SPDL1

UniProt ID: Q96EA4
Organism: Homo sapiens
Review Status: DRAFT
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Gene Description

SPDL1 (Spindly/CCDC99) encodes a coiled-coil protein that functions as a kinetochore-specific adaptor for cytoplasmic dynein during mitosis. It is recruited to the outer kinetochore via the RZZ complex (Rod/ZW10/Zwilch) in an Aurora B-regulated manner, and its C-terminal farnesylation is required for kinetochore targeting. At kinetochores, Spindly recruits the dynein-dynactin complex, which is essential for initial lateral kinetochore-microtubule interactions, chromosome congression, and correct spindle orientation. Spindly also drives kinetochore corona expansion by promoting oligomerization of RZZ-Spindly complexes, independent of dynein. Following microtubule attachment, dynein-mediated removal of Spindly from kinetochores is the critical event for spindle assembly checkpoint silencing, though in human cells (unlike Drosophila) Spindly is not absolutely required for checkpoint protein stripping. Spindly also functions as a dynein-dynactin cargo adaptor that converts dynein from a non-processive to a highly processive motor. Outside mitosis, Spindly interacts with the deubiquitinase USP45 and plays a role in cell migration. Spindly is monoubiquitinated and deubiquitinated by USP45.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0000132 establishment of mitotic spindle orientation
IBA
GO_REF:0000033
ACCEPT
Summary: IBA annotation for establishment of mitotic spindle orientation inferred by phylogenetic analysis. This is strongly supported by experimental evidence in human cells from PMID:19468067, which showed that hSpindly depletion induces striking spindle rotation that is rescued by co-depletion of dynein, demonstrating a direct role for kinetochore dynein in spindle orientation.
Supporting Evidence:
PMID:19468067
depletion of hSpindly induces a striking spindle rotation, which can be rescued by co-depletion of dynein
GO:0000922 spindle pole
IBA
GO_REF:0000033
ACCEPT
Summary: IBA annotation for spindle pole localization. Supported by direct experimental evidence (IDA) from PMID:19468067, which showed Spindly relocalizes to spindle poles before metaphase. Spindly is transported poleward by dynein along kinetochore fibers after microtubule attachment.
Supporting Evidence:
PMID:19468067
hSpindly decorated KTs in early prometaphase before it relocalized to the spindle poles before metaphase
GO:0000940 outer kinetochore
IBA
GO_REF:0000033
ACCEPT
Summary: IBA annotation for outer kinetochore localization. Strongly supported by IDA evidence from PMID:19468067 showing Spindly localizes to the outer kinetochore in early prometaphase. This is a core localization for Spindly, where it recruits dynein-dynactin to drive chromosome movements. Falcon deep research further localizes this to the kinetochore fibrous corona, the dynamic outer-kinetochore layer assembled in early mitosis.
Supporting Evidence:
PMID:19468067
localization of human Spindly (hSpindly) to KTs is controlled by the Rod/Zw10/Zwilch (RZZ) complex and Aurora B
file:human/SPDL1/SPDL1-deep-research-falcon.md
Spindly is specifically enriched at the **kinetochore fibrous corona** in early mitosis where it enables dynein–dynactin recruitment
GO:0007080 mitotic metaphase chromosome alignment
IBA
GO_REF:0000033
ACCEPT
Summary: IBA annotation for mitotic metaphase chromosome alignment. Strongly supported by IMP evidence from PMID:19468067, which showed that hSpindly depletion results in severe chromosome misalignment. This is a core biological process for Spindly.
Supporting Evidence:
PMID:19468067
hSpindly depletion results in reduced inter-KT tension, unstable KT fibers, an extensive prometaphase delay, and severe chromosome misalignment
GO:0034501 protein localization to kinetochore
IBA
GO_REF:0000033
ACCEPT
Summary: IBA annotation for protein localization to kinetochore. Supported by IMP evidence from PMID:19468067 and PMID:17576797. Spindly recruits dynein and dynactin to the kinetochore; depletion abolishes kinetochore dynein. This is a core function of Spindly. Falcon deep research details the recruitment mechanism: Spindly is targeted to kinetochores by the RZZ complex, with C-terminal farnesylation engaging the Rod beta-propeller as a farnesyl receptor.
Supporting Evidence:
PMID:19468067
Mitotic control of kinetochore-associated dynein and spindle orientation by human Spindly
PMID:17576797
After the depletion of Spindly, dynein cannot target to kinetochores
file:human/SPDL1/SPDL1-deep-research-falcon.md
Spindly is recruited to kinetochores primarily through the **RZZ complex** (ROD–ZW10–ZWILCH). A key targeting mechanism is **C-terminal farnesylation**, with the **Rod β-propeller** acting as a **farnesyl receptor** in humans
GO:0043515 kinetochore binding
IBA
GO_REF:0000033
ACCEPT
Summary: IBA annotation for kinetochore binding. Supported by IDA evidence from PMID:19468067 showing direct localization to kinetochores. Spindly binds kinetochores via the RZZ complex, requiring C-terminal farnesylation for this interaction (PMID:25825516).
Supporting Evidence:
PMID:19468067
localization of human Spindly (hSpindly) to KTs is controlled by the Rod/Zw10/Zwilch (RZZ) complex and Aurora B
GO:0000922 spindle pole
IEA
GO_REF:0000044
ACCEPT
Summary: IEA annotation for spindle pole based on UniProt subcellular location mapping. Redundant with the IBA annotation for the same term, and both are supported by experimental IDA evidence from PMID:19468067.
GO:0000940 outer kinetochore
IEA
GO_REF:0000104
ACCEPT
Summary: IEA annotation for outer kinetochore based on UniRule transfer. Redundant with the IBA annotation for the same term, both supported by IDA from PMID:19468067.
GO:0005634 nucleus
IEA
GO_REF:0000044
KEEP AS NON CORE
Summary: IEA annotation for nucleus based on UniProt subcellular location mapping. Supported by IDA evidence from PMID:19468067 showing Spindly localizes to the nucleus during interphase. This is a non-core localization representing the interphase state.
Reason: Nuclear localization is the interphase state. The core localizations are the outer kinetochore and spindle pole during mitosis.
GO:0005813 centrosome
IEA
GO_REF:0000044
KEEP AS NON CORE
Summary: IEA annotation for centrosome based on UniProt subcellular location vocabulary mapping. UniProt lists centrosome as a subcellular location. This is plausible given that Spindly localizes to spindle poles (which contain centrosomes) during mitosis, though the primary experimental evidence places Spindly at the kinetochore and spindle pole rather than explicitly at the centrosome per se. This is a non-core secondary localization.
Reason: Centrosome localization is implied by spindle pole localization but is not the primary or core localization for this protein.
GO:0007094 mitotic spindle assembly checkpoint signaling
IEA
GO_REF:0000002
ACCEPT
Summary: IEA annotation for SAC signaling based on InterPro domain mapping (IPR028593). The role of Spindly in SAC signaling is complex. In Drosophila, Spindly depletion prevents SAC silencing (PMID:17576797). In human cells, hSpindly depletion does NOT abolish removal of checkpoint proteins MAD2 and ZW10 from kinetochores (PMID:19468067), but Spindly mutants that cannot recruit dynein DO prevent checkpoint silencing (PMID:20439434). Thus Spindly is involved in SAC signaling primarily through its role in checkpoint silencing via dynein-mediated removal of checkpoint components. Falcon deep research updates this model with Ide et al. 2023: the checkpoint-silencing role of Spindly-recruited dynein is restricted primarily to disassembly of the fibrous corona, rather than wholesale removal of all checkpoint proteins from the outer kinetochore.
Supporting Evidence:
PMID:19468067
in contrast to Drosophila, hSpindly depletion does not abolish the removal of MAD2 and ZW10 from KTs
PMID:17576797
Spindly, a novel protein essential for silencing the spindle assembly checkpoint, recruits dynein to the kinetochore
file:human/SPDL1/SPDL1-deep-research-falcon.md
kinetochore dynein’s checkpoint-silencing role is **restricted primarily to disassembly of the fibrous corona**, rather than wholesale removal of checkpoint proteins from the entire outer kinetochore
GO:0034501 protein localization to kinetochore
IEA
GO_REF:0000120
ACCEPT
Summary: IEA annotation for protein localization to kinetochore via combined automated annotation. Redundant with IBA and IMP annotations for the same term. Well supported by experimental evidence.
GO:0043515 kinetochore binding
IEA
GO_REF:0000104
ACCEPT
Summary: IEA annotation for kinetochore binding based on UniRule transfer. Redundant with IBA and IDA annotations for the same term. Well supported.
GO:0005515 protein binding
IPI
PMID:25416956
A proteome-scale map of the human interactome network.
REMOVE
Summary: Protein binding annotation based on large-scale interactome study (Rolland et al. 2014). This is a generic, uninformative term. Spindly interacts with CA8, DNAAF4, PPP1R18, RTP5, TRAF4, USP15 in this dataset. These are high-throughput yeast two-hybrid results. The interactions with CA8 and DNAAF4 have no clear biological context for Spindly function.
Reason: Protein binding is uninformative per GO curation guidelines. The specific biologically relevant interactions (with RZZ complex, dynein, dynactin, USP45) are captured by more specific terms.
Supporting Evidence:
PMID:25416956
A proteome-scale map of the human interactome network
GO:0005515 protein binding
IPI
PMID:25910212
Widespread macromolecular interaction perturbations in human...
REMOVE
Summary: Protein binding annotation from large-scale interactome perturbation study (Sahni et al. 2015). Uninformative generic term from high-throughput data.
Reason: Protein binding is uninformative per GO curation guidelines.
Supporting Evidence:
PMID:25910212
Widespread macromolecular interaction perturbations in human genetic disorders
GO:0005515 protein binding
IPI
PMID:26871637
Widespread Expansion of Protein Interaction Capabilities by ...
REMOVE
Summary: Protein binding annotation from alternative splicing interactome study (Yang et al. 2016). Uninformative generic term from high-throughput data.
Reason: Protein binding is uninformative per GO curation guidelines.
Supporting Evidence:
PMID:26871637
Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing
GO:0005515 protein binding
IPI
PMID:33961781
Dual proteome-scale networks reveal cell-specific remodeling...
REMOVE
Summary: Protein binding annotation from BioPlex 3.0 dual proteome-scale network study (Huttlin et al. 2021). Uninformative generic term.
Reason: Protein binding is uninformative per GO curation guidelines.
Supporting Evidence:
PMID:33961781
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome
GO:0005515 protein binding
IPI
PMID:30258100
USP45 and Spindly are part of the same complex implicated in...
REMOVE
Summary: Protein binding annotation based on the USP45-Spindly interaction study (Conte et al. 2018). The IPI is with USP45 (Q70EL2). While the specific interaction is real and biologically relevant, protein binding is too generic. A more informative term would be enzyme binding (already captured elsewhere) or deubiquitinase binding.
Reason: Protein binding is uninformative. The USP45 interaction is better captured by more specific MF terms.
Supporting Evidence:
PMID:30258100
we have identified Spindly as a new target of USP45
GO:0005515 protein binding
IPI
PMID:19468067
Mitotic control of kinetochore-associated dynein and spindle...
REMOVE
Summary: Protein binding annotation from Chan et al. 2009. The IPI partners are KNTC1/Rod (O43264) and KNTC2/ZW10 (P50748), components of the RZZ complex. These interactions are biologically central to Spindly function, as Spindly is recruited to kinetochores via the RZZ complex. However, protein binding is too generic; kinetochore binding (GO:0043515) and dynein complex binding (GO:0070840) are more informative.
Reason: Protein binding is uninformative. The specific RZZ complex interaction is functionally captured by kinetochore binding and the dynein recruitment function.
Supporting Evidence:
PMID:19468067
RZZ members (ZW10 and Rod), but not dynein, could be coimmunoprecipitated with hSpindly
GO:0016477 cell migration
IMP
PMID:30258100
USP45 and Spindly are part of the same complex implicated in...
KEEP AS NON CORE
Summary: IMP annotation for cell migration based on Conte et al. 2018, which showed that cells lacking Spindly migrate slower than wild-type cells. This was supported by an earlier report showing Spindly associates with the cell cortex and colocalizes with dynein/dynactin at the leading edge of migrating cells. This is a real but non-core function of Spindly; its primary evolved function is in mitotic kinetochore-dynein regulation.
Reason: Cell migration is a documented secondary function of Spindly, but it is not the core evolved function. The core function is dynein recruitment to kinetochores during mitosis.
Supporting Evidence:
PMID:30258100
cells lacking Spindly migrate slower than wild type cells and that this effect is rescued by re-expression of wild-type Spindly
GO:0019899 enzyme binding
IPI
PMID:23382074
A high-confidence interaction map identifies SIRT1 as a medi...
KEEP AS NON CORE
Summary: Enzyme binding annotation from Armour et al. 2013 SIRT1 interactome study. The IPI partner is SIRT1 (Q96EB6). SPDL1 was identified as a SIRT1-interacting protein in a high-throughput screen. The biological significance of the SIRT1-Spindly interaction is unclear. This paper is primarily about USP22 and SAGA complex regulation; Spindly was a background hit. This is unlikely to represent a core function.
Reason: The SIRT1 interaction is from a large-scale screen and its functional significance for Spindly is not established. However, enzyme binding is more informative than protein binding and the interaction data are real.
Supporting Evidence:
PMID:23382074
a comprehensive analysis of SIRT1 binding proteins yielding a high-confidence interaction map
GO:0005829 cytosol
TAS
Reactome:R-HSA-141409
KEEP AS NON CORE
Summary: Cytosol annotation from Reactome pathway "Mad1 binds kinetochore." Spindly is included as a participant in SAC-related Reactome reactions. Multiple redundant TAS annotations for the same GO term from different Reactome reactions. The cytosol localization is correct as the interphase/soluble pool of Spindly, but this is non-core. Consolidating all Reactome cytosol entries into a single review.
Reason: Cytosol is a valid but non-core localization for Spindly representing the soluble pool outside of mitosis.
GO:0005829 cytosol
TAS
Reactome:R-HSA-141422
KEEP AS NON CORE
Summary: Redundant cytosol TAS annotation from Reactome. Same assessment as above.
GO:0005829 cytosol
TAS
Reactome:R-HSA-141431
KEEP AS NON CORE
Summary: Redundant cytosol TAS annotation from Reactome. Same assessment as above.
GO:0005829 cytosol
TAS
Reactome:R-HSA-141439
KEEP AS NON CORE
Summary: Redundant cytosol TAS annotation from Reactome. Same assessment as above.
GO:0005829 cytosol
TAS
Reactome:R-HSA-1638803
KEEP AS NON CORE
Summary: Redundant cytosol TAS annotation from Reactome. Same assessment as above.
GO:0005829 cytosol
TAS
Reactome:R-HSA-1638821
KEEP AS NON CORE
Summary: Redundant cytosol TAS annotation from Reactome. Same assessment as above.
GO:0005829 cytosol
TAS
Reactome:R-HSA-2467809
KEEP AS NON CORE
Summary: Redundant cytosol TAS annotation from Reactome. Same assessment as above.
GO:0005829 cytosol
TAS
Reactome:R-HSA-2467811
KEEP AS NON CORE
Summary: Redundant cytosol TAS annotation from Reactome. Same assessment as above.
GO:0005829 cytosol
TAS
Reactome:R-HSA-2468287
KEEP AS NON CORE
Summary: Redundant cytosol TAS annotation from Reactome. Same assessment as above.
GO:0005829 cytosol
TAS
Reactome:R-HSA-2484822
KEEP AS NON CORE
Summary: Redundant cytosol TAS annotation from Reactome. Same assessment as above.
GO:0005829 cytosol
TAS
Reactome:R-HSA-375302
KEEP AS NON CORE
Summary: Redundant cytosol TAS annotation from Reactome. Same assessment as above.
GO:0005829 cytosol
TAS
Reactome:R-HSA-5666129
KEEP AS NON CORE
Summary: Redundant cytosol TAS annotation from Reactome. Same assessment as above.
GO:0005829 cytosol
TAS
Reactome:R-HSA-5666160
KEEP AS NON CORE
Summary: Redundant cytosol TAS annotation from Reactome. Same assessment as above.
GO:0005829 cytosol
TAS
Reactome:R-HSA-5666169
KEEP AS NON CORE
Summary: Redundant cytosol TAS annotation from Reactome. Same assessment as above.
GO:0005829 cytosol
TAS
Reactome:R-HSA-9648114
KEEP AS NON CORE
Summary: Redundant cytosol TAS annotation from Reactome. Same assessment as above.
GO:0000132 establishment of mitotic spindle orientation
IMP
PMID:19468067
Mitotic control of kinetochore-associated dynein and spindle...
ACCEPT
Summary: IMP annotation for establishment of mitotic spindle orientation from Chan et al. 2009. hSpindly depletion induces striking spindle rotation that is rescued by co-depletion of dynein, demonstrating that kinetochore dynein (recruited by Spindly) is critical for spindle orientation. This is a core biological process for Spindly.
Supporting Evidence:
PMID:19468067
depletion of hSpindly induces a striking spindle rotation, which can be rescued by co-depletion of dynein
GO:0000922 spindle pole
IDA
PMID:19468067
Mitotic control of kinetochore-associated dynein and spindle...
ACCEPT
Summary: IDA annotation for spindle pole localization from Chan et al. 2009. Direct observation that Spindly relocalizes to spindle poles before metaphase via dynein-mediated poleward transport.
Supporting Evidence:
PMID:19468067
hSpindly decorated KTs in early prometaphase before it relocalized to the spindle poles before metaphase
GO:0000940 outer kinetochore
IDA
PMID:19468067
Mitotic control of kinetochore-associated dynein and spindle...
ACCEPT
Summary: IDA annotation for outer kinetochore localization from Chan et al. 2009. Direct observation by immunofluorescence showing Spindly localizes to the outer kinetochore in early prometaphase. This is the primary and core localization for Spindly during mitosis.
Supporting Evidence:
PMID:19468067
localization of human Spindly (hSpindly) to KTs is controlled by the Rod/Zw10/Zwilch (RZZ) complex and Aurora B
GO:0005515 protein binding
IPI
PMID:19468067
Mitotic control of kinetochore-associated dynein and spindle...
REMOVE
Summary: Protein binding annotation from Chan et al. 2009 based on interaction with KNTC1/Rod and ZW10. Uninformative term; the specific interactions are better captured by kinetochore binding.
Reason: Protein binding is uninformative per GO curation guidelines.
Supporting Evidence:
PMID:19468067
RZZ members (ZW10 and Rod), but not dynein, could be coimmunoprecipitated with hSpindly
GO:0005634 nucleus
IDA
PMID:19468067
Mitotic control of kinetochore-associated dynein and spindle...
KEEP AS NON CORE
Summary: IDA annotation for nuclear localization from Chan et al. 2009. Spindly localizes to the nucleus in interphase. This is a non-core secondary localization reflecting the interphase distribution. Falcon deep research corroborates the cell-cycle localization dynamics: nuclear in interphase, then kinetochore in prometaphase.
Reason: Nuclear localization is the interphase state; the core mitotic localizations are outer kinetochore and spindle pole.
Supporting Evidence:
PMID:19468067
Interphase localization of hSpindly was mainly nuclear
file:human/SPDL1/SPDL1-deep-research-falcon.md
**Interphase:** nuclear localization.
GO:0007080 mitotic metaphase chromosome alignment
IMP
PMID:19468067
Mitotic control of kinetochore-associated dynein and spindle...
ACCEPT
Summary: IMP annotation for mitotic metaphase chromosome alignment from Chan et al. 2009. hSpindly depletion causes severe chromosome misalignment with reduced inter-KT tension and unstable KT fibers. This is a core biological process for Spindly.
Supporting Evidence:
PMID:19468067
hSpindly depletion results in reduced inter-KT tension, unstable KT fibers, an extensive prometaphase delay, and severe chromosome misalignment
GO:0034501 protein localization to kinetochore
IMP
PMID:19468067
Mitotic control of kinetochore-associated dynein and spindle...
ACCEPT
Summary: IMP annotation for protein localization to kinetochore from Chan et al. 2009. Spindly is required for the recruitment of dynein and dynactin to kinetochores. Depletion abolishes kinetochore dynein. This is a core function of Spindly.
Supporting Evidence:
PMID:19468067
localization of human Spindly (hSpindly) to KTs is controlled by the Rod/Zw10/Zwilch (RZZ) complex and Aurora B
PMID:17576797
After the depletion of Spindly, dynein cannot target to kinetochores
GO:0043515 kinetochore binding
IDA
PMID:19468067
Mitotic control of kinetochore-associated dynein and spindle...
ACCEPT
Summary: IDA annotation for kinetochore binding from Chan et al. 2009. Spindly directly binds kinetochores, as demonstrated by immunofluorescence microscopy. This binding is mediated via the RZZ complex and requires C-terminal farnesylation of Spindly (PMID:25825516). This is a core molecular function.
Supporting Evidence:
PMID:19468067
localization of human Spindly (hSpindly) to KTs is controlled by the Rod/Zw10/Zwilch (RZZ) complex and Aurora B
GO:0070840 dynein complex binding
IDA
PMID:19468067
Mitotic control of kinetochore-associated dynein and spindle...
NEW
Summary: NEW annotation. Spindly directly recruits the dynein-dynactin complex to kinetochores. Chan et al. 2009 showed that hSpindly depletion abolishes dynein localization to kinetochores. McKenney et al. 2014 demonstrated that Spindly functions as a cargo adaptor that physically links dynein to dynactin and activates processive motility. This is more informative than the generic protein binding annotations and represents a core molecular function. Falcon deep research specifies the binding logic of this activating adaptor: a CC1 box binding pocket engages a conserved amphipathic helix in dynein LIC, while the Spindly motif engages the dynactin pointed-end.
Supporting Evidence:
PMID:19468067
localization of human Spindly (hSpindly) to KTs is controlled by the Rod/Zw10/Zwilch (RZZ) complex and Aurora B
PMID:25035494
Activation of cytoplasmic dynein motility by dynactin-cargo adapter complexes
file:human/SPDL1/SPDL1-deep-research-bioreason-sft.md
The dynein-adapter core enforces dynein targeting to microtubule minus ends and kinetochore receptors
file:human/SPDL1/SPDL1-deep-research-falcon.md
**CC1 box**: creates a binding pocket for a conserved amphipathic helix in **dynein LIC (light intermediate chain)**.
GO:0007018 microtubule-based movement
IMP
PMID:19468067
Mitotic control of kinetochore-associated dynein and spindle...
NEW
Summary: NEW annotation. Spindly is required for dynein-dependent poleward chromosome movements during mitosis. hSpindly depletion results in reduced inter-KT tension and unstable KT fibers, consistent with impaired microtubule-based movement at kinetochores. Additionally, Spindly functions as a dynein-dynactin cargo adaptor that activates processive microtubule-based motility (PMID:25035494). Falcon deep research notes that Spindly-dependent dynein stripping (poleward transport of corona material) is triggered after end-coupled microtubule attachment.
Supporting Evidence:
PMID:19468067
hSpindly depletion results in reduced inter-KT tension, unstable KT fibers, an extensive prometaphase delay, and severe chromosome misalignment
file:human/SPDL1/SPDL1-deep-research-falcon.md
Spindly-dependent dynein stripping is triggered after **end-coupled microtubule attachment**, enabling removal of corona components (including Mad1–Mad2) and promoting kinetochore remodeling/compaction

Core Functions

Kinetochore-specific dynein adaptor that recruits cytoplasmic dynein-dynactin to the outer kinetochore during mitosis, enabling lateral kinetochore-microtubule interactions, poleward chromosome movements, chromosome congression, and spindle orientation control.

Supporting Evidence:
  • PMID:19468067
    hSpindly depletion results in reduced inter-KT tension, unstable KT fibers, an extensive prometaphase delay, and severe chromosome misalignment
  • PMID:17576797
    After the depletion of Spindly, dynein cannot target to kinetochores
  • file:human/SPDL1/SPDL1-deep-research-falcon.md
    Kinetochore-localized **dynein–dynactin activating adaptor**; assembles DDS at fibrous corona

Dynein-dynactin cargo adaptor that activates processive dynein motility. Facilitates the interaction between dynein and dynactin and converts dynein from a non-processive to a highly processive motor.

Molecular Function:
dynein complex binding
Directly Involved In:
Cellular Locations:
Supporting Evidence:
  • PMID:25035494
    Activation of cytoplasmic dynein motility by dynactin-cargo adapter complexes

Participates in spindle assembly checkpoint signaling through dynein-mediated removal of checkpoint proteins from kinetochores upon microtubule attachment. Spindly removal from attached kinetochores is the critical event for checkpoint silencing.

Supporting Evidence:
  • PMID:20439434
    Removal of Spindly from microtubule-attached kinetochores controls spindle checkpoint silencing in human cells

References

Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features
Combined Automated Annotation using Multiple IEA Methods
Spindly, a novel protein essential for silencing the spindle assembly checkpoint, recruits dynein to the kinetochore.
  • Spindly was discovered as a kinetochore protein required for dynein recruitment and SAC silencing in Drosophila; a human homologue was identified with similar function.
    "After the depletion of Spindly, dynein cannot target to kinetochores, and, as a result, cells arrest in metaphase with high levels of kinetochore-bound Mad2 and RZZ"
Mitotic control of kinetochore-associated dynein and spindle orientation by human Spindly.
  • Human Spindly localizes to the outer kinetochore via the RZZ complex, recruits dynein-dynactin, and is required for chromosome alignment and spindle orientation. Unlike Drosophila, human Spindly is not required for checkpoint protein stripping from kinetochores.
    "hSpindly depletion results in reduced inter-KT tension, unstable KT fibers, an extensive prometaphase delay, and severe chromosome misalignment...depletion of hSpindly induces a striking spindle rotation, which can be rescued by co-depletion of dynein...in contrast to Drosophila, hSpindly depletion does not abolish the removal of MAD2 and ZW10 from KTs"
A high-confidence interaction map identifies SIRT1 as a mediator of acetylation of USP22 and the SAGA coactivator complex.
  • SPDL1 was identified as a SIRT1-interacting protein in a high-throughput interaction screen. The biological significance of this interaction for Spindly function is unclear.
    "a comprehensive analysis of SIRT1 binding proteins yielding a high-confidence interaction map"
Activation of cytoplasmic dynein motility by dynactin-cargo adapter complexes.
  • Spindly functions as a cargo adaptor that links the dynein motor complex to various cargos and converts dynein from a non-processive to a highly processive motor in the presence of dynactin.
    "Recombinant SNAPf-tagged Rab11-FIP3, human Spindly, and Hook3 (fig"
A proteome-scale map of the human interactome network.
  • Large-scale yeast two-hybrid interactome study detecting SPDL1 interactions with multiple partners including CA8, DNAAF4, PPP1R18, RTP5, TRAF4, USP15.
    "A proteome-scale map of the human interactome network"
Widespread macromolecular interaction perturbations in human genetic disorders.
  • Follow-up interactome perturbation study; SPDL1 interactions detected in high-throughput screen.
    "Widespread macromolecular interaction perturbations in human genetic disorders"
Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.
  • Alternative splicing interactome study; SPDL1 isoform interactions detected.
    "Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing"
USP45 and Spindly are part of the same complex implicated in cell migration.
  • USP45 and Spindly form a complex; Spindly is monoubiquitinated and deubiquitinated by USP45; both play roles in cell migration.
    "Here, we also show that Spindly is mono-ubiquitylated and this can be specifically removed by USP45 in its active form but not by the catalytic inactive form"
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
  • BioPlex 3.0 dual proteome-scale interactome study; SPDL1 interactions detected in high-throughput AP-MS.
    "Dual proteome-scale networks reveal cell-specific remodeling of the human interactome"
Removal of Spindly from microtubule-attached kinetochores controls spindle checkpoint silencing in human cells.
  • Dynein-mediated removal of Spindly from microtubule-attached kinetochores is the critical reaction in checkpoint silencing. A conserved Spindly motif is essential for dynein targeting to kinetochores.
    "we identify a conserved motif in Spindly that is essential for kinetochore targeting of dynein"
Dynamic kinetochore size regulation promotes microtubule capture and chromosome biorientation in mitosis.
  • Spindly and RZZ drive kinetochore corona expansion in a dynein-independent manner. C-terminal farnesylation and MPS1 kinase activity cause Spindly conformational changes promoting oligomerization of RZZ-Spindly complexes.
    "the dynein adaptor Spindly and the RZZ (ROD-Zwilch-ZW10) complex drive kinetochore expansion in a dynein-independent manner"
file:human/SPDL1/SPDL1-deep-research-bioreason-sft.md
BioReason deep research on SPDL1 (Spindly)
  • BioReason analysis correctly identifies the dynein-adapter core architecture and kinetochore adaptor function. Contains some errors regarding specific binding partners (BUB1B, NDC80, SKA, CENP-F, HOX-D13, MKLN1) that are not supported by published literature.
file:human/SPDL1/SPDL1-deep-research-falcon.md
Falcon (Edison) deep research on human SPDL1 (Spindly, Q96EA4)
  • Spindly is a coiled-coil activating adaptor that links the minus-end motor cytoplasmic dynein-1 and its cofactor dynactin to the kinetochore fibrous corona during mitosis, enabling dynein recruitment and activation at kinetochores.
    "links the microtubule minus-end motor **cytoplasmic dynein-1** and its cofactor **dynactin** to the **kinetochore fibrous corona** during mitosis, enabling dynein recruitment/activation at kinetochores"
  • Spindly operates within the RZZ-Spindly pathway to recruit dynein-dynactin to the fibrous corona and to promote dynein-dependent poleward stripping of corona material, contributing to SAC silencing.
    "Spindly operates within the **RZZ–Spindly pathway** to recruit dynein–dynactin to this region and to promote **dynein-dependent “stripping”** (poleward transport/removal) of corona material"
  • Domain architecture: a CC1 box creates a binding pocket for a conserved amphipathic helix in dynein LIC; the Spindly motif engages the dynactin pointed-end; a C-terminal CAAX motif enables farnesylation.
    "**Spindly motif**: contributes to interaction with the **dynactin pointed-end**."
  • Spindly is recruited to kinetochores via the RZZ complex (ROD-ZW10-ZWILCH) and C-terminal farnesylation, with the Rod beta-propeller acting as a farnesyl receptor in humans.
    "Spindly is recruited to kinetochores primarily through the **RZZ complex** (ROD–ZW10–ZWILCH). A key targeting mechanism is **C-terminal farnesylation**, with the **Rod β-propeller** acting as a **farnesyl receptor** in humans"
  • Full-length Spindly is autoinhibited, adopting a closed conformation that occludes the CC1 box and Spindly motif and prevents productive dynein-dynactin binding in solution until activated at kinetochores.
    "full-length Spindly is autoinhibited"
  • Updated 2023 model (Ide et al.): the checkpoint-silencing role of kinetochore dynein recruited via Spindly is restricted primarily to disassembly of the fibrous corona rather than wholesale removal of all outer-kinetochore checkpoint proteins.
    "kinetochore dynein’s checkpoint-silencing role is **restricted primarily to disassembly of the fibrous corona**, rather than wholesale removal of checkpoint proteins from the entire outer kinetochore"
  • Localization is cell-cycle dependent: nuclear in interphase, kinetochore in prometaphase, relocalizing toward spindle poles before metaphase, and lost after chromosome congression.
    "**Prometaphase:** kinetochore localization."
  • A rare SPDL1 missense variant p.Arg20Gln (rs116483731) is associated with idiopathic pulmonary fibrosis, and shows antagonistic pleiotropy with increased IPF risk but decreased cancer risk.
    "the same SPDL1 missense allele shows **antagonistic pleiotropy**: increased IPF risk but decreased cancer risk"
Reactome:R-HSA-141409
Mad1 binds kinetochore
Reactome:R-HSA-141422
MAD2 converted to an inhibitory state via interaction with Mad1
Reactome:R-HSA-141431
MAD2 associates with the Mad1 kinetochore complex
Reactome:R-HSA-141439
Release of activated MAD2 from kinetochores
Reactome:R-HSA-1638803
Phosphorylation of cohesin by PLK1 at centromeres
Reactome:R-HSA-1638821
PP2A-B56 dephosphorylates centromeric cohesin
Reactome:R-HSA-2467809
ESPL1 (Separase) cleaves centromeric cohesin
Reactome:R-HSA-2467811
Separation of sister chromatids
Reactome:R-HSA-2468287
CDK1 phosphorylates CDCA5 (Sororin) at centromeres
Reactome:R-HSA-2484822
Kinetochore assembly
Reactome:R-HSA-375302
Kinetochore capture of astral microtubules
Reactome:R-HSA-5666129
CDC42:GTP recruits DIAPH2-2 to kinetochores
Reactome:R-HSA-5666160
AURKB phosphorylates DIAPH2-2 at kinetochores
Reactome:R-HSA-5666169
Kinetochore capture of astral microtubules is positively regulated by CDC42:GTP:p-S196-DIAPH2-2
Reactome:R-HSA-9648114
EML4 recruits NUDC to mitotic spindle

Suggested Questions for Experts

Q: What is the precise structural basis for the Spindly-RZZ interaction, and how does farnesylation of the Spindly C-terminus promote this interaction?

Suggested experts: Geert Kops, Reto Gassmann

Q: Does Spindly have a direct role in kinetochore corona formation beyond its RZZ interaction, and what is the functional significance of RZZ-Spindly oligomerization for microtubule capture?

Suggested experts: Carlos Sacristan, Andrea Musacchio

Q: What is the biological significance of Spindly monoubiquitination by USP45 for cell migration, and what is the relevant E3 ubiquitin ligase?

Suggested experts: Ana Belen Perez-Oliva, Eric Griffis

Suggested Experiments

Experiment: Generate ubiquitination-site mutants of Spindly and test their effect on cell migration, cortical dynein recruitment, and USP45 interaction using wound-healing and transwell assays combined with live-cell imaging.

Hypothesis: Spindly monoubiquitination regulates its localization or interaction partners during cell migration.

Type: cell biology

Experiment: Use separation-of-function mutants that retain corona expansion but lack dynein recruitment (Spindly motif mutants from Gassmann et al. 2010) to assess microtubule capture efficiency, attachment error rates, and chromosome segregation fidelity by live-cell imaging with kinetochore markers.

Hypothesis: The dynein-independent corona expansion function of Spindly is separable from its dynein recruitment function and has distinct contributions to chromosome segregation fidelity.

Type: cell biology

Deep Research

Bioreason Pro

(SPDL1-deep-research-bioreason-sft.md)
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Thinking Trace

The architecture begins with IPR028593 (Protein Spindly, chordates family) spanning residues 1605, covering the full polypeptide and defining a chordate-specific kinetochore adaptor scaffold. Nested within this, residues 3468 carry IPR051149 (Spindly/BICDR Dynein Motor Adapter family), a hallmark of coiled-coil adaptors that couple cytoplasmic dynein to diverse cargo. The placement of the dynein-adapter core inside the broader Spindly family envelope indicates a bipartite design: an N-terminal-to-mid-region motor-adapter module that binds dynein and its regulatory subunits, and a C-terminal region within the full-length family signature that engages kinetochore receptors. This arrangement causes selective recruitment of dynein to kinetochores and spindle poles, and it provides a platform for regulatory enzymes at the kinetochore.

From this domain logic, the molecular function centers on assembling and positioning a motor-enzymatic module. The dynein-adapter core enforces dynein targeting to microtubule minus ends and kinetochore receptors, while the scaffolded surfaces accommodate regulatory enzymes. This supports GO:0019899 enzyme binding, as the adaptor is poised to bind kinases and phosphatases that tune kinetochore-microtubule attachments and checkpoint signaling.

The same architecture drives specific biological processes. By docking dynein at kinetochores, the adaptor generates poleward forces that align chromosomes at the metaphase plate, matching GO:0007080 mitotic metaphase plate congression. Dynein recruitment also biases spindle geometry and microtubule flux, enabling GO:0000132 establishment of mitotic spindle orientation. The scaffold’s ability to capture outer-kinetochore receptors and concentrate regulatory enzymes directly implements GO:0034501 protein localization to kinetochore. Outside mitosis, dynein-based transport along microtubules contributes to directed cell movement; by positioning dynein at specific cortical or Golgi sites, the adaptor can influence cytoskeletal polarity and vesicle trafficking, aligning with GO:0016477 cell migration.

The cellular context follows from the same chain. The dynein-adapter module and kinetochore-binding surfaces place the protein at the GO:0000940 outer kinetochore during mitosis, where it forms the GO:0098806 Spindly-BICDR complex that couples dynein to kinetochore receptors. Minus-end-directed transport and motor loading explain accumulation at the GO:0000922 spindle pole. Between divisions and during interphase transport, a soluble pool resides in the GO:0005829 cytosol, while regulatory cycles and chromatin-proximal functions rationalize presence in the GO:0005634 nucleus.

Mechanistically, the adaptor binds outer-kinetochore receptors such as BUB1B/BUB3 and the NDC80 complex to anchor dynein and its cofactors, creating a dynein–dynactin–adaptor assembly that exerts poleward forces on attached kinetochores. Phosphorylation by PLK1 and checkpoint factors modulates its affinity and timing, while association with MKLN1 (BICDR) tunes dynein loading in interphase. Through these regulated interactions, it promotes bi-orientation, error correction, and timely anaphase onset. The same scaffold can engage additional kinetochore modules (SKA1/2/3, CENP-F) to stabilize end-on attachments and coordinate with APC/C activation via CDC20. In non-mitotic contexts, adaptor-mediated dynein targeting to Golgi membranes and cortical sites can drive vesicle trafficking and polarity, contributing to cell migration. The observed partners—BUB1 beta, CENP-F, SKA1/2/3, BIO1, PLK1, CDC20, NDC80, and even developmental regulators like HOX-D13—fit a model in which the adaptor integrates checkpoint, structural, and regulatory inputs to choreograph dynein-dependent transport and kinetochore mechanics.

## Functional Summary

A dynein-recruiting kinetochore adaptor that assembles a motorregulatory module to capture and load dyneindynactin at kinetochores and spindle poles. By anchoring to outer-kinetochore receptors and engaging checkpoint and structural factors, it generates poleward forces for chromosome alignment and proper spindle orientation, coordinates the timing of anaphase onset, and modulates kinetochoremicrotubule attachments. In interphase, association with a dynein cofactor tunes dynein loading and extends its role to Golgi-directed transport and polarity programs that support cell migration. The protein cycles between cytosol and nucleus, concentrates at kinetochores during mitosis, and forms a dedicated adaptor complex with its dynein-binding partner.

## UniProt Summary

Kinetochore adapter protein which recruits the dynein motor complex to kinetochores. Required for chromosome alignment and spindle orientation during mitosis. May also regulate the onset of anaphase and kinetochore microtubule attachment. Association with MKLN1/BICDR regulates dynein loading by SPINDLY onto the Golgi apparatus.

## InterPro Domains

    - IPR028593: Protein Spindly, chordates (family) [1-605]
- IPR051149: Spindly/BICDR Dynein Motor Adapter (family) [3-468]

## GO Term Predictions

### Molecular Function


### Biological Process


### Cellular Component

Falcon

(SPDL1-deep-research-falcon.md)
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 35 citations 1 artifacts 2026-05-30T01:40:42.250532

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research Report: Human SPDL1 (Spindly; UniProt Q96EA4) Functional Annotation

0) Target verification (mandatory)

SPDL1 in this report refers specifically to human Spindly (hSpindly) encoded by SPDL1 (also referenced as CCDC99) with UniProt accession Q96EA4 and a length of ~605 aa. This matches the mitotic dynein–dynactin activating adaptor described in kinetochore/corona literature, including explicit UniProt mapping and domain schematics in a 2023 review. (gassmann2023dyneinatthe pages 5-6, gassmann2023dyneinatthe pages 4-5, d’amico2022conformationaltransitionsof pages 1-2, feng2024emergingroleand pages 1-2)

1) Key concepts, definitions, and current understanding

1.1 What SPDL1/Spindly is

Spindly (SPDL1) is a coiled-coil activating adaptor that links the microtubule minus-end motor cytoplasmic dynein-1 and its cofactor dynactin to the kinetochore fibrous corona during mitosis, enabling dynein recruitment/activation at kinetochores. (gassmann2023dyneinatthe pages 4-5, gassmann2023dyneinatthe pages 5-6)

A core organizing concept is that “activating adaptors” are not merely tethers: they stabilize the dynein–dynactin interaction and promote formation of a motile dynein–dynactin–adaptor complex (here, DDS = dynein–dynactin–Spindly). (gassmann2023dyneinatthe pages 4-5)

1.2 Kinetochore/corona and spindle assembly checkpoint (SAC) silencing

The fibrous corona is a dynamic outer kinetochore layer that concentrates microtubule-binding and checkpoint proteins early in mitosis. Spindly operates within the RZZ–Spindly pathway to recruit dynein–dynactin to this region and to promote dynein-dependent “stripping” (poleward transport/removal) of corona material, including checkpoint effectors, as kinetochores achieve productive microtubule attachments—an important mechanism contributing to SAC silencing and error avoidance. (gassmann2023dyneinatthe pages 4-5, gassmann2023dyneinatthe pages 3-4)

2) Molecular mechanism: domains, interactions, and regulation

2.1 Domain architecture and dynein/dynactin binding logic

A domain schematic from a 2023 review summarizes Spindly’s key motifs and post-translational targeting signal, including:
- CC1 box: creates a binding pocket for a conserved amphipathic helix in dynein LIC (light intermediate chain).
- Spindly motif: contributes to interaction with the dynactin pointed-end.
- C-terminal CAAX motif enabling farnesylation.
- N-terminal functional partitioning (roughly 1–275 for dynein/dynactin recruitment; 276–605 for kinetochore targeting/corona formation). (gassmann2023dyneinatthe pages 4-5, gassmann2023dyneinatthe pages 5-6)

Image evidence: The Spindly domain architecture and the kinetochore recruitment model are shown schematically in the cited review figures. (gassmann2023dyneinatthe media 046141ea, gassmann2023dyneinatthe media fb7cb4cf)

2.2 Recruitment to kinetochores via RZZ and farnesylation

Spindly is recruited to kinetochores primarily through the RZZ complex (ROD–ZW10–ZWILCH). A key targeting mechanism is C-terminal farnesylation, with the Rod β-propeller acting as a farnesyl receptor in humans. (gassmann2023dyneinatthe pages 6-7, barbosa2020rzzspindlydyneinyougot pages 5-7)

2.3 Autoinhibition and kinetochore-dependent activation (structural/biochemical understanding)

A major mechanistic insight from structure–function work is that full-length Spindly is autoinhibited: it adopts a folded/closed conformation that occludes the CC1 box and Spindly motif, preventing productive binding to dynein–dynactin in solution. (d’amico2022conformationaltransitionsof pages 1-2, d’amico2022conformationaltransitionsof pages 11-13)

Importantly, RZZ binding alone is insufficient to fully “open” Spindly into a dynein–dynactin-binding competent state; the data support a multi-trigger activation model at kinetochores (RZZ plus at least one additional kinetochore cue/receptor). (d’amico2022conformationaltransitionsof pages 11-13, d’amico2022conformationaltransitionsof pages 13-14, gassmann2023dyneinatthe pages 6-7)

A 2023 synthesis describes a regulatory segment in CC2 (residues ~276–306) folding back onto the CC1 box to enforce autoinhibition, thereby preventing inappropriate dynein activation away from kinetochores and coupling activation to corona assembly. (gassmann2023dyneinatthe pages 6-7)

2.4 Kinase regulation and corona dynamics

Multiple mitotic kinases regulate the RZZ–Spindly–dynein module:
- MPS1 activity is required for robust RZZ–Spindly recruitment/corona expansion; MPS1-dependent ROD phosphorylation promotes expansion. (barbosa2020rzzspindlydyneinyougot pages 5-7, barbosa2022theroleof pages 17-18, gassmann2023dyneinatthe pages 7-8)
- PLK1/Polo phosphorylates Spindly to tune coupling/uncoupling between RZZ and dynein, helping prevent premature stabilization of erroneous attachments early in mitosis and allowing later transition to stable end-on attachments. (barbosa2020rzzspindlydyneinyougot pages 1-3, barbosa2020rzzspindlydyneinyougot pages 3-5, barbosa2020rzzspindlydyneinyougot pages 5-7)

3) Cellular functions (experimentally supported)

3.1 Spindle assembly checkpoint silencing via corona disassembly (updated model)

A key 2023 mechanistic advance is that kinetochore dynein’s checkpoint-silencing role is restricted primarily to disassembly of the fibrous corona, rather than wholesale removal of checkpoint proteins from the entire outer kinetochore. Spindly is central because it recruits dynein to the corona. (ide2023theroleof pages 1-2, ide2023theroleof pages 9-10)

Quantitative evidence from the 2023 study: a Spindly mutant (SpindlyΔCCS) that fails to recruit dynein but allows corona expansion yields strong mitotic arrest phenotypes (mitotic index 63.9% with wild-type Mad1). Disrupting corona-localized Mad1/Mad2 (Mad1-3EK) in the same SpindlyΔCCS background reduces the mitotic index (30.8%) and increases mitotic exit over 15 h (49% vs 8% for SpindlyΔCCS + WT Mad1), supporting that dynein recruited through Spindly is essential to remove a potent corona-derived inhibitory signal when few kinetochores remain unattached. (ide2023theroleof pages 9-10)

3.2 Promoting correct kinetochore–microtubule attachments and limiting segregation errors

A 2023 review describes that Spindly-dependent dynein stripping is triggered after end-coupled microtubule attachment, enabling removal of corona components (including Mad1–Mad2) and promoting kinetochore remodeling/compaction. Perturbations that prevent Spindly-dependent dynein recruitment/stripping can lead to merotelic attachments and chromosome mis-segregation. (gassmann2023dyneinatthe pages 4-5, gassmann2023dyneinatthe pages 3-4)

4) Subcellular localization

A 2024 SPDL1-focused review summarizes Spindly localization dynamics:
- Interphase: nuclear localization.
- Prometaphase: kinetochore localization.
- Pre-metaphase/metaphase: relocalization toward spindle poles.
- Loss after chromosome congression. (feng2024emergingroleand pages 1-2)

Consistent with the mechanistic literature, Spindly is specifically enriched at the kinetochore fibrous corona in early mitosis where it enables dynein–dynactin recruitment. (d’amico2022conformationaltransitionsof pages 1-2, ide2023theroleof pages 1-2)

5) Recent developments and latest research (prioritizing 2023–2024)

5.1 2023: dynein/Spindly in checkpoint silencing refined to corona disassembly

The 2023 Molecular Biology of the Cell study provides a refined checkpoint-silencing model emphasizing that dynein recruited via Spindly primarily removes corona-localized checkpoint effectors, effectively “priming” the checkpoint system for stable end-on attachment signals. (ide2023theroleof pages 1-2, ide2023theroleof pages 9-10)

5.2 2024: disease-focused synthesis of SPDL1 (review)

A 2024 Open Medicine review provides a consolidated picture of SPDL1/Spindly biology and disease relevance, summarizing SPDL1 structure (~605 aa; farnesylation; kinetochore-binding segment), core mitotic functions (SAC silencing, microtubule attachment), and diverse disease associations including pulmonary fibrosis and multiple cancers. (feng2024emergingroleand pages 1-2, feng2024emergingroleand pages 6-7)

5.3 2024: oncology example—ESCC functional targeting and prognostic modeling

A 2024 PLOS ONE study in esophageal squamous cell carcinoma (ESCC) reports SPDL1 is overexpressed in tumor tissue datasets (TCGA/GEO), correlates with survival through SPDL1-related lncRNA risk scores (P<0.05), and that SPDL1 inhibition in TE-1 cells suppresses proliferation, migration, and invasion (P<0.05), supporting biomarker/target hypotheses in a real tumor setting. (liu2024inhibitingtheexpression pages 1-2)

5.4 2024: large-scale human genetics (preprint) implicating SPDL1 in prostate cancer risk

A May 2024 medRxiv meta-analysis of rare coding germline variation in prostate cancer (37,184 cases; 331,329 male controls overall) reports rare non-synonymous variants in SPDL1 among genes associated with decreased prostate cancer risk (preprint; not peer-reviewed). (mitchell2024characterisingthecontribution pages 1-4)

6) Human disease associations and statistics (with emphasis on fibrosis genetics)

6.1 Idiopathic pulmonary fibrosis (IPF): replicated SPDL1 missense association

A 2021 Communications Biology sequencing study identifies a rare SPDL1 missense variant p.Arg20Gln (rs116483731) associated with IPF:
- Discovery: 752 sporadic IPF cases vs 119,055 controls; allele frequency 2.2% in cases vs 0.78% controls; OR 2.87 (95% CI 2.03–4.07), p=2.4×10−7.
- Replication: FinnGen 1028 cases vs 196,986 controls; case frequency 6.9% vs control 3.0%; OR 3.13 (95% CI 2.37–4.14), p=1.0×10−15.
- Combined evidence: p=2.2×10−20.
The authors highlight SPDL1/Spindly as a mitotic checkpoint signaling gene not previously tied to fibrosis, suggesting a new mechanistic axis for IPF biology and drug discovery. (dhindsa2021identificationofa pages 2-3, dhindsa2021identificationofa pages 1-2)

Clinical context reported in the same study: median diagnosis age 71 years, median survival 39.4 months, underscoring unmet need and the potential value of genetic stratification for etiology and therapy development. (dhindsa2021identificationofa pages 1-2)

6.2 Antagonistic pleiotropy (IPF risk vs cancer protection) and somatic chromosomal alterations (preprint)

A 2021 medRxiv analysis using FinnGen/UK Biobank data reports the same SPDL1 missense allele shows antagonistic pleiotropy: increased IPF risk but decreased cancer risk. In FinnGen, the SPDL1 missense allele is associated with IPF risk (HR 2.27, 95% CI 1.86–2.76; P=4.46×10−16) and reduced overall cancer risk (OR 0.81, 95% CI 0.77–0.85; P=2.05×10−15; longitudinal cancer HR 0.83). The allele is also associated with reduced mosaic chromosomal alterations (OR 0.71, 95% CI 0.63–0.79; P=5.36×10−9), supporting a hypothesis that reduced accumulation of chromosomal alterations may protect against cancer while predisposing to fibrosis/senescence pathways (preprint). (koskela2021geneticvariantin pages 7-10)

7) Current applications and real-world implementations

  1. Clinical genetics / risk stratification in IPF: The replicated association of SPDL1 p.Arg20Gln with IPF (OR ~2.9–3.1; strong replication; large cohorts) supports its use as a genetic risk marker in research and potentially in clinical genetic panels for pulmonary fibrosis risk assessment/stratification, alongside known loci such as MUC5B and telomere-related genes (implementation depends on local practice and validation studies). (dhindsa2021identificationofa pages 2-3, dhindsa2021identificationofa pages 1-2)

  2. Therapeutic discovery for IPF: By implicating a mitotic checkpoint/kinetochore–dynein pathway in IPF—distinct from telomere-length mechanisms—SPDL1 provides a mechanistically distinct hypothesis space for target discovery, though direct SPDL1-targeted therapies are not established. (dhindsa2021identificationofa pages 1-2, dhindsa2021identificationofa pages 3-5)

  3. Oncology biomarker/target exploration: A 2024 ESCC study supports SPDL1 as a prognostic/biology-linked marker and suggests suppressing SPDL1 can inhibit malignant cell phenotypes in vitro, motivating exploratory targeting strategies in specific tumor contexts; however, prognostic directionality appears cancer-type dependent per review synthesis. (liu2024inhibitingtheexpression pages 1-2, feng2024emergingroleand pages 6-7)

8) Expert synthesis and interpretation (authoritative perspectives)

  • A 2023 Journal of Cell Science review frames SPDL1/Spindly as a kinetochore-localized activating adaptor that couples dynein recruitment to motor activation, and emphasizes that dynein/Spindly-dependent corona stripping is integrated with establishment of correct end-on attachments and checkpoint silencing; several mechanistic parameters (stoichiometry of DDS; triggers of Spindly activation; full corona architecture) remain open. (gassmann2023dyneinatthe pages 4-5, gassmann2023dyneinatthe pages 3-4, gassmann2023dyneinatthe pages 6-7)

  • A 2024 SPDL1-focused review synthesizes broader disease connections, emphasizing mitotic checkpoint silencing, microtubule attachment and potential roles in migration/drug response as recurring biological themes; it highlights heterogeneity and contradictions in cancer associations as an area requiring more rigorous clinical validation. (feng2024emergingroleand pages 1-2, feng2024emergingroleand pages 6-7)

9) Summary tables

9.1 Core functional annotation (mechanism-level)

Aspect Current best-supported annotation for human SPDL1/Spindly Key sources
Molecular role Kinetochore-localized dynein–dynactin activating adaptor; assembles DDS at fibrous corona (gassmann2023dyneinatthe pages 4-5)
Recruitment platform RZZ complex (ROD/ZW10/ZWILCH); oligomerization contributes to corona organization (gassmann2023dyneinatthe pages 6-7, gassmann2023dyneinatthe pages 7-8)
Targeting PTM C-terminal farnesylation (CAAX); Rod β-propeller is farnesyl receptor (gassmann2023dyneinatthe pages 6-7, barbosa2020rzzspindlydyneinyougot pages 5-7)
Dynein binding CC1 box → dynein LIC amphipathic helix; additional motifs engage dynein/dynactin (gassmann2023dyneinatthe pages 4-5, barbosa2020rzzspindlydyneinyougot pages 3-5)
Dynactin binding Spindly motif engages dynactin pointed-end (gassmann2023dyneinatthe pages 4-5, barbosa2020rzzspindlydyneinyougot pages 3-5)
Regulation Autoinhibition (closed conformation occludes CC1 box/Spindly motif); activated at kinetochores (d’amico2022conformationaltransitionsof pages 1-2, d’amico2022conformationaltransitionsof pages 11-13)
Checkpoint role Dynein recruited by Spindly disassembles corona and removes corona-localized checkpoint effectors (ide2023theroleof pages 1-2, ide2023theroleof pages 9-10)

9.2 Selected recent/impactful studies with quantitative data

Year Study Topic Key quantitative findings URL
2023 Ide et al., Mol Biol Cell Dynein/Spindly in SAC silencing via corona disassembly SpindlyΔCCS + WT Mad1 mitotic index 63.9% vs SpindlyΔCCS + Mad1-3EK 30.8%; mitotic exit over 15h 8% vs 49% https://doi.org/10.1091/mbc.e23-04-0130
2024 Feng et al., Open Medicine (review) SPDL1 in health/disease synthesis Reports 605-aa Q96EA4 protein; summarizes mitotic roles and disease links https://doi.org/10.1515/med-2024-0922
2024 Liu et al., PLOS ONE ESCC biomarker/functional study SPDL1 inhibition suppresses TE-1 proliferation/migration/invasion (P<0.05); risk models correlate with OS (P<0.05) https://doi.org/10.1371/journal.pone.0302312
2024 Mitchell et al., medRxiv (preprint) Prostate cancer rare variant meta-analysis Cohort sizes 37,184 cases; 331,329 controls; SPDL1 rare variants associated with decreased risk (no OR in excerpt) https://doi.org/10.1101/2024.05.10.24307164
2021 Dhindsa et al., Commun Biol IPF genetics p.Arg20Gln (rs116483731) OR 2.87 (p=2.4×10−7) discovery; OR 3.13 (p=1.0×10−15) replication; combined p=2.2×10−20 https://doi.org/10.1038/s42003-021-01910-y
2021 Koskela et al., medRxiv (preprint) IPF–cancer antagonistic pleiotropy IPF HR 2.27; cancer OR 0.81; mosaic chromosomal alterations OR 0.71 https://doi.org/10.1101/2021.05.07.21255988

10) Notes on evidence limitations

  • Some 2024 oncology/genetics results are preprints (medRxiv) and should be interpreted as provisional until peer reviewed. (mitchell2024characterisingthecontribution pages 1-4, koskela2021geneticvariantin pages 7-10)
  • Cancer associations for SPDL1 appear context-dependent (tumor type–specific directionality), per 2024 synthesis. (feng2024emergingroleand pages 6-7)

Key cited visuals

  • Spindly domain architecture and kinetochore recruitment pathway cartoons (used as visual evidence in this report). (gassmann2023dyneinatthe media 046141ea, gassmann2023dyneinatthe media fb7cb4cf)

References

  1. (gassmann2023dyneinatthe pages 5-6): Reto Gassmann. Dynein at the kinetochore. Journal of cell science, Mar 2023. URL: https://doi.org/10.1242/jcs.220269, doi:10.1242/jcs.220269. This article has 24 citations and is from a domain leading peer-reviewed journal.

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  6. (gassmann2023dyneinatthe media 046141ea): Reto Gassmann. Dynein at the kinetochore. Journal of cell science, Mar 2023. URL: https://doi.org/10.1242/jcs.220269, doi:10.1242/jcs.220269. This article has 24 citations and is from a domain leading peer-reviewed journal.

  7. (gassmann2023dyneinatthe media fb7cb4cf): Reto Gassmann. Dynein at the kinetochore. Journal of cell science, Mar 2023. URL: https://doi.org/10.1242/jcs.220269, doi:10.1242/jcs.220269. This article has 24 citations and is from a domain leading peer-reviewed journal.

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  11. (d’amico2022conformationaltransitionsof pages 13-14): Ennio A. d’Amico, Misbha Ud Din Ahmad, Verena Cmentowski, Mathias Girbig, Franziska Müller, Sabine Wohlgemuth, Andreas Brockmeyer, Stefano Maffini, Petra Janning, Ingrid R. Vetter, Andrew P. Carter, Anastassis Perrakis, and Andrea Musacchio. Conformational transitions of the spindly adaptor underlie its interaction with dynein and dynactin. The Journal of Cell Biology, Sep 2022. URL: https://doi.org/10.1083/jcb.202206131, doi:10.1083/jcb.202206131. This article has 34 citations.

  12. (barbosa2022theroleof pages 17-18): João Barbosa, Claudio E. Sunkel, and Carlos Conde. The role of mitotic kinases and the rzz complex in kinetochore-microtubule attachments: doing the right link. Frontiers in Cell and Developmental Biology, Jan 2022. URL: https://doi.org/10.3389/fcell.2022.787294, doi:10.3389/fcell.2022.787294. This article has 18 citations.

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  14. (barbosa2020rzzspindlydyneinyougot pages 1-3): João Barbosa, Carlos Conde, and Claudio Sunkel. Rzz-spindly-dynein: you got to keep ‘em separated. Cell Cycle, 19:1716-1726, Jun 2020. URL: https://doi.org/10.1080/15384101.2020.1780382, doi:10.1080/15384101.2020.1780382. This article has 10 citations and is from a peer-reviewed journal.

  15. (barbosa2020rzzspindlydyneinyougot pages 3-5): João Barbosa, Carlos Conde, and Claudio Sunkel. Rzz-spindly-dynein: you got to keep ‘em separated. Cell Cycle, 19:1716-1726, Jun 2020. URL: https://doi.org/10.1080/15384101.2020.1780382, doi:10.1080/15384101.2020.1780382. This article has 10 citations and is from a peer-reviewed journal.

  16. (ide2023theroleof pages 1-2): Amy H. Ide, Keith F. DeLuca, O’Neil Wiggan, Steven M. Markus, and Jennifer G. DeLuca. The role of kinetochore dynein in checkpoint silencing is restricted to disassembly of the corona. Jun 2023. URL: https://doi.org/10.1091/mbc.e23-04-0130, doi:10.1091/mbc.e23-04-0130. This article has 10 citations and is from a domain leading peer-reviewed journal.

  17. (ide2023theroleof pages 9-10): Amy H. Ide, Keith F. DeLuca, O’Neil Wiggan, Steven M. Markus, and Jennifer G. DeLuca. The role of kinetochore dynein in checkpoint silencing is restricted to disassembly of the corona. Jun 2023. URL: https://doi.org/10.1091/mbc.e23-04-0130, doi:10.1091/mbc.e23-04-0130. This article has 10 citations and is from a domain leading peer-reviewed journal.

  18. (feng2024emergingroleand pages 6-7): Yuejiao Feng, Donghao Tang, and Jie Wang. Emerging role and function of spdl1 in human health and diseases. Open Medicine, Jan 2024. URL: https://doi.org/10.1515/med-2024-0922, doi:10.1515/med-2024-0922. This article has 4 citations and is from a peer-reviewed journal.

  19. (liu2024inhibitingtheexpression pages 1-2): Tao Liu, Juan Xu, Qun-xian Zhang, Yan-Jiao Huang, Wei Wang, and Zhu Fu. Inhibiting the expression of spindle appendix cooled coil protein 1 can suppress tumor cell growth and metastasis and is associated with cancer immune cells in esophageal squamous cell carcinoma. PLOS ONE, 19(8):e0302312, Aug 2024. URL: https://doi.org/10.1371/journal.pone.0302312, doi:10.1371/journal.pone.0302312. This article has 1 citations and is from a peer-reviewed journal.

  20. (mitchell2024characterisingthecontribution pages 1-4): Jonathan Mitchell, Niedzica Camacho, Patrick Shea, Konrad H. Stopsack, Vijai Joseph, Oliver Burren, Ryan Dhindsa, Abhishek Nag, Jacob E. Berchuck, Amanda O’Neill, Ali Abbasi, Anthony W. Zoghbi, Jesus Alegre-Díaz, Pablo Kuri-Morales, Jaime Berumen, Roberto Tapia-Conyer, Jonathan Emberson, Jason M. Torres, Rory Collins, Quanli Wang, David Goldstein, Athena Matakidou, Carolina Haefliger, Lauren Anderson-Dring, Ruth March, Vaidehi Jobanputra, Brian Dougherty, Keren Carss, Slavé Petrovski, Philip W. Kantoff, Kenneth Offit, Lorelei A. Mucci, Mark Pomerantz, and Margarete A. Fabre. Characterising the contribution of rare protein-coding germline variants to prostate cancer risk and severity in 37,184 cases. medRxiv, May 2024. URL: https://doi.org/10.1101/2024.05.10.24307164, doi:10.1101/2024.05.10.24307164. This article has 4 citations.

  21. (dhindsa2021identificationofa pages 2-3): Ryan S. Dhindsa, Johan Mattsson, Abhishek Nag, Quanli Wang, Louise V. Wain, Richard Allen, Eleanor M. Wigmore, Kristina Ibanez, Dimitrios Vitsios, Sri V. V. Deevi, Sebastian Wasilewski, Maria Karlsson, Glenda Lassi, Henric Olsson, Daniel Muthas, Susan Monkley, Alex Mackay, Lynne Murray, Simon Young, Carolina Haefliger, Toby M. Maher, Maria G. Belvisi, Gisli Jenkins, Philip L. Molyneaux, Adam Platt, and Slavé Petrovski. Identification of a missense variant in spdl1 associated with idiopathic pulmonary fibrosis. Communications Biology, Mar 2021. URL: https://doi.org/10.1038/s42003-021-01910-y, doi:10.1038/s42003-021-01910-y. This article has 69 citations and is from a peer-reviewed journal.

  22. (dhindsa2021identificationofa pages 1-2): Ryan S. Dhindsa, Johan Mattsson, Abhishek Nag, Quanli Wang, Louise V. Wain, Richard Allen, Eleanor M. Wigmore, Kristina Ibanez, Dimitrios Vitsios, Sri V. V. Deevi, Sebastian Wasilewski, Maria Karlsson, Glenda Lassi, Henric Olsson, Daniel Muthas, Susan Monkley, Alex Mackay, Lynne Murray, Simon Young, Carolina Haefliger, Toby M. Maher, Maria G. Belvisi, Gisli Jenkins, Philip L. Molyneaux, Adam Platt, and Slavé Petrovski. Identification of a missense variant in spdl1 associated with idiopathic pulmonary fibrosis. Communications Biology, Mar 2021. URL: https://doi.org/10.1038/s42003-021-01910-y, doi:10.1038/s42003-021-01910-y. This article has 69 citations and is from a peer-reviewed journal.

  23. (koskela2021geneticvariantin pages 7-10): Jukka T. Koskela, Paavo Häppölä, Aoxing Liu, Juulia Partanen, Giulio Genovese, Mykyta Artomov, Mikko N.M. Myllymäki, Masahiro Kanai, Wei Zhou, Juha M. Karjalainen, Teemu Palviainen, Justiina Ronkainen, Sylvain Sebert, Taru Tukiainen, Priit Palta, Jaakko Kaprio, Mitja Kurki, Andrea Ganna, Aarno Palotie, Tarja Laitinen, Marjukka Myllärniemi, and Mark J. Daly. Genetic variant in spdl1 reveals novel mechanism linking pulmonary fibrosis risk and cancer protection. MedRxiv, May 2021. URL: https://doi.org/10.1101/2021.05.07.21255988, doi:10.1101/2021.05.07.21255988. This article has 11 citations.

  24. (dhindsa2021identificationofa pages 3-5): Ryan S. Dhindsa, Johan Mattsson, Abhishek Nag, Quanli Wang, Louise V. Wain, Richard Allen, Eleanor M. Wigmore, Kristina Ibanez, Dimitrios Vitsios, Sri V. V. Deevi, Sebastian Wasilewski, Maria Karlsson, Glenda Lassi, Henric Olsson, Daniel Muthas, Susan Monkley, Alex Mackay, Lynne Murray, Simon Young, Carolina Haefliger, Toby M. Maher, Maria G. Belvisi, Gisli Jenkins, Philip L. Molyneaux, Adam Platt, and Slavé Petrovski. Identification of a missense variant in spdl1 associated with idiopathic pulmonary fibrosis. Communications Biology, Mar 2021. URL: https://doi.org/10.1038/s42003-021-01910-y, doi:10.1038/s42003-021-01910-y. This article has 69 citations and is from a peer-reviewed journal.

Artifacts

## Context ID: pqac-00000031 The requested schematics are found in Figures 2 and 3 of the document. Figure 2A illustrates the domain architecture of Spindly (SP

Citations

  1. gassmann2023dyneinatthe pages 4-5
  2. gassmann2023dyneinatthe pages 6-7
  3. ide2023theroleof pages 9-10
  4. feng2024emergingroleand pages 1-2
  5. liu2024inhibitingtheexpression pages 1-2
  6. mitchell2024characterisingthecontribution pages 1-4
  7. dhindsa2021identificationofa pages 1-2
  8. koskela2021geneticvariantin pages 7-10
  9. feng2024emergingroleand pages 6-7
  10. gassmann2023dyneinatthe pages 5-6
  11. gassmann2023dyneinatthe pages 3-4
  12. barbosa2020rzzspindlydyneinyougot pages 5-7
  13. barbosa2022theroleof pages 17-18
  14. gassmann2023dyneinatthe pages 7-8
  15. barbosa2020rzzspindlydyneinyougot pages 1-3
  16. barbosa2020rzzspindlydyneinyougot pages 3-5
  17. ide2023theroleof pages 1-2
  18. dhindsa2021identificationofa pages 2-3
  19. dhindsa2021identificationofa pages 3-5
  20. https://doi.org/10.1091/mbc.e23-04-0130
  21. https://doi.org/10.1515/med-2024-0922
  22. https://doi.org/10.1371/journal.pone.0302312
  23. https://doi.org/10.1101/2024.05.10.24307164
  24. https://doi.org/10.1038/s42003-021-01910-y
  25. https://doi.org/10.1101/2021.05.07.21255988
  26. https://doi.org/10.1242/jcs.220269,
  27. https://doi.org/10.1083/jcb.202206131,
  28. https://doi.org/10.1515/med-2024-0922,
  29. https://doi.org/10.1080/15384101.2020.1780382,
  30. https://doi.org/10.3389/fcell.2022.787294,
  31. https://doi.org/10.1091/mbc.e23-04-0130,
  32. https://doi.org/10.1371/journal.pone.0302312,
  33. https://doi.org/10.1101/2024.05.10.24307164,
  34. https://doi.org/10.1038/s42003-021-01910-y,
  35. https://doi.org/10.1101/2021.05.07.21255988,

📚 Additional Documentation

Notes

(SPDL1-notes.md)

SPDL1 (Spindly) Gene Review Notes

Gene Overview

SPDL1 (also known as CCDC99, Spindly, hSpindly) encodes Protein Spindly, a coiled-coil domain-containing protein that functions as a dynein adaptor at kinetochores during mitosis. UniProt: Q96EA4. 605 amino acids. Chromosome 5.

Key Publications and Findings

PMID:17576797 - Griffis et al. 2007, J Cell Biol

  • Title: "Spindly, a novel protein essential for silencing the spindle assembly checkpoint, recruits dynein to the kinetochore."
  • VERIFIED: REAL - Published in J Cell Biol 177:1005-1015 (2007). Authors: Griffis ER, Stuurman N, Vale RD. HHMI/UCSF.
  • This is the discovery paper for Spindly. Identified via RNAi screen in Drosophila S2 cells.
  • Key findings: Spindly accumulates on unattached kinetochores; required for SAC silencing in Drosophila; dynein cannot target to kinetochores after Spindly depletion; human homologue identified with similar function.
  • PMID:17576797

PMID:19468067 - Chan et al. 2009, J Cell Biol

  • Title: "Mitotic control of kinetochore-associated dynein and spindle orientation by human Spindly."
  • VERIFIED: REAL - Published in J Cell Biol 185:859-874 (2009). Authors: Chan YW, Fava LL, Uldschmid A, Schmitz MH, Gerlich DW, Nigg EA, Santamaria A.
  • The primary characterization paper for human Spindly. This is the main reference for most experimental GO annotations.
  • Key findings:
  • hSpindly KT localization controlled by RZZ complex and Aurora B
  • Depletion causes reduced inter-KT tension, unstable KT fibers, prometaphase delay, severe chromosome misalignment
  • Depletion induces striking spindle rotation (rescued by co-depletion of dynein)
  • In contrast to Drosophila, hSpindly depletion does NOT abolish removal of MAD2 and ZW10 from KTs
  • Interacts with KNTC1 (Rod) and ZW10 (interactions appear weak/transient)
  • Localizes to outer kinetochore (IDA), spindle pole (IDA), nucleus in interphase (IDA)
  • PMID:19468067

PMID:25035494 - McKenney et al. 2014, Science

  • Title: "Activation of cytoplasmic dynein motility by dynactin-cargo adapter complexes."
  • VERIFIED: REAL - Published in Science 345:337-341 (2014). Authors: McKenney RJ, Huynh W, Tanenbaum ME, Bhabha G, Vale RD.
  • Key finding: Spindly acts as an adapter protein linking the dynein motor complex to cargo; converts dynein from non-processive to highly processive motor in the presence of dynactin.
  • This paper established the paradigm for dynein-dynactin activation by cargo adaptors (including BICD2, Spindly, etc.)

PMID:30258100 - Conte et al. 2018, Sci Rep

  • Title: "USP45 and Spindly are part of the same complex implicated in cell migration."
  • VERIFIED: REAL - Published in Sci Rep 8:14375 (2018). Authors: Conte C, Griffis ER, Hickson I, Perez-Oliva AB.
  • Key findings:
  • Spindly identified as a new interactor of USP45 by mass spectrometry
  • Interaction depends on catalytic activity of USP45
  • Spindly is monoubiquitinated; USP45 removes this monoubiquitin
  • USP45 has preferential activity on K48 ubiquitin chains
  • USP45 plays a role in cell migration similar to Spindly
  • PMID:30258100

PMID:23382074 - Armour et al. 2013, Mol Cell Biol

  • Title: "A high-confidence interaction map identifies SIRT1 as a mediator of acetylation of USP22 and the SAGA coactivator complex."
  • VERIFIED: REAL - Published in Mol Cell Biol 33:1487-1502 (2013).
  • This paper is about SIRT1/USP22/SAGA complex. SPDL1 interaction with SIRT1 is likely a high-throughput finding from the interaction screen. The enzyme binding annotation (GO:0019899) from this paper is based on SPDL1 appearing in the SIRT1 interactome. The GOA annotation says the IPI is with Q96EB6 (SIRT1). This is from a large-scale interaction study.

PMID:25416956 - Rolland et al. 2014, Cell

  • Title: "A proteome-scale map of the human interactome network."
  • VERIFIED: REAL - Large-scale yeast two-hybrid study. SPDL1 interactions detected: CA8, RTP5, PPP1R18, DNAAF4, TRAF4, USP15.

PMID:25910212 - Sahni et al. 2015, Cell

  • Title: "Widespread macromolecular interaction perturbations in human genetic disorders."
  • VERIFIED: REAL - Follow-up to the interactome network study.

PMID:26871637 - Yang et al. 2016, Cell

  • Title: "Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing."
  • VERIFIED: REAL - Studies alternative splicing effects on protein interactions.

PMID:33961781 - Huttlin et al. 2021, Cell

  • Title: "Dual proteome-scale networks reveal cell-specific remodeling of the human interactome."
  • VERIFIED: REAL - BioPlex 3.0 interactome study.

Additional key papers (not in current annotations):

PMID:20439434 - Gassmann et al. 2010, Genes Dev

  • "Removal of Spindly from microtubule-attached kinetochores controls spindle checkpoint silencing in human cells."
  • Identified conserved Spindly motif essential for dynein targeting to KT. Dynein-mediated removal of Spindly from KTs is the critical reaction in checkpoint silencing.

PMID:20427577 - Barisic et al. 2010, Mol Biol Cell

  • "Spindly/CCDC99 is required for efficient chromosome congression and mitotic checkpoint regulation."
  • Showed Spindly is a mitotic phosphoprotein, interacts with RZZ, and levels at KT are regulated by MT attachment and tension.

PMID:29915359 - Sacristan et al. 2018, Nat Cell Biol

  • "Dynamic kinetochore size regulation promotes microtubule capture and chromosome biorientation in mitosis."
  • Showed Spindly and RZZ drive kinetochore expansion (corona formation) in a dynein-independent manner. C-terminal farnesylation and MPS1 activity cause Spindly conformational changes promoting RZZ-Spindly oligomerization.

PMID:25825516 - Moudgil et al. 2015, J Cell Biol

  • Showed hSpindly undergoes farnesylation at C-terminal cysteine, essential for KT localization and RZZ interaction.

BioReason Analysis Assessment

Verified claims in BioReason's deep research:

  • Correct: IPR028593 (Protein Spindly, chordates) and IPR051149 (Spindly/BICDR Dynein Motor Adapter)
  • Correct: Dynein adapter function at kinetochores
  • Correct: Coiled-coil architecture (residues 2-442)
  • Correct: Roles in chromosome alignment, spindle orientation, protein localization to KT

Questionable/unverified claims in BioReason:

  • Claims about "BUB1B/BUB3" and "NDC80 complex" as direct Spindly receptors at the outer kinetochore: Not supported. Spindly binds via the RZZ complex (Rod/ZW10/Zwilch), not directly to BUB1B or NDC80. This is a significant error.
  • Claims about "SKA1/2/3" and "CENP-F" as Spindly interactors: Not supported by literature. SKA complex and CENP-F are outer KT components but not established Spindly interactors.
  • Claims about "HOX-D13" as a partner: No evidence for this. Likely hallucinated.
  • Claims about "MKLN1 (BICDR)" association: BICDR1/BICDL1 (not MKLN1) is the related dynein adaptor. MKLN1 is muskelin, not the same protein. This is an error.
  • The mention of GO:0098806 "Spindly-BICDR complex" needs verification - this GO term may not exist.
  • Claims about "Golgi-directed transport" via Spindly: The cell migration role is documented but the Golgi mechanism is speculative.

Summary of BioReason accuracy:

The BioReason analysis gets the broad strokes correct (dynein adaptor, kinetochore localization, chromosome alignment, spindle orientation) but contains several specific errors about binding partners (BUB1B, NDC80, SKA, CENP-F, HOX-D13, MKLN1) that are not supported by the literature. The actual RZZ complex interaction is underemphasized.

Bioreason Sft Review

(SPDL1-bioreason-sft-review.md)

BioReason SFT Review: SPDL1 (Spindly)

UniProt: Q96EA4 | Gene: SPDL1 (CCDC99) | Organism: Homo sapiens

Overall Assessment

BioReason's SFT model analysis of SPDL1 captures the broad functional profile correctly but contains several specific factual errors about binding partners and molecular mechanisms that are not supported by the published literature.

Accuracy grade: B- (core function identified correctly; significant errors in molecular details)

Correct Claims

  1. Domain architecture: Correctly identifies IPR028593 (Protein Spindly, chordates, residues 1-605) and IPR051149 (Spindly/BICDR Dynein Motor Adapter, residues 3-468). The coiled-coil N-terminal/mid-region as the motor-adapter module is accurately described.

  2. Core function as dynein adaptor: The central description of Spindly as a dynein-recruiting kinetochore adaptor is correct. PMID:17576797 (Griffis et al. 2007) and PMID:19468067 (Chan et al. 2009) established this function.

  3. GO term associations: The functional summary correctly associates Spindly with GO:0019899 (enzyme binding), GO:0007080 (mitotic metaphase chromosome alignment), GO:0000132 (establishment of mitotic spindle orientation), GO:0034501 (protein localization to kinetochore), GO:0016477 (cell migration), GO:0000940 (outer kinetochore), GO:0000922 (spindle pole), GO:0005829 (cytosol), and GO:0005634 (nucleus). All are validated by experimental evidence.

  4. Cell migration role: Correctly notes the cell migration function, supported by PMID:30258100 (Conte et al. 2018).

  5. Subcellular localization cycle: Accurately describes Spindly cycling between cytosol/nucleus (interphase), outer kinetochore (prometaphase), and spindle pole (metaphase).

Errors and Unsupported Claims

Error 1: Binding partners - BUB1B/BUB3 and NDC80 complex

Claim: "the adaptor binds outer-kinetochore receptors such as BUB1B/BUB3 and the NDC80 complex to anchor dynein"
Verdict: INCORRECT. Spindly is recruited to kinetochores via the RZZ complex (Rod/ZW10/Zwilch), NOT via BUB1B/BUB3 or NDC80. While NDC80/Hec1 is required upstream for RZZ recruitment to kinetochores (PMID:19468067), Spindly does not directly bind NDC80. The Spindly-RZZ interaction is well-documented: "RZZ members (ZW10 and Rod), but not dynein, could be coimmunoprecipitated with hSpindly" (PMID:19468067).

Error 2: SKA1/2/3 and CENP-F interactions

Claim: "The same scaffold can engage additional kinetochore modules (SKA1/2/3, CENP-F) to stabilize end-on attachments"
Verdict: UNSUPPORTED. There is no published evidence that Spindly directly engages the SKA complex or CENP-F. These are independent outer kinetochore components with distinct recruitment mechanisms.

Error 3: HOX-D13 as a partner

Claim: lists "developmental regulators like HOX-D13" as an observed partner
Verdict: HALLUCINATED. There is no evidence in any published study linking Spindly to HOXD13. This appears to be a model confabulation.

Error 4: MKLN1 (muskelin) confused with BICDR

Claim: "association with MKLN1 (BICDR) tunes dynein loading in interphase"
Verdict: INCORRECT identification. MKLN1 is muskelin, a kelch-repeat/LisH-domain protein involved in the CTLH complex. The related dynein adaptor is BICDL1/BICDR1 (BICD family-like cargo adapter 1), encoded by BICDL1 (not MKLN1). These are entirely different proteins.

Error 5: GO:0098806 "Spindly-BICDR complex"

Claim: presence in "GO:0098806 Spindly-BICDR complex"
Verdict: This GO term does not appear to exist in the Gene Ontology. The Spindly/BICDR family relationship is at the InterPro domain level (IPR051149), not as a named GO complex.

Error 6: PLK1 and CDC20 as direct Spindly regulatory partners

Claim: "Phosphorylation by PLK1 and checkpoint factors modulates its affinity and timing"
Verdict: PARTIALLY CORRECT but misleading. PLK1 phosphorylates dynein intermediate chains (PMID:21507953), which affects kinetochore dynein recruitment. However, PLK1 phosphorylation of Spindly itself is not the primary regulatory mechanism. Aurora B, not PLK1, is the established kinase controlling Spindly kinetochore localization (PMID:19468067). The Spindly-CDC20 interaction is not established in the literature.

Missing Key Information

  1. Farnesylation requirement: BioReason fails to mention that C-terminal farnesylation of Spindly is essential for kinetochore targeting and RZZ interaction (PMID:25825516, PMID:25808490). This is a major mechanistic detail.

  2. Corona expansion function: The recently discovered dynein-independent function of Spindly in driving kinetochore corona/fibrous corona expansion through RZZ-Spindly oligomerization (PMID:29915359, Sacristan et al. 2018) is not mentioned.

  3. Conserved Spindly motif: The conserved motif essential for dynein recruitment, identified in PMID:20439434 (Gassmann et al. 2010), is not discussed.

  4. USP45 interaction and monoubiquitination: While cell migration is mentioned, the specific mechanism involving USP45-mediated deubiquitination of monoubiquitinated Spindly (PMID:30258100) is not described.

  5. Species-specific differences: The critical finding that human Spindly, unlike Drosophila Spindly, is NOT required for checkpoint protein (MAD2, ZW10) removal from kinetochores (PMID:19468067) is absent.

GO Term Prediction Assessment

BioReason's GO predictions section was empty (no specific MF, BP, or CC predictions made beyond the thinking trace), which is a missed opportunity given the well-characterized functions of this protein.

Reference Verification Summary

All PMIDs cited in the GOA annotations for SPDL1 were verified as real publications:
- PMID:17576797 - Griffis et al. 2007, J Cell Biol (discovery paper)
- PMID:19468067 - Chan et al. 2009, J Cell Biol (human characterization)
- PMID:23382074 - Armour et al. 2013, Mol Cell Biol (SIRT1 interactome)
- PMID:25035494 - McKenney et al. 2014, Science (dynein activation)
- PMID:25416956 - Rolland et al. 2014, Cell (interactome)
- PMID:25910212 - Sahni et al. 2015, Cell (interactome perturbations)
- PMID:26871637 - Yang et al. 2016, Cell (alternative splicing)
- PMID:30258100 - Conte et al. 2018, Sci Rep (USP45-Spindly)
- PMID:33961781 - Huttlin et al. 2021, Cell (BioPlex 3.0)

All Reactome pathway references are valid entries in the Reactome database.

Conclusion

BioReason's analysis demonstrates competence at identifying broad protein function from domain architecture (InterPro) but exhibits weaknesses in specific protein-protein interaction details and regulatory mechanisms. The model appears to hallucinate specific binding partners (BUB1B, NDC80 as direct Spindly receptors; SKA complex; CENP-F; HOX-D13) and confuses related but distinct proteins (MKLN1 vs BICDL1). For curation purposes, the analysis is useful as a starting framework but requires substantial verification and correction of molecular details.

📄 View Raw YAML

id: Q96EA4
gene_symbol: SPDL1
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  SPDL1 (Spindly/CCDC99) encodes a coiled-coil protein that functions as a
  kinetochore-specific adaptor for cytoplasmic dynein during mitosis. It is
  recruited to the outer kinetochore via the RZZ complex (Rod/ZW10/Zwilch) in
  an Aurora B-regulated manner, and its C-terminal farnesylation is required
  for kinetochore targeting. At kinetochores, Spindly recruits the
  dynein-dynactin complex, which is essential for initial lateral
  kinetochore-microtubule interactions, chromosome congression, and correct
  spindle orientation. Spindly also drives kinetochore corona expansion by
  promoting oligomerization of RZZ-Spindly complexes, independent of dynein.
  Following microtubule attachment, dynein-mediated removal of Spindly from
  kinetochores is the critical event for spindle assembly checkpoint silencing,
  though in human cells (unlike Drosophila) Spindly is not absolutely required
  for checkpoint protein stripping. Spindly also functions as a dynein-dynactin
  cargo adaptor that converts dynein from a non-processive to a highly
  processive motor. Outside mitosis, Spindly interacts with the deubiquitinase
  USP45 and plays a role in cell migration. Spindly is monoubiquitinated and
  deubiquitinated by USP45.
alternative_products:
- name: '1'
  id: Q96EA4-1
- name: '2'
  id: Q96EA4-2
  sequence_note: VSP_022777
- name: '3'
  id: Q96EA4-3
  sequence_note: VSP_054244
existing_annotations:
- term:
    id: GO:0000132
    label: establishment of mitotic spindle orientation
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for establishment of mitotic spindle orientation inferred by
      phylogenetic analysis. This is strongly supported by experimental evidence
      in human cells from PMID:19468067, which showed that hSpindly depletion
      induces striking spindle rotation that is rescued by co-depletion of
      dynein, demonstrating a direct role for kinetochore dynein in spindle
      orientation.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        depletion of hSpindly induces a striking spindle rotation, which can
        be rescued by co-depletion of dynein
- term:
    id: GO:0000922
    label: spindle pole
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for spindle pole localization. Supported by direct
      experimental evidence (IDA) from PMID:19468067, which showed Spindly
      relocalizes to spindle poles before metaphase. Spindly is transported
      poleward by dynein along kinetochore fibers after microtubule attachment.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        hSpindly decorated KTs in early prometaphase before it relocalized to
        the spindle poles before metaphase
- term:
    id: GO:0000940
    label: outer kinetochore
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for outer kinetochore localization. Strongly supported by
      IDA evidence from PMID:19468067 showing Spindly localizes to the outer
      kinetochore in early prometaphase. This is a core localization for
      Spindly, where it recruits dynein-dynactin to drive chromosome movements.
      Falcon deep research further localizes this to the kinetochore fibrous
      corona, the dynamic outer-kinetochore layer assembled in early mitosis.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        localization of human Spindly (hSpindly) to KTs is controlled by the
        Rod/Zw10/Zwilch (RZZ) complex and Aurora B
    - reference_id: file:human/SPDL1/SPDL1-deep-research-falcon.md
      supporting_text: >-
        Spindly is specifically enriched at the **kinetochore fibrous corona**
        in early mitosis where it enables dynein–dynactin recruitment
- term:
    id: GO:0007080
    label: mitotic metaphase chromosome alignment
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for mitotic metaphase chromosome alignment. Strongly
      supported by IMP evidence from PMID:19468067, which showed that hSpindly
      depletion results in severe chromosome misalignment. This is a core
      biological process for Spindly.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        hSpindly depletion results in reduced inter-KT tension, unstable KT
        fibers, an extensive prometaphase delay, and severe chromosome
        misalignment
- term:
    id: GO:0034501
    label: protein localization to kinetochore
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for protein localization to kinetochore. Supported by IMP
      evidence from PMID:19468067 and PMID:17576797. Spindly recruits dynein and
      dynactin to the kinetochore; depletion abolishes kinetochore dynein. This
      is a core function of Spindly. Falcon deep research details the recruitment
      mechanism: Spindly is targeted to kinetochores by the RZZ complex, with
      C-terminal farnesylation engaging the Rod beta-propeller as a farnesyl
      receptor.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        Mitotic control of kinetochore-associated dynein and spindle
        orientation by human Spindly
    - reference_id: PMID:17576797
      supporting_text: >-
        After the depletion of Spindly, dynein cannot target to kinetochores
    - reference_id: file:human/SPDL1/SPDL1-deep-research-falcon.md
      supporting_text: >-
        Spindly is recruited to kinetochores primarily through the **RZZ
        complex** (ROD–ZW10–ZWILCH). A key targeting mechanism is **C-terminal
        farnesylation**, with the **Rod β-propeller** acting as a **farnesyl
        receptor** in humans
- term:
    id: GO:0043515
    label: kinetochore binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for kinetochore binding. Supported by IDA evidence from
      PMID:19468067 showing direct localization to kinetochores. Spindly binds
      kinetochores via the RZZ complex, requiring C-terminal farnesylation for
      this interaction (PMID:25825516).
    action: ACCEPT
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        localization of human Spindly (hSpindly) to KTs is controlled by the
        Rod/Zw10/Zwilch (RZZ) complex and Aurora B
- term:
    id: GO:0000922
    label: spindle pole
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      IEA annotation for spindle pole based on UniProt subcellular location
      mapping. Redundant with the IBA annotation for the same term, and both
      are supported by experimental IDA evidence from PMID:19468067.
    action: ACCEPT
- term:
    id: GO:0000940
    label: outer kinetochore
  evidence_type: IEA
  original_reference_id: GO_REF:0000104
  review:
    summary: >-
      IEA annotation for outer kinetochore based on UniRule transfer. Redundant
      with the IBA annotation for the same term, both supported by IDA from
      PMID:19468067.
    action: ACCEPT
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      IEA annotation for nucleus based on UniProt subcellular location mapping.
      Supported by IDA evidence from PMID:19468067 showing Spindly localizes
      to the nucleus during interphase. This is a non-core localization
      representing the interphase state.
    action: KEEP_AS_NON_CORE
    reason: >-
      Nuclear localization is the interphase state. The core localizations are
      the outer kinetochore and spindle pole during mitosis.
- term:
    id: GO:0005813
    label: centrosome
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      IEA annotation for centrosome based on UniProt subcellular location
      vocabulary mapping. UniProt lists centrosome as a subcellular location.
      This is plausible given that Spindly localizes to spindle poles (which
      contain centrosomes) during mitosis, though the primary experimental
      evidence places Spindly at the kinetochore and spindle pole rather than
      explicitly at the centrosome per se. This is a non-core secondary
      localization.
    action: KEEP_AS_NON_CORE
    reason: >-
      Centrosome localization is implied by spindle pole localization but is not
      the primary or core localization for this protein.
- term:
    id: GO:0007094
    label: mitotic spindle assembly checkpoint signaling
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      IEA annotation for SAC signaling based on InterPro domain mapping
      (IPR028593). The role of Spindly in SAC signaling is complex. In
      Drosophila, Spindly depletion prevents SAC silencing (PMID:17576797). In
      human cells, hSpindly depletion does NOT abolish removal of checkpoint
      proteins MAD2 and ZW10 from kinetochores (PMID:19468067), but Spindly
      mutants that cannot recruit dynein DO prevent checkpoint silencing
      (PMID:20439434). Thus Spindly is involved in SAC signaling primarily
      through its role in checkpoint silencing via dynein-mediated removal of
      checkpoint components. Falcon deep research updates this model with Ide
      et al. 2023: the checkpoint-silencing role of Spindly-recruited dynein is
      restricted primarily to disassembly of the fibrous corona, rather than
      wholesale removal of all checkpoint proteins from the outer kinetochore.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        in contrast to Drosophila, hSpindly depletion does not abolish the
        removal of MAD2 and ZW10 from KTs
    - reference_id: PMID:17576797
      supporting_text: >-
        Spindly, a novel protein essential for silencing the spindle assembly
        checkpoint, recruits dynein to the kinetochore
    - reference_id: file:human/SPDL1/SPDL1-deep-research-falcon.md
      supporting_text: >-
        kinetochore dynein’s checkpoint-silencing role is **restricted
        primarily to disassembly of the fibrous corona**, rather than wholesale
        removal of checkpoint proteins from the entire outer kinetochore
- term:
    id: GO:0034501
    label: protein localization to kinetochore
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA annotation for protein localization to kinetochore via combined
      automated annotation. Redundant with IBA and IMP annotations for the
      same term. Well supported by experimental evidence.
    action: ACCEPT
- term:
    id: GO:0043515
    label: kinetochore binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000104
  review:
    summary: >-
      IEA annotation for kinetochore binding based on UniRule transfer.
      Redundant with IBA and IDA annotations for the same term. Well supported.
    action: ACCEPT
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25416956
  review:
    summary: >-
      Protein binding annotation based on large-scale interactome study (Rolland
      et al. 2014). This is a generic, uninformative term. Spindly interacts
      with CA8, DNAAF4, PPP1R18, RTP5, TRAF4, USP15 in this dataset. These are
      high-throughput yeast two-hybrid results. The interactions with CA8 and
      DNAAF4 have no clear biological context for Spindly function.
    action: REMOVE
    reason: >-
      Protein binding is uninformative per GO curation guidelines. The specific
      biologically relevant interactions (with RZZ complex, dynein, dynactin,
      USP45) are captured by more specific terms.
    supported_by:
    - reference_id: PMID:25416956
      supporting_text: >-
        A proteome-scale map of the human interactome network
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25910212
  review:
    summary: >-
      Protein binding annotation from large-scale interactome perturbation study
      (Sahni et al. 2015). Uninformative generic term from high-throughput data.
    action: REMOVE
    reason: >-
      Protein binding is uninformative per GO curation guidelines.
    supported_by:
    - reference_id: PMID:25910212
      supporting_text: >-
        Widespread macromolecular interaction perturbations in human genetic
        disorders
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:26871637
  review:
    summary: >-
      Protein binding annotation from alternative splicing interactome study
      (Yang et al. 2016). Uninformative generic term from high-throughput data.
    action: REMOVE
    reason: >-
      Protein binding is uninformative per GO curation guidelines.
    supported_by:
    - reference_id: PMID:26871637
      supporting_text: >-
        Widespread Expansion of Protein Interaction Capabilities by
        Alternative Splicing
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:33961781
  review:
    summary: >-
      Protein binding annotation from BioPlex 3.0 dual proteome-scale network
      study (Huttlin et al. 2021). Uninformative generic term.
    action: REMOVE
    reason: >-
      Protein binding is uninformative per GO curation guidelines.
    supported_by:
    - reference_id: PMID:33961781
      supporting_text: >-
        Dual proteome-scale networks reveal cell-specific remodeling of the
        human interactome
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:30258100
  review:
    summary: >-
      Protein binding annotation based on the USP45-Spindly interaction study
      (Conte et al. 2018). The IPI is with USP45 (Q70EL2). While the specific
      interaction is real and biologically relevant, protein binding is too
      generic. A more informative term would be enzyme binding (already
      captured elsewhere) or deubiquitinase binding.
    action: REMOVE
    reason: >-
      Protein binding is uninformative. The USP45 interaction is better captured
      by more specific MF terms.
    supported_by:
    - reference_id: PMID:30258100
      supporting_text: >-
        we have identified Spindly as a new target of USP45
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19468067
  review:
    summary: >-
      Protein binding annotation from Chan et al. 2009. The IPI partners are
      KNTC1/Rod (O43264) and KNTC2/ZW10 (P50748), components of the RZZ
      complex. These interactions are biologically central to Spindly function,
      as Spindly is recruited to kinetochores via the RZZ complex. However,
      protein binding is too generic; kinetochore binding (GO:0043515) and
      dynein complex binding (GO:0070840) are more informative.
    action: REMOVE
    reason: >-
      Protein binding is uninformative. The specific RZZ complex interaction is
      functionally captured by kinetochore binding and the dynein recruitment
      function.
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        RZZ members (ZW10 and Rod), but not dynein, could be
        coimmunoprecipitated with hSpindly
- term:
    id: GO:0016477
    label: cell migration
  evidence_type: IMP
  original_reference_id: PMID:30258100
  review:
    summary: >-
      IMP annotation for cell migration based on Conte et al. 2018, which
      showed that cells lacking Spindly migrate slower than wild-type cells.
      This was supported by an earlier report showing Spindly associates with
      the cell cortex and colocalizes with dynein/dynactin at the leading edge
      of migrating cells. This is a real but non-core function of Spindly;
      its primary evolved function is in mitotic kinetochore-dynein regulation.
    action: KEEP_AS_NON_CORE
    reason: >-
      Cell migration is a documented secondary function of Spindly, but it is
      not the core evolved function. The core function is dynein recruitment to
      kinetochores during mitosis.
    supported_by:
    - reference_id: PMID:30258100
      supporting_text: >-
        cells lacking Spindly migrate slower than wild type cells and that
        this effect is rescued by re-expression of wild-type Spindly
- term:
    id: GO:0019899
    label: enzyme binding
  evidence_type: IPI
  original_reference_id: PMID:23382074
  review:
    summary: >-
      Enzyme binding annotation from Armour et al. 2013 SIRT1 interactome
      study. The IPI partner is SIRT1 (Q96EB6). SPDL1 was identified as a
      SIRT1-interacting protein in a high-throughput screen. The biological
      significance of the SIRT1-Spindly interaction is unclear. This paper is
      primarily about USP22 and SAGA complex regulation; Spindly was a
      background hit. This is unlikely to represent a core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      The SIRT1 interaction is from a large-scale screen and its functional
      significance for Spindly is not established. However, enzyme binding is
      more informative than protein binding and the interaction data are real.
    supported_by:
    - reference_id: PMID:23382074
      supporting_text: >-
        a comprehensive analysis of SIRT1 binding proteins yielding a
        high-confidence interaction map
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-141409
  review:
    summary: >-
      Cytosol annotation from Reactome pathway "Mad1 binds kinetochore." Spindly
      is included as a participant in SAC-related Reactome reactions. Multiple
      redundant TAS annotations for the same GO term from different Reactome
      reactions. The cytosol localization is correct as the interphase/soluble
      pool of Spindly, but this is non-core. Consolidating all Reactome cytosol
      entries into a single review.
    action: KEEP_AS_NON_CORE
    reason: >-
      Cytosol is a valid but non-core localization for Spindly representing the
      soluble pool outside of mitosis.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-141422
  review:
    summary: >-
      Redundant cytosol TAS annotation from Reactome. Same assessment as above.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-141431
  review:
    summary: >-
      Redundant cytosol TAS annotation from Reactome. Same assessment as above.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-141439
  review:
    summary: >-
      Redundant cytosol TAS annotation from Reactome. Same assessment as above.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-1638803
  review:
    summary: >-
      Redundant cytosol TAS annotation from Reactome. Same assessment as above.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-1638821
  review:
    summary: >-
      Redundant cytosol TAS annotation from Reactome. Same assessment as above.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-2467809
  review:
    summary: >-
      Redundant cytosol TAS annotation from Reactome. Same assessment as above.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-2467811
  review:
    summary: >-
      Redundant cytosol TAS annotation from Reactome. Same assessment as above.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-2468287
  review:
    summary: >-
      Redundant cytosol TAS annotation from Reactome. Same assessment as above.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-2484822
  review:
    summary: >-
      Redundant cytosol TAS annotation from Reactome. Same assessment as above.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-375302
  review:
    summary: >-
      Redundant cytosol TAS annotation from Reactome. Same assessment as above.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5666129
  review:
    summary: >-
      Redundant cytosol TAS annotation from Reactome. Same assessment as above.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5666160
  review:
    summary: >-
      Redundant cytosol TAS annotation from Reactome. Same assessment as above.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5666169
  review:
    summary: >-
      Redundant cytosol TAS annotation from Reactome. Same assessment as above.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9648114
  review:
    summary: >-
      Redundant cytosol TAS annotation from Reactome. Same assessment as above.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0000132
    label: establishment of mitotic spindle orientation
  evidence_type: IMP
  original_reference_id: PMID:19468067
  review:
    summary: >-
      IMP annotation for establishment of mitotic spindle orientation from Chan
      et al. 2009. hSpindly depletion induces striking spindle rotation that is
      rescued by co-depletion of dynein, demonstrating that kinetochore dynein
      (recruited by Spindly) is critical for spindle orientation. This is a core
      biological process for Spindly.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        depletion of hSpindly induces a striking spindle rotation, which can
        be rescued by co-depletion of dynein
- term:
    id: GO:0000922
    label: spindle pole
  evidence_type: IDA
  original_reference_id: PMID:19468067
  review:
    summary: >-
      IDA annotation for spindle pole localization from Chan et al. 2009. Direct
      observation that Spindly relocalizes to spindle poles before metaphase via
      dynein-mediated poleward transport.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        hSpindly decorated KTs in early prometaphase before it relocalized to
        the spindle poles before metaphase
- term:
    id: GO:0000940
    label: outer kinetochore
  evidence_type: IDA
  original_reference_id: PMID:19468067
  review:
    summary: >-
      IDA annotation for outer kinetochore localization from Chan et al. 2009.
      Direct observation by immunofluorescence showing Spindly localizes to the
      outer kinetochore in early prometaphase. This is the primary and core
      localization for Spindly during mitosis.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        localization of human Spindly (hSpindly) to KTs is controlled by the
        Rod/Zw10/Zwilch (RZZ) complex and Aurora B
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19468067
  review:
    summary: >-
      Protein binding annotation from Chan et al. 2009 based on interaction
      with KNTC1/Rod and ZW10. Uninformative term; the specific interactions
      are better captured by kinetochore binding.
    action: REMOVE
    reason: >-
      Protein binding is uninformative per GO curation guidelines.
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        RZZ members (ZW10 and Rod), but not dynein, could be
        coimmunoprecipitated with hSpindly
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:19468067
  review:
    summary: >-
      IDA annotation for nuclear localization from Chan et al. 2009. Spindly
      localizes to the nucleus in interphase. This is a non-core secondary
      localization reflecting the interphase distribution. Falcon deep research
      corroborates the cell-cycle localization dynamics: nuclear in interphase,
      then kinetochore in prometaphase.
    action: KEEP_AS_NON_CORE
    reason: >-
      Nuclear localization is the interphase state; the core mitotic
      localizations are outer kinetochore and spindle pole.
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        Interphase localization of hSpindly was mainly nuclear
    - reference_id: file:human/SPDL1/SPDL1-deep-research-falcon.md
      supporting_text: >-
        **Interphase:** nuclear localization.
- term:
    id: GO:0007080
    label: mitotic metaphase chromosome alignment
  evidence_type: IMP
  original_reference_id: PMID:19468067
  review:
    summary: >-
      IMP annotation for mitotic metaphase chromosome alignment from Chan et al.
      2009. hSpindly depletion causes severe chromosome misalignment with
      reduced inter-KT tension and unstable KT fibers. This is a core
      biological process for Spindly.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        hSpindly depletion results in reduced inter-KT tension, unstable KT
        fibers, an extensive prometaphase delay, and severe chromosome
        misalignment
- term:
    id: GO:0034501
    label: protein localization to kinetochore
  evidence_type: IMP
  original_reference_id: PMID:19468067
  review:
    summary: >-
      IMP annotation for protein localization to kinetochore from Chan et al.
      2009. Spindly is required for the recruitment of dynein and dynactin to
      kinetochores. Depletion abolishes kinetochore dynein. This is a core
      function of Spindly.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        localization of human Spindly (hSpindly) to KTs is controlled by the
        Rod/Zw10/Zwilch (RZZ) complex and Aurora B
    - reference_id: PMID:17576797
      supporting_text: >-
        After the depletion of Spindly, dynein cannot target to kinetochores
- term:
    id: GO:0043515
    label: kinetochore binding
  evidence_type: IDA
  original_reference_id: PMID:19468067
  review:
    summary: >-
      IDA annotation for kinetochore binding from Chan et al. 2009. Spindly
      directly binds kinetochores, as demonstrated by immunofluorescence
      microscopy. This binding is mediated via the RZZ complex and requires
      C-terminal farnesylation of Spindly (PMID:25825516). This is a core
      molecular function.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        localization of human Spindly (hSpindly) to KTs is controlled by the
        Rod/Zw10/Zwilch (RZZ) complex and Aurora B
- term:
    id: GO:0070840
    label: dynein complex binding
  evidence_type: IDA
  original_reference_id: PMID:19468067
  review:
    summary: >-
      NEW annotation. Spindly directly recruits the dynein-dynactin complex to
      kinetochores. Chan et al. 2009 showed that hSpindly depletion abolishes
      dynein localization to kinetochores. McKenney et al. 2014 demonstrated
      that Spindly functions as a cargo adaptor that physically links dynein
      to dynactin and activates processive motility. This is more informative
      than the generic protein binding annotations and represents a core
      molecular function. Falcon deep research specifies the binding logic of
      this activating adaptor: a CC1 box binding pocket engages a conserved
      amphipathic helix in dynein LIC, while the Spindly motif engages the
      dynactin pointed-end.
    action: NEW
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        localization of human Spindly (hSpindly) to KTs is controlled by the
        Rod/Zw10/Zwilch (RZZ) complex and Aurora B
    - reference_id: PMID:25035494
      supporting_text: >-
        Activation of cytoplasmic dynein motility by dynactin-cargo adapter
        complexes
    - reference_id: file:human/SPDL1/SPDL1-deep-research-bioreason-sft.md
      supporting_text: >-
        The dynein-adapter core enforces dynein targeting to microtubule
        minus ends and kinetochore receptors
    - reference_id: file:human/SPDL1/SPDL1-deep-research-falcon.md
      supporting_text: >-
        **CC1 box**: creates a binding pocket for a conserved amphipathic helix
        in **dynein LIC (light intermediate chain)**.
- term:
    id: GO:0007018
    label: microtubule-based movement
  evidence_type: IMP
  original_reference_id: PMID:19468067
  review:
    summary: >-
      NEW annotation. Spindly is required for dynein-dependent poleward
      chromosome movements during mitosis. hSpindly depletion results in
      reduced inter-KT tension and unstable KT fibers, consistent with
      impaired microtubule-based movement at kinetochores. Additionally,
      Spindly functions as a dynein-dynactin cargo adaptor that activates
      processive microtubule-based motility (PMID:25035494). Falcon deep
      research notes that Spindly-dependent dynein stripping (poleward transport
      of corona material) is triggered after end-coupled microtubule attachment.
    action: NEW
    supported_by:
    - reference_id: PMID:19468067
      supporting_text: >-
        hSpindly depletion results in reduced inter-KT tension, unstable KT
        fibers, an extensive prometaphase delay, and severe chromosome
        misalignment
    - reference_id: file:human/SPDL1/SPDL1-deep-research-falcon.md
      supporting_text: >-
        Spindly-dependent dynein stripping is triggered after **end-coupled
        microtubule attachment**, enabling removal of corona components
        (including Mad1–Mad2) and promoting kinetochore remodeling/compaction
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with 
    GO terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: >-
    Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: GO_REF:0000104
  title: >-
    Electronic Gene Ontology annotations created by transferring manual GO
    annotations between related proteins based on shared sequence features
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:17576797
  title: >-
    Spindly, a novel protein essential for silencing the spindle assembly
    checkpoint, recruits dynein to the kinetochore.
  findings:
  - statement: >-
      Spindly was discovered as a kinetochore protein required for dynein
      recruitment and SAC silencing in Drosophila; a human homologue was
      identified with similar function.
    supporting_text: >-
      After the depletion of Spindly, dynein cannot target to kinetochores,
      and, as a result, cells arrest in metaphase with high levels of
      kinetochore-bound Mad2 and RZZ
- id: PMID:19468067
  title: >-
    Mitotic control of kinetochore-associated dynein and spindle orientation by
    human Spindly.
  findings:
  - statement: >-
      Human Spindly localizes to the outer kinetochore via the RZZ complex,
      recruits dynein-dynactin, and is required for chromosome alignment and
      spindle orientation. Unlike Drosophila, human Spindly is not required for
      checkpoint protein stripping from kinetochores.
    supporting_text: >-
      hSpindly depletion results in reduced inter-KT tension, unstable KT
      fibers, an extensive prometaphase delay, and severe chromosome
      misalignment...depletion of hSpindly induces a striking spindle
      rotation, which can be rescued by co-depletion of dynein...in contrast
      to Drosophila, hSpindly depletion does not abolish the removal of MAD2
      and ZW10 from KTs
- id: PMID:23382074
  title: >-
    A high-confidence interaction map identifies SIRT1 as a mediator of
    acetylation of USP22 and the SAGA coactivator complex.
  full_text_unavailable: true
  findings:
  - statement: >-
      SPDL1 was identified as a SIRT1-interacting protein in a high-throughput
      interaction screen. The biological significance of this interaction for
      Spindly function is unclear.
    supporting_text: >-
      a comprehensive analysis of SIRT1 binding proteins yielding a
      high-confidence interaction map
- id: PMID:25035494
  title: >-
    Activation of cytoplasmic dynein motility by dynactin-cargo adapter complexes.
  findings:
  - statement: >-
      Spindly functions as a cargo adaptor that links the dynein motor complex
      to various cargos and converts dynein from a non-processive to a highly
      processive motor in the presence of dynactin.
    supporting_text: >-
      Recombinant SNAPf-tagged Rab11-FIP3, human Spindly, and Hook3 (fig
- id: PMID:25416956
  title: A proteome-scale map of the human interactome network.
  findings:
  - statement: >-
      Large-scale yeast two-hybrid interactome study detecting SPDL1
      interactions with multiple partners including CA8, DNAAF4, PPP1R18,
      RTP5, TRAF4, USP15.
    full_text_unavailable: true
    supporting_text: >-
      A proteome-scale map of the human interactome network
- id: PMID:25910212
  title: >-
    Widespread macromolecular interaction perturbations in human genetic disorders.
  findings:
  - statement: >-
      Follow-up interactome perturbation study; SPDL1 interactions detected
      in high-throughput screen.
    full_text_unavailable: true
    supporting_text: >-
      Widespread macromolecular interaction perturbations in human genetic
      disorders
- id: PMID:26871637
  title: >-
    Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.
  findings:
  - statement: >-
      Alternative splicing interactome study; SPDL1 isoform interactions
      detected.
    full_text_unavailable: true
    supporting_text: >-
      Widespread Expansion of Protein Interaction Capabilities by Alternative
      Splicing
- id: PMID:30258100
  title: >-
    USP45 and Spindly are part of the same complex implicated in cell migration.
  findings:
  - statement: >-
      USP45 and Spindly form a complex; Spindly is monoubiquitinated and
      deubiquitinated by USP45; both play roles in cell migration.
    supporting_text: >-
      Here, we also show that Spindly is mono-ubiquitylated and this can be
      specifically removed by USP45 in its active form but not by the
      catalytic inactive form
- id: PMID:33961781
  title: >-
    Dual proteome-scale networks reveal cell-specific remodeling of the human
    interactome.
  findings:
  - statement: >-
      BioPlex 3.0 dual proteome-scale interactome study; SPDL1 interactions
      detected in high-throughput AP-MS.
    full_text_unavailable: true
    supporting_text: >-
      Dual proteome-scale networks reveal cell-specific remodeling of the
      human interactome
- id: PMID:20439434
  title: >-
    Removal of Spindly from microtubule-attached kinetochores controls spindle
    checkpoint silencing in human cells.
  full_text_unavailable: true
  findings:
  - statement: >-
      Dynein-mediated removal of Spindly from microtubule-attached
      kinetochores is the critical reaction in checkpoint silencing.
      A conserved Spindly motif is essential for dynein targeting to
      kinetochores.
    supporting_text: >-
      we identify a conserved motif in Spindly that is essential for
      kinetochore targeting of dynein
- id: PMID:29915359
  title: >-
    Dynamic kinetochore size regulation promotes microtubule capture and
    chromosome biorientation in mitosis.
  findings:
  - statement: >-
      Spindly and RZZ drive kinetochore corona expansion in a
      dynein-independent manner. C-terminal farnesylation and MPS1 kinase
      activity cause Spindly conformational changes promoting
      oligomerization of RZZ-Spindly complexes.
    supporting_text: >-
      the dynein adaptor Spindly and the RZZ (ROD-Zwilch-ZW10) complex drive
      kinetochore expansion in a dynein-independent manner
- id: file:human/SPDL1/SPDL1-deep-research-bioreason-sft.md
  title: >-
    BioReason deep research on SPDL1 (Spindly)
  findings:
  - statement: >-
      BioReason analysis correctly identifies the dynein-adapter core
      architecture and kinetochore adaptor function. Contains some errors
      regarding specific binding partners (BUB1B, NDC80, SKA, CENP-F,
      HOX-D13, MKLN1) that are not supported by published literature.
- id: file:human/SPDL1/SPDL1-deep-research-falcon.md
  title: >-
    Falcon (Edison) deep research on human SPDL1 (Spindly, Q96EA4)
  findings:
  - statement: >-
      Spindly is a coiled-coil activating adaptor that links the minus-end
      motor cytoplasmic dynein-1 and its cofactor dynactin to the kinetochore
      fibrous corona during mitosis, enabling dynein recruitment and activation
      at kinetochores.
    reference_section_type: RESULTS
    supporting_text: >-
      links the microtubule minus-end motor **cytoplasmic dynein-1** and its
      cofactor **dynactin** to the **kinetochore fibrous corona** during
      mitosis, enabling dynein recruitment/activation at kinetochores
  - statement: >-
      Spindly operates within the RZZ-Spindly pathway to recruit
      dynein-dynactin to the fibrous corona and to promote dynein-dependent
      poleward stripping of corona material, contributing to SAC silencing.
    reference_section_type: RESULTS
    supporting_text: >-
      Spindly operates within the **RZZ–Spindly pathway** to recruit
      dynein–dynactin to this region and to promote **dynein-dependent
      “stripping”** (poleward transport/removal) of corona material
  - statement: >-
      Domain architecture: a CC1 box creates a binding pocket for a conserved
      amphipathic helix in dynein LIC; the Spindly motif engages the dynactin
      pointed-end; a C-terminal CAAX motif enables farnesylation.
    reference_section_type: RESULTS
    supporting_text: >-
      **Spindly motif**: contributes to interaction with the **dynactin
      pointed-end**.
  - statement: >-
      Spindly is recruited to kinetochores via the RZZ complex (ROD-ZW10-ZWILCH)
      and C-terminal farnesylation, with the Rod beta-propeller acting as a
      farnesyl receptor in humans.
    reference_section_type: RESULTS
    supporting_text: >-
      Spindly is recruited to kinetochores primarily through the **RZZ
      complex** (ROD–ZW10–ZWILCH). A key targeting mechanism is **C-terminal
      farnesylation**, with the **Rod β-propeller** acting as a **farnesyl
      receptor** in humans
  - statement: >-
      Full-length Spindly is autoinhibited, adopting a closed conformation that
      occludes the CC1 box and Spindly motif and prevents productive
      dynein-dynactin binding in solution until activated at kinetochores.
    reference_section_type: RESULTS
    supporting_text: >-
      full-length Spindly is autoinhibited
  - statement: >-
      Updated 2023 model (Ide et al.): the checkpoint-silencing role of
      kinetochore dynein recruited via Spindly is restricted primarily to
      disassembly of the fibrous corona rather than wholesale removal of all
      outer-kinetochore checkpoint proteins.
    reference_section_type: RESULTS
    supporting_text: >-
      kinetochore dynein’s checkpoint-silencing role is **restricted primarily
      to disassembly of the fibrous corona**, rather than wholesale removal of
      checkpoint proteins from the entire outer kinetochore
  - statement: >-
      Localization is cell-cycle dependent: nuclear in interphase, kinetochore
      in prometaphase, relocalizing toward spindle poles before metaphase, and
      lost after chromosome congression.
    reference_section_type: RESULTS
    supporting_text: >-
      **Prometaphase:** kinetochore localization.
  - statement: >-
      A rare SPDL1 missense variant p.Arg20Gln (rs116483731) is associated with
      idiopathic pulmonary fibrosis, and shows antagonistic pleiotropy with
      increased IPF risk but decreased cancer risk.
    reference_section_type: RESULTS
    supporting_text: >-
      the same SPDL1 missense allele shows **antagonistic pleiotropy**:
      increased IPF risk but decreased cancer risk
- id: Reactome:R-HSA-141409
  title: Mad1 binds kinetochore
  findings: []
- id: Reactome:R-HSA-141422
  title: MAD2 converted to an inhibitory state via interaction with Mad1
  findings: []
- id: Reactome:R-HSA-141431
  title: MAD2 associates with the Mad1 kinetochore complex
  findings: []
- id: Reactome:R-HSA-141439
  title: Release of activated MAD2 from kinetochores
  findings: []
- id: Reactome:R-HSA-1638803
  title: Phosphorylation of cohesin by PLK1 at centromeres
  findings: []
- id: Reactome:R-HSA-1638821
  title: PP2A-B56 dephosphorylates centromeric cohesin
  findings: []
- id: Reactome:R-HSA-2467809
  title: ESPL1 (Separase) cleaves centromeric cohesin
  findings: []
- id: Reactome:R-HSA-2467811
  title: Separation of sister chromatids
  findings: []
- id: Reactome:R-HSA-2468287
  title: CDK1 phosphorylates CDCA5 (Sororin) at centromeres
  findings: []
- id: Reactome:R-HSA-2484822
  title: Kinetochore assembly
  findings: []
- id: Reactome:R-HSA-375302
  title: Kinetochore capture of astral microtubules
  findings: []
- id: Reactome:R-HSA-5666129
  title: CDC42:GTP recruits DIAPH2-2 to kinetochores
  findings: []
- id: Reactome:R-HSA-5666160
  title: AURKB phosphorylates DIAPH2-2 at kinetochores
  findings: []
- id: Reactome:R-HSA-5666169
  title: >-
    Kinetochore capture of astral microtubules is positively regulated by
    CDC42:GTP:p-S196-DIAPH2-2
  findings: []
- id: Reactome:R-HSA-9648114
  title: EML4 recruits NUDC to mitotic spindle
  findings: []
core_functions:
- description: >-
    Kinetochore-specific dynein adaptor that recruits cytoplasmic
    dynein-dynactin to the outer kinetochore during mitosis, enabling lateral
    kinetochore-microtubule interactions, poleward chromosome movements,
    chromosome congression, and spindle orientation control.
  molecular_function:
    id: GO:0070840
    label: dynein complex binding
  directly_involved_in:
  - id: GO:0034501
    label: protein localization to kinetochore
  - id: GO:0007080
    label: mitotic metaphase chromosome alignment
  - id: GO:0000132
    label: establishment of mitotic spindle orientation
  supported_by:
  - reference_id: PMID:19468067
    supporting_text: >-
      hSpindly depletion results in reduced inter-KT tension, unstable KT
      fibers, an extensive prometaphase delay, and severe chromosome
      misalignment
  - reference_id: PMID:17576797
    supporting_text: >-
      After the depletion of Spindly, dynein cannot target to kinetochores
  - reference_id: file:human/SPDL1/SPDL1-deep-research-falcon.md
    supporting_text: >-
      Kinetochore-localized **dynein–dynactin activating adaptor**; assembles
      DDS at fibrous corona
  in_complex:
    id: GO:0000940
    label: outer kinetochore
- description: >-
    Dynein-dynactin cargo adaptor that activates processive dynein motility.
    Facilitates the interaction between dynein and dynactin and converts dynein
    from a non-processive to a highly processive motor.
  molecular_function:
    id: GO:0070840
    label: dynein complex binding
  directly_involved_in:
  - id: GO:0007018
    label: microtubule-based movement
  locations:
  - id: GO:0000922
    label: spindle pole
  supported_by:
  - reference_id: PMID:25035494
    supporting_text: >-
      Activation of cytoplasmic dynein motility by dynactin-cargo adapter
      complexes
  in_complex:
    id: GO:0000940
    label: outer kinetochore
- description: >-
    Participates in spindle assembly checkpoint signaling through dynein-mediated
    removal of checkpoint proteins from kinetochores upon microtubule attachment.
    Spindly removal from attached kinetochores is the critical event for
    checkpoint silencing.
  molecular_function:
    id: GO:0043515
    label: kinetochore binding
  directly_involved_in:
  - id: GO:0007094
    label: mitotic spindle assembly checkpoint signaling
  supported_by:
  - reference_id: PMID:20439434
    supporting_text: >-
      Removal of Spindly from microtubule-attached kinetochores controls
      spindle checkpoint silencing in human cells
  in_complex:
    id: GO:0000940
    label: outer kinetochore
suggested_questions:
- question: >-
    What is the precise structural basis for the Spindly-RZZ interaction, and
    how does farnesylation of the Spindly C-terminus promote this interaction?
  experts:
  - Geert Kops
  - Reto Gassmann
- question: >-
    Does Spindly have a direct role in kinetochore corona formation beyond its
    RZZ interaction, and what is the functional significance of RZZ-Spindly
    oligomerization for microtubule capture?
  experts:
  - Carlos Sacristan
  - Andrea Musacchio
- question: >-
    What is the biological significance of Spindly monoubiquitination by USP45
    for cell migration, and what is the relevant E3 ubiquitin ligase?
  experts:
  - Ana Belen Perez-Oliva
  - Eric Griffis
suggested_experiments:
- hypothesis: >-
    Spindly monoubiquitination regulates its localization or interaction
    partners during cell migration.
  description: >-
    Generate ubiquitination-site mutants of Spindly and test their effect on
    cell migration, cortical dynein recruitment, and USP45 interaction using
    wound-healing and transwell assays combined with live-cell imaging.
  experiment_type: cell biology
- hypothesis: >-
    The dynein-independent corona expansion function of Spindly is separable
    from its dynein recruitment function and has distinct contributions to
    chromosome segregation fidelity.
  description: >-
    Use separation-of-function mutants that retain corona expansion but lack
    dynein recruitment (Spindly motif mutants from Gassmann et al. 2010) to
    assess microtubule capture efficiency, attachment error rates, and
    chromosome segregation fidelity by live-cell imaging with kinetochore
    markers.
  experiment_type: cell biology