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Research plan status: All objectives completed. We verified identity and assembled recent and foundational sources, extracted quantitative data, mapped disease relevance, and synthesized below.
Title: VBP1 (PFDN3, VHL-binding protein 1) in human proteostasis, gene regulation, and hypoxia/VHL signaling: recent advances (2023–2024) and foundational insights
Executive summary
VBP1 encodes the α-type prefoldin subunit 3, a component of the heterohexameric prefoldin cochaperone that captures nascent polypeptides—most prominently actin and tubulin monomers—and delivers them to the TRiC/CCT chaperonin for ATP-dependent folding. Beyond its canonical cytoplasmic role, human prefoldin has nuclear functions influencing transcription elongation and co‑transcriptional splicing. VBP1 physically binds pVHL (the VHL tumor suppressor), contributes to pVHL maturation/anti‑aggregation within the prefoldin–Hsp70–TRiC network, and thereby supports HIFα degradation. Recent 2024 studies report disease relevance: in melanoma, loss of VBP1 is sufficient to accumulate HIF1A and promote migratory phenotypes; in esophageal squamous cell carcinoma (ESCC), VBP1 is part of a hypoxia-related prognostic signature and promotes proliferation in vitro and tumor growth in vivo. Together, these findings position VBP1 as a critical node coupling proteostasis with hypoxia signaling and cancer progression (millanzambrano2014nuclearfunctionsof pages 1-2, payanbravo2018functionalcontributionsof pages 1-3, payanbravo2021humanprefoldinmodulates pages 1-4, heritz2024molecularchaperonesguardians pages 13-14, miao2024vbp1promotestumor pages 1-3, schorghofer2024latestagemelanoma pages 1-2, miao2024vbp1promotestumor pages 5-9, schorghofer2024latestagemelanoma pages 3-4, tahmaz2022prefoldinfunctionin pages 9-11, goff2016aggregationdynamicsand pages 14-16, goff2016aggregationdynamicsand pages 12-14, goff2016aggregationdynamicsand pages 1-4).
| Claim/Topic | Key Finding (1–2 sentences) | Experimental System | Year | Source (first author/journal) | URL/DOI |
|---|---|---|---|---|---|
| Prefoldin α-subunit; architecture & cytoskeletal co-chaperone | VBP1 (PFDN3) is an α-type prefoldin subunit in a heterohexameric "jellyfish-like" complex that captures nascent actin/tubulin and delivers them to the TRiC/CCT chaperonin for folding. | Reviews; biochemical and cellular studies across eukaryotes | 2014, 2018 | Millán‑Zambrano / Open Biology; Payán‑Bravo / Adv Exp Med Biol (millanzambrano2014nuclearfunctionsof pages 1-2, payanbravo2018functionalcontributionsof pages 1-3) | https://doi.org/10.1098/rsob.140085; https://doi.org/10.1007/978-3-030-00737-9_1 |
| Nuclear roles; co-transcriptional splicing & chromatin association | Prefoldin subunits including PFDN3 localize nucleo-cytoplasmically and modulate transcription elongation and co-transcriptional splicing; loss of prefoldin decreases RNA Pol II Ser2 phosphorylation and impairs splicing efficiency. | Genome-wide chromatin/functional assays in human cells; reviews | 2021, 2024 | Payán‑Bravo / Nucleic Acids Research; Ostio (2024) (payanbravo2021humanprefoldinmodulates pages 1-4, ostio2024humanprefoldinregulates pages 88-91) | https://doi.org/10.1101/2020.06.14.150466; No DOI available |
| Direct interaction with pVHL; stabilization/anti-aggregation; HIF consequences | PFDN3/VBP1 binds pVHL and, as part of the prefoldin complex, helps prevent pVHL aggregation and promotes its maturation; reduced PFDN3 destabilizes the prefoldin complex and correlates with impaired pVHL function and altered HIF regulation. | Biochemical studies and fission-yeast Pac10 genetic models showing quantitative changes in pVHL inclusions; review summaries of human data | 2016, 2022 | Goff / Journal of Cell Science; Tahmaz / Front Cell Dev Biol (goff2016aggregationdynamicsand pages 14-16, tahmaz2022prefoldinfunctionin pages 9-11) | https://doi.org/10.1242/jcs.184846; https://doi.org/10.3389/fcell.2021.816214 |
| 2024 melanoma — VBP1 loss → HIF1A accumulation & prognosis | siRNA-mediated VBP1 depletion causes HIF1A accumulation and upregulation of HIF targets; VBP1 expression correlates with patient prognosis and influences migratory/tumor phenotypes in melanoma models. | Human melanoma cell lines, tumorspheres, organoid grafts, patient histology | 2024 | Schörghofer / British Journal of Cancer (schorghofer2024latestagemelanoma pages 1-2) | https://doi.org/10.1038/s41416-024-02758-9 |
| 2024 ESCC — VBP1 in hypoxia signature & tumor proliferation | VBP1 is part of a four-gene hypoxia-related prognostic signature in esophageal squamous cell carcinoma; higher VBP1 expression associates with poorer survival and promotes proliferation in vitro and tumor growth in xenografts. | RNA‑Seq, TCGA/GEO analysis, qRT‑PCR/IHC, cell proliferation assays, xenografts | 2024 | Miao / Human Cell (miao2024vbp1promotestumor pages 1-3, miao2024vbp1promotestumor pages 5-9) | https://doi.org/10.1007/s13577-024-01068-9 |
| Chaperone/tumor-suppressor review: prefoldin supports pVHL folding with TRiC/CCT | Reviews synthesize evidence that prefoldin/VBP1 cooperates with Hsp70 and TRiC/CCT to fold and stabilize pVHL, linking chaperone-mediated maturation to maintenance of HIF regulation and tumor suppressor function. | Review / synthesis of biochemical and cell-based studies | 2024 | Heritz / Oncotarget (heritz2024molecularchaperonesguardians pages 13-14) | https://doi.org/10.18632/oncotarget.28653 |
Table: Compact table summarizing key foundational and recent (2021–2024) evidence on human VBP1/PFDN3 covering prefoldin structure/function, nuclear roles, pVHL interaction and recent cancer-focused findings; citations point to the underlying sources used.
1) Key concepts and definitions with current understanding
- Identity and family: VBP1 (UniProt P61758) is prefoldin subunit 3 (PFDN3), an α-class subunit of the canonical eukaryotic prefoldin complex. Prefoldin is a jellyfish-like heterohexamer (two α- and four β-subunits) with six coiled-coil “tentacles” forming a cavity that binds unfolded proteins (structural concept; canonical function) (millanzambrano2014nuclearfunctionsof pages 1-2, payanbravo2018functionalcontributionsof pages 1-3).
- Canonical molecular function: Prefoldin binds nascent cytoskeletal polypeptides (actin, α/β‑tubulin) cotranslationally and hands them to TRiC/CCT for productive folding; loss of prefoldin subunits disrupts microtubule dynamics and cytoskeletal homeostasis (millanzambrano2014nuclearfunctionsof pages 1-2, payanbravo2018functionalcontributionsof pages 1-3).
- Nuclear/non-canonical functions: Human prefoldin localizes to transcribed chromatin, modulates RNA polymerase II CTD phosphorylation (Ser2/Ser5) and co‑transcriptional splicing efficiency, especially affecting long intron-rich genes under stimulation; some subunits have roles in removal/ubiquitination of nuclear substrates (e.g., HIV integrase) (payanbravo2021humanprefoldinmodulates pages 1-4, millanzambrano2014nuclearfunctionsof pages 4-5, ostio2024humanprefoldinregulates pages 88-91, millanzambrano2014nuclearfunctionsof pages 2-3).
- Interaction with VHL/pVHL and hypoxia axis: VBP1 (historically termed VHL-binding protein 1, VBP-1) binds the C-terminus of pVHL; as part of the prefoldin network, it protects pVHL against aggregation, supports folding/assembly into the VCB E3 ligase that targets HIFα for degradation, thus linking VBP1 to HIF pathway control (tahmaz2022prefoldinfunctionin pages 9-11, goff2016aggregationdynamicsand pages 14-16, goff2016aggregationdynamicsand pages 12-14, goff2016aggregationdynamicsand pages 1-4, heritz2024molecularchaperonesguardians pages 13-14).
2) Recent developments and latest research (2023–2024)
- Melanoma (2024, British Journal of Cancer): NLGN4X suppression downregulates VBP1; siRNA VBP1 knockdown in melanoma cell lines is sufficient to accumulate HIF1A and activate HIF targets (TXNIP, HMOX1), promoting migratory properties. Clinically, higher NLGN4X and VBP1 associate with improved survival. Functional rescue by NLGN4X reduces tumor growth in human-skin organoid grafts (publication date: June 2024; URL/DOI in table) (schorghofer2024latestagemelanoma pages 1-2, schorghofer2024latestagemelanoma pages 3-4).
- ESCC (2024, Human Cell): A four-gene hypoxia-related prognostic signature (VBP1, BGN, CDKN1A, PPFIA1) identified/validated via TCGA/GEO; VBP1 expression is elevated in tumors by qRT‑PCR and IHC, correlates with worse OS/DFS, and drives proliferation in vitro (EdU, CCK‑8, colony assays) and tumor growth in xenografts (publication date: May 2024; URL/DOI in table) (miao2024vbp1promotestumor pages 1-3, miao2024vbp1promotestumor pages 5-9, miao2024vbp1promotestumor pages 14-15).
- Chaperone–tumor suppressor interface (2024, review): Synthesis highlights prefoldin/VBP1 cooperation with Hsp70 and TRiC/CCT to stabilize pVHL against aggregation/degradation, tightening the mechanistic link between cochaperones and integrity of tumor suppressors governing HIF signaling (publication date: Oct 2024; URL/DOI in table) (heritz2024molecularchaperonesguardians pages 13-14).
3) Current applications and real-world implementations
- Biomarker/prognosis: In ESCC, VBP1 integrates into a hypoxia-related risk model with measurable predictive performance (e.g., GEO AUC ≈0.71 reported), and higher VBP1 associates with poorer outcomes; IHC/qRT‑PCR assays are feasible for clinical correlation (miao2024vbp1promotestumor pages 5-9).
- Therapeutic hypothesis generation: The melanoma study supports targeting upstream axes that restore VBP1 levels or function to restrain HIF1A stabilization, suggesting VHL/prefoldin chaperone pathways as potential nodes in anti‑metastatic strategies; organoid graft models demonstrate translational feasibility for testing (schorghofer2024latestagemelanoma pages 1-2, schorghofer2024latestagemelanoma pages 3-4).
- Proteostasis-informed oncology: Reviews argue that enhancing prefoldin‑TRiC folding capacity or preventing pVHL aggregation could preserve HIF regulation in tumors with intact VHL alleles but chaperone imbalance, informing combination strategies with HIF pathway inhibitors (heritz2024molecularchaperonesguardians pages 13-14, tahmaz2022prefoldinfunctionin pages 9-11).
4) Expert opinions and analysis from authoritative sources
- Open Biology and Nucleic Acids Research syntheses: Prefoldin (including PFDN3/VBP1) is positioned as a nexus of cytoskeletal folding and nuclear gene regulation, with mechanistic evidence for association with chromatin and splicing machinery; these journals are authoritative in cell biology and transcription fields (millanzambrano2014nuclearfunctionsof pages 1-2, payanbravo2021humanprefoldinmodulates pages 1-4, millanzambrano2014nuclearfunctionsof pages 4-5).
- Journal of Cell Science mechanistic data: Yeast models quantify the requirement of the VBP1 homolog Pac10 for pVHL stability and inclusion dynamics, supporting a conserved chaperone role modulating tumor suppressor proteostasis (goff2016aggregationdynamicsand pages 14-16, goff2016aggregationdynamicsand pages 12-14, goff2016aggregationdynamicsand pages 1-4).
- Oncotarget review perspective (2024): Although Oncotarget has variable reputation, the review collates peer-reviewed mechanistic work indicating prefoldin/VBP1 assistance in pVHL maturation with consequences for HIF signaling, aligning with independent primary literature (heritz2024molecularchaperonesguardians pages 13-14).
5) Relevant statistics and data from recent studies
- Melanoma (2024): VBP1 knockdown elevates HIF1A protein and induces HIF target genes TXNIP and HMOX1; higher VBP1 correlates with better survival in patient cohorts; re-expression of NLGN4X (which upregulates VBP1) reduces tumor growth in organoid grafts (publication: June 2024; British Journal of Cancer; URL/DOI in table) (schorghofer2024latestagemelanoma pages 1-2, schorghofer2024latestagemelanoma pages 3-4).
- ESCC (2024): VBP1 mRNA upregulated in tumors (qRT‑PCR paired t-test p≈4.0×10^−3), protein up by IHC; survival associations significant (e.g., TCGA OS p≈3.4×10^−2; DFS p≈2.5×10^−2; independent IHC cohort OS p≈3.48×10^−6); risk model AUC≈0.71; VBP1 overexpression increases proliferation and xenograft growth (publication: May 2024; Human Cell) (miao2024vbp1promotestumor pages 5-9, miao2024vbp1promotestumor pages 1-3, miao2024vbp1promotestumor pages 14-15).
- pVHL chaperoning/aggregation (foundational): In fission yeast, deletion of the VBP1 homolog pac10 reduces large pVHL inclusions (LSA) from ~32.4% in WT to ~6.5% in pac10Δ; aggregation-prone pVHL mutant P146A forms more LSA in pac10Δ (~19.5%) than WT VHL213 (~6.5%), indicating Pac10/VBP1 normally stabilizes pVHL and modulates aggregation thresholds (goff2016aggregationdynamicsand pages 12-14).
Functional roles, pathways, and localization
- Primary role: Non-enzymatic cochaperone subunit. VBP1 contributes structurally and functionally to substrate capture and handoff to TRiC/CCT. Substrate specificity at the complex level encompasses cytoskeletal clients (actin, tubulins). As an α‑subunit, VBP1 helps form the tentacle architecture that engages unfolded chains (millanzambrano2014nuclearfunctionsof pages 1-2, payanbravo2018functionalcontributionsof pages 1-3).
- Cellular compartment(s): Predominantly cytoplasmic for canonical folding of actin/tubulin; detectable nuclear localization for the canonical complex with functions at transcribed chromatin influencing RNA Pol II phosphorylation and co‑transcriptional splicing; perinuclear/nuclear co-localization with VHL in contexts of substrate ubiquitination (ostio2024humanprefoldinregulates pages 88-91, payanbravo2021humanprefoldinmodulates pages 1-4, millanzambrano2014nuclearfunctionsof pages 4-5).
- Pathways: Proteostasis (prefoldin–Hsp70–TRiC axis), cytoskeletal assembly, and VHL E3 ligase pathway (via pVHL maturation enabling HIFα ubiquitination); nuclear gene expression/splicing pathways via effects on RNA Pol II CTD phosphorylation and factor recruitment (payanbravo2021humanprefoldinmodulates pages 1-4, heritz2024molecularchaperonesguardians pages 13-14, millanzambrano2014nuclearfunctionsof pages 1-2).
Notes on gene/protein identification and domain/family validation
- Verified match: VBP1 (PFDN3) in Homo sapiens; prefoldin α-subunit; functions and domains consistent with UniProt P61758 and literature usage. If ambiguous symbols exist in other organisms, they are not used here; all cited functional literature maps to human VBP1 or its direct yeast homolog Pac10 for mechanistic inference (millanzambrano2014nuclearfunctionsof pages 1-2, payanbravo2018functionalcontributionsof pages 1-3, goff2016aggregationdynamicsand pages 12-14).
Limitations and open questions
- Direct structural details of human VBP1–pVHL binding and the precise folding trajectory in human cells remain areas for deeper structural biology. Many nuclear functions have been defined at the complex level; VBP1’s specific nuclear interactome warrants further delineation. Context-dependent roles in cancer appear bidirectional (e.g., melanoma vs ESCC associations) and may reflect differences in upstream regulation or tumor lineage.
References: URLs and publication dates are provided in the embedded table, and claims throughout are supported by the following sources: (millanzambrano2014nuclearfunctionsof pages 1-2, payanbravo2018functionalcontributionsof pages 1-3, payanbravo2021humanprefoldinmodulates pages 1-4, ostio2024humanprefoldinregulates pages 88-91, millanzambrano2014nuclearfunctionsof pages 4-5, heritz2024molecularchaperonesguardians pages 13-14, miao2024vbp1promotestumor pages 1-3, miao2024vbp1promotestumor pages 5-9, schorghofer2024latestagemelanoma pages 3-4, tahmaz2022prefoldinfunctionin pages 9-11, goff2016aggregationdynamicsand pages 14-16, goff2016aggregationdynamicsand pages 12-14, goff2016aggregationdynamicsand pages 1-4).
References
(millanzambrano2014nuclearfunctionsof pages 1-2): Gonzalo Millán-Zambrano and Sebastián Chávez. Nuclear functions of prefoldin. Open Biology, 4:140085, Jul 2014. URL: https://doi.org/10.1098/rsob.140085, doi:10.1098/rsob.140085. This article has 90 citations and is from a peer-reviewed journal.
(payanbravo2018functionalcontributionsof pages 1-3): Laura Payán-Bravo, Xenia Peñate, and Sebastián Chávez. Functional contributions of prefoldin to gene expression. Advances in experimental medicine and biology, 1106:1-10, Jan 2018. URL: https://doi.org/10.1007/978-3-030-00737-9_1, doi:10.1007/978-3-030-00737-9_1. This article has 20 citations and is from a peer-reviewed journal.
(payanbravo2021humanprefoldinmodulates pages 1-4): Laura Payán-Bravo, Sara Fontalva, Xenia Peñate, Ildefonso Cases, José Antonio Guerrero-Martínez, Yerma Pareja-Sánchez, Yosu Odriozola-Gil, Esther Lara, Silvia Jimeno-González, Carles Suñé, Mari Cruz Muñoz-Centeno, José C. Reyes, and Sebastián Chávez. Human prefoldin modulates co-transcriptional pre-mrna splicing. Nucleic Acids Research, 49:6267-6280, Jun 2021. URL: https://doi.org/10.1101/2020.06.14.150466, doi:10.1101/2020.06.14.150466. This article has 13 citations and is from a highest quality peer-reviewed journal.
(heritz2024molecularchaperonesguardians pages 13-14): Jennifer A. Heritz, Sarah J. Backe, and Mehdi Mollapour. Molecular chaperones: guardians of tumor suppressor stability and function. Oncotarget, 15:679-696, Oct 2024. URL: https://doi.org/10.18632/oncotarget.28653, doi:10.18632/oncotarget.28653. This article has 8 citations and is from a poor quality or predatory journal.
(miao2024vbp1promotestumor pages 1-3): Huikai Miao, Wuyou Gao, Leqi Zhong, Hongmu Li, Dongni Chen, Chunmei Xu, Zhesheng Wen, and Youfang Chen. Vbp1 promotes tumor proliferation as a part of the hypoxia-related signature in esophageal squamous cell carcinoma. Human Cell, 37:1141-1155, May 2024. URL: https://doi.org/10.1007/s13577-024-01068-9, doi:10.1007/s13577-024-01068-9. This article has 4 citations and is from a peer-reviewed journal.
(schorghofer2024latestagemelanoma pages 1-2): David Schörghofer, Laurenz Vock, Madalina A. Mirea, Oliver Eckel, Anna Gschwendtner, Jürgen Neesen, Erika Richtig, Markus Hengstschläger, and Mario Mikula. Late stage melanoma is hallmarked by low nlgn4x expression leading to hif1a accumulation. British Journal of Cancer, 131:468-480, Jun 2024. URL: https://doi.org/10.1038/s41416-024-02758-9, doi:10.1038/s41416-024-02758-9. This article has 7 citations and is from a domain leading peer-reviewed journal.
(miao2024vbp1promotestumor pages 5-9): Huikai Miao, Wuyou Gao, Leqi Zhong, Hongmu Li, Dongni Chen, Chunmei Xu, Zhesheng Wen, and Youfang Chen. Vbp1 promotes tumor proliferation as a part of the hypoxia-related signature in esophageal squamous cell carcinoma. Human Cell, 37:1141-1155, May 2024. URL: https://doi.org/10.1007/s13577-024-01068-9, doi:10.1007/s13577-024-01068-9. This article has 4 citations and is from a peer-reviewed journal.
(schorghofer2024latestagemelanoma pages 3-4): David Schörghofer, Laurenz Vock, Madalina A. Mirea, Oliver Eckel, Anna Gschwendtner, Jürgen Neesen, Erika Richtig, Markus Hengstschläger, and Mario Mikula. Late stage melanoma is hallmarked by low nlgn4x expression leading to hif1a accumulation. British Journal of Cancer, 131:468-480, Jun 2024. URL: https://doi.org/10.1038/s41416-024-02758-9, doi:10.1038/s41416-024-02758-9. This article has 7 citations and is from a domain leading peer-reviewed journal.
(tahmaz2022prefoldinfunctionin pages 9-11): Ismail Tahmaz, Somayeh Shahmoradi Ghahe, and Ulrike Topf. Prefoldin function in cellular protein homeostasis and human diseases. Frontiers in Cell and Developmental Biology, Jan 2022. URL: https://doi.org/10.3389/fcell.2021.816214, doi:10.3389/fcell.2021.816214. This article has 48 citations and is from a poor quality or predatory journal.
(goff2016aggregationdynamicsand pages 14-16): Xavier Le Goff, Franck Chesnel, Olivier Delalande, Anne Couturier, Stéphane Dréano, Cathy Le Goff, Cécile Vigneau, and Yannick Arlot-Bonnemains. Aggregation dynamics and identification of aggregation-prone mutants of the von hippel–lindau tumor suppressor protein. Journal of Cell Science, 129:2638-2650, Jul 2016. URL: https://doi.org/10.1242/jcs.184846, doi:10.1242/jcs.184846. This article has 17 citations and is from a domain leading peer-reviewed journal.
(goff2016aggregationdynamicsand pages 12-14): Xavier Le Goff, Franck Chesnel, Olivier Delalande, Anne Couturier, Stéphane Dréano, Cathy Le Goff, Cécile Vigneau, and Yannick Arlot-Bonnemains. Aggregation dynamics and identification of aggregation-prone mutants of the von hippel–lindau tumor suppressor protein. Journal of Cell Science, 129:2638-2650, Jul 2016. URL: https://doi.org/10.1242/jcs.184846, doi:10.1242/jcs.184846. This article has 17 citations and is from a domain leading peer-reviewed journal.
(goff2016aggregationdynamicsand pages 1-4): Xavier Le Goff, Franck Chesnel, Olivier Delalande, Anne Couturier, Stéphane Dréano, Cathy Le Goff, Cécile Vigneau, and Yannick Arlot-Bonnemains. Aggregation dynamics and identification of aggregation-prone mutants of the von hippel–lindau tumor suppressor protein. Journal of Cell Science, 129:2638-2650, Jul 2016. URL: https://doi.org/10.1242/jcs.184846, doi:10.1242/jcs.184846. This article has 17 citations and is from a domain leading peer-reviewed journal.
(ostio2024humanprefoldinregulates pages 88-91): SF Ostio. Human prefoldin regulates gene transcription through fact-mediated chromatin dynamics. Unknown journal, 2024.
(millanzambrano2014nuclearfunctionsof pages 4-5): Gonzalo Millán-Zambrano and Sebastián Chávez. Nuclear functions of prefoldin. Open Biology, 4:140085, Jul 2014. URL: https://doi.org/10.1098/rsob.140085, doi:10.1098/rsob.140085. This article has 90 citations and is from a peer-reviewed journal.
(millanzambrano2014nuclearfunctionsof pages 2-3): Gonzalo Millán-Zambrano and Sebastián Chávez. Nuclear functions of prefoldin. Open Biology, 4:140085, Jul 2014. URL: https://doi.org/10.1098/rsob.140085, doi:10.1098/rsob.140085. This article has 90 citations and is from a peer-reviewed journal.
(miao2024vbp1promotestumor pages 14-15): Huikai Miao, Wuyou Gao, Leqi Zhong, Hongmu Li, Dongni Chen, Chunmei Xu, Zhesheng Wen, and Youfang Chen. Vbp1 promotes tumor proliferation as a part of the hypoxia-related signature in esophageal squamous cell carcinoma. Human Cell, 37:1141-1155, May 2024. URL: https://doi.org/10.1007/s13577-024-01068-9, doi:10.1007/s13577-024-01068-9. This article has 4 citations and is from a peer-reviewed journal.