MTRNR2L10 is a nuclear human locus on the X chromosome that resembles the humanin small open reading frame of the mitochondrial large-subunit rRNA gene MT-RNR2, one of thirteen such MT-RNR2-like sequences in the human genome that are generally interpreted as nuclear insertions of mitochondrial DNA. Its predicted product, humanin-like 10 (HN10), is a 24-residue peptide (MTTRGFSCLLLLIREIDLSAKRRI) that matches humanin at 17 of 24 aligned positions, differing by Ala2->Thr, Pro3->Thr, Thr13->Ile, Ser14->Arg, Pro19->Ser, Val20->Ala and Ala24->Ile; it retains the Leu9-Leu12 stretch but is the only member of the family that alters both residues of the Pro19-Val20 segment humanin requires for secretion, and it carries substitutions at three positions whose mutation abolishes or reduces humanin activity. The locus is transcribed: RT-PCR detects it in human tissues, most strongly in testis, and its transcript is down-regulated 6 hours and up-regulated 24 hours after staurosporine treatment of cultured cells. Whether a peptide is actually made from this transcript, and what it does, is unestablished: no HN10 peptide has been detected by mass spectrometry in human tissue or fluid, no molecular activity has been measured for it, and no binding partner or receptor interaction has been reported; reports of reduced serum humanin-like 10 in restless legs syndrome rest on an immunoassay that has not been shown to discriminate this peptide from humanin or from its nuclear siblings. The humanin peptide from which it is named is cytoprotective and antiapoptotic, binds BAX, BID, BIM and IGFBP3 intracellularly and signals through FPRL1/FPR2 and a CNTFR-alpha/WSX-1/gp130 complex when secreted, but those properties were measured on the mitochondrially encoded peptide and on synthetic analogues of it, not on this gene product.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005576 extracellular region | IEA GO_REF:0000044 | REMOVE | Summary: Electronic mapping of UniProt's Secreted subcellular-location line for P0CJ77. That line is itself annotated ECO:0000250 by similarity to humanin (UniProtKB:Q8IVG9), so the row carries no observation made on MTRNR2L10. Reason: MTRNR2L10 is known only as a transcript (UniProt protein existence level 2); no peptide from this locus has been detected in any compartment by mass spectrometry. UniProt's Secreted and Cytoplasm lines for P0CJ77 are themselves ECO:0000250 by-similarity statements transferred from humanin (file:human/MTRNR2L10/MTRNR2L10-uniprot.txt), so both the ISS row (donor UniProtKB:Q8IVG9) and the subcellular-location IEA row state the same humanin claim, once directly and once via the controlled-vocabulary mapping. Secretion of humanin is not a generic property of the sequence: it depends on Leu9-Leu11 and on Pro19-Val20 [PMID:35372353], and Bodzioch et al. proposed on the alignment that position 19 is what decides whether a nuclear isoform is secreted at all [PMID:19477263]. HN10 is the one member of MTRNR2L1-10 that alters both residues of the Pro19-Val20 segment, carrying Pro19->Ser and Val20->Ala, while humanin Pro19->Arg and Val20->Arg each abolish secretion (file:human/MT-RNR2__Q8IVG9/MT-RNR2__Q8IVG9-uniprot.txt). Because the asserted location depends on secretion determinants that are altered at both positions in this peptide, the row is not merely unverified but positively doubtful, and I remove it. Supporting Evidence: PMID:35372353 HN was found to be an extracellularly secreted factor whereby two amino acid structures, Leu9-Leu11, and Pro19-Va120, appear to be essential for the secretion of HN peptide PMID:19477263 Proline vs serine in position 19 may determine whether the peptide is secreted or not, while threonine in position 13 may be important for cell surface receptor binding. file:human/MTRNR2L10/MTRNR2L10-uniprot.txt SUBCELLULAR LOCATION: Secreted |
| GO:0005576 extracellular region | ISS GO_REF:0000024 | REMOVE | Summary: Curator transfer of humanin's secreted location to MTRNR2L10 on sequence similarity. Humanin's own extracellular annotations are IDA/EXP from several studies, so the donor side is sound; the question is only whether the transfer is safe. Reason: MTRNR2L10 is known only as a transcript (UniProt protein existence level 2); no peptide from this locus has been detected in any compartment by mass spectrometry. Secretion of humanin depends on Leu9-Leu11 and on Pro19-Val20 [PMID:35372353], and Bodzioch et al. singled out position 19 as the determinant of whether a nuclear isoform is secreted [PMID:19477263]. In HN10 Leu9-Leu11 is intact but both Pro19 and Val20 are substituted, which is the most complete loss of a humanin secretion determinant anywhere in this family. The transfer therefore fails on the target side and I remove it. The reported reduction of serum humanin-like 10 in restless legs syndrome [PMID:38630326] does not rescue the row, because that measurement is an ELISA for a peptide that matches humanin at 17 of 24 positions and its nuclear siblings more closely still, and no locus-specific immunodetection has been demonstrated for this family. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG FUNCTIONAL DIVERGENCE Sources checked: UniProtKB:Q8IVG9 · MT-RNR2 SUPPORTS SOURCE BUT NOT TARGET Humanin, the mitochondrially encoded peptide. Its secreted location is directly observed and the source annotation is sound. What does not transfer is the premise: this nuclear MT-RNR2-like sequence is a paralogous genomic copy rather than an ortholog of a protein-coding gene, no peptide product of it has been observed, and the residues humanin needs in order to be secreted are altered at both positions of the Pro19-Val20 segment. Supporting Evidence: PMID:35372353 HN was found to be an extracellularly secreted factor whereby two amino acid structures, Leu9-Leu11, and Pro19-Va120, appear to be essential for the secretion of HN peptide PMID:35372353 It is predicted that these various isoforms might contribute to differential neuroprotective effects and receptor binding, but their individual roles remain to be investigated. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | MARK AS OVER ANNOTATED | Summary: Electronic mapping of UniProt's Cytoplasm line, which is itself a by-similarity statement transferred from humanin. Reason: MTRNR2L10 is known only as a transcript (UniProt protein existence level 2); no peptide from this locus has been detected in any compartment. UniProt's Secreted and Cytoplasm lines for P0CJ77 are themselves ECO:0000250 by-similarity statements transferred from humanin (file:human/MTRNR2L10/MTRNR2L10-uniprot.txt), so both the ISS row (donor UniProtKB:Q8IVG9) and the subcellular-location IEA row state the same humanin claim, once directly and once via the controlled-vocabulary mapping. A translated 24-residue peptide would plausibly be cytosolic, and no mapped determinant argues against it the way the Pro19-Val20 substitutions argue against secretion, which is why this row is marked over-annotated rather than removed; but it is asserted from humanin, not observed here, and it adds nothing to the record of this locus. Supporting Evidence: PMID:35372353 It is predicted that these various isoforms might contribute to differential neuroprotective effects and receptor binding, but their individual roles remain to be investigated. file:human/MTRNR2L10/MTRNR2L10-uniprot.txt Cytoplasm {ECO:0000250|UniProtKB:Q8IVG9} |
| GO:0005737 cytoplasm | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: Curator transfer of humanin's cytoplasmic location on sequence similarity; humanin's own cytoplasm annotations are IDA/EXP. Reason: The same humanin claim as the paired IEA row. A translated 24-residue peptide would plausibly be cytosolic, and unlike the secretion claim nothing in the HN10 sequence contradicts it. But no HN10 peptide has been observed in any compartment, so the row states a plausible inference about the humanin sequence rather than an observation about this gene product. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG Sources checked: UniProtKB:Q8IVG9 · MT-RNR2 SUPPORTS SOURCE BUT NOT TARGET Humanin has direct cytoplasmic localisation evidence, so the source is sound; the transfer assumes a peptide product of this nuclear locus that has never been detected. Supporting Evidence: PMID:35372353 It is predicted that these various isoforms might contribute to differential neuroprotective effects and receptor binding, but their individual roles remain to be investigated. file:human/MTRNR2L10/MTRNR2L10-uniprot.txt Cytoplasm {ECO:0000250|UniProtKB:Q8IVG9} |
| GO:0048019 receptor antagonist activity | IBA GO_REF:0000033 | REMOVE | Summary: Phylogenetic propagation of humanin's receptor antagonist activity to MTRNR2L10 from the humanin-family node PANTHER:PTN002141596. The grounding experiment is humanin competing with amyloid-beta at FPRL1 [PMID:15153530]; nothing comparable has been done with HN10. Reason: The IBD behind this row places the activity at the humanin-family node, and the placement is reasonable for the mitochondrial peptide: humanin is a genuine FPRL1 ligand and the antagonism of amyloid-beta at that receptor is directly observed [PMID:15153530]. Arguing with the row means asking whether MTRNR2L10 sits inside the clade that inherited the function, and the difficulty is that the question is not really phylogenetic. The nuclear MT-RNR2-like loci are copies of a mitochondrial rRNA segment, so descent in this tree tracks genomic sequence rather than a protein-coding lineage, and membership of the node does not establish that the ORF is translated, that the peptide is stable, or that it reaches a receptor. On residues HN10 fails precisely where a receptor-level claim needs support. It carries Ser14->Arg, which UniProt records as one of the humanin substitutions that abolishes activity, and Thr13->Ile, the only substitution in this family with a direct measurement - the polymorphic HN5 variant carrying exactly Thr13->Ile has reduced cytoprotection [PMID:19477263] - and Thr13 is the position Bodzioch et al. singled out as the one that may matter for cell-surface receptor binding [PMID:19477263]. Pro3 is lost as well. The usual counterweight in this family, that synthetic HN5 keeps activity despite Leu12->Ser, does not apply here, because HN10 retains Leu12 and diverges instead at the positions where HN5 remained humanin-like. A second, term-level point applies to every member of this node: receptor antagonist activity describes humanin's competition with amyloid-beta at FPRL1, which is a property measured in a specific assay, whereas humanin also carries receptor ligand activity by IDA - so even for the donor the term captures one facet of the interaction. I therefore remove the row rather than marking it over-annotated: the substitutions are at the positions where humanin receptor-level activity has been experimentally mapped, so the inheritance assumption fails on the target side. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN002141596 SUPPORTS SOURCE BUT NOT TARGET Humanin-family ancestral node. The assertion is correctly placed for the mitochondrially encoded peptide, which has the experimental grounding; its mechanical descent to nuclear MT-RNR2-like copies carries no evidence that those copies yield a peptide with receptor-level activity, and HN10 has lost Thr13 and Ser14. UniProtKB:Q8IVG9 · MT-RNR2 SUPPORTS SOURCE BUT NOT TARGET Humanin, with IDA for this term from the FPRL1 competition experiments [PMID:15153530]. Sound at source; all assays used synthetic humanin. Supporting Evidence: PMID:15153530 Humanin shares human FPRL1 and mouse FPR2 with Abeta(42) and suggest that Humanin may exert its neuroprotective effects by competitively inhibiting the access of FPRL1 to Abeta(42). PMID:19477263 Proline vs serine in position 19 may determine whether the peptide is secreted or not, while threonine in position 13 may be important for cell surface receptor binding. PMID:19477263 Cytoprotection against the STS-induced apoptosis conferred by the polymorphic HN5 variant, in which threonine in position 13 is replaced with isoleucine, is reduced compared to the wild type HN5 peptide. |
| GO:1900118 negative regulation of execution phase of apoptosis | IBA GO_REF:0000033 | REMOVE | Summary: Phylogenetic propagation of negative regulation of the execution phase of apoptosis to MTRNR2L10 from the humanin-family node. The co-listed donor is UniProtKB:P0CJ72 (MTRNR2L5), whose own evidence for this term is an IMP from an assay on synthetic HN5 peptide [PMID:19477263]. Reason: The antiapoptotic function is the best-supported property of this family, and the IBD placement is sensible: humanin blocks BAX, BID and BIM and is antiapoptotic in many systems, and synthetic HN5 peptide - the product of one of these very nuclear loci - is cytoprotective against staurosporine-induced apoptosis [PMID:19477263]. For HN10, though, that same HN5 experiment is the argument against the row rather than for it. The HN5 variant that was measured to be less cytoprotective is the one carrying Thr13->Ile [PMID:19477263], which is exactly the substitution HN10 carries, and HN10 adds Ser14->Arg, listed in UniProt among the humanin substitutions that abolish neuroprotective activity, plus the loss of Pro3 (file:human/MT-RNR2__Q8IVG9/MT-RNR2__Q8IVG9-uniprot.txt). The usual mitigation for this family does not apply, because HN10 retains Leu12 and diverges instead at the positions HN5 kept. What the row also lacks is anything specific to this locus. Its transcript is detectable and staurosporine-responsive [PMID:19477263], but a transcript is not a peptide, no apoptosis assay has used HN10, and the systematic human-genetics lookup across all thirteen loci found no association with disease and no expression QTL that would argue for a functional product [PMID:31753007]. The one clinical paper that names this locus as neuroprotective selected it out of a differential-expression list by this very GO term [PMID:38630326], so it cannot be used as independent support without closing a loop. I remove the row. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN002141596 SUPPORTS SOURCE BUT NOT TARGET Humanin-family node. The ancestral antiapoptotic assertion is well placed for humanin and for the synthetic HN5 peptide, but descent in this tree is descent of a mitochondrial rRNA segment copied into the nucleus, and says nothing about whether this copy is translated. UniProtKB:P0CJ72 · MTRNR2L5 SUPPORTS SOURCE BUT NOT TARGET MTRNR2L5/HN5, the only nuclear humanin-like sequence with a functional assay. Its synthetic peptide is cytoprotective, which supports the node, but the HN5 variant carrying Thr13->Ile - the substitution HN10 carries constitutively - is measurably less protective [PMID:19477263], so this donor argues against the transfer to HN10 specifically. Supporting Evidence: PMID:19477263 Cytoprotection against the STS-induced apoptosis conferred by the polymorphic HN5 variant, in which threonine in position 13 is replaced with isoleucine, is reduced compared to the wild type HN5 peptide. PMID:19477263 At least ten of these nuclear genes are expressed in human tissues, and respond to staurosporine (STS) and beta-carotene. PMID:31753007 None of the found associations were statistically significant after correction for multiple testing. PMID:38630326 Two genes, MTRNR2L10 and MTRNR2L3, involved negative regulation of the execution phase of apoptosis were highlighted in GO analysis. |
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Download this section (compressed HTML)Q: Is a peptide produced from the MTRNR2L10 locus at all? Everything annotated to this gene follows from the assumption that it is, and the assumption rests on an intact open reading frame plus RT-PCR detection of the transcript [PMID:19477263]. Targeted mass spectrometry of testis for the HN10-specific tryptic peptides would settle it, and HN10 is unusually tractable for this because the IREIDLSA region differs from humanin at four positions.
Suggested experts: Alan Saghatelian, Pinchas Cohen, Jonathan Wren
Q: What does the serum humanin-like 10 ELISA actually measure? Reduced levels are reported in restless legs syndrome [PMID:38630326], but HN10 matches humanin at 17 of 24 positions and its nuclear siblings more closely, and no locus-specific immunodetection has been demonstrated anywhere in this family. Epitope mapping of the antibody against synthetic HN1-HN13 and humanin would establish what the clinical literature on humanin-like peptides is reporting.
Suggested experts: Pinchas Cohen
Q: How should GO treat a family in which one member has all the experimental evidence and twelve nuclear copies have none? The present solution propagates humanin's activity to every copy through PANTHER:PTN002141596, which produces thirteen gene products annotated as receptor antagonists and apoptosis regulators on the strength of one mitochondrial peptide. A node restricted to MT-RNR2 plus MTRNR2L5, the two sequences with functional data, would say what is actually known. MTRNR2L10 shows the downstream cost - a clinical study selected this locus for investigation on the basis of the propagated term [PMID:38630326], so the annotation is now generating the literature that appears to confirm it.
Q: Do the rat sequences manipulated in the status-epilepticus study [PMID:42289503] correspond to human MTRNR2L1 and MTRNR2L10? These are pericentromeric nuclear insertions of mitochondrial rRNA, so one-to-one orthology across rodents and primates should not be assumed, and knockdown constructs against one such sequence may hit several. Stating the rat loci and the construct specificity controls would make that work interpretable for human gene annotation.
Experiment: Targeted (PRM) mass spectrometry of human testis and of plasma for peptides unique to HN10, using the positions at which it differs from humanin (Ala2->Thr, Pro3->Thr, Thr13->Ile, Ser14->Arg, Pro19->Ser, Val20->Ala and Ala24->Ile) to design discriminating transitions. This is the one experiment that would convert the entire annotation set on this gene from inference to observation.
Experiment: Ribosome profiling or ORF-capture of the MTRNR2L10 transcript in testis, to test whether the predicted ORF is translated rather than merely transcribed.
Experiment: Synthesise the HN10 peptide and test it side by side with humanin and with HN5 in the secretion assay used to map the humanin Pro19-Val20 determinant, and in staurosporine- and amyloid-beta-induced death, FPRL1 competition and BAX binding. HN10 is the natural test of whether the Pro19-Val20 segment is required for secretion in a natural sequence context rather than only in arginine-substituted mutants, and whether Thr13->Ile plus Ser14->Arg together abolish cytoprotection as the single-substitution data predict.
Experiment: Epitope mapping of the commercial humanin-like 10 antibody against synthetic humanin and all thirteen HN-like peptides, to determine whether published serum measurements [PMID:38630326] are locus-specific. This is a prerequisite for interpreting any clinical study of this family.
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