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PreprintCited by 7Advanced Proteomics Techniques and ApplicationsOvarian cancer diagnosis and treatmentMass Spectrometry Techniques and Applications

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Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization

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Tristan, Cardon, Rio, Diego Garcia-del, Derhourhi, Mehdi, Bonnefond, Amelie, Leblanc, Sebastien, Guilloy, Noe, Roucou, Xavier, Eyckerman, Sven, Gevaert, Kris, Salzet, Michel·2024·Cell Death and Disease
DOI 10.21203/rs.3.rs-3972487/v1PMC PMC11442847

Preprint — published as 10.1038/s41419-024-07046-1 · Paper page

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Abstract

Proteogenomics is becoming a powerful tool in personalized medicine by linking genomics, transcriptomics and mass spectrometry (MS)-based proteomics. Due to increasing evidence of alternative open reading frame-encoded proteins (AltProts), proteogenomics has a high potential to unravel the characteristics, variants and expression levels of the alternative proteome, in addition to already annotated proteins (RefProts). To obtain a broader view of the proteome of ovarian cancer cells compared to ovarian epithelial cells, cell-specific total RNA-sequencing profiles and customized protein databases were generated. In total, 128 RefProts and 30 AltProts were identified exclusively in SKOV-3 and PEO-4 cells. Among them, an AltProt variant of IP_715944, translated from DHX8, was found mutated (p.Leu44Pro). We show high variation in protein expression levels of RefProts and AltProts in different subcellular compartments. The presence of 117 RefProt and two AltProt variants was described, along with their possible implications in the different physiological/pathological characteristics. To identify the possible involvement of AltProts in cellular processes, crosslinking-MS (XL-MS) was performed in each cell line to identify AltProt-RefProt interactions. This approach revealed an interaction between POLD3 and the AltProt IP_183088, which after molecular docking, was placed between POLD3-POLD2 binding sites, highlighting its possibility of the involvement in DNA replication and repair.

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  1. The UniProt Consortium (2015) UniProt: a hub for protein information. Nucleic Acids Research, 43, D204–D212. · DOI · Paper page
  2. Breuza,L., Poux,S., Estreicher,A., Famiglietti,M.L., Magrane,M., Tognolli,M., Bridge,A., Baratin,D., Redaschi,N., and UniProt Consortium (2016) The UniProtKB guide to the human proteome. Database (Oxford), 2016, bav120.
  3. Mouilleron,H., Delcourt,V. and Roucou,X. (2016) Death of a dogma: eukaryotic mRNAs can code for more than one protein. Nucleic Acids Res, 44, 14–23. · DOI
  4. Hao,Y., Zhang,L., Niu,Y., Cai,T., Luo,J., He,S., Zhang,B., Zhang,D., Qin,Y., Yang,F., et al. (2018) SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci. Briefings in Bioinformatics, 19, 636–643.
  5. Galindo,M.I., Pueyo,J.I., Fouix,S., Bishop,S.A. and Couso,J.P. (2007) Peptides Encoded by Short ORFs Control Development and Define a New Eukaryotic Gene Family. PLOS Biology, 5, e106. · DOI
  6. Albuquerque,J.P., Tobias-Santos,V., Rodrigues,A.C., Mury,F.B. and Fonseca,R.N. da (2015) small ORFs: A new class of essential genes for development. Genet. Mol. Biol., 38, 278–283. · DOI
  7. Ruiz-Orera,J., Messeguer,X., Subirana,J.A. and Alba,M.M. (2014) Long non-coding RNAs as a source of new peptides. eLife, 3, e03523. · DOI
  8. Slavoff,S.A., Heo,J., Budnik,B.A., Hanakahi,L.A. and Saghatelian,A. (2014) A human short open reading frame (sORF)-encoded polypeptide that stimulates DNA end joining. J Biol Chem, 289, 10950–10957. · DOI
  9. Brunet,M.A., Brunelle,M., Lucier,J.-F., Delcourt,V., Levesque,M., Grenier,F., Samandi,S., Leblanc,S., Aguilar,J.-D., Dufour,P., et al. (2018) OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. Nucleic Acids Research, 10.1093/nar/gky936. · DOI
  10. Cardon,T., Fournier,I. and Salzet,M. (2021) Shedding Light on the Ghost Proteome. Trends in Biochemical Sciences, 46, 239–250. · DOI
  11. Brunet,M.A. and Roucou,X. (2019) Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames. JoVE (Journal of Visualized Experiments), 10.3791/59589. · DOI
  12. Kozak,M. (1999) Initiation of translation in prokaryotes and eukaryotes. Gene, 234, 187–208. · DOI · Paper page
  13. Kozak,M. (2006) Rethinking some mechanisms invoked to explain translational regulation in eukaryotes. Gene, 382, 1–11. · DOI
  14. Boeckmann,B., Bairoch,A., Apweiler,R., Blatter,M.-C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O’Donovan,C., Phan,I., et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Research, 31, 365–370. · DOI
  15. Brunet,M.A., Lucier,J.-F., Levesque,M., Leblanc,S., Jacques,J.-F., Al-Saedi,H.R.H., Guilloy,N., Grenier,F., Avino,M., Fournier,I., et al. (2021) OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. Nucleic Acids Research, 49, D380–D388. · DOI
  16. Guilloy,N., Brunet,M.A., Leblanc,S., Jacques,J.-F., Hardy,M.-P., Ehx,G., Lanoix,J., Thibault,P., Perreault,C. and Roucou,X. (2023) OpenCustomDB: Integration of Unannotated Open Reading Frames and Genetic Variants to Generate More Comprehensive Customized Protein Databases. J. Proteome Res., 22, 1492–1500. · DOI
  17. Cao,X., Khitun,A., Harold,C.M., Bryant,C.J., Zheng,S.-J., Baserga,S.J. and Slavoff,S.A. (2022) Nascent alt-protein chemoproteomics reveals a pre-60S assembly checkpoint inhibitor. Nat Chem Biol, 18, 643–651. · DOI
  18. Cardon,T., Salzet,M., Franck,J. and Fournier,I. (2019) Nuclei of HeLa cells interactomes unravel a network of ghost proteins involved in proteins translation. Biochimica et Biophysica Acta (BBA) - General Subjects, 1863, 1458–1470. · DOI
  19. D’Lima,N.G., Ma,J., Winkler,L., Chu,Q., Loh,K.H., Corpuz,E.O., Budnik,B.A., Lykke-Andersen,J., Saghatelian,A. and Slavoff,S.A. (2017) A human microprotein that interacts with the mRNA decapping complex. Nat Chem Biol, 13, 174–180. · DOI
  20. Matsumoto,A., Pasut,A., Matsumoto,M., Yamashita,R., Fung,J., Monteleone,E., Saghatelian,A., Nakayama,K.I., Clohessy,J.G. and Pandolfi,P.P. (2017) mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide. Nature, 541, 228–232. · DOI
  21. Stein,C.S., Jadiya,P., Zhang,X., McLendon,J.M., Abouassaly,G.M., Witmer,N.H., Anderson,E.J., Elrod,J.W. and Boudreau,R.L. (2018) Mitoregulin: A lncRNA-Encoded Microprotein that Supports Mitochondrial Supercomplexes and Respiratory Efficiency. Cell Rep, 23, 3710–3720.e8. · DOI
  22. Cardon,T., Ozcan,B., Aboulouard,S., Kobeissy,F., Duhamel,M., Rodet,F., Fournier,I. and Salzet,M. (2020) Epigenetic Studies Revealed a Ghost Proteome in PC1/3 KD Macrophages under Antitumoral Resistance Induced by IL-10. ACS Omega, 10.1021/acsomega.0c02530. · DOI
  23. Delcourt,V., Franck,J., Leblanc,E., Narducci,F., Robin,Y.-M., Gimeno,J.-P., Quanico,J., Wisztorski,M., Kobeissy,F., Jacques,J.-F., et al. (2017) Combined Mass Spectrometry Imaging and Top-down Microproteomics Reveals Evidence of a Hidden Proteome in Ovarian Cancer. EBioMedicine, 21, 55–64. · DOI
  24. Huang,J.-Z., Chen,M., Chen,D., Gao,X.-C., Zhu,S., Huang,H., Hu,M., Zhu,H. and Yan,G.-R. (2017) A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth. Molecular Cell, 68, 171–184.e6. · DOI
  25. Polycarpou-Schwarz,M., Groß,M., Mestdagh,P., Schott,J., Grund,S.E., Hildenbrand,C., Rom,J., Aulmann,S., Sinn,H.-P., Vandesompele,J., et al. (2018) The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation. Oncogene, 37, 4750–4768. · DOI
  26. Brunet,M.A., Jacques,J.-F., Nassari,S., Tyzack,G.E., McGoldrick,P., Zinman,L., Jean,S., Robertson,J., Patani,R. and Roucou,X. (2020) The FUS gene is dual-coding with both proteins contributing to FUS‐mediated toxicity. EMBO reports, 10.15252/embr.202050640. · DOI
  27. Cao,X., Chen,Y., Khitun,A. and Slavoff,S.A. (2023) BONCAT-based Profiling of Nascent Small and Alternative Open Reading Frame-encoded Proteins. Bio Protoc, 13, e4585.
  28. Slavoff,S.A., Mitchell,A.J., Schwaid,A.G., Cabili,M.N., Ma,J., Levin,J.Z., Karger,A.D., Budnik,B.A., Rinn,J.L. and Saghatelian,A. (2013) Peptidomic discovery of short open reading frame–encoded peptides in human cells. Nat Chem Biol, 9, 59–64. · DOI
  29. Garcia-del Rio,D.F., Fournier,I., Cardon,T. and Salzet,M. (2023) Protocol to identify human subcellular alternative protein interactions using cross-linking mass spectrometry. STAR Protocols, 4, 102380. · DOI
  30. Vanderperre,B., Staskevicius,A.B., Tremblay,G., McCoy,M., O’Neill,M.A., Cashman,N.R. and Roucou,X. (2011) An overlapping reading frame in the PRNP gene encodes a novel polypeptide distinct from the prion protein. The FASEB Journal, 25, 2373–2386. · DOI
  31. Zhang,Q., Vashisht,A.A., O’Rourke,J., Corbel,S.Y., Moran,R., Romero,A., Miraglia,L., Zhang,J., Durrant,E., Schmedt,C., et al. (2017) The microprotein Minion controls cell fusion and muscle formation. Nat Commun, 8, 15664. · DOI
  32. Yosten,G.L.C., Liu,J., Ji,H., Sandberg,K., Speth,R. and Samson,W.K. (2016) A 5′-upstream short open reading frame encoded peptide regulates angiotensin type 1a receptor production and signalling via the β-arrestin pathway. The Journal of Physiology, 594, 1601–1605. · DOI
  33. Hevler,J.F., Lukassen,M.V., Cabrera-Orefice,A., Arnold,S., Pronker,M.F., Franc,V. and Heck,A.J.R. (2021) Selective cross-linking of coinciding protein assemblies by in-gel cross-linking mass spectrometry. The EMBO Journal, 40, e106174. · DOI
  34. Berek,J.S., Renz,M., Kehoe,S., Kumar,L. and Friedlander,M. (2021) Cancer of the ovary, fallopian tube, and peritoneum: 2021 update. International Journal of Gynecology & Obstetrics, 155, 61–85. · DOI
  35. Wentzensen,N., Poole,E.M., Trabert,B., White,E., Arslan,A.A., Patel,A.V., Setiawan,V.W., Visvanathan,K., Weiderpass,E., Adami,H.-O., et al. (2016) Ovarian Cancer Risk Factors by Histologic Subtype: An Analysis From the Ovarian Cancer Cohort Consortium. J Clin Oncol, 34, 2888–2898. · DOI · Paper page
  36. Stewart,C., Ralyea,C. and Lockwood,S. (2019) Ovarian Cancer: An Integrated Review. Seminars in Oncology Nursing, 35, 151–156. · DOI
  37. Kanehisa,M. and Goto,S. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res, 28, 27–30. · DOI · Paper page
  38. Soga,T. (2013) Cancer metabolism: Key players in metabolic reprogramming. Cancer Science, 104, 275–281. · DOI
  39. Warburg,O. (1925) The Metabolism of Carcinoma Cells1. The Journal of Cancer Research, 9, 148–163. · DOI
  40. Vander Heiden,M.G., Cantley,L.C. and Thompson,C.B. (2009) Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science, 324, 1029–1033. · DOI · Paper page
  41. Wolf,C.R., Hayward,I.P., Lawrie,S.S., Buckton,K., McIntyre,M.A., Adams,D.J., Lewis,A.D., Scott,A.R.R. and Smyth,J.F. (1987) Cellular heterogeneity and drug resistance in two ovarian adenocarcinoma cell lines derived from a single patient. International Journal of Cancer, 39, 695–702. · DOI
  42. Fogh,J., Fogh,J.M. and Orfeo,T. (1977) One hundred and twenty-seven cultured human tumor cell lines producing tumors in nude mice. J Natl Cancer Inst, 59, 221–226. · DOI · Paper page
  43. Hernandez,L., Kim,M.K., Lyle,L.T., Bunch,K.P., House,C.D., Ning,F., Noonan,A.M. and Annunziata,C.M. (2016) Characterization of ovarian cancer cell lines as in vivo models for preclinical studies. Gynecol Oncol, 142, 332–340. · DOI · Paper page
  44. Hallas-Potts,A., Dawson,J.C. and Herrington,C.S. (2019) Ovarian cancer cell lines derived from non-serous carcinomas migrate and invade more aggressively than those derived from high-grade serous carcinomas. Sci Rep, 9, 5515. · DOI · Paper page
  45. Tabb,D.L., Eng,J.K. and Yates,J.R. (2001) Protein Identification by SEQUEST. In James,P. (ed), Proteome Research: Mass Spectrometry, Principles and Practice. Springer, Berlin, Heidelberg, pp. 125–142. · DOI
  46. McGinnis,S. and Madden,T.L. (2004) BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res, 32, W20-25. · DOI
  47. Jones,P., Binns,D., Chang,H.-Y., Fraser,M., Li,W., McAnulla,C., McWilliam,H., Maslen,J., Mitchell,A., Nuka,G., et al. (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics, 30, 1236–1240. · DOI
  48. Käll,L., Krogh,A. and Sonnhammer,E.L.L. (2004) A Combined Transmembrane Topology and Signal Peptide Prediction Method. Journal of Molecular Biology, 338, 1027–1036. · DOI
  49. Sherman,B.T., Hao,M., Qiu,J., Jiao,X., Baseler,M.W., Lane,H.C., Imamichi,T. and Chang,W. (2022) DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Research, 50, W216–W221. · DOI
  50. Dong,X.-C., Jing,L.-M., Wang,W.-X. and Gao,Y.-X. (2016) Down-regulation of SIRT3 promotes ovarian carcinoma metastasis. Biochem Biophys Res Commun, 475, 245–250. · DOI
  51. Sebastián,C., Zwaans,B.M.M., Silberman,D.M., Gymrek,M., Goren,A., Zhong,L., Ram,O., Truelove,J., Guimaraes,A.R., Toiber,D., et al. (2012) The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. Cell, 151, 1185–1199. · DOI · Paper page
  52. Zhang,J., Yin,X.-J., Xu,C.-J., Ning,Y.-X., Chen,M., Zhang,H., Chen,S.-F. and Yao,L.-Q. (2015) The histone deacetylase SIRT6 inhibits ovarian cancer cell proliferation via down-regulation of Notch 3 expression. Eur Rev Med Pharmacol Sci, 19, 818–824.
  53. Shannon,P., Markiel,A., Ozier,O., Baliga,N.S., Wang,J.T., Ramage,D., Amin,N., Schwikowski,B. and Ideker,T. (2003) Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Res., 13, 2498–2504. · DOI · Paper page
  54. Jensen,L.J., Kuhn,M., Stark,M., Chaffron,S., Creevey,C., Muller,J., Doerks,T., Julien,P., Roth,A., Simonovic,M., et al. (2009) STRING 8–a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res, 37, D412-416. · DOI
  55. Doncheva,N.T., Morris,J.H., Gorodkin,J. and Jensen,L.J. (2019) Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data. J Proteome Res, 18, 623–632. · DOI
  56. Oughtred,R., Rust,J., Chang,C., Breitkreutz,B.-J., Stark,C., Willems,A., Boucher,L., Leung,G., Kolas,N., Zhang,F., et al. (2021) The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. Protein Sci, 30, 187–200. · DOI · Paper page
  57. Orchard,S., Ammari,M., Aranda,B., Breuza,L., Briganti,L., Broackes-Carter,F., Campbell,N.H., Chavali,G., Chen,C., del-Toro,N., et al. (2014) The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Research, 42, D358–D363. · DOI
  58. Bindea,G., Mlecnik,B., Hackl,H., Charoentong,P., Tosolini,M., Kirilovsky,A., Fridman,W.-H., Pagès,F., Trajanoski,Z. and Galon,J. (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics, 25, 1091–1093. · DOI · Paper page
  59. Yang,J., Yan,R., Roy,A., Xu,D., Poisson,J. and Zhang,Y. (2015) The I-TASSER Suite: protein structure and function prediction. Nat Methods, 12, 7–8. · DOI · Paper page
  60. Kozakov,D., Hall,D.R., Xia,B., Porter,K.A., Padhorny,D., Yueh,C., Beglov,D. and Vajda,S. (2017) The ClusPro web server for protein–protein docking. Nat Protoc, 12, 255–278. · DOI
  61. Becker,K.G., Barnes,K.C., Bright,T.J. and Wang,S.A. (2004) The genetic association database. Nat Genet, 36, 431–432. · DOI
  62. Käll,L., Canterbury,J.D., Weston,J., Noble,W.S. and MacCoss,M.J. (2007) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods, 4, 923–925. · DOI · Paper page
  63. The,M., MacCoss,M.J., Noble,W.S. and Käll,L. (2016) Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0. J. Am. Soc. Mass Spectrom., 27, 1719–1727. · DOI · Paper page
  64. Paulo,J.A., Gaun,A., Kadiyala,V., Ghoulidi,A., Banks,P.A., Conwell,D.L. and Steen,H. (2013) Subcellular Fractionation Enhances Proteome Coverage of Pancreatic Duct Cells. Biochim Biophys Acta, 1834, 791–797. · DOI
  65. Na,Z., Dai,X., Zheng,S.-J., Bryant,C.J., Loh,K.H., Su,H., Luo,Y., Buhagiar,A.F., Cao,X., Baserga,S.J., et al. (2022) Mapping subcellular localizations of unannotated microproteins and alternative proteins with MicroID. Molecular Cell, 82, 2900–2911.e7. · DOI
  66. Eyckerman,S., Titeca,K., Van Quickelberghe,E., Cloots,E., Verhee,A., Samyn,N., De Ceuninck,L., Timmerman,E., De Sutter,D., Lievens,S., et al. (2016) Trapping mammalian protein complexes in viral particles. Nat Commun, 7, 11416. · DOI
  67. Alam,M.S. (2018) Proximity Ligation Assay (PLA). Curr Protoc Immunol, 123, e58. · DOI
  68. Zheng,Z.-Y., Elsarraj,H., Lei,J.T., Hong,Y., Anurag,M., Feng,L., Kennedy,H., Shen,Y., Lo,F., Zhao,Z., et al. (2022) Elevated NRAS expression during DCIS is a potential driver for progression to basal-like properties and local invasiveness. Breast Cancer Research, 24, 68. · DOI
  69. Birkeland,E., Wik,E., Mjøs,S., Hoivik,E.A., Trovik,J., Werner,H.M.J., Kusonmano,K., Petersen,K., Raeder,M.B., Holst,F., et al. (2012) KRAS gene amplification and overexpression but not mutation associates with aggressive and metastatic endometrial cancer. Br J Cancer, 107, 1997–2004. · DOI
  70. Zhou,J.-D., Yao,D.-M., Li,X.-X., Zhang,T.-J., Zhang,W., Ma,J.-C., Guo,H., Deng,Z.-Q., Lin,J. and Qian,J. (2017) KRAS overexpression independent of RAS mutations confers an adverse prognosis in cytogenetically normal acute myeloid leukemia. Oncotarget, 8, 66087–66097. · DOI
  71. Jung,J., Cho,K.-J., Naji,A.K., Clemons,K.N., Wong,C.O., Villanueva,M., Gregory,S., Karagas,N.E., Tan,L., Liang,H., et al. (2019) HRAS-driven cancer cells are vulnerable to TRPML1 inhibition. EMBO reports, 20, e46685. · DOI
  72. Miglietta,G., Gouda,A.S., Cogoi,S., Pedersen,E.B. and Xodo,L.E. (2015) Nucleic Acid Targeted Therapy: G4 Oligonucleotides Downregulate HRAS in Bladder Cancer Cells through a Decoy Mechanism. ACS Med. Chem. Lett., 6, 1179–1183. · DOI
  73. November 2020,19 (2020) The Human Protein Atlas: A 20-year journey into the body. Science | AAAS.
  74. Ouyang,S., Zhang,Q., Lou,L., Zhu,K., Li,Z., Liu,P. and Zhang,X. (2022) The Double-Edged Sword of SIRT3 in Cancer and Its Therapeutic Applications. Frontiers in Pharmacology, 13. · DOI
  75. Chen,G., Gharib,T.G., Huang,C.-C., Taylor,J.M.G., Misek,D.E., Kardia,S.L.R., Giordano,T.J., Iannettoni,M.D., Orringer,M.B., Hanash,S.M., et al. (2002) Discordant Protein and mRNA Expression in Lung Adenocarcinomas *. Molecular & Cellular Proteomics, 1, 304–313. · DOI
  76. Bauernfeind,A.L. and Babbitt,C.C. (2017) The predictive nature of transcript expression levels on protein expression in adult human brain. BMC Genomics, 18, 322. · DOI
  77. Perl,K., Ushakov,K., Pozniak,Y., Yizhar-Barnea,O., Bhonker,Y., Shivatzki,S., Geiger,T., Avraham,K.B. and Shamir,R. (2017) Reduced changes in protein compared to mRNA levels across non-proliferating tissues. BMC Genomics, 18, 305. · DOI
  78. Fukao,Y. (2015) Discordance between protein and transcript levels detected by selected reaction monitoring. Plant Signal Behav, 10, e1017697. · DOI
  79. Brion,C., Lutz,S.M. and Albert,F.W. (2020) Simultaneous quantification of mRNA and protein in single cells reveals post-transcriptional effects of genetic variation. eLife, 9, e60645. · DOI
  80. De Marco,C., Rinaldo,N., Bruni,P., Malzoni,C., Zullo,F., Fabiani,F., Losito,S., Scrima,M., Marino,F.Z., Franco,R., et al. (2013) Multiple genetic alterations within the PI3K pathway are responsible for AKT activation in patients with ovarian carcinoma. PLoS One, 8, e55362. · DOI
  81. Wang,G., Yang,X., Li,C., Cao,X., Luo,X. and Hu,J. (2014) PIK3R3 Induces Epithelial-to-Mesenchymal Transition and Promotes Metastasis in Colorectal Cancer. Molecular Cancer Therapeutics, 13, 1837–1847. · DOI
  82. Stronach,E.A., Chen,M., Maginn,E.N., Agarwal,R., Mills,G.B., Wasan,H. and Gabra,H. (2011) DNA-PK mediates AKT activation and apoptosis inhibition in clinically acquired platinum resistance. Neoplasia, 13, 1069–1080. · DOI
  83. Liu,Q., Turner,K.M., Alfred Yung,W.K., Chen,K. and Zhang,W. (2014) Role of AKT signaling in DNA repair and clinical response to cancer therapy. Neuro Oncol, 16, 1313–1323. · DOI
  84. Arlt,C., Ihling,C.H. and Sinz,A. (2015) Structure of full-length p53 tumor suppressor probed by chemical cross-linking and mass spectrometry. PROTEOMICS, 15, 2746–2755. · DOI
  85. Wells,M., Tidow,H., Rutherford,T.J., Markwick,P., Jensen,M.R., Mylonas,E., Svergun,D.I., Blackledge,M. and Fersht,A.R. (2008) Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain. Proceedings of the National Academy of Sciences, 105, 5762–5767.
  86. Hoyos,D., Greenbaum,B. and Levine,A.J. (2022) The genotypes and phenotypes of missense mutations in the proline domain of the p53 protein. Cell Death Differ, 29, 938–945. · DOI
  87. Schildkraut,J.M., Goode,E.L., Clyde,M.A., Iversen,E.S., Moorman,P.G., Berchuck,A., Marks,J.R., Lissowska,J., Brinton,L., Peplonska,B., et al. (2009) Single Nucleotide Polymorphisms in the TP53 Region and Susceptibility to Invasive Epithelial Ovarian Cancer. Cancer Research, 69, 2349–2357. · DOI
  88. Yaginuma,Y. and Westphal,H. (1992) Abnormal structure and expression of the p53 gene in human ovarian carcinoma cell lines. Cancer Res, 52, 4196–4199.
  89. Willis,S., Villalobos,V.M., Gevaert,O., Abramovitz,M., Williams,C., Sikic,B.I. and Leyland-Jones,B. (2016) Single Gene Prognostic Biomarkers in Ovarian Cancer: A Meta-Analysis. PLoS One, 11, e0149183. · DOI
  90. Weberpals,J.I., Pugh,T.J., Marco-Casanova,P., Goss,G.D., Andrews Wright,N., Rath,P., Torchia,J., Fortuna,A., Jones,G.N., Roudier,M.P., et al. (2021) Tumor genomic, transcriptomic, and immune profiling characterizes differential response to first‐line platinum chemotherapy in high grade serous ovarian cancer. Cancer Med, 10, 3045–3058. · DOI
  91. Murga,M., Lecona,E., Kamileri,I., Díaz,M., Lugli,N., Sotiriou,S.K., Anton,M.E., Méndez,J., Halazonetis,T.D. and Fernandez-Capetillo,O. (2016) POLD3 Is Haploinsufficient for DNA Replication in Mice. Molecular Cell, 63, 877–883. · DOI
  92. Perez-Riverol,Y., Bai,J., Bandla,C., García-Seisdedos,D., Hewapathirana,S., Kamatchinathan,S., Kundu,D.J., Prakash,A., Frericks-Zipper,A., Eisenacher,M., et al. (2022) The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Research, 50, D543–D552. · DOI · Paper page

Metadata

Authors
Tristan, C., Rio, D. G.-D., Derhourhi, M., Bonnefond, A., Leblanc, S., Guilloy, N., Roucou, X., Eyckerman, S., Gevaert, K., & Salzet, M.
Affiliations
  • Unversité de Lille, Inserm, CHU Lille
  • Centre National de la Recherche Scientifique (FR)
  • Université de Lille
  • Université de Sherbrooke
  • Université de Sherbrooke (CA)
  • Ghent University (BE)
  • Inserm (FR)
Corresponding author
Salzet, Michel
ORCID
Venue
Cell Death and Disease
Publisher
Springer Science and Business Media LLC
Published
2024-04-09
Volume
15
Issue
9
Pages
712-712
ISSN
2041-4889 (ISSN-L)
DOI
10.21203/rs.3.rs-3972487/v1
PMC
PMC11442847
OpenAlex
W4402983075
Cited by
7
References
1
Citations by year
2026: 2 · 2025: 5
FWCI
0.87
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell Death and Disease (publishedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by)
  • Ghent University Academic Bibliography (Ghent University) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • LillOA (Université de Lille (University Of Lille)) (submittedVersion)
Funders
  • Université de Lille
  • Institut National de la Santé et de la Recherche Médicale
  • Fonds Wetenschappelijk Onderzoek (G008018N)
  • Vlaamse regering
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Health Sciences › Medicine › Oncology › Ovarian cancer diagnosis and treatment
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
Keywords
ovarian cancer, proteogenomics, POLD3, protein-protein interaction, cross-linking mass spectrometry, SKOV3 cells, DNA replication and repair
MeSH terms
Proteogenomics, Female, Humans, Ovarian Neoplasms, Open Reading Frames, Proteome, Cell Line, Tumor

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