Identification of novel protein biomarkers and drug targets for colorectal cancer by integrating human plasma proteome with genome

Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, et al. Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA Cancer J Clin. 2021;71(3):209–49.

Article  PubMed  Google Scholar 

Biller LH, Schrag D. Diagnosis and treatment of metastatic colorectal cancer: a review. JAMA. 2021;325(7):669–85.

Article  CAS  PubMed  Google Scholar 

Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics. 2002;1(11):845–67.

Article  CAS  PubMed  Google Scholar 

Suhre K, McCarthy MI, Schwenk JM. Genetics meets proteomics: perspectives for large population-based studies. Nat Rev Genet. 2021;22(1):19–37.

Article  CAS  PubMed  Google Scholar 

Tsilidis KK, Branchini C, Guallar E, Helzlsouer KJ, Erlinger TP, Platz EA. C-reactive protein and colorectal cancer risk: a systematic review of prospective studies. Int J Cancer. 2008;123(5):1133–40.

Article  CAS  PubMed  Google Scholar 

Murphy N, Carreras-Torres R, Song M, Chan AT, Martin RM, Papadimitriou N, et al. Circulating Levels of Insulin-like Growth Factor 1 and Insulin-like Growth Factor Binding Protein 3 Associate With Risk of Colorectal Cancer Based on Serologic and Mendelian Randomization Analyses. Gastroenterology. 2020;158(5):1300-1312.e1320.

Article  CAS  PubMed  Google Scholar 

Mehta RS, Song M, Bezawada N, Wu K, Garcia-Albeniz X, Morikawa T, et al. A prospective study of macrophage inhibitory cytokine-1 (MIC-1/GDF15) and risk of colorectal cancer. J Natl Cancer Institute. 2014;106(4):dju016.

Article  Google Scholar 

Sun X, Shu XO, Lan Q, Laszkowska M, Cai Q, Rothman N, et al. Prospective proteomic study identifies potential circulating protein biomarkers for colorectal cancer Risk. Cancers. 2022;14(13):3261.

Kakourou A, Koutsioumpa C, Lopez DS, Hoffman-Bolton J, Bradwin G, Rifai N, et al. Interleukin-6 and risk of colorectal cancer: results from the CLUE II cohort and a meta-analysis of prospective studies. Cancer Causes Control. 2015;26(10):1449–60.

Article  PubMed  PubMed Central  Google Scholar 

Pietzner M, Wheeler E, Carrasco-Zanini J, Cortes A, Koprulu M, Wörheide MA, et al. Mapping the proteo-genomic convergence of human diseases. Science (New York, NY). 2021;374(6569):eabj1541.

Article  Google Scholar 

Ferkingstad E, Sulem P, Atlason BA, Sveinbjornsson G, Magnusson MI, Styrmisdottir EL, et al. Large-scale integration of the plasma proteome with genetics and disease. Nat Genet. 2021;53(12):1712–21.

Article  CAS  PubMed  Google Scholar 

Sun BB, Maranville JC, Peters JE, Stacey D, Staley JR, Blackshaw J, et al. Genomic atlas of the human plasma proteome. Nature. 2018;558(7708):73–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sun BB, Chiou J, Traylor M, Benner C, Hsu Y-H, Richardson TG, et al. Genetic regulation of the human plasma proteome in 54,306 UK Biobank participants. bioRxiv. 2022. https://doi.org/10.1101/2022.06.17.496443.

Suhre K, Arnold M, Bhagwat AM, Cotton RJ, Engelke R, Raffler J, et al. Connecting genetic risk to disease end points through the human blood plasma proteome. Nat Commun. 2017;8:14357.

Folkersen L, Gustafsson S, Wang Q, Hansen DH, Hedman ÅK, Schork A, et al. Genomic and drug target evaluation of 90 cardiovascular proteins in 30,931 individuals. Nat Metab. 2020;2(10):1135–48.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yao C, Chen G, Song C, Keefe J, Mendelson M, Huan T, et al. Genome-wide mapping of plasma protein QTLs identifies putatively causal genes and pathways for cardiovascular disease. Nat Commun. 2018;9(1):3268.

Article  PubMed  PubMed Central  Google Scholar 

Davies NM, Holmes MV, Davey Smith G. Reading Mendelian randomisation studies: a guide, glossary, and checklist for clinicians. BMJ (Clinical research ed). 2018;362:k601.

Mishra A, Malik R, Hachiya T, Jürgenson T, Namba S, Posner DC, et al. Stroke genetics informs drug discovery and risk prediction across ancestries. Nature. 2022;611(7934):115–23.

Yazdanpanah N, Yazdanpanah M, Wang Y, Forgetta V, Pollak M, Polychronakos C, et al. Clinically relevant circulating protein biomarkers for type 1 diabetes: evidence from a two-sample mendelian randomization study. Diabetes care. 2022;45(1):169–77.

Article  CAS  PubMed  Google Scholar 

Wingo AP, Liu Y, Gerasimov ES, Gockley J, Logsdon BA, Duong DM, et al. Integrating human brain proteomes with genome-wide association data implicates new proteins in Alzheimer’s disease pathogenesis. Nature genetics. 2021;53(2):143–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zheng J, Haberland V, Baird D, Walker V, Haycock PC, Hurle MR, et al. Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases. Nat Genet. 2020;52(10):1122–31.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Considine DPC, Jia G, Shu X, Schildkraut JM, Pharoah PDP, Zheng W, et al. Genetically predicted circulating protein biomarkers and ovarian cancer risk. Gynecol Oncol. 2021;160(2):506–13.

Article  CAS  PubMed  Google Scholar 

Li X, Timofeeva M, Spiliopoulou A, McKeigue P, He Y, Zhang X, et al. Prediction of colorectal cancer risk based on profiling with common genetic variants. Int J Cancer. 2020;147(12):3431–7.

Article  CAS  PubMed  Google Scholar 

Kurki MI, Karjalainen J, Palta P, Sipilä TP, Kristiansson K, Donner K, et al. FinnGen: Unique genetic insights from combining isolated population and national health register data. medRxiv. 2022. https://doi.org/10.1101/2022.03.03.22271360.

Bycroft C, Freeman C, Petkova D, Band G, Elliott LT, Sharp K, et al. The UK Biobank resource with deep phenotyping and genomic data. Nature. 2018;562(7726):203–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rashkin SR, Graff RE, Kachuri L, Thai KK, Alexeeff SE, Blatchins MA, et al. Pan-cancer study detects genetic risk variants and shared genetic basis in two large cohorts. Nat Commun. 2020;11(1):4423.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Papadimitriou N, Dimou N, Tsilidis KK, Banbury B, Martin RM, Lewis SJ, et al. Physical activity and risks of breast and colorectal cancer: a Mendelian randomisation analysis. Nat Commun. 2020;11(1):597.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hemani G, Zheng J, Elsworth B, Wade KH, Haberland V, Baird D, et al. The MR-Base platform supports systematic causal inference across the human phenome. eLife. 2018;7:e34408.

Bowden J, Davey Smith G, Haycock PC, Burgess S. Consistent estimation in mendelian randomization with some invalid instruments using a weighted median estimator. Genet Epidemiol. 2016;40(4):304–14.

Article  PubMed  PubMed Central  Google Scholar 

Giambartolomei C, Vukcevic D, Schadt EE, Franke L, Hingorani AD, Wallace C, et al. Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet. 2014;10(5):e1004383.

Article  PubMed  PubMed Central  Google Scholar 

Liu B, Gloudemans MJ, Rao AS, Ingelsson E, Montgomery SB. Abundant associations with gene expression complicate GWAS follow-up. NatGenet. 2019;51(5):768–9.

CAS  Google Scholar 

Wu Y, Zeng J, Zhang F, Zhu Z, Qi T, Zheng Z, et al. Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits. Nat Commun. 2018;9(1):918.

Article  PubMed  PubMed Central  Google Scholar 

Wang R, Li J, Zhou X, Mao Y, Wang W, Gao S, et al. Single-cell genomic and transcriptomic landscapes of primary and metastatic colorectal cancer tumors. Genome Med. 2022;14(1):93.

Article  PubMed  PubMed Central  Google Scholar 

Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018;36(5):411–20.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aran D, Looney AP, Liu L, Wu E, Fong V, Hsu A, et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat Immunol. 2019;20(2):163–72.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Freshour SL, Kiwala S, Cotto KC, Coffman AC, McMichael JF, Song JJ, et al. Integration of the Drug-Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts. Nucleic Acids Res. 2021;49(D1):D1144-d1151.

Article  CAS  PubMed  Google Scholar 

Mendez D, Gaulton A, Bento AP, Chambers J, De Veij M, Félix E, et al. ChEMBL: towards direct deposition of bioassay data. Nucleic Acids Res. 2019;47(D1):D930-d940.

Article  CAS  PubMed  Google Scholar 

Wishart DS, Feunang YD, Guo AC, Lo EJ, Marcu A, Grant JR, et al. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res. 2018;46(D1):D1074-d1082.

Article  CAS  PubMed  Google Scholar 

Bach DH, Park HJ, Lee SK. The Dual Role of Bone Morphogenetic Proteins in Cancer. Mol Ther Oncolytics. 2018;8:1–13.

Kupfer SS, Skol AD, Hong E, Ludvik A, Kittles RA, Keku TO, et al. Shared and independent colorectal cancer risk alleles in TGFβ-related genes in African and European Americans. Carcinogenesis. 2014;35(9):2025–30.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kobayashi H, Gieniec KA, Wright JA, Wang T, Asai N, Mizutani Y, et al. The Balance of Stromal BMP Signaling Mediated by GREM1 and ISLR Drives Colorectal Carcinogenesis. Gastroenterology. 2021;160(4):1224-1239.e1230.

Article  CAS  PubMed 

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