Neoplastic cell enrichment of tumor tissues using coring and laser microdissection for proteomic and genomic analyses of pancreatic ductal adenocarcinoma

Siegel RL, Miller KD, Fuchs HE, Jemal A. Cancer statistics, 2022. CA Cancer J Clin. 2022. https://doi.org/10.3322/caac.21708.

Article  PubMed  Google Scholar 

Ryan DP, Hong TS, Bardeesy N. Pancreatic adenocarcinoma. N Engl J Med. 2014;371:1039–49.

Article  CAS  Google Scholar 

Hruban RH, Gaida MM, Thompson E, Hong SM, Noe M, Brosens LA, Jongepier M, Offerhaus GJA, Wood LD. Why is pancreatic cancer so deadly? The pathologist’s view. J Pathol. 2019;248:131–41.

Article  Google Scholar 

Zaid M, Elganainy D, Dogra P, Dai A, Widmann L, Fernandes P, Wang Z, Pelaez MJ, Ramirez JR, Singhi AD, Dasyam AK, Brand RE, Park WG, Rahmanuddin S, Rosenthal MH, Wolpin BM, Khalaf N, Goel A, Von Hoff DD, Tamm EP, Maitra A, Cristini V, Koay EJ. Imaging-based subtypes of pancreatic ductal adenocarcinoma exhibit differential growth and metabolic patterns in the pre-diagnostic period: implications for early detection. Front Oncol. 2020;10: 596931.

Article  Google Scholar 

Lee AYL, Dubois CL, Sarai K, Zarei S, Schaeffer DF, Sander M, Kopp JL. Cell of origin affects tumor development and phenotype in pancreatic ductal adenocarcinoma. Gut. 2019;68:487–98.

Article  CAS  Google Scholar 

Nicolle R, Blum Y, Duconseil P, Vanbrugghe C, Brandone N, Poizat F, Roques J, Bigonnet M, Gayet O, Rubis M, Elarouci N, Armenoult L, Ayadi M, Reyniès A, Giovannini M, Grandval P, Garcia S, Canivet C, Cros J, Bournet B, Buscail L, BACAP Consortium, Moutardier V, Gilabert M, Iovanna J, Dusetti N. Establishment of a pancreatic adenocarcinoma molecular gradient (PAMG) that predicts the clinical outcome of pancreatic cancer. EBioMedicine. 2020;57:102858.

Article  Google Scholar 

Beel S, Kolloch L, Apken LH, Jürgens L, Bolle A, Sudhof N, Ghosh S, Wardelmann E, Meisterernst M, Steinestel K, Oeckinghaus A. κB-Ras and Ral GTPases regulate acinar to ductal metaplasia during pancreatic adenocarcinoma development and pancreatitis. Nat Commun. 2020;11:3409.

Article  CAS  Google Scholar 

Noë M, Niknafs N, Fischer CG, Hackeng WM, Beleva Guthrie V, Hosoda W, Debeljak M, Papp E, Adleff V, White JR, Luchini C, Pea A, Scarpa A, Butturini G, Zamboni G, Castelli P, Hong SM, Yachida S, Hiraoka N, Gill AJ, Samra JS, Offerhaus GJA, Hoorens A, Verheij J, Jansen C, Adsay NV, Jiang W, Winter J, Albores-Saavedra J, Terris B, Thompson ED, Roberts NJ, Hruban RH, Karchin R, Scharpf RB, Brosens LAA, Velculescu VE, Wood LD. Genomic characterization of malignant progression in neoplastic pancreatic cysts. Nat Commun. 2020;11:4085.

Article  Google Scholar 

Saha B, Chhatriya B, Pramanick S, Goswami S. Bioinformatic analysis and integration of transcriptome and proteome results identify key coding and noncoding genes predicting malignancy in intraductal papillary mucinous neoplasms of the pancreas. Biomed Res Int. 2021;2021:1056622.

Article  Google Scholar 

Zhou W, Capello M, Fredolini C, Piemonti L, Liotta LA, Novelli F, Petricoin EF. Proteomic analysis of pancreatic ductal adenocarcinoma cells reveals metabolic alterations. J Proteome Res. 2011;10:1944–52.

Article  CAS  Google Scholar 

Bailey P, Chang DK, Nones K, Johns AL, Patch AM, Gingras MC, Miller DK, Christ AN, Bruxner TJ, Quinn MC, Nourse C, Murtaugh LC, Harliwong I, Idrisoglu S, Manning S, Nourbakhsh E, Wani S, Fink L, Holmes O, Chin V, Anderson MJ, Kazakoff S, Leonard C, Newell F, Waddell N, Wood S, Xu Q, Wilson PJ, Cloonan N, Kassahn KS, Taylor D, Quek K, Robertson A, Pantano L, Mincarelli L, Sanchez LN, Evers L, Wu J, Pinese M, Cowley MJ, Jones MD, Colvin EK, Nagrial AM, Humphrey ES, Chantrill LA, Mawson A, Humphris J, Chou A, Pajic M, Scarlett CJ, Pinho AV, Giry-Laterriere M, Rooman I, Samra JS, Kench JG, Lovell JA, Merrett ND, Toon CW, Epari K, Nguyen NQ, Barbour A, Zeps N, Moran-Jones K, Jamieson NB, Graham JS, Duthie F, Oien K, Hair J, Grützmann R, Maitra A, Iacobuzio-Donahue CA, Wolfgang CL, Morgan RA, Lawlor RT, Corbo V, Bassi C, Rusev B, Capelli P, Salvia R, Tortora G, Mukhopadhyay D, Petersen GM, Australian Pancreatic Cancer Genome Initiative, Munzy DM, Fisher WE, Karim SA, Eshleman JR, Hruban RH, Pilarsky C, Morton JP, Sansom OJ, Scarpa A, Musgrove EA, Bailey UM, Hofmann O, Sutherland RL, Wheeler DA, Gill AJ, Gibbs RA, Pearson JV, Waddell N, Biankin AV, Grimmond SM. Genomic analyses identify molecular subtypes of pancreatic cancer. Nature. 2016;531:47–52.

Article  CAS  Google Scholar 

Cancer Genome Atlas Research Network. Integrated genomic characterization of pancreatic ductal adenocarcinoma. Cancer Cell. 2017;32:185–203.

Article  Google Scholar 

Kuboki Y, Fischer CG, Beleva Guthrie V, Huang W, Yu J, Chianchiano P, Hosoda W, Zhang H, Zheng L, Shao X, Thompson ED, Waters K, Poling J, He J, Weiss MJ, Wolfgang CL, Goggins MG, Hruban RH, Roberts NJ, Karchin R, Wood LD. Single-cell sequencing defines genetic heterogeneity in pancreatic cancer precursor lesions. J Pathol. 2019;247:347–56.

Article  CAS  Google Scholar 

Coleman O, Henry M, O’Neill F, Roche S, Swan N, Geoghegan J, Conlon K, McVey G, Moriarty M, Meleady P, Clynes M. Proteomic analysis of cell lines and primary tumors in pancreatic cancer identifies proteins expressed only in vitro and only in vivo. Pancreas. 2020;49:1109–16.

Article  CAS  Google Scholar 

Law HC, Lagundžin D, Clement EJ, Qiao F, Wagner ZS, Krieger KL, Costanzo-Garvey D, Caffrey TC, Grem JL, DiMaio DJ, Grandgenett PM, Cook LM, Fisher KW, Yu F, Hollingsworth MA, Woods NT. The proteomic landscape of pancreatic ductal adenocarcinoma liver metastases identifies molecular subtypes and associations with clinical response. Clin Cancer Res. 2020;26:1065–76.

Article  CAS  Google Scholar 

Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H, Clinical Proteomic Tumor Analysis Consortium. Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell. 2021;184:5031–52.

Article  CAS  Google Scholar 

Eser S, Schnieke A, Schneider G, Saur D. Oncogenic KRAS signalling in pancreatic cancer. Br J Cancer. 2014;111:817–22.

Article  CAS  Google Scholar 

Buscail L, Bournet B, Cordelier P. Role of oncogenic KRAS in the diagnosis, prognosis and treatment of pancreatic cancer. Nat Rev Gastroenterol Hepatol. 2020;17:153–68.

Article  CAS  Google Scholar 

Thompson ED, Roberts NJ, Wood LD, Eshleman JR, Goggins MG, Kern SE, Klein AP, Hruban RH. The genetics of ductal adenocarcinoma of the pancreas in the year 2020: dramatic progress, but far to go. Mod Pathol. 2020;33:2544–63.

Article  Google Scholar 

Singh K, Pruski M, Bland R, Younes M, Guha S, Thosani N, Maitra A, Cash BD, McAllister F, Logsdon CD, Chang JT, Bailey-Lundberg JM. Kras mutation rate precisely orchestrates ductal derived pancreatic intraepithelial neoplasia and pancreatic cancer. Lab Invest. 2021;101:177–92.

Article  CAS  Google Scholar 

Yoshihara K, Shahmoradgoli M, Martínez E, Vegesna R, Kim H, Torres-Garcia W, Treviño V, Shen H, Laird PW, Levine DA, Carter SL, Getz G, Stemke-Hale K, Mills GB, Verhaak RG. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun. 2013;4:2612.

Article  Google Scholar 

Öhlund D, Handly-Santana A, Biffi G, Elyada E, Almeida AS, Ponz-Sarvise M, Corbo V, Oni TE, Hearn SA, Lee EJ, Chio II, Hwang CI, Tiriac H, Baker LA, Engle DD, Feig C, Kultti A, Egeblad M, Fearon DT, Crawford JM, Clevers H, Park Y. Tuveson DA Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic cancer. J Exp Med. 2017;214:579–96.

Article  Google Scholar 

Maurer C, Holmstrom SR, He J, Laise P, Su T, Ahmed A, Hibshoosh H, Chabot JA, Oberstein PE, Sepulveda AR, Genkinger JM, Zhang J, Iuga AC, Bansal M, Califano A, Olive KP. Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes. Gut. 2019;68:1034–43.

Article  CAS  Google Scholar 

Kalimuthu SN, Wilson GW, Grant RC, Seto M, O’Kane G, Vajpeyi R, Notta F, Gallinger S, Chetty R. Morphological classification of pancreatic ductal adenocarcinoma that predicts molecular subtypes and correlates with clinical outcome. Gut. 2020;69:317–28.

Article  Google Scholar 

Shekouh AR, Thompson CC, Prime W, Campbell F, Hamlett J, Herrington CS, Lemoine NR, Crnogorac-Jurcevic T, Buechler MW, Friess H, Neoptolemos JP, Pennington SR, Costello E. Application of laser capture microdissection combined with two-dimensional electrophoresis for the discovery of differentially regulated proteins in pancreatic ductal adenocarcinoma. Proteomics. 2003;3:1988–2001.

Article  CAS  Google Scholar 

Rodriguez AS, Espina BH, Espina V, Liotta LA. Automated laser capture microdissection for tissue proteomics. Methods Mol Biol. 2008;441:71–90.

Article  CAS  Google Scholar 

Padden J, Ahrens M, Kälsch J, Bertram S, Megger DA, Bracht T, Eisenacher M, Kocabayoglu P, Meyer HE, Sipos B, Baba HA, Sitek B. Immunohistochemical Markers Distinguishing Cholangiocellular Carcinoma (CCC) from Pancreatic Ductal Adenocarcinoma (PDAC) Discovered by Proteomic Analysis of Microdissected Cells. Mol Cell Proteomics. 2016;15:1072–82.

Article  CAS  Google Scholar 

Moffitt RA, Marayati R, Flate EL, Volmar KE, Loeza SG, Hoadley KA, Rashid NU, Williams LA, Eaton SC, Chung AH, Smyla JK, Anderson JM, Kim HJ, Bentrem DJ, Talamonti MS, Iacobuzio-Donahue CA, Hollingsworth MA, Yeh JJ. Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma. Nat Genet. 2015;47:1168–78.

Article  CAS  Google Scholar 

Le Large TY, Mantini G, Meijer LL, Pham TV, Funel N, van Grieken NC, Kok B, Knol J, van Laarhoven HW, Piersma SR, Jimenez CR, Kazemier G, Giovannetti E, Bijlsma MF. Microdissected pancreatic cancer proteomes reveal tumor heterogeneity and therapeutic targets. JCI Insight. 2020;5: e138290.

Article  Google Scholar 

Oppong KW, Bekkali NLH, Leeds JS, Johnson SJ, Nayar MK, Darné A, Egan M, Bassett P, Haugk B. Fork-tip needle biopsy versus fine-needle aspiration in endoscopic ultrasound-guided sampling of solid pancreatic masses: a randomized crossover study. Endoscopy. 2020;52:454–61.

Article  Google Scholar 

Mertins P, Tang LC, Krug K, Clark DJ, Gritsenko MA, Chen L, Clauser KR, Clauss TR, Shah P, Gillette MA, Petyuk VA, Thomas SN, Mani DR, Mundt F, Moore RJ, Hu Y, Zhao R, Schnaubelt M, Keshishian H, Monroe ME, Zhang Z, Udeshi ND, Mani D, Davies SR, Townsend RR, Chan DW, Smith RD, Zhang H, Liu T, Carr SA. Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry. Nat Protoc. 2018;13:1632–61.

Article  CAS  Google Scholar 

Kim S, Pevzner PA. MS-GF+ makes progress towards a universal database search tool for proteomics. Nat Commun. 2014;5:5277. https://doi.org/10.1038/ncomms6277.

Article  CAS  PubMed  Google Scholar 

Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümüş ZH, Geiszler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H, Clinical Proteomic Tumor Analysis Consortium. Integrated proteogenomic characterization of clear cell renal cell carcinoma. Cell. 2019;179:964–83.

Article  CAS  Google Scholar 

Zhang B, Chambers MC, Tabb DL. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J Proteome Res. 2007;6:3549–57.

Article  CAS 

留言 (0)

沒有登入
gif