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Genomic alterations drive metastases formation in pancreatic ductal adenocarcinoma cancer: deciphering the role of CDKN2A and CDKN2B in mediating liver tropism

Oncogene volume 41, pages 1468–1481 (2022)Cite this article

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Abstract

Metastases are often the direct cause of death from pancreatic ductal adenocarcinoma (PDAC). The role of genomic alterations (GA) in mediating tropism and metastasis formation by PDAC cells is currently unknown. We aimed to identify GAs predisposing colonization of PDAC cells to the liver and decipher mechanisms enabling this process. In order to reveal specific genes, we studied the frequency of GA in 8,880 local and 7,983 metastatic PDAC samples. We observed differential pattern of GA in the local tumor and specific metastatic sites, with liver metastases characterized by deletion of CDKN2A/B (encoding p16/p15, respectively). The role of CDKN2A/B in promoting liver metastasis was evidenced by enhanced tumorigenic phenotype of p15/p16-deleted PDAC cells when exposed to hepatocytes conditioned media. The liver is characterized by high-ammonia low-glutamine environment and transcriptomic assays indicated unique adaptation of PDAC cells to these conditions, including regulation of genes leading to reduced glutaminolysis, like overexpression of GLUL and reduction in GLS2. Furthermore, metabolic assays indicated an increase in glutamate derived from [U-13C]-glucose in p15/p16-deleted cells. Importantly, these cells thrived under high ammonia condition. These data suggest a unique role for genomic alterations in mediating tropism of PDAC. Among these alterations, p15/16 deletion was identified as a promoter of liver metastases. Further studies indicated a unique role for p15/16 in regulating glutaminolysis. These findings reveal vulnerabilities in PDAC cells, which may pave the way for the development of novel therapeutic strategies aiming at the prevention of liver metastases formation.

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Fig. 1: Increased prevalence CDKN2A/B deletion in PDAC liver metastasis relative to local tumors and other metastatic sites.
Fig. 2: CDKN2A/p16 and CDKN2B/p15 co-deletion enhances aggressive phenotypes in PDAC cell lines.
Fig. 3: p15/p16 co-deletion enhances tumorigenicity of PDAC cells in hepatocyte-conditioned media.
Fig. 4: p15/p16 co-deletion increases aggressive gene signature in pancreatic cancer cells.
Fig. 5: p15/p16 silencing differentially regulates glutamine metabolism.
Fig. 6: p15/p16 deletion confers resistance to ammonia toxicity through glutamine metabolism.

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Data availability

The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.

References

  1. Siegel R, Naishadham D, Jemal A. Cancer statistics, 2012. CA: A Cancer J Clin. 2012;62:10–29.

    Google Scholar 

  2. Pokorny AMJ, Chin VT, Nagrial AM, Yip D, Chantrill LA. Metastatic pancreatic ductal adenocarcinoma: diagnosis and treatment with a view to the future. Intern Med J. 2018;48:637–44.

    Article  PubMed  Google Scholar 

  3. Ryan DP, Hong TS, Bardeesy N. Pancreatic adenocarcinoma. N Engl J Med. 2014;371:2140–1.

    Article  PubMed  Google Scholar 

  4. Hess KR, Varadhachary GR, Taylor SH, Wei W, Raber MN, Lenzi R, et al. Metastatic patterns in adenocarcinoma. Cancer. 2006;106:1624–33.

    Article  PubMed  Google Scholar 

  5. Weissmueller S, Manchado E, Saborowski M, Morris JP,4th, Wagenblast E, Davis CA. et al. Mutant p53 drives pancreatic cancer metastasis through cell-autonomous PDGF receptor β signaling. Cell. 2014;157:382–94.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Yachida S, White CM, Naito Y, Zhong Y, Brosnan JA, Macgregor-Das AM, et al. Clinical significance of the genetic landscape of pancreatic cancer and implications for identification of potential long-term survivors. Clin Cancer Res. 2012;18:6339–47.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Makohon-Moore AP, Zhang M, Reiter JG, Bozic I, Allen B, Kundu D, et al. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nat Genet. 2017;49:358–66.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Connor AA, Denroche RE, Jang GH, Lemire M, Zhang A, Chan-Seng-Yue M, et al. Integration of genomic and transcriptional features in pancreatic cancer reveals increased cell cycle progression in metastases. Cancer Cell. 2019;35:267–82.e7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Kennecke H, Yerushalmi R, Woods R, Cheang MC, Voduc D, Speers CH, et al. Metastatic behavior of breast cancer subtypes. J Clin Oncol. 2010;28:3271–7.

    Article  PubMed  Google Scholar 

  10. Spinelli JB, Yoon H, Ringel AE, Jeanfavre S, Clish CB, Haigis MC. Metabolic recycling of ammonia via glutamate dehydrogenase supports breast cancer biomass. Science. 2017;358:941–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Hatting M, Tavares CDJ, Sharabi K, Rines AK, Puigserver P. Insulin regulation of gluconeogenesis. Ann NY Acad Sci. 2018;1411:21–35.

    Article  CAS  PubMed  Google Scholar 

  12. Kumar A, Cherukumilli M, Mahmoudpour SH, Brand K, Bandapalli OR. ShRNA-mediated knock-down of CXCL8 inhibits tumor growth in colorectal liver metastasis. Biochem Biophys Res Commun. 2018;500:731–7.

    Article  CAS  PubMed  Google Scholar 

  13. Caldas C, Hahn SA, da Costa LT, Redston MS, Schutte M, Seymour AB, et al. Frequent somatic mutations and homozygous deletions of the p16 (MTS1) gene in pancreatic adenocarcinoma. Nat Genet. 1994;8:27–32.

    Article  CAS  PubMed  Google Scholar 

  14. Kamb A, Gruis NA, Weaver-Feldhaus J, Liu Q, Harshman K, Tavtigian SV, et al. A cell cycle regulator potentially involved in genesis of many tumor types. Science. 1994;264:436–40.

    Article  CAS  PubMed  Google Scholar 

  15. Naumann M, Savitskaia N, Eilert C, Schramm A, Kalthoff H, Schmiegel W. Frequent codeletion of p16/MTS1 and p15/MTS2 and genetic alterations in p16/MTS1 in pancreatic tumors. Gastroenterology. 1996;110:1215–24.

    Article  CAS  PubMed  Google Scholar 

  16. Nobori T, Miura K, Wu DJ, Lois A, Takabayashi K, Carson DA. Deletions of the cyclin-dependent kinase-4 inhibitor gene in multiple human cancers. Nature. 1994;368:753–6.

    Article  CAS  PubMed  Google Scholar 

  17. Deer EL, Gonzalez-Hernandez J, Coursen JD, Shea JE, Ngatia J, Scaife CL, et al. Phenotype and genotype of pancreatic cancer cell lines. Pancreas. 2010;39:425–35.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Morgan RT, Woods LK, Moore GE, Quinn LA, McGavran L, Gordon SG. Human cell line (COLO 357) of metastatic pancreatic adenocarcinoma. Int J Cancer. 1980;25:591–8.

    Article  CAS  PubMed  Google Scholar 

  19. Sipos B, Moser S, Kalthoff H, Torok V, Lohr M, Kloppel G. A comprehensive characterization of pancreatic ductal carcinoma cell lines: towards the establishment of an in vitro research platform. Virchows Arch: Int J Pathol. 2003;442:444–52.

    Article  Google Scholar 

  20. Serrano M, Hannon GJ, Beach D. A new regulatory motif in cell-cycle control causing specific inhibition of cyclin D/CDK4. Nature. 1993;366:704–7.

    Article  CAS  PubMed  Google Scholar 

  21. Häussinger D, Graf D, Weiergräber OH. Glutamine and cell signaling in liver. J Nutr. 2001;131:2509S–14S. discussion 23S-4S

    Article  PubMed  Google Scholar 

  22. Walker V. Ammonia metabolism and hyperammonemic disorders. Adv Clin Chem. 2014;67:73–150.

    Article  CAS  PubMed  Google Scholar 

  23. Watford M. Glutamine and glutamate metabolism across the liver sinusoid. J Nutr. 2000;130:983s–7s.

    Article  CAS  PubMed  Google Scholar 

  24. Cluntun AA, Lukey MJ, Cerione RA, Locasale JW. Glutamine metabolism in cancer: understanding the heterogeneity. Trends Cancer. 2017;3:169–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Eng CH, Yu K, Lucas J, White E, Abraham RT. Ammonia derived from glutaminolysis is a diffusible regulator of autophagy. Sci Signal. 2010;3:ra31.

    Article  PubMed  Google Scholar 

  26. Bott AJ, Shen J, Tonelli C, Zhan L, Sivaram N, Jiang YP, et al. Glutamine anabolism plays a critical role in pancreatic cancer by coupling carbon and nitrogen metabolism. Cell Rep. 2019;29:1287–98. e6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Reiter JG, Makohon-Moore AP, Gerold JM, Heyde A, Attiyeh MA, Kohutek ZA, et al. Minimal functional driver gene heterogeneity among untreated metastases. Science. 2018;361:1033–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Tanaka M, Mihaljevic AL, Probst P, Heckler M, Klaiber U, Heger U, et al. Meta-analysis of recurrence pattern after resection for pancreatic cancer. Br J Surg. 2019;106:1590–601.

    Article  CAS  PubMed  Google Scholar 

  29. Kietzmann T, Roth U, Freimann S, Jungermann K. Arterial oxygen partial pressures reduce the insulin-dependent induction of the perivenously located glucokinase in rat hepatocyte cultures: mimicry of arterial oxygen pressures by H2O2. Biochemical J. 1997;321:17–20.

    Article  CAS  Google Scholar 

  30. Häussinger D, Schliess F. Glutamine metabolism and signaling in the liver. Front Biosci. 2007;12:371–91.

    Article  PubMed  Google Scholar 

  31. Zinger L, Merenbakh-Lamin K, Klein A, Elazar A, Journo S, Boldes T, et al. Ligand-binding domain-activating mutations of ESR1 rewire cellular metabolism of breast cancer cells. Clin Cancer Res. 2019;25:2900–14.

    Article  CAS  PubMed  Google Scholar 

  32. Yuan L, Sheng X, Willson AK, Roque DR, Stine JE, Guo H, et al. Glutamine promotes ovarian cancer cell proliferation through the mTOR/S6 pathway. Endocr-Relat Cancer. 2015;22:577–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Yang L, Moss T, Mangala LS, Marini J, Zhao H, Wahlig S, et al. Metabolic shifts toward glutamine regulate tumor growth, invasion and bioenergetics in ovarian cancer. Mol Syst Biol. 2014;10:728.

    Article  PubMed  PubMed Central  Google Scholar 

  34. Hao Y, Samuels Y, Li Q, Krokowski D, Guan BJ, Wang C, et al. Oncogenic PIK3CA mutations reprogram glutamine metabolism in colorectal cancer. Nat Commun. 2016;7:11971.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Kim GW, Lee DH, Jeon YH, Yoo J, Kim SY, Lee SW, et al. Glutamine synthetase as a therapeutic target for cancer treatment. Int J Mol Sci. 2021;22:1701–18.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Hayashi N, Sugimoto Y, Tsuchiya E, Ogawa M, Nakamura Y. Somatic mutations of the MTS (multiple tumor suppressor) 1/CDK4l (cyclin-dependent kinase-4 inhibitor) gene in human primary non-small cell lung carcinomas. Biochemical biophysical Res Commun. 1994;202:1426–30.

    Article  CAS  Google Scholar 

  37. Yu T, Ma P, Wu D, Shu Y, Gao W. Functions and mechanisms of microRNA-31 in human cancers. Biomedicine Pharmacother = Biomedecine pharmacotherapie. 2018;108:1162–9.

    Article  CAS  Google Scholar 

  38. Kent OA, Mendell JT, Rottapel R. Transcriptional regulation of miR-31 by oncogenic KRAS mediates metastatic phenotypes by repressing RASA1. Mol Cancer Res. 2016;14:267–77.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Frampton GM, Fichtenholtz A, Otto GA, Wang K, Downing SR, He J, et al. Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nat Biotechnol. 2013;31:1023–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Chalmers ZR, Connelly CF, Fabrizio D, Gay L, Ali SM, Ennis R, et al. Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden. Genome Med. 2017;9:34.

    Article  PubMed  PubMed Central  Google Scholar 

  41. Edwards M, Houseman L, Phillips IR, Shephard EA. Isolation of mouse hepatocytes. Methods Mol Biol. 2013;987:283–93.

    Article  CAS  PubMed  Google Scholar 

  42. Melamud E, Vastag L, Rabinowitz JD. Metabolomic analysis and visualization engine for LC-MS data. Anal Chem. 2010;82:9818–26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Boldes T, Merenbakh-Lamin K, Journo S, Shachar E, Lipson D, Yeheskel A, et al. R269C variant of ESR1: high prevalence and differential function in a subset of pancreatic cancers. BMC Cancer. 2020;20:531.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was financially supported by the Israel Science Foundation to I.W. (grant no. 1320/14); the Israel Cancer Association to I.W. (grant no. 20160053); The Margaret Stultz foundation for Pancreatic Cancer Research, the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; and TASMC excellence fund. The funding sources had no implications on the study design, collections, analysis, and interpretation of data or writing the manuscript. Israel Cancer Association, ISF, Pancreatic Cancer Foundation

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  1. These authors contributed equally: Ido Wolf, Tami Rubinek

Authors and Affiliations

  1. Institute of Oncology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel

    Shani Journo, Anat Klein Goldberg, Lotem Zinger, Dor Simkin, Sivan Fuchs, Ido Wolf & Tami Rubinek

  2. Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel

    Shani Journo, Lotem Zinger, Ido Wolf & Tami Rubinek

  3. Foundation Medicine, Inc., Cambridge, MA, 02141, USA

    Ethan S Sokol

  4. Bioinformatics Unit, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel

    Metsada Pasmanik-Chor

  5. Faculty of Computer Science at Technion; and Faculty of Biology at Technion, Haifa, Israel

    Boris Sarvin & Tomer Shlomi

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Contributions

SJ- Collected the data, performed the analysis of in vitro assays, and wrote the paper. AKG- Collected the data, performed the analysis of in vitro assays. ES- Conceived and designed the analysis, collected the data, contributed data and analysis tools, performed analysis, and participated in writing of the paper. LZ- Collected the data and performed analysis. MPC- Contributed data and analysis tools, performed analysis of RNA sequencing, and participated in writing. BS- Collected data, performed analysis and participated in writing. DS- Performed analysis of RNA sequencing. SF- Collected data and performed analysis. TS- Designed and performed analysis and participated in writing. TR- Conceived and designed the analysis, collected the data, performed analysis, and wrote the paper. IW- Conceived and designed the analysis, collected the data, performed analysis, and wrote the paper. All authors read and approved the final manuscript.

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Correspondence to Ido Wolf or Tami Rubinek.

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Journo, S., Goldberg, A.K., Sokol, E.S. et al. Genomic alterations drive metastases formation in pancreatic ductal adenocarcinoma cancer: deciphering the role of CDKN2A and CDKN2B in mediating liver tropism. Oncogene 41, 1468–1481 (2022). https://doi.org/10.1038/s41388-022-02184-2

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