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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.

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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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