Exploring the Genomic Landscape of Hepatobiliary Cancers to Establish a Novel Molecular Classification System

Anthony J. Scholer, Rebecca K. Marcus, Mary Garland-Kledzik, Debopriya Ghosh, Miquel Ensenyat-Mendez, Joshua Germany, Juan A. Santamaria-Barria, Adam Khader, Javier I.J. Orozco, Melanie Goldfarb

Research output: Contribution to journalArticlepeer-review


Taxonomy of hepatobiliary cancer (HBC) categorizes tumors by location or histopathology (tissue of origin, TO). Tumors originating from different TOs can also be grouped by overlapping genomic alterations (GA) into molecular subtypes (MS). The aim of this study was to create novel HBC MSs. Next-generation sequencing (NGS) data from the AACR-GENIE database were used to examine the genomic landscape of HBCs. Machine learning and gene enrichment analysis identified MSs and their oncogenomic pathways. Descriptive statistics were used to compare subtypes and their associations with clinical and molecular variables. Integrative analyses generated three MSs with different oncogenomic pathways independent of TO (n = 324; p < 0.05). HC-1 “hyper-mutated-proliferative state” MS had rapidly dividing cells susceptible to chemotherapy; HC-2 “adaptive stem cell-cellular senescence” MS had epigenomic alterations to evade immune system and treatment-resistant mechanisms; HC-3 “metabolic-stress pathway” MS had metabolic alterations. The discovery of HBC MSs is the initial step in cancer taxonomy evolution and the incorporation of genomic profiling into the TNM system. The goal is the development of a precision oncology machine learning algorithm to guide treatment planning and improve HBC outcomes. Future studies should validate findings of this study, incorporate clinical outcomes, and compare the MS classification to the AJCC 8th staging system.

Original languageEnglish (US)
Article number325
Issue number2
StatePublished - Jan 2024


  • hepatobiliary cancer
  • molecular subtypes
  • next-generation sequencing
  • oncogenic pathways

ASJC Scopus subject areas

  • Oncology
  • Cancer Research


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