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Original research
Novel microenvironment-based classification of intrahepatic cholangiocarcinoma with therapeutic implications
  1. Miguel A Martin-Serrano1,
  2. Benjamin Kepecs2,
  3. Miguel Torres-Martin3,
  4. Emily R Bramel1,4,
  5. Philipp K Haber1,
  6. Elliot Merritt2,5,
  7. Alexander Rialdi1,6,
  8. Nesteene Joy Param4,6,
  9. Miho Maeda1,
  10. Katherine E Lindblad1,4,5,6,
  11. James K Carter1,4,
  12. Marina Barcena-Varela1,5,6,
  13. Vincenzo Mazzaferro7,
  14. Myron Schwartz8,
  15. Silvia Affo9,
  16. Robert F Schwabe10,
  17. Augusto Villanueva1,
  18. Ernesto Guccione1,6,
  19. Scott L Friedman1,
  20. Amaia Lujambio1,4,5,6,
  21. Anna Tocheva2,5,
  22. Josep M Llovet1,3,11,
  23. Swan N Thung12,
  24. Alexander M Tsankov2,
  25. Daniela Sia1
  1. 1Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
  2. 2Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
  3. 3Translational Research in Hepatic Oncology, Liver Unit, IDIBAPS, Hospital Clinic, University of Barcelona, Barcelona, Catalunya, Spain
  4. 4Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
  5. 5The Precision Immunology Institute (PrIISM), Icahn School of Medicine at Mount Sinai, New York, New York, USA
  6. 6Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
  7. 7General Surgery and Liver Transplantation Unit, Department of Oncology and Hemato-Oncology, University of Milan and Istituto Nazionale Tumori, IRCCS Foundation, Milano, Lombardia, Italy
  8. 8Department of Surgery, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
  9. 9Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalunya, Spain
  10. 10Department of Medicine, Columbia University, New York, New York, USA
  11. 11Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
  12. 12Department of Pathology, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
  1. Correspondence to Dr Daniela Sia, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Liver Cancer Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA; daniela.sia{at}mssm.edu

Abstract

Objective The diversity of the tumour microenvironment (TME) of intrahepatic cholangiocarcinoma (iCCA) has not been comprehensively assessed. We aimed to generate a novel molecular iCCA classifier that incorporates elements of the stroma, tumour and immune microenvironment (‘STIM’ classification).

Design We applied virtual deconvolution to transcriptomic data from ~900 iCCAs, enabling us to devise a novel classification by selecting for the most relevant TME components. Murine models were generated through hydrodynamic tail vein injection and compared with the human disease.

Results iCCA is composed of five robust STIM classes encompassing both inflamed (35%) and non-inflamed profiles (65%). The inflamed classes, named immune classical (~10%) and inflammatory stroma (~25%), differ in oncogenic pathways and extent of desmoplasia, with the inflammatory stroma showing T cell exhaustion, abundant stroma and KRAS mutations (p<0.001). Analysis of cell–cell interactions highlights cancer-associated fibroblast subtypes as potential mediators of immune evasion. Among the non-inflamed classes, the desert-like class (~20%) harbours the lowest immune infiltration with abundant regulatory T cells (p<0.001), whereas the hepatic stem-like class (~35%) is enriched in ‘M2-like’ macrophages, mutations in IDH1/2 and BAP1, and FGFR2 fusions. The remaining class (tumour classical: ~10%) is defined by cell cycle pathways and poor prognosis. Comparative analysis unveils high similarity between a KRAS/p19 murine model and the inflammatory stroma class (p=0.02). The KRAS-SOS inhibitor, BI3406, sensitises a KRAS-mutant iCCA murine model to anti-PD1 therapy.

Conclusions We describe a comprehensive TME-based stratification of iCCA. Cross-species analysis establishes murine models that align closely to human iCCA for the preclinical testing of combination strategies.

  • cholangiocarcinoma
  • immune response
  • molecular biology
  • gene expression
  • immunotherapy

Data availability statement

Data are available in a public, open access repository. RNA-sequencing data generated in this study have been deposited in the GEO database (GSE171443). Previously published datasets analysed in this study are indicated in main Methods and detailed in online supplemental table 1.

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Data availability statement

Data are available in a public, open access repository. RNA-sequencing data generated in this study have been deposited in the GEO database (GSE171443). Previously published datasets analysed in this study are indicated in main Methods and detailed in online supplemental table 1.

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Footnotes

  • BK and MT-M contributed equally.

  • Contributors DS designed the research, obtained funding and acts as guarantor for the overall content; MAM-S, MM, ST, MB-V, KL, NJP and EB performed the experiments. MAM-S, MM, JC and EB performed immunohistochemical analysis. DS, AV, BK, MT-M and PH conducted the in silico analyses. EM, AR, EG and AT performed coculture experiments. SA, RS and AL provided plasmids and advised on the murine models. VM, MS, SLF and JL collected the tissues and clinical data. BK performed scRNA-seq and ligand bulk RNA-seq correlation analyses designed by AMT, DS, MAM-S, BK and AMT, interpreted the results. DS, MAM-S, BK and AMT, interpreted the results. DS wrote the manuscript. All authors reviewed, edited and approved the manuscript.

  • Funding This study was partially funded by the 2019 PhD Scientist Innovative Research Award and the Dr. Franklin Klion Young Scientist Award (DS), and the Cholangiocarcinoma Foundation (MAM-S). MAM-S is supported by the Margaret M. Brown Memorial Research Fellowship from the Cholangiocarcinoma Foundation. PH is supported by the fellowship grant of the German Research Foundation (DFG, HA 8754/1-1). JC is supported by grants from National Institutes of Health (T32GM007280 and T32GM062754). KL is supported by NIH T32 AI78892-12. MB-V is supported by the Asociación Española por el Estudio del Hígado (AEEH). SA is supported by a fellowship from 'la Caixa' Foundation (ID 100010434) and from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 847648. AL is supported by Damon Runyon-Rachleff Innovation Award (DR52-18), R37 Merit Award (R37CA230636), and Icahn School of Medicine at Mount Sinai. The Tisch Cancer Institute and related research facilities are supported by P30 CA196521. JML acknowledges his research funding from the Accelerator Award (HUNTER, Ref. C9380/A26813, partnership between the CRUK, AECC and AIRC), Samuel Waxman Cancer Research Foundation, Spanish National Health Institute (PID2019-105378RB-100), the Generalitat de Catalunya/AGAUR (SGR-1358). DS is supported by the Tisch Cancer Institute and Icahn School of Medicine at Mount Sinai. SLF is supported by the US Department of Defense (CA150272P3) and NIDDK (R01 DK56621 and R01 DK128289). AMT is supported by US Department of Defense (W81XWH2210079) and Icahn School of Medicine at Mount Sinai.

  • Competing interests JML is receiving research support from Bayer HealthCare Pharmaceuticals, Eisai Inc, Bristol-Myers Squibb, Boehringer-Ingelheim and Ipsen, and consulting fees from Eli Lilly, Bayer HealthCare Pharmaceuticals, Bristol-Myers Squibb, Eisai Inc, Celsion Corporation, Exelixis, Merck, Ipsen, Genentech, Roche, Glycotest, Nucleix, Sirtex, Mina Alpha Ltd and AstraZeneca. AV has received consulting fees from Genentech, Guidepoint, Fujifilm, Boehringer Ingelheim, FirstWord, and MHLife Sciences; advisory board fees from Exact Sciences, Nucleix, Gilead and NGM Pharmaceuticals; and research support from Eisai.

  • Patient and public involvement Patients and/or the public were not involved in the design, or conduct, or reporting, or dissemination plans of this research.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Supplemental material This content has been supplied by the author(s). It has not been vetted by BMJ Publishing Group Limited (BMJ) and may not have been peer-reviewed. Any opinions or recommendations discussed are solely those of the author(s) and are not endorsed by BMJ. BMJ disclaims all liability and responsibility arising from any reliance placed on the content. Where the content includes any translated material, BMJ does not warrant the accuracy and reliability of the translations (including but not limited to local regulations, clinical guidelines, terminology, drug names and drug dosages), and is not responsible for any error and/or omissions arising from translation and adaptation or otherwise.

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