Gastroenterology

Gastroenterology

Volume 153, Issue 3, September 2017, Pages 812-826
Gastroenterology

Original Research
Full Report: Basic and Translational—Liver
Identification of an Immune-specific Class of Hepatocellular Carcinoma, Based on Molecular Features

https://doi.org/10.1053/j.gastro.2017.06.007Get rights and content

Background & aims

Agents that induce an immune response against tumors by altering T-cell regulation have increased survival times of patients with advanced-stage tumors, such as melanoma or lung cancer. We aimed to characterize molecular features of immune cells that infiltrate hepatocellular carcinomas (HCCs) to determine whether these types of agents might be effective against liver tumors.

Methods

We analyzed HCC samples from 956 patients. We separated gene expression profiles from tumor, stromal, and immune cells using a non-negative matrix factorization algorithm. We then analyzed the gene expression pattern of inflammatory cells in HCC tumor samples. We correlated expression patterns with the presence of immune cell infiltrates and immune regulatory molecules, determined by pathology and immunohistochemical analyses, in a training set of 228 HCC samples. We validated the correlation in a validation set of 728 tumor samples. Using data from 190 tumors in the Cancer Genome Atlas, we correlated immune cell gene expression profiles with numbers of chromosomal aberrations (based on single-nucleotide polymorphism array) and mutations (exome sequence data).

Results

We found approximately 25% of HCCs to have markers of an inflammatory response, with high expression levels of the CD274 molecule (programmed death-ligand 1) and programmed cell death 1, markers of cytolytic activity, and fewer chromosomal aberrations. We called this group of tumors the Immune class. It contained 2 subtypes, characterized by markers of an adaptive T-cell response or exhausted immune response. The exhausted immune response subclass expressed many genes regulated by transforming growth factor beta 1 that mediate immunosuppression. We did not observe any differences in numbers of mutations or expression of tumor antigens between the immune-specific class and other HCCs.

Conclusions

In an analysis of HCC samples from 956 patients, we found almost 25% to express markers of an inflammatory response. We identified 2 subclasses, characterized by adaptive or exhausted immune responses. These findings indicate that some HCCs might be susceptible to therapeutic agents designed to block the regulatory pathways in T cells, such as programmed death-ligand 1, programmed cell death 1, or transforming growth factor beta 1 inhibitors.

Section snippets

Patients and Samples

For the purpose of the study, gene expression profile from a total of 956 HCC human samples was analyzed (Figure 1), including a training cohort of 228 surgically resected fresh frozen (FF) samples (Heptromic dataset, GSE63898). All samples of the training set were previously obtained from 2 institutions of the HCC Genomic Consortium upon institutional review board approval: IRCCS Istituto Nazionale Tumori (Milan, Italy) and Hospital Clínic (Barcelona, Spain). RNA profiling and methylation data

A Novel Immune Class of HCC

To isolate immune-related genomic signals from bulk gene expression data in HCC tumors, we performed NMF analysis of 228 resected HCC samples (training cohort, Figure 1). Clinical characteristics of the training cohort are summarized in Table 1. Among the distinct expression patterns identified by NMF, one was attributed to the presence of inflammatory response and immune cells through integration with a previously reported immune enrichment score (Supplementary Figure 1A). Analysis of the

Discussion

Our study represents a comprehensive characterization of the immunologic profile of human HCC tumors. The use of virtual separation analytical approaches enabled us to deconvolute the gene expression signals deriving from the intratumoral immune infiltrates; this identified a previously unnoticed robust class of HCC (∼27% of 956 patients), herein named Immune class. The immune nature of our classifier is supported by the overlap with gene signatures identifying immune cells (ie, T cells and

Acknowledgments

We thank Prof Jessica Zucman-Rossi for her advice and revision of the paper. We thank Wei Quiang Leow and Agrin Moeini for their support. The results shown here are in part based on data generated by the TCGA Research Network: http://cancergenome.nih.gov/.

References (42)

  • J.M. Llovet et al.

    Hepatocellular carcinoma

    Nat Rev Dis Primers

    (2016)
  • J.M. Llovet et al.

    Sorafenib in advanced hepatocellular carcinoma

    N Engl J Med

    (2008)
  • J.M. Llovet et al.

    Advances in targeted therapies for hepatocellular carcinoma in the genomic era

    Nat Rev Clin Oncol

    (2015)
  • W. Zou et al.

    PD-L1 (B7-H1) and PD-1 pathway blockade for cancer therapy: mechanisms, response biomarkers, and combinations

    Sci Transl Med

    (2016)
  • E.B. Garon et al.

    Pembrolizumab for the treatment of non-small-cell lung cancer

    N Engl J Med

    (2015)
  • S.L. Topalian et al.

    Safety, activity, and immune correlates of anti-PD-1 antibody in cancer

    N Engl J Med

    (2012)
  • R.R. Ji et al.

    An immune-active tumor microenvironment favors clinical response to ipilimumab

    Cancer Immunol Immunother

    (2012)
  • D.T. Le et al.

    PD-1 Blockade in tumors with mismatch-repair deficiency

    N Engl J Med

    (2015)
  • T. Bald et al.

    Immune cell-poor melanomas benefit from PD-1 blockade after targeted type I IFN activation

    Cancer Discov

    (2014)
  • S. Spranger et al.

    Melanoma-intrinsic beta-catenin signalling prevents anti-tumour immunity

    Nature

    (2015)
  • R.A. Moffitt et al.

    Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma

    Nat Genet

    (2015)

    • Cited by (0)

    Conflicts of interest The authors disclose the following: DS, AV, and JML are co-inventors of the patent “Identification of an immune-specific class of hepatocellular carcinoma, based on molecular features” (Application N62/519,711). The remaining authors disclose no conflicts.

    Funding This project has received funding from the Tisch Cancer Institute at Mount Sinai (P30 CA196521–Cancer Center Support Grant). J.M.L. is supported by grants from the US Department of Defense (CA150272P3), European Commission Framework Program 7 (HEPTROMIC, proposal number 259744), and Horizon 2020 Program (HEPCAR, proposal number 667273–2), the Asociación Española Contra el Cáncer, Samuel Waxman Cancer Research Foundation, Spanish National Health Institute (SAF2013–41027), and Grup de Recerca Consolidat–Recerca Translacional en Oncologia Hepàtica, AGAUR (Generalitat de Catalunya), SGR 1162. I.M.-Q. is supported by the European Commission HEPCAR grant. O.K. is supported by Onlus Prometeo, Hepato-Oncology Research Project, Istituto Nazionale Tumori (National Cancer Institute) IRCCS Foundation (Milan, Italy). L.B. is supported by the Juan de la Cierva Fellowship. V.M. is supported by grants from Associazione Italiana per la Ricerca sul Cancro and the Oncology Research Project of the Italian Ministry of Health. S.L.F. is supported by the US Department of Defense (CA150272P3) and National Institutes of Health (R01DK56621). A.V. is supported by the US Department of Defense (CA150272P3), The Tisch Cancer Institute, and the American Association for the Study of Liver Diseases Foundation Alan Hofmann Clinical and Translational Award.

    Gene Expression Omnibus accession number: GSE93647, and previously deposited data from our group (GSE63898, GSE20140) and others [GPL1528, GSE1898, GPL2094 a), GPL80b), GPL96 E-TABM-36, GPL5474, GSE10186].

    Author names in bold designate shared co-first authorship.

    View full text
    © 2017 by the AGA Institute