Copy number alteration burden differentially impacts immune profiles and molecular features of hepatocellular carcinoma
Clinical Cancer Research
Chromosomal instability is a hallmark of cancer that results in broad and focal copy number alterations (CNAs), two events associated with distinct molecular, immunological and clinical features. In hepatocellular carcinoma (HCC) the CNAs role has not been thoroughly assessed. Thus, we dissected the impact of CNA burdens on HCC molecular and immune features. We analyzed SNP-array data from 452 paired tumor/adjacent resected HCCs and 25 dysplastic nodules. For each sample, broad and focal CNA
... ad and focal CNA burdens were quantified using CNApp, and the resulting broad scores (BS) and focal scores (FS) were correlated with transcriptomic, mutational and methylation profiles, tumor immune composition, and with clinico-pathological data. HCCs with low broad CNA burdens (defined as BS≤4; 17%) presented high inflammation, active infiltrate signalling, high cytolytic activity, and enrichment of the 'HCC-Immune-Class' and gene signatures related to antigen presentation. Conversely, tumors with chromosomal instability (high broad CNA loads, BS≥11; 40%), displayed immune excluded traits and were linked to proliferation, TP53 dysfunction, and DNA repair. Candidate determinants of the low cytotoxicity and immune exclusion features of high-BS tumors included alterations in antigen presenting machinery (i.e. HLA), widespread hypomethylation and decreased rates of observed/expected neoantigenic mutations. High focal scores were independent of tumor immune features, but were related to proliferation, TP53 dysfunction and progenitor cell traits. HCCs with high chromosomal instability exhibit features of immune exclusion, whereas tumors displaying low burdens of broad CNAs present an immune active profile. These CNA scores can be tested to predict response to immunotherapies.