Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

Abstract

Background Although mutated HLA ligands are considered ideal cancer-specific immunotherapy targets, evidence for their presentation is lacking in hepatocellular carcinomas (HCCs). Employing a unique multi-omics approach comprising a neoepitope identification pipeline, we assessed exome-derived mutations naturally presented as HLA class I ligands in HCCs. Methods In-depth multi-omics analyses included whole exome and transcriptome sequencing to define individual patient-specific search spaces of neoepitope candidates. Evidence for the natural presentation of mutated HLA ligands was investigated through an in silico pipeline integrating proteome and HLA ligandome profiling data. Results The approach was successfully validated in a state-of-the-art dataset from malignant melanoma, and despite multi-omics evidence for somatic mutations, mutated naturally presented HLA ligands remained elusive in HCCs. An analysis of extensive cancer datasets confirmed fundamental differences of tumor mutational burden in HCC and malignant melanoma, challenging the notion that exome-derived mutations contribute relevantly to the expectable neoepitope pool in malignancies with only few mutations. Conclusions This study suggests that exome-derived mutated HLA ligands appear to be rarely presented in HCCs, inter alia resulting from a low mutational burden as compared to other malignancies such as malignant melanoma. Our results therefore demand widening the target scope for personalized immunotherapy beyond this limited range of mutated neoepitopes, particularly for malignancies with similar or lower mutational burden. Electronic supplementary material The online version of this article (10.1186/s13073-019-0636-8) contains supplementary material, which is available to users.

Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy

“…HLA ligandomics was performed by reversed phase liquid chromatography coupled mass spectrometry as previously described [15,24,25]. The monoclonal antibodies W6/32, Tü39, and L243 (in-house production at the Department of Immunology, University of Tuebingen, Tuebingen, Germany) were used for immunoaffinity purification of HLA class I and II peptide complexes.…”

“…One important requirement for the recognition and killing of cancer cells by specialized cells of the immune system, such as cytotoxic CD8 + T lymphocytes (CTL), is the presentation of tumor-specific peptides by major histocompatibility complex (MHC; also human leukocyte antigen (HLA)) molecules on the cell surfaces of the cancer cells. We have previously characterized the landscape of HLA-presented peptides, termed the HLA ligandome, of several cancer entities to identify HLA class I-and class II-restricted peptides [13][14][15][16][17]. In cancer therapy, such peptides are exploited in vaccines or adoptive T cell therapy (ACT) to activate CTLs and prime them for the killing of a patient's cancer cells [18][19][20].…”

High Somatic Mutation and Neoantigen Burden Do Not Correlate with Decreased Progression-Free Survival in HCC Patients not Undergoing Immunotherapy

“…Hepatocellular carcinoma (HCC) ranks as a medium-variable tumor, with an average mutational burden of 5 somatic mutations per Mb, corresponding to approximately 60 non-synonymous substitutions within expressed genes [31]. In such a setting of low mutational burden, mutated human leukocyte antigen (HLA) ligands appear to be rarely presented in HCC, and identification of naturally presented neo-antigens by high-efficiency mass spectrometry has failed [32].…”

Targeting Neoantigens in Hepatocellular Carcinoma for Immunotherapy: A Futile Strategy?

“…A recent study on the neoantigen landscape in HCC raised concern about the potential pitfalls of targeting neoantigens in this type of tumor (13). Of 1039 nonsynonymous mutations identified in 16 HCC patients, no neoepitopes were detected in HLA class I complexes upon mass spectrometry analysis.…”