BackgroundAberrant translation of the non-coding genome in cancer can generate novel peptides capable of presentation by major histocompatibility complex class I (MHC-I; HLA-I in humans) and these ...non-canonical peptide sources can broaden the landscape of potentially targetable antigens in low-to-intermediate mutational burden malignancies. While emerging evidence suggests that translation of unannotated open reading frames (uORFs) can give rise to MHC class I-associated peptides (MAPs) across a range of malignancies, it is currently unknown to what extent these translation products are truly cancer-restricted and how effectively the resulting non-canonical MAPs (ncMAPs) can elicit a T cell response.MethodsWe leveraged twelve pancreatic cancer (PDAC) patient-derived organoids (PDOs) to purify the malignant compartment from low tumor cellularity tumor specimens. We developed a cutting-edge proteogenomics pipeline, coupled with high-depth immunopeptidomics to identify pancreatic cancer MAPs derived from somatic mutations, retained introns, and uORFs. To investigate the cancer-specificity of ncMAPs, we developed a translation-centric analysis pipeline that examines translation of uORFs encoding ncMAPs across a range of healthy tissues, including healthy thymus. To evaluate for immunogenicity, we employed a highly sensitive ex vivo platform to prime and expand ncMAP-specific cytotoxic T lymphocytes (CTLs) and evaluate cytolytic potential.ResultsWe demonstrate that ncMAPs are abundant and predominate over mutation-derived peptides in the pancreatic cancer immunopeptidome, establishing a novel class of recurrent cancer-restricted epitopes available for immune recognition. We observed widespread translation and MHC-I presentation of numerous ncMAPs across many healthy tissues, highlighting the importance of our translation-centric approach to assess cancer-restriction. Excitingly, we nominated over 500 ncMAPs that exhibit cancer-specific translation patterns. Approximately 30% of ncMAPs exhibited bona fide cancer-restricted translation patterns, and a substantial subset of these were shared among patients. We next interrogated immunogenicity using a highly sensitive ex vivo vaccination platform and demonstrated that the majority of cancer-restricted ncMAPs evaluated were highly immunogenic. Remarkably, the proportion of ncMAPs harboring immunogenic potential was substantially higher than mutation-derived neoepitopes and tumor-associated antigens, underscoring their therapeutic potential relative to traditional immunotherapy targets.ConclusionsThese findings demonstrate that aberrant translation in pancreatic cancer can give rise to recurrent cancer-restricted ncMAPs capable of recognition by cytotoxic T lymphocytes. Collectively, our findings furnish a novel set of recurrent, cancer-restricted immunotherapy targets not subject to central tolerance. We believe these findings will prompt translation-centric investigations in other solid tumors. We envision that these novel antigens will augment ongoing efforts to treat pancreatic cancer patients with vaccines and cell-based therapies.Ethics ApprovalInformed consent was obtained from patients at least 18 years old with pancreatic cancer under Dana-Farber/Harvard Cancer Center Institutional Review Board (IRB)-approved protocols 11–104, 17–000, 03–189, and/or 14–408 for tissue collection, molecular analysis, and organoid generation.
To examine the incidence of hepatocellular carcinoma (HCC) in western Sydney over the last 14 years, to assess risk factors for the disease among ethnic groups of Australian residents, and to ...consider the opportunities for improving its usually poor outcome.
Retrospective case-record review of clinical features in all (122) patients discharged from a 900-bed tertiary-referral teaching hospital with a diagnosis of HCC from January 1979 to March 1993.
Annual number of new cases; risk factors according to birthplace; surgical resectability of tumours.
New cases admitted each year at least doubled between 1979-1985 and 1986-1992. This apparent increase involved individuals born in Australia (50% of all patients) as well as immigrants. Cirrhosis was found in 93% at liver biopsy or autopsy. Excessive alcohol intake was an associated risk factor for 46% of Australian-born patients and for 13% of those born overseas. Among the latter, HCC was associated with markers of hepatitis B virus infection in 64%. Since hepatitis C virus (HCV) tests became available in 1990, five of nine patients tested were anti-HCV positive. Surveillance screening of patients known to have cirrhosis detected eight cases of early HCC. Seven of these had surgical resection and all are alive.
New diagnoses of HCC have increased recently, irrespective of country of birth. In Australian-born patients alcoholic liver disease remains a major aetiological factor but the role of HCV requires further evaluation. Among immigrants, cirrhosis from chronic viral hepatitis accounts for most cases. We propose that prevention of cirrhosis caused by chronic viral hepatitis should have the greatest long-term impact on prevention of HCC in Australia. The role of surveillance of people with cirrhosis to detect small and potentially resectable tumours should be explored.
