Advances in the molecular characterization of liver tumors

Mutational burden and signatures

To understand the molecular origins of the intrinsically aggressive disease trajectories of HB malignancies, increased mutational burden and/or rates may be suggested as a plausible mechanism. Surprisingly, comparative mutational profiling across cancers indicates these subsets of tumors are exceptionally unremarkable in this regard, falling approximately midway between leukemias (toward the lower end) and melanomas (at the upper end of the spectrum). On average, whole-exome sequencing (WES) studies have detected nonsynonymous mutation frequencies of 39 per tumor (median) in intrahepatic CCA (iCCA; see Chapter 50 ), 35 per tumor (median) in extrahepatic CCA (eCCA; see Chapter 51 ), 64 per tumor (median) in GBC (see Chapter 49 ), and 64 per tumor (median) in HCC (see Chapter 89 ). Although it is clear that there is significant variation in mutational burden between HB cancers, significant heterogeneity also exists within HB cancer subtypes. Certain etiologic backgrounds have been confirmed to correlate with higher mutational loads, such as liver fluke-associated CCA versus noninfected CCA. The mutation loads of HB tumors are of particular interest, given that tumor mutation burden (TMB) is positively correlated with increased likelihood of neoantigen production, potentially resulting in beneficial response to checkpoint inhibitor therapies.

Beyond the exome, whole-genome sequencing (WGS) studies remain somewhat underevaluated in HB cancers, with some notable exceptions, but this approach holds significant potential to inform on important features of cancer biology. Such areas include the pro-tumorigenic impact of retrotransposon reanimation, viral integration with insertional mutagenesis, enhancer function, and intergenic long ncRNAs (lncRNAs). WGS analysis has also been applied to successfully discern multicentric HCC from HCC with intrahepatic metastasis, a distinction that is important in determining patient eligibility for surgical resection.

Diverse exogenous and endogenous mutagenic processes are active in individual HB patients, collectively contributing to the total mutation burden of a given tumor. Analysis of mutational signature patterns in whole-exome and whole-genome sequencing data enable such mutagenic processes to be extrapolated, providing insight into the evolutionary processes that shaped the cancer genome. In total, 81 mutational signatures have been identified, although the causative mutagenic process is only known for some of these signatures. General signatures found across HB cancers include those associated with nucleotide excision repair deficiency, 5-methylcytosine deamination, and aging. ^{, ,} Examples of mutation signatures found to be enriched in specific HB cancers include an aflatoxin-associated signature in HCC ^, and an APOBEC-associated signature in eCCA and GBC. Further, a liver cancer–specific signature has also been identified, associating with alcohol exposure, transcription-coupled damage, and beta-catenin ( CTNNB1) mutations. The existence of such a liver-specific signature is perhaps unsurprising, given the associated hepatic exposure to diverse mutagens when carrying out its physiologic function in detoxification.