Elsevier

Journal of Hepatology

Volume 65, Issue 5, November 2016, Pages 1031-1042
Journal of Hepatology

Review
Genetic profiling of hepatocellular carcinoma using next-generation sequencing

https://doi.org/10.1016/j.jhep.2016.05.035Get rights and content

Summary

Hepatocellular carcinoma (HCC) is a highly heterogeneous disease, both clinically and from a molecular standpoint. The advent of next-generation sequencing technologies has provided new opportunities to extensively analyze molecular defects in HCC samples. This has uncovered major cancer driver genes and associated oncogenic pathways operating in HCC. More sophisticated analyses of sequencing data have linked specific nucleotide patterns to external toxic agents and defined so-called ‘mutational signatures’ in HCC. Molecular signatures, taking into account intra- and inter-tumor heterogeneity, and their functional validation could provide useful data to predict treatment response to molecular therapies. In this review we will focus on the current knowledge of deep sequencing in HCC and its foreseeable clinical impact.

Introduction

Hepatocellular carcinoma (HCC) is the second cause of cancer-related mortality worldwide [1]. Its mortality is rising and considering the dismal results of recent clinical trials testing systemic agents [2], it seems more difficult to treat than initially anticipated. Each HCC is composed of a unique combination of somatic alterations including genetic, epigenetic, transcriptomic and metabolic events that form its unique molecular fingerprint [3], [4]. Regarding genetic changes, the progressive accumulation of mutations in cancer cells is the result of spontaneous events in the context of enhanced cell division, exposure to viruses (e.g., hepatitis B), carcinogens (e.g., aflatoxin B1) and defects in the DNA repair processes [5]. Moreover, the strong association between cirrhosis and HCC could be partially explained by an accelerated acquisition of genetic alterations in senescent cirrhotic hepatocytes exposed to chronic inflammation and oxidative stress [6]. Genome wide sequencing using next-generation technologies has exponentially improved our ability to explore the cancer genome [7]. Identification of the key driver genes and mechanisms underlying mutation occurrence could help understand HCC pathogenesis and develop new therapeutic strategies [2]. Herein, we will review the main advances in our knowledge of the HCC genome obtained by next-generation sequencing (NGS) and its potential future impact in clinical practice.

Section snippets

Methodological insights of next-generation sequencing

It took almost 40 years between the identification of the structure of DNA [8] by Watson, Crick and Wilkins (Nobel Prize 1962) and the first draft of the complete sequence of the human genome after 10 years of work for almost 4 billion US dollars [9]. NGS technologies developed in the beginning of the 21st century considerably accelerated our ability to explore the DNA structure at a significant lower cost (less than $5000 for a whole human genome performed in less than 24 h) [10]. NGS generates

Mutational landscape in hepatocellular carcinoma

The accumulation of alterations in cancer driver genes and associated pathways are major triggers for hepatocarcinogenesis and tumor progression. Specific discrepancies in HCC mutation rates of major cancer drivers are thought to be dependent on the clinical profile of each patient such as etiology of the liver disease, stage of cancer progression, selective pressure under treatment, and presence or not of an underlying chronic liver disease. Therefore, deciphering the mutational landscape of

Mutational signatures in hepatocellular carcinoma

In addition to identifying mutations in specific genes and their potential contribution to the malignant phenotype, a more global view on mutational patterns has been recently developed at the Wellcome Trust Sanger Institute. The so-called ‘nucleotide or mutational signatures’ link distinct intrinsic processes such as defective DNA repair or exposure to external toxic agents (e.g., UV light, tobacco) with specific patterns of mutations at the nucleotide level. Taking into account a nucleotide

Genetic basis of telomerase reactivation in hepatocellular carcinoma

Telomeres are short non-coding DNA repeats (TTAGGG) localized at the extremity of the chromosome and coated by sheltering proteins [31]. They protect coding regions from DNA losses induced by the shortening of the end of the chromosome due to the end replication problem observed during cell division [32], [33]. However, at each round of cell replication, telomeres shortened and, when they reach a critical point, cell senescence is triggered through induction of the P53/P21 and P16/RB

Consequences of viral infection for the genome of hepatocellular carcinoma

The most common mechanism leading to HCC in patients with chronic viral infection remains the occurrence of chronic liver disease and cirrhosis due to persistent inflammation and oxidative stress [3]. A direct oncogenic role of HCV proteins is still controversial, and since HCV is an RNA virus no integrations in the tumor genome have been described [55]. This mechanism explains most HCV-related HCC since these patients almost always develop HCC on cirrhosis. In contrast, a direct oncogenic

Molecular heterogeneity in hepatocellular carcinoma

The issue of cancer molecular heterogeneity has sparked notorious scientific debate in the last years. The concept assumes that somatic molecular alterations in cancer are not uniformly distributed throughout the whole tumor mass. One of the key issues is to determine if this diversity significantly impacts predictions based on single biopsies, and ultimately, clinical decision-making in the precision medicine era. Molecular heterogeneity expands the model of clonal cancer evolution, which was

Clinical implementation of sequencing data

One of the most notorious successes of anticancer therapy came from the selective blockage of cancer drivers [98]. Some of them are the result of aberrant activation of tyrosine kinases due to somatic mutation. Well-known examples include erlotinib in EGFR-mutated lung cancer, vemurafenib in BRAF-mutated melanoma or crizotinib in lung cancer with anaplastic lymphoma kinase (ALK) rearrangements. Unfortunately, biomarker-driven clinical trials haven’t dominated drug development in HCC. Probably

Conclusions and future perspectives

The tremendous impact that NGS had in biomedical research is indisputable. Like in previous occasions, technological breakthroughs had preceded major scientific discoveries. In the case of HCC, one of the deadliest malignancies known to humans, NGS has provided a comprehensive landscape of recurrence molecular alterations including somatic mutations, chromosomal alterations and viral integrations. Further analytical refinements of NGS data will soon allow to better understand tumor

Conflict of interest

The authors declared that they do not have anything to disclose regarding funding or conflict of interest with respect to this manuscript.

Acknowledgments

AV is the recipient of the American Association for the Study of Liver Diseases Foundation Alan Hofmann Clinical and Translational Research Award.

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