Hepatocellular carcinoma (HCC) is the most common type of liver cancer that accounts for 4.7% of the total number of new cases of cancer worldwide every year. HCC is a highly heterogeneous and complex disease with an estimated 5-year survival rate of only 18%. A better understanding of the mechanisms involved in the development, progression and recurrence of this tumour could not only guide us in the improvement of preventive strategies but also in the expansion of alternative target therapies for HCC patients.

The aim of this thesis is to investigate new diagnostic and prognostic markers, both on genetic and molecular levels, in the context of HCC. The results section is divided in two, called Chapter I and Chapter II.

HCC presents a distinct mutational landscape and Chapter I describes how we developed a HCC-specific custom made sequencing panel, containing the genes most commonly affected by somatic mutations and copy number alterations (CNAs) in the disease. We created a panel that was tested in different kinds of patient biopsies: frozen tissues, formalin-fixed paraffin-embedded (FFPE) tissues and also liquid biopsies. Moreover, to have reliable and reproducible sequencing data, we created a solid and user friendly somatic variant calling pipeline specific for Ion Torrent sequencing data.

In Chapter II, we aimed to investigate the molecular mechanism of HMGA1 in HCC and to explore its molecular targets. HMGA1 is an architectural transcription factor that was found often overexpressed in HCCs. We explored its DNA-binding landscape and, after deregulating HMGA1 in a HCC in vitro environment, its expression signature both at the RNA and protein levels. With the analysis of the binding partners of HMGA1, we recognised the vast range of mechanisms of action of this complex protein. We identified several RNA regulators that bind HMGA1, including Alyref, which plays a role in the regulation of the transcription. Further work should aim to determine the non-canonical role of HMGA1 involved in the binding and the regulation not only at the DNA but also at the RNA level.

Both chapters describe the steps of this work on the identification and the functional understanding of HCC biomarkers. This may lead in the future to more individualised treatment approaches, a need that in cancers with low survival rate such as HCC is not only highly desirable but is also a necessity.