A primer on a hepatocellular carcinoma bioresource bank using the cancer genome atlas guidelines: practical issues and pitfalls

Role of Biobanks for Cancer Research and Precision Medicine in Hepatocellular Carcinoma

INTRODUCTION

Hepatocellular carcinoma (HCC) is a highly complex and deadly cancer. There is an urgent need for new and effective treatment modalities. Since the primary goal in the management of cancer is to cure and improve survival, personalized therapy can increase survival, reduce mortality rates, and improve quality of life. Biobanks hold potential in leading to breakthroughs in biomedical research and precision medicine (PM). They serve as a biorepository, collecting, processing, storing, and supplying specimens and relevant data for basic, translational, and clinical research.

OBJECTIVE

We aimed to highlight the fundamental role of biobanks, harboring high quality, sustainable collections of patient samples in adequate size and variability, for developing diagnostic, prognostic, and predictive biomarkers to develop and PM approaches in the management of HCC.

METHOD

We obtained information from previously published articles and BBMRI directory.

RESULTS AND CONCLUSION

Biobanking of high-quality biospecimens along with patient clinical information provides a fundamental scientific infrastructure for basic, translational, and clinical research. Biobanks that control and eliminate pre-analytical variability of biospecimens, provide a platform to identify reliable biomarkers for the application of PM. We believe, establishing HCC biobanks will empower to underpin molecular mechanisms of HCC and generate strategies for PM. Thus, first, we will review current therapy approaches in HCC care. Then, we will summarize challenges in HCC management. Lastly, we will focus on the best practices for establishing HCC biobanking to support research, translational medicine in the light of new experimental research conducted with the aim of delivering PM for HCC patients.

BRIT1 dysfunction confers synergistic inhibition of hepatocellular carcinoma by targeting poly (ADP-ribose) polymerases and PI3K

BRIT1 has emerged as a novel key player in homologous recombination (HR). It is located in 8p23, a locus frequently deleted in hepatocellular carcinoma (HCC). Previously, we found that BRIT1-deficiency triggered genomic instability and tumor formation in our mouse model. Here we aim to determine whether BRIT1 aberrations are implicated in HCC and, if so, whether they can be used for targeted therapy with PARP inhibitors and other agents. We analyzed HCC samples for BRIT1 alterations at DNA, RNA and protein levels. BRIT1 was found deleted and/or downregulated in ~30% of HCC samples; BRIT1 mutant K659fsX10 identified in HCC abolished DNA repair function. Notably, BRIT1 deletion was correlated with poor survival and high recurrence of HCC. To determine the role of BRIT1 deficiency in potentiating the drug response, we subsequently generated BRIT1-deficient HCC cells, determined their HR defects, and assessed their response to the PARPi olaparib and PI3K inhibitor in vitro and in mice. BRIT1-deficient HCC cells were HR defective and hypersensitive to olaparib alone or in combination with PI3K inhibitor BEZ235, both in vitro and in vivo. The cytotoxicity of olaparib alone or in combination with BEZ235 was largely alleviated by ectopic BRIT1. We also found that BEZ235 markedly enhanced the production of poly (ADP-ribose) and the level of double-strand breaks (DSB) and single-strand breaks (SSB) in BRIT1-deficient cells. In summary, our results identify BRIT1 deficiency as a potential driver for HCC development, and BRIT1 status is critical to sensitivity to treatment with olaparib and/or BEZ235. PI3K inhibition induces substantial DNA damage and makes cells more dependent on PARP activity in the context of BRIT1 deficiency, thus, BRIT1 depletion facilitates enhancing synthetic lethality of PARP inhibitors and PI3K inhibitors in HCC. This study provides a new mechanistic foundation for significantly expanding the application of PARPi in HCC therapy.

Shift in VEGFA isoform balance towards more angiogenic variants is associated with tumor stage and differentiation of human hepatocellular carcinoma

BACKGROUND

Hepatocellular carcinoma (HCC) is the most common and aggressive type of malignant liver tumor. HCC progression depends significantly on its vascularization and formation of new blood vessels. Vascular endothelial growth factor A (VEGFA) is a crucial regulator of tumor vascularization and components of VEGF-induced cell signaling pathways are important targets of therapeutical drugs that demonstrated the highest efficiency in case of advanced HCC (sorafenib and regorafenib). VEGFA is expressed as a set of isoforms with different functional properties, thus VEGFA isoform expression pattern may affect tumor sensitivity to anti-angiogenic drugs. However, information about VEGFA isoforms expression in HCC is still incomplete and contradictory. The present study aims to quantitatively investigate VEGFA isoform expression aberrations in HCC tissue.

METHODS

A total of 50 pairs of HCC and non-tumor tissue samples were used to evaluate the VEGFA isoform spectrum using RT-PCR and quantitatively estimate changes in isoform expression using RT-qPCR. Correlations between these changes and tumor clinicopathological characteristics were analyzed.

RESULTS

We identified VEGFA-189, VEGFA-165, and VEGFA-121 as predominant isoforms in liver tissue. Anti-angiogenic VEGFA-xxxb variants constituted no more than 5% of all mature VEGFA transcripts detected and their expression was not changed significantly in HCC tissue. We demonstrated for the first time that the least active variant VEGFA-189 is frequently repressed in HCC (p < 0.001), while no uniform changes were detected for potent angiogenesis stimulators VEGFA-165 and VEGFA-121. Isoform balance in HCC shifts from VEGFA-189 towards VEGFA-165 or VEGFA-121 in the majority of cases (p < 0.001). Changes in fractions, but not expression levels, of VEGFA-189 (decrease) and VEGFA-121 (increase) correlated with advanced Tumor-Node-Metastasis (TNM) and Barcelona Clinic Liver Cancer (BCLC) tumor stages (p < 0.05), VEGFA-189 fraction reduction was also associated with poor tumor differentiation (p < 0.05).

DISCUSSION

A distinct shift in VEGFA isoform balance towards more pro-angiogenic variants occurs in HCC tissue and may modulate overall impact of VEGFA signaling. We suppose that the ratio between VEGFA isoforms is an important parameter governing HCC angiogenesis that may affect HCC progression and be used for optimizing the strategy of HCC therapy by predicting the response to anti-angiogenic drugs.