• hepatocellular carcinoma
• liver
• liver immunology
• molecular genetics

Malignant tumours are composed of a heterogeneous collection of single cells with different molecular and phenotypic features, a phenomenon termed intratumoural heterogeneity (ITH) that is involved in tumour growth, progression, invasion and metastasis. This multilesion scenario represents a serious hurdle to accurate diagnoses and effective treatments that should be urgently circumvented to improve the clinical management of oncologic patients. To this end, many efforts have been devoted to investigate the morphological, environmental and molecular principles of ITH, specifically in hepatocellular carcinoma (HCC).1 Understanding tumour immunogenicity is a central topic in cancer therapy as immune microenvironment, human leucocyte antigen heterogeneity and tumour-specific neoantigens may lead to next-generation vaccination strategies.2 Genetic variation has been appointed as a source of ITH in HCC with pharmacological implication, although caution should be taken in the interpretation of mutational signatures3 that should be subjected to further validation. In this regard, orthogonal analyses combining complementary approaches to analyse different layers of biological information are currently providing a more precise phenotypic description to the molecular complexity resulting from ITH. The study of ITH by integrating different sources of information was already proposed in 1983 and in recent years the use of genome-wide exploration technologies is emerging as a resource with unprecedented capabilities …