ABSTRACT
Interplays among lineage-specific nuclear proteins, chromatin modifying enzymes, and the basal transcription machinery govern cellular differentiation, but their dynamics of action and coordination with transcriptional control are not fully understood. Alterations in chromatin structure appear to establish a permissive state for gene activation at some loci, but they play an integral role in activation at other loci. To determine the predominant roles of chromatin states and factor occupancy in directing gene regulation during differentiation, we mapped chromatin accessibility, histone modifications, and nuclear factor occupancy genome-wide during mouse erythroid differentiation dependent on the master regulatory transcription factor GATA1. Notably, despite extensive changes in gene expression, the chromatin state profiles (proportions of a gene in a chromatin state dominated by activating or repressive histone modifications) and accessibility remain largely unchanged during GATA1-induced erythroid differentiation. In contrast, gene induction and repression are strongly associated with changes in patterns of transcription factor occupancy. Our results indicate that during erythroid differentiation, the broad features of chromatin states are established at the stage of lineage commitment, largely independently of GATA1. These determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors.
Subject(s)
Cell Differentiation/genetics , Epigenesis, Genetic , Erythropoiesis/genetics , GATA1 Transcription Factor/metabolism , Animals , Basic Helix-Loop-Helix Transcription Factors/metabolism , Cell Line , Chromatin Assembly and Disassembly , Chromatin Immunoprecipitation , Estradiol/pharmacology , Estradiol/physiology , GATA1 Transcription Factor/genetics , GATA2 Transcription Factor/metabolism , Gene Expression Profiling , Gene Silencing , Mice , Multivariate Analysis , Peptide Hydrolases/metabolism , Protein Binding , Proto-Oncogene Proteins/metabolism , Receptors, Estrogen/genetics , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Regulatory Sequences, Nucleic Acid , T-Cell Acute Lymphocytic Leukemia Protein 1ABSTRACT
BACKGROUND: Paediatric hepatocellular carcinomas (HCC) traditionally arise in the context of a normal structural and functional liver and carry a dismal prognosis. While chemotherapy is the frontline standard, there is emerging interest in the study of immunotherapies for paediatric patients with relapsed/refractory disease. There is limited data to support whether immunotherapies will be of utility in this patient population. METHODS: Six paediatric patients (median age:16 years, range: 12-17 at the time of treatment) with advanced hepatocellular neosplams, either conventional hepatocellular or fibrolamellar carcinoma, were treated with immunotherapy. Patients were consented to institutional genomic profiling and biobanking protocols. Baseline samples and serial tissue samples, when available, were evaluated for somatic mutation rate, actionable gene mutations, and pan-immune bulk RNA expression profiling. Results were correlated with clinical course. FINDINGS: Three patients responded to checkpoint inhibition: one achieved a complete, durable response and the other two, prolonged stable disease. Three additional patients progressed. Diagnostic tissue from the complete responder demonstrated a higher relative mutational burden and robust immune infiltrate. Pre-treatment samples from the three responders demonstrated decreased expression of genes associated with T-cell dysfunction. INTERPRETATION: A subset of patients with primary paediatric hepatocellular tumours will respond to immunotherapy. Immunotherapies are currently under prospective study for relapsed/refractory liver tumours in paediatric patients. Results from this report support the prospective collection of serial serum and tissue samples which may further identify genomic and immunophenotypic patterns predictive of response. FUNDING: This work was supported by Philanthropic funds (Pan Mass Challenge, Team Angus and Team Perspective).
Subject(s)
Carcinoma, Hepatocellular , Immunophenotyping , Immunotherapy , Liver Neoplasms , Humans , Liver Neoplasms/therapy , Liver Neoplasms/immunology , Liver Neoplasms/pathology , Carcinoma, Hepatocellular/therapy , Carcinoma, Hepatocellular/immunology , Carcinoma, Hepatocellular/pathology , Carcinoma, Hepatocellular/genetics , Male , Female , Child , Adolescent , Immunotherapy/methods , Mutation , Treatment Outcome , Biomarkers, Tumor , Gene Expression ProfilingABSTRACT
To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome.