Functional-genetic dissection of HDAC dependencies in mouse lymphoid and myeloid malignancies.

Histone deacetylase (HDAC) inhibitors (HDACis) have demonstrated activity in hematological and solid malignancies. Vorinostat, romidepsin, belinostat, and panobinostat are Food and Drug Administration-approved for hematological malignancies and inhibit class II and/or class I HDACs, including HDAC1, 2, 3, and 6. We combined genetic and pharmacological approaches to investigate whether suppression of individual or multiple Hdacs phenocopied broad-acting HDACis in 3 genetically distinct leukemias and lymphomas. Individual Hdacs were depleted in murine acute myeloid leukemias (MLL-AF9;Nras(G12D); PML-RARα acute promyelocytic leukemia [APL] cells) and Eµ-Myc lymphoma in vitro and in vivo. Strikingly, Hdac3-depleted cells were selected against in competitive assays for all 3 tumor types. Decreased proliferation following Hdac3 knockdown was not prevented by BCL-2 overexpression, caspase inhibition, or knockout of Cdkn1a in Eµ-Myc lymphoma, and depletion of Hdac3 in vivo significantly reduced tumor burden. Interestingly, APL cells depleted of Hdac3 demonstrated a more differentiated phenotype. Consistent with these genetic studies, the HDAC3 inhibitor RGFP966 reduced proliferation of Eµ-Myc lymphoma and induced differentiation in APL. Genetic codepletion of Hdac1 with Hdac2 was pro-apoptotic in Eµ-Myc lymphoma in vitro and in vivo and was phenocopied by the HDAC1/2-specific agent RGFP233. This study demonstrates the importance of HDAC3 for the proliferation of leukemia and lymphoma cells, suggesting that HDAC3-selective inhibitors could prove useful for the treatment of hematological malignancies. Moreover, our results demonstrate that codepletion of Hdac1 with Hdac2 mediates a robust pro-apoptotic response. Our integrated genetic and pharmacological approach provides important insights into the individual or combinations of HDACs that could be prioritized for targeting in a range of hematological malignancies.

How do tumor cells respond to HDAC inhibition?

It is now well recognized that mutations, deregulated expression, and aberrant recruitment of epigenetic readers, writers, and erasers are fundamentally important processes in the onset and maintenance of many human tumors. The molecular, biological, and biochemical characteristics of a particular class of epigenetic erasers, the histone deacetylases (HDACs), have been extensively studied and small-molecule HDAC inhibitors (HDACis) have now been clinically approved for the treatment of human hemopoietic malignancies. This review explores our current understanding of the biological and molecular effects on tumor cells following HDACi treatment. The predominant responses include induction of tumor cell death and inhibition of proliferation that in experimental models have been linked to therapeutic efficacy. However, tumor cell-intrinsic responses to HDACi, including modulating tumor immunogenicity have also been described and may have substantial roles in mediating the antitumor effects of HDACi. We posit that the field has failed to fully reconcile the biological consequences of exposure to HDACis with the molecular events that underpin these responses, however progress is being made. Understanding the pleiotrophic activities of HDACis on tumor cells will hopefully fast track the development of more potent and selective HDACi that may be used alone or in combination to improve patient outcomes.

Histone deacetylases and their inhibitors in cancer, neurological diseases and immune disorders.

Epigenetic aberrations, which are recognized as key drivers of several human diseases, are often caused by genetic defects that result in functional deregulation of epigenetic proteins, their altered expression and/or their atypical recruitment to certain gene promoters. Importantly, epigenetic changes are reversible, and epigenetic enzymes and regulatory proteins can be targeted using small molecules. This Review discusses the role of altered expression and/or function of one class of epigenetic regulators--histone deacetylases (HDACs)--and their role in cancer, neurological diseases and immune disorders. We highlight the development of small-molecule HDAC inhibitors and their use in the laboratory, in preclinical models and in the clinic.

A high-throughput, multiplex cell death assay using an RNAi screening approach.

This protocol outlines a high-throughput, multiplex cell death assay and its use in conjunction with a genome-scale siRNA screen to identify genes that cooperate with a drug to induce apoptosis. The assay, ApoLive-Glo (Promega), measures viability of drug-treated, reverse-transfected cells via the fluorescent CellTiter-Fluor reagent, which includes a substrate that is cleaved by a live cell protease. ApoLive-Glo also quantitates cell death by the amount of cleaved caspases 3 and 7 using a luminescent Caspase-Glo 3/7 caspase activation assay. The advantage of the multiplex assay is that it distinguishes rapid cell death from the slower activation of caspase activity, permitting measurement of different stages of cell death in the same sample at a single time point. In parallel, a high-content imaging protocol involving 4',6-diamidino-2-phenylindole-stained nuclei is used as a cost-effective way to quantitate viability of vehicle-treated control cells. Automation and robotic liquid handling are built into the protocol to increase speed of workflow and improve reproducibility. A screen using these assays will identify gene targets that are essential for viability irrespective of drug treatment and gene targets that cause a synergistic enhancement of cell death in the presence of drug. Candidate target activity can then be validated by conventional flow cytometry-based assays.

High-throughput approaches to measuring cell death.

Cell death is integral to developmental and disease processes, and high-throughput screening (HTS) has been instrumental both for understanding biological mechanisms underlying cell death and for discovering novel therapeutic agents targeting these pathways. The various cell death modalities and their distinctive morphological and biochemical features have led to the development of a staggering variety of assays to measure these features, many of which have been adapted to HTS format. Although not all cell death assays are readily amenable to a high-throughput format, the potential power of HTS assays and increasing accessibility to associated technology make it likely that new approaches will continue to emerge. In particular, many recent studies in this field have used multiplex assays and high-content imaging to measure several features concurrently. Here, we discuss a broad array of considerations for designing HTS cell death assays, including some common challenges and pitfalls. We aim to provide a framework for deciding the most appropriate biological readouts, assay strategy and mode, workflow, controls, validation, and bioinformatics.

Genome-wide functional genomic and transcriptomic analyses for genes regulating sensitivity to vorinostat.

Identification of mechanisms of resistance to histone deacetylase inhibitors, such as vorinostat, is important in order to utilise these anticancer compounds more efficiently in the clinic. Here, we present a dataset containing multiple tiers of stringent siRNA screening for genes that when knocked down conferred sensitivity to vorinostat-induced cell death. We also present data from a miRNA overexpression screen for miRNAs contributing to vorinostat sensitivity. Furthermore, we provide transcriptomic analysis using massively parallel sequencing upon knockdown of 14 validated vorinostat-resistance genes. These datasets are suitable for analysis of genes and miRNAs involved in cell death in the presence and absence of vorinostat as well as computational biology approaches to identify gene regulatory networks.

Adipose-derived stem cells promote angiogenesis and tissue formation for in vivo tissue engineering.

Adult mesenchymal stem cells secrete a variety of angiogenic cytokines and growth factors, so we proposed that these paracrine mechanisms may be used to promote vascularization and growth for tissue engineering in vivo. We tested whether or not human adipose-derived stem cells (ASCs) promote tissue formation in rats. ASCs were evaluated in vitro for mRNA expression of angiogenic factors, including the vascular endothelial growth factor, basic fibroblast growth factor, interleukin-8 (IL-8), and stromal cell-derived factor-1 (SDF-1) and proliferative activity on human microvascular endothelial cells. For in vivo analysis, CM-DiI-labeled ASCs were implanted with a rat cardiac extracellular matrix (ECM) extract-derived hydrogel into a chamber with a femoral arteriovenous loop in the groin of male nude rats for 7 days. Vascularization in newly generated tissue was estimated by histomorphometry after endothelial nitric oxide synthase (eNOS) immunostaining. ASCs expressed growth factor mRNA and produced an angiogenic activity in vitro. After implantation, ASCs survived, but remained suspended in the ECM and relatively few were incorporated into the newly formed tissue. The volume of newly generated tissue was significantly higher in chambers containing ASCs and it was enriched with vasculature when compared with the ECM alone. We conclude that human ASCs promote tissue growth and angiogenesis in the rat vascularized chamber, thereby showing promise for tissue-engineering applications for regenerative therapy.