Research Interests:
The thought that one day we might understand mechanistically how cells decide whether to continue to proliferate or to differentiate has always been dreamlike to me. Recent advances in molecular and computational biology have made possible to study, genome-wide, transcriptional regulatory networks, to put them in hierarchical order and establish their relevance to the control of cell proliferation and differentiation. We apply this knowledge towards understanding changes occurring in cancer cells. Epigenetic mechanisms play an important role in determining fate of every cell in the organism, in normal development as well as in cancer. In particular, H3K4me3 is a robust epigenetic modification essential for activation of gene expression. in vivo mechanisms regulating binding and activity of epigenetic factors and associated transcription factors at genomic sites exhibiting H3K4me3 modification are very poorly defined. We study recruitment of such factors at the genome scale in collaboration with Dr. Nuria Lopez-Bigas, the leader of Biomedical Genomics Group in IRB, Barcelona. Through a combination of molecular and bioinformatics approaches, we hope to achieve a better understanding of how epigenetic factors regulate gene expression and operate as oncogenes and tumor suppressors.

• Role of RBP2/KDM5A in RB pathway and in differentiation
  Inactivation of the retinoblastoma gene (RB1) is viewed as a necessary step in the development of human cancers. It might be a result of mutation in the RB1 gene or, more common, due to pRB hyperphosphorylation. Both types of inactivation lead to deregulation of normal biological processes, and molecularly this can be explained by abrogation of pRB protein-protein interactions. In fact, the view on the pRB as a tumor suppressor has been dominated by its contribution to repressor complexes with E2F family of transcription factors that results in cessation of cell cycle progression. However, another tumor suppressor function of pRB has been connected to its ability to promote differentiation, a process during which cell stops dividing and attributes a certain cell fate, but the critical pRB interacting protein was unknown. We isolated RBP2 (now known as KDM5A histone demethylase) among several pRB-interacting proteins that modulated the ability of pRB to promote differentiation. We showed that the ability of pRB to promote differentiation requires pRB binding to and inhibiting KDM5A. Genetic loss of KDM5A resulted in enhanced ability to execute differentiation program and overridden requirement of pRB for differentiation. Thus, the histone H3K4 demethylase KDM5A is a critical factor in a pRB tumor suppressor function related to the switch from cellular proliferation to differentiation.
• Role of mitochondrial function in progression to differentiation
  Using genome-wide approaches, we found that pRB and KDM5A are critical for regulation of mitochondrial functions in cells that were induced to differentiation. Cells lacking pRB displayed a number of mitochondrial defects, and KDM5A loss in these cells significantly rescued the defects. We found that KDM5A is a direct repressor of metabolic regulatory genes, thus explaining the compensatory role of KDM5A loss in restoring mitochondrial functions. Significantly, KDM5A-dependent metabolic effects were both necessary and sufficient to induce the expression of a network of cell-type specific signaling and structural genes. In addition, activation of mitochondrial function by the mitochondrial biogenesis regulator PGC-1α, a co-activator of the KDM5A target genes, was sufficient to override the differentiation block. The rescue of differentiation by KDM5A loss or by activation of mitochondrial biogenesis reveals the switch to oxidative phosphorylation as an essential step in restoring differentiation and a less aggressive cancer phenotype.
• KDM5A effects on gene expression
  We think that if we reach global understanding of the central effector of RB pathway such as KDM5A, we will know better how to treat cancer. Using a combination of gene expression analysis and immunoprecipitation with massively parallel sequencing (ChIP-seq), we were able to correlate gene transcript level with KDM5A binding and H3K4me3 level. A number of experiments attributed not only repressing but activating activities to the KDM5A. The major question that stands out from my previous research is how KDM5A accommodates the two functions on different genes. We are using gene knockdown and CRISPR techniques to investigate factors modifying the outcome of KDM5A binding at the genomic loci.
• Cooperation between histone methylation enzymes in establishment cancer-specific gene expression
  We study histone modifications and transcriptional activity of the targets of enzymes involved in histone methylation in human tumors. By analyzing cancers of different aggressiveness, we hope to identify the main contributing epigenetic marks and affected genomic loci.
• Control of gene expression by KDM5B/PLU1, the closest KDM5A homolog
  Increased level of KDM5B has been associated with several human malignancies. We study KDM5B function using a variety of breast cancer models, in order to better understand why cancer cell growth depends on KDM5B. We are interested in identifying similarities and differences between KDM5A and KDM5B, and between H3K4me3-dependent and independent mechanisms.

Selected Publications

• Váraljai, R., A.B.M.M.K. Islam, M. L. Beshiri, J. Rehman, N. Lopez-Bigas, and E.V. Benevolenskaya. Increased mitochondrial function downstream from KDM5A histone demethylase rescues differentiation in pRB-deficient cells. Genes & Dev. 2015; 29: 1817-1834. PMCID: PMC4573855
• Benevolenskaya, E.V., and M.V. Frolov. 2015. Emerging links between E2F control and mitochondrial function. Cancer Res. 75(4): 619-623. PMCID: PMC4332890
• Jene-Sanz, A., R. Váraljai, A.V.Vilkova, G.F. Khramtsova, A.I. Khramtsov, O.I. Olopade, N. Lopez-Bigas, and E.V. Benevolenskaya. 2013. Expression of Polycomb targets predicts breast cancer prognosis. Mol. Cell. Biol. 33(19): 3962-3971. PMCID: PMC3811872
• Beshiri, M.L., K. B. Holmes, W. F. Richter, S. Hess, A.B.M.M.K. Islam, Qin Yan, L. Plante, N. Gévry, N. Lopez-Bigas, W. G. Kaelin, Jr., and E.V. Benevolenskaya. 2012. Demethylation by KDM5A contributes to repression of cell cycle genes during differentiation. PNAS 109(45): 18499-18504. PMCID: PMC3494949
• Lopez-Bigas, N., T.A. Kisiel, D.C. DeWaal, K. Holmes, T. Volkert, S. Gupta, J. Love, H.L. Murray, R.A. Young, and E.V. Benevolenskaya. 2008. Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation. Molecular Cell 31: 520-530. PMCID: PMC3003864

PhD Moscow State University, Russia (advisor Dr. Vladimir Gvozdev)
Post-doc University of Missouri-Columbia (advisor Dr. James Birchler)
Res. Associate Harvard Medical School & Dana-Farber Cancer Institute (advisor Dr. William Kaelin, Jr.)