Black Family Stem Cell Institute

Epigenetics

Epigenetic regulation is critical for inducing and maintaining pluripotency of various stem cell populations, and for determining cell fate decisions.

Members of the Black Family Stem Cell Institute faculty study various epigenetic processes across a wide range of biological systems, including embryonic stem cell totipotency and pluripotency; somatic cell reprogramming; differentiation towards distinct lineages, such as various epithelial cell compartments and red blood cells; and cancer.

We study epigenetic mechanisms such as regulation by histone modifiers including but not limited to histone deacetylases, arginine and lysine methyltransferases, and Polycomb repressive complexes; DNA methylation; histone variants; and transcription factors, including lineage-specific and pluripotency factors. Institute staff use a wide range of tools to study these epigenetic mechanisms entailing genomic, epigenomic, and proteomic approaches; mouse modeling; high throughput screens; and genome editing.

Investigators with a major focus in epigenetics include:

Emily Bernstein, PhD

Emily Bernstein, PhD, is a Professor of Oncological Sciences and Dermatology at the Icahn School of Medicine at Mount Sinai and co-leader of the Cancer Mechanisms Program of The Tisch Cancer Institute, an NCI-designated center. She also organizes numerous epigenetics events including Mount Sinai’s Chromatin Club. Her team studies epigenetic mechanisms underlying normal development and cancer with a focus on histone variant proteins that replace canonical histones within the nucleosome core particle. Histone variants are specialized in function and represent an important layer of regulation to diversify the structural characteristics and functional outputs of chromatin. Her laboratory discovered a key role for H2A histone variants such as macroH2A and H2A.Z in melanoma malignancy and reprogramming towards pluripotency.

Ongoing research interests include:

  • Investigating histone variant-deficient mice in normal development, stem cell populations, and tumor initiation/progression
  • Understanding the role of the epigenome and non-coding DNA elements in cancer progression and drug resistance
  • Modeling pediatric cancer mutations in chromatin factors by directed differentiation protocols of human pluripotent stem cells

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James J. Bieker, PhD

James J. Bieker, PhD, is a Professor in the Department of Cell, Developmental, and Regenerative Biology at the Icahn School of Medicine at Mount Sinai. The laboratory's interest is in the transcriptional regulation of red blood cell-specific gene expression, and in identifying the molecular events that confer the ability to express lineage-specific genes in uncommitted, pluripotent hematopoietic stem cells. These issues are being addressed by the functional analysis of a novel, erythroid-specific gene that the Bieker Laboratory identified a number of years ago named erythroid Krüppel-like factor; EKLF. Biochemical, molecular, cellular, developmental, and genetic studies in mice and humans have established that EKLF is an essential component required for globin switching and completion of the definitive erythroid program.

Using our model system, we aim to disentangle genotype from phenotype and cell-type and identify disease relevant common and unique pathways that hold promise for future therapies.

Ongoing research interests include:

  • Analyzing EKLF protein/protein interactions and how they result in altered transcriptional and epigenetic changes at target loci
  • Determining how molecular controls converge to regulate late events in erythropoiesis, particularly enucleation
  • Analyzing EKLF upstream regulators to explain its exquisite tissue-restricted expression pattern, and to possibly link alteration of its expression level to aberrant red cell biology
  • Determining the mechanism by which a human mutation in EKLF leads to congenital dyserythropoietic anemia.

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Timothy A. Blenkinsop, PhD

Timothy A. Blenkinsop, PhD, is an Assistant Professor in the Department of Cell, Development, and Regenerative Biology at the Icahn School of Medicine at Mount Sinai, as well as member of the Ophthalmology Department, the Black Family Stem Cell Institute, and Mount Sinai’s Eye and Vision Research Institute. His team is interested in understanding human retina development in normal and pathological situations, as well as in modeling in vitro various eye diseases. The lab’s primary interest lies in retina stem cell biology, cell replacement therapy, and endogenous retina regeneration potential. The lab uses adult human tissues and pluripotent stem cells-derived differentiated cells to probe retina physiology and model diseases such as age-related macular degeneration, proliferative vitreoretinopathy, and proliferative diabetic retinopathy. The main goal is to identify epigenetic regulation of cell plasticity for stimulating it with therapeutic benefit, while also modeling diseases where plasticity leads to disease.

Ongoing research interests include:

  • Exploring signaling transduction pathways involved in retinal pigment epithelium plasticity
  • Exploring cell replacement therapy for age-related macular degeneration
  • Researching cell fate specification of developing human eye field

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Kristen Brennand, PhD

Kristen Brennand, PhD, is an Associate Professor of Genetics and Genomics, Neuroscience, and Psychiatry at the Icahn School of Medicine at Mount Sinai. She trained in developmental and stem cell biology at Harvard University and in neuroscience during her postdoctoral studies at the Salk Institute for Biological Studies. By blending expertise in stem cell biology and neurobiology, she has pioneered a new approach to study psychiatric disease. By developing a G16 based model for the study of predisposition to neuropsychiatric disease, and combining it with CRISPR-based genomic engineering, the Brennand Laboratory has established a new approach by which to systematically test the impact of causal variants in human cells. The future of psychiatry requires a model of precision medicine, in which doctors consider how the patient’s genetic variants—and the many interactions among them—affect disease course and treatment response before prescribing any medication.

Ongoing research interests include:

  • Understanding the genetic mechanisms underlying schizophrenia
  • Developing personalized screening platforms to identify new therapeutics for the treatment of this debilitating disorder

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Elena Ezhkova, PhD

Elena Ezhkova, PhD, is an Associate Professor in the Cell, Developmental, and Regenerative Biology Department. Her laboratory implements an array of powerful cellular and high-throughput molecular biology tools to dissect how epigenetic gene regulators, specifically the polycomb repressive complexes 1 and 2 (PRC1 and PRC2), play a role in cell fate determination, homeostasis, and regeneration. Her lab has recently showed that PRC1 functions both as a transcriptional repressor and as a transcriptional activator during skin development. Importantly, PRC1-mediated gene activating functions are critical for hair follicle development and for the establishment of the adult bulge stem cell compartment. Identification of these molecular mechanisms that control cell fate determination, commitment, and differentiation aids in expanding our understanding of tissue development and the progression of various tissue disorders, including cancer. 

Ongoing research interests include:

  • Uncovering the molecular mechanism of PRC-mediated gene regulation in skin development, homeostasis, and regeneration
  • Dissecting the canonical and non-canonical PRC function in different epithelial tissues, including skin and oral epithelia
  • Uncovering the molecular mechanisms controlling Merkel cell development and maintenance and Merkel cell carcinoma formation

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Ernesto Guccione, PhD

Ernesto Guccione, PhD, is an Associate Professor of Oncological Sciences, and Pharmacological Sciences at the Icahn School of Medicine at Mount Sinai. His team studies transcriptional and post-transcriptional mechanisms regulating development and cancer with a focus on mammalian protein methyltransferases and the function of alternative splicing. The team uses biochemistry, mouse models, next generation sequencing and splice switching antisense oligonucleotide (AON)-based approaches to understand the molecular mechanisms of action of candidate PMTs or specific isoforms. The range of techniques and approaches used in the lab has allowed researchers to characterize the mechanism of action of specific PMTs (e.g., PRMT5 and PRDM15) or oncogenic isoforms (e.g., MDM4l/s), which are of great interest for their clinical applications.

Ongoing research interests include:

  • Investigating the role of PRMTs and PRDMs in normal development, stem cell populations, and tumor initiation/progression
  • Using AON-based approaches to uncover the function of specific alternative splicing isoforms
  • Exploring use of pharmacogenomic approaches to identify new therapies for hematological and solid tumors

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Samuele G. Marro

Samuele G. Marro, PhD, is an Assistant Professor in the Nash Family Department of Neuroscience and co-Director of the Stem Cell Engineering Core at the Icahn School of Medicine at Mount Sinai. His research team focuses on the regulation of synaptic plasticity and its dysfunction in Fragile X syndrome, the number one genetic cause of autism. To accomplish this, the group studies human neurons directly differentiated from pluripotent stem cells that are genetically modified using CRISPR/Cas9 tools. The institutional Stem Cell Engineering Core itself provides services and resources at a reduced cost to the Icahn School of Medicine community that include the derivation of iPS from patient blood samples; iPS differentiation into different cell types; and gene-editing to create or repair putative disease mutations.

      

Ongoing research interests include:

  • Investigating protein homeostasis in human neurons
  • Exploring epigenetic regulation of synaptic plasticity
  • Understanding and correcting the epigenetic silencing in Fragile X syndrome

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Sarah E. Millar

Sarah E. Millar, PhD, is Director of the Black Family Stem Cell Institute, and Lillian and Henry M. Stratton Professorial Chair in the Departments of Cell, Developmental, and Regenerative Biology, and Dermatology at the Icahn School of Medicine at Mount Sinai. Understanding the molecular and cellular mechanisms regulating the development, patterning, and postnatal renewal of the skin and ectodermal appendage organs such as hair follicles, teeth, and taste papillae, and identifying stem and progenitor cell populations in these organs, is critical for developing new therapies to accelerate wound healing, treat hair loss diseases, repair or replace diseased teeth, and ameliorate taste dysfunction. Research in the Millar Laboratory focuses on cell-cell signaling and epigenetic mechanisms that underlie these processes. In published research, researchers identified Wnt/beta-catenin signaling as a key pathway required for initiating the formation of ectodermal appendages from multipotent cells in mammalian embryos, and in controlling development and patterning of haired versus hairy skin. By analyzing genetic mouse models and tissues from human patients carrying mutations in the WNT10A gene, we showed that Wnt signaling plays a key role in regulating the functions of a wide variety of adult epithelial stem cells, as well as in controlling specialized differentiation programs in palmoplantar skin. We have also identified critical functions for epigenetic regulators including micro-RNAs and chromatin modifiers in skin development and regeneration.

Ongoing research interests include:

  • Investigating mechanisms that cause ectodermal dysplasia in patients with mutations in the WNT10A gene, and testing potential therapeutic strategies
  • Determining the mechanisms that underlie the formation and maintenance of hairy versus hairless skin and regulate hair patterning
  • Delineating the functions of histone deacetylase chromatin modifiers in skin development, stem cells, and cancer
  • Identifying pioneer transcription factors that control development and stem cell activity in skin and oral epithelia

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Robert Sebra, PhD

Robert Sebra, PhD, is an Associate Professor in the Department of Genetics and Genomic Sciences at the Icahn School of Medicine at Mount Sinai and Director of Technology Development and the Genomics Core Facility for the Icahn Institute for Data Science and Genomic Technology. His research lab centers on creating and applying bulk and single cell molecular methods to generate highly resolved data using genomics technology for variant discovery and annotation. This research integrates single molecular and cellular genomics data with assays to assess chromatin accessibility, proteomics, and epigenetics data to decipher factors of pathogenesis versus normal cellular functions. Determining which cellular niches and mechanisms in complex primary tissues drive disease or resilience facilitates translation of functional genomics data using model systems for screening possible downstream regenerative and therapeutic potential using high throughput methods.

Ongoing research interests include:

  • Developing novel molecular methods and genome sequencing technologies
  • Advancing high-throughput functional genomics
  • Exploring whole genome and repeat content characterization for disease association
  • Analyzing surveillance and genomic characterization of pathogen transmission
  • Using genomics to temporally characterize development and pathogenesis
  • Translating genomic data in various oncologic diseases including gynecologic and breast cancers

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Alexander M. Tsankov

Alexander M. Tsankov, PhD, is an Assistant Professor in Genetics and Genomic Sciences at Icahn School of Medicine at Mount Sinai. He completed his PhD in electrical engineering and computer science at MIT and his postdoctoral training at the Broad Institute and Harvard University (Alex Meissner and Aviv Regev’s lab). The Tsankov lab overall vision is to use genomics to build data-driven, predictive models that improve diagnosis, find new drug-able pathways, and personalize treatment of patients with lung cancer and respiratory diseases. The lab specializes in next generation sequencing (NGS) technologies (e.g. single-cell transcriptomic, epigenomic, and spatial data) and computational analysis with the goal of unraveling how the underlying regulatory mechanisms, cell-cell interactions, and regenerative lineages have changed in lung disease compared to normal lung tissue homeostasis.

Ongoing research interests include:

  • Using single-cell technologies to reconstruct the regenerative lineages in the human lung and to understand how these have been hijacked in cancer or altered in lung disease
  • Investigating cell-cell interactions and their role on lung regeneration, disease progression, and immunosuppression.
  • Dissecting the cell-type specific regulatory mechanisms underlying normal lung homeostasis and changes that arise in respiratory disease and lung cancer

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