Mechanisms Regulating Stem Cell Potency and Cell Fate Decisions

Development  2019  146: dev182170 doi: 10.1242/dev.182170

During development and lineage specification, pluripotent and adult stem cells generate the diverse arrays of specialized cells of the adult body. Once a cell type is specified, the mechanisms that restrict and maintain cell fate are important in ensuring tissue integrity, and their dysregulation often results in disease, particularly cancer.

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Our current research aims to understand the post-transcriptional & epigenetic mechanisms that govern stem cell potency and cell fate decisions, and determine how to exploit these mechanisms to develop new therapeutic strategies.

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Towards this goal, our lab employs diverse approaches and tools including human and mouse embryonic stem cells, adult progenitor cell cultures, 3D organoids, cellular reprogramming, transdifferentiation, in vivo mouse models, genome editing with CRISPR-Cas nucleases, and genome-wide techniques (e.g. scRNA-seq, ATAC-seq, ChIP-seq, CLIP-seq).

RESEARCH AREAS

Mechanisms Governing Stem Cell Potency and Lineage Commitment

Functional Role of RNA Condensates in Cell Fate Decisions

Alternative Polyadenylation in Cancer 

Cell fate decisions require precise coordination of gene expression programs. The study of spatiotemporal regulation of gene expression and its function in controlling cell fate transitions has been largely limited to mechanisms that control RNA transcription. However, it is increasingly evident that post-transcriptional mechanisms facilitate cell fate changes during development and tissue homeostasis.

Our current goal is to elucidate the role of post-transcriptional regulation in mammalian cell fate.

The localization of RNAs in the cell can influence their folding, editing, splicing, translation, degradation, and even the fate of the proteins they encode. Recently, RNAs have been shown to be selectively sequestered in cytoplasmic condensates, however, the functional role and composition of RNA condensates during cell fate specification remain unknown. In our lab we are testing the hypothesis that the sequestration of RNAs in cytoplasmic condensates plays a crucial role during early developmental transitions. Moreover, my lab is testing the hypothesis that RNA sequestration is critical to maintaining adult tissue homeostasis.

Recently, we made the exciting discovery that alternative polyadenylation (APA), a post-transcriptional mechanism that generates distinct transcript isoforms by using different poly(A) sites, controls establishment and maintenance of cell identity across different lineages. It has been estimated that ~70% of mammalian mRNAs are subject to APA, providing a potent strategy to regulate global gene expression patterns. While transcripts utilizing proximal poly(A) sites are generally highly expressed and associated with transformed and proliferative cells, transcripts utilizing distal poly(A) sites are generally modestly expressed and associated with differentiated and senescent cells.

One of the goals of our team is to dissect the molecular and functional roles APA play in tumorigenesis.

JOIN OUR RESEARCH TEAM!

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We are currently recruiting graduate students and postdocs

with a focus on stem cells, cancer, epigenetics, and RNA biology

Please submit CV and contact information for 3 references by email to Dr. Bruno Di Stefano

Lab Members

Bruno Di Stefano, Ph.D.

Principal Investigator

CPRIT scholar

Assistant Professor in Molecular and Cellular Biology

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Bruno received his BSc and MSc in Molecular Biology from the University of Pavia and the University School for Advanced Studies IUSS Pavia. He performed his graduate studies in the lab of Dr. Thomas Graf at the CRG. There his work focused on the mechanisms that control transcription factor-induced cell fate change. He developed the first rapid, ultra-efficient system to reprogram B cells into induced pluripotent stem cells. In 2016, he joined the lab of Dr. Konrad Hochedlinger as an EMBO long-term postdoctoral fellow at Harvard University. His postdoctoral work focused on the role of post-transcriptional mechanisms in mammalian cell fate.

Patrizia Pessina, Ph.D.

Staff Scientist

Patrizia received her MS in Biological Sciences and her PhD in Translational and Molecular Medicine from the University of Milano Bicocca. She completed her postdoctoral training in the Muñoz-Canoves Lab at the University of Pompeu Fabra where she studied muscle stem cells and fibrosis. From 2016 to 2020, Patrizia worked as Staff Scientist in the Carla Kim lab at Harvard Medical School studying stem cell function in lung fibrosis and aging. She joined the Di Stefano lab in October 2020.

Florencia Levin Ferreyra

Research Assistant

Florencia received her Bachelor's degree in Biotechnology engineering from the ORT University in Uruguay. During her studies, she joined the team of the Molecular Human Genetics laboratory at the Pasteur Institut of Montevideo. Her work focused on developing a new zebrafish transgenic line to label adipocytes in development. She joined the Di Stefano lab in May 2021.

Srikanth Kodali, Ph.D.

Postdoc

Srikanth obtained his B.S. and M.S. in Biomedical Engineering from The University of Texas at Austin and Duke University, respectively. He received his Ph.D. in Integrative Molecular and Biomedical Sciences from Baylor College of Medicine, where he worked in the lab of Dr. Jin Wang. His research was focused on the molecular mechanisms underlying memory B cell development and survival. Srikanth joined the Di Stefano lab in May 2021.

Featured Publications

• Di Stefano B, Luo EC, Haggerty C, Aigner S, Charlton J, Brumbaugh J, Ji F, Jiménez IR, Clowers KJ, Huebner AJ, Clement K, Lipchina I, de Kort MAC, Anselmo A, Pulice J, Gerli MFM, Gu H, Gygi SP, Sadreyev RI, Meissner A, Yeo GW,  Hochedlinger K. The RNA helicase DDX6 controls cellular plasticity by modulating P-body homeostasis. Cell Stem Cell 2019 Nov 7; 25 (5), 622-638.e13.

Cover of Cell Stem Cell 2019 Nov; Commented in Cell Stem Cell 2019 Nov 7; 25:589-1.

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• Francesconi M*, Di Stefano B*, Berenguer C, de Andrés-Aguayo L, Plana-Carmona M, Mendez-Lago M, Guillaumet-Adkins A, Rodriguez-Esteban G, Gut M, Gut IG, Heyn H, Lehner B, Graf T. Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming. Elife 2019 Mar 12;8. pii: e41627. 

• Di Stefano B, Ueda M, Sabri S, Brumbaugh J, Huebner A, Sahakyan A, Clement K, Clowers KJ, Erickson AE, Shioda K, Gygi SP, Gu H, Shioda T, Meissner A, Takashima Y, Plath K, Hochedlinger K. Reduced MEK inhibition confers a growth advantage and preserves genomic stability in naïve human ES cells. Nat Methods 2018 Sep;15(9):732-740.

• Brumbaugh J*, Di Stefano B*, Wang X, Borkent M, Forouzmand E, Clowers KJ, Ji F, Schwarz BA, Kalocsay M, Elledge SJ, Chen Y, Sadreyev RI, Gygi SP, Hu G, Shi Y, Hochedlinger K. Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling. Cell 2018 Jan 11; 172(1-2):106-120.e21.

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• Krijger PHL*, Di Stefano B*, de Wit E*, Limone F, Van Oevelen C, de Laat W, Graf T. Cell-of-Origin-specific 3D genome structure acquired during somatic cell reprogramming. Cell Stem Cell 2016 May 5;18(5):597-6.

Commented in Nat Rev Genet. 2016 May;17(5):253 and Cell Stem Cell. 2016 May 5;18(5):557-9. 

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• Di Stefano B*,§, Collombet S*, Jakobsen JS*, Wierer M, Sardina JL, Lackner A, Stadhouders R, Segura-Morales C, Francesconi M, Limone F, Mann M, Porse B, Thieffry D, Graf T§. C/EBPa creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4. Nat Cell Biol 2016 Apr;18(4):371-81.

Cover of Nature Cell Biology 2016 Apr. and F1000 recommended.

• Di Stefano B, Sardina JL, van Oevelen C, Collombet S, Kallin EM, Vicent GP, Lu J, Thieffry D, Beato M and Graf T. C/EBPa poises B cells for rapid reprogramming into induced pluripotent stem cells. Nature 2014, 506, 235–239. ​

Di Stefano Lab

Stem Cells and Regenerative Medicine Center (STaR)

Center for Cell and Gene Therapy

Department of Molecular and Cellular Biology

Baylor College of Medicine

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One Baylor Plaza
Alkek Bldg Room N1020
77030, Houston, Texas, US