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).

Mechanisms Governing Stem Cell Potency and Lineage Commitment

Role of RNA sequestration in mammalian cell fate

Reprogramming RNA processing mechanisms in hematopoietic cells

Cell fate decisions, including events that occur naturally (e.g., development, differentiation, regeneration, and homeostasis) and experimentally (e.g., reprogramming to induced pluripotent stem (iPS) cells, directed differentiation, transdifferentiation), are typically mediated by transcription factors in concert with epigenetic modifications. These crucial regulators direct gene expression changes to establish cell-type specific transcriptional profiles. Mechanistically, a wide range of chromatin-related processes are involved (DNA and histone modifications, histone variants, genome topology, RNA processing and many more). The interplay between all these layers of epigenetic regulation finally controls the transcriptional output of the conversion process, thus determining the final cell fate. Our current goal is to elucidate molecular mechanisms regulating establishment and maintenance of mammalian cell identity.

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.

Hematopoietic stem and progenitor cells (HSPCs) have the capacity to self-renew and commit to fully mature specialized blood cell types. HSPC self-renewal and differentiation potential are tightly regulated and kept in balance. Disruption of this balance results in severe disease, including cancer. Thus, uncovering and understanding new molecular and cellular pathways that govern HSPC cell fate is critical for basic biology and to develop new therapeutic strategies for hematologic disorders. One of the main goals of the lab is to answer the following important questions: i) Does RNA processing have a pivotal role in maintenance of HSPC identity? ii) How do post-transcriptional mechanisms instruct hematopoiesis? iii) Does dysregulation of RNA processing promote hematologic malignancies? Addressing these questions will yield fundamental insights into the underpinnings of hematopoiesis and will pave the way for efforts aimed at targeting post-transcriptional regulators as a new therapeutic strategy for blood-related diseases.

JOIN OUR RESEARCH TEAM!

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We are currently recruiting postdocs

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

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

Bruno Di Stefano, Ph.D.

Principal Investigator

CPRIT Scholar

Assistant Professor in Molecular and Cellular Biology

Florencia Levin Ferreyra

Graduate Student

Emily Park

Graduate Student

Emily graduated with a B.A. in Neuroscience from Wellesley College. Afterwards, she worked as a research assistant for Dr. Paul Greengard at Rockefeller University until she joined Baylor’s MD/PhD program in 2019. She is currently a graduate student in the DDMT program. Emily joined the Di Stefano lab in March 2022. 

Yingzhi Cui

Graduate Student

Yingzhi received her B.A. and M.Sci. in Natural Sciences from the University of Cambridge, UK. She then worked as a research assistant in Ji's lab at Shenzhen University. She joined Baylor's PhD program in 2021. She is currently a graduate student in the DDMT program. Yingzhi joined the Di Stefano lab in May 2022.

Núria Lupión García

Research Assistant

Núria received her B.A. and M.Sci. in Genetics from the Autonomous University of Barcelona and the Vall d’Hebron Institute of Oncology. Her work focused on the epigenetic characterization of IDH1 mutant cholangiocarcinomas. She joined the Di Stefano lab in December 2022. 

• Wang D, Wu W, Callen E, Pavani R, Zolnerowich N, Kodali S, Zong D, Wong N, Noriega S, Nathan WJ, Matos-Rodrigues G, Chari R, Kruhlak MJ, Livak F, Ward M, Caldecott K, Di Stefano B, Nussenzweig A. Active DNA demethylation promotes cell fate specification and the DNA damage response. Science 2022 378;6623. 

          Commented in Science . 2022 Dec 2;378(6623):948-949.

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• Di Stefano B. Cell identity and plasticity uncoupled. Nature Cell Biology 2022 Sep;24(9):1326-1327.

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• 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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• 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. ​

The Nancy Chang, Ph.D. Award
for Research Excellence