In this proposal, I detail a plan to program cells to pancreatic and intestinal fates through computationally predictive understanding of how transcription factors dictate cellular identity. This 5-year plan outlines how I will transition toan independent tenure-track investigator bridging the fields of stem cells, genomics, and computational biology in order to pursue my long-term goal of enabling stem cell-derived cell and organ transplant therapy for diabetes and digestive diseases. To attain these goals, I will be advised by Dr. Richard Maas and Dr. David Gifford, well-established experts in, respectively, developmental and stem cell biology and computational biology and genomics. The planned research and career development activities will be carried out at the Brigham and Women's Hospital and Harvard Medical School, where I plan to take advantage of the excellent research and training environment. The ability to manipulate cell identity to produce large numbers of pancreatic and intestinal cells de novo would transform the study and treatment of diabetes and digestive diseases. Current approaches to derive therapeutically relevant cell types from stem cells are laborious and empirical, and we believe that developing a predictive understanding of how transcription factors guide cell fate decisions will significantly improve our ability to produe therapeutically relevant pancreatic and intestinal cells for disease modeling and transplantation. We have recently developed an experimental- computational pipeline based on a genomic technology called DNase-Seq that transforms our ability to understand dynamic transcription factor binding and function, and we have employed this pipeline to reveal a binding hierarchy that explains how transcription factors populate regulatory DNA. In this project, we will develop and test predictive models to explain how intercellular signaling pathways that are used in all tissues act specifically in endoderm to promote adoption of pancreatic and intestinal cell fates. To accomplish this goal, we will answer the following questions: (i) Can we develop a fully predictive model to explain the binding decisions of pioneer transcription factors, which sit atop the hierarchy of transcription factor binding? (ii) Can we develop a predictive understanding of the dynamic binding of transcription factors downstream of the key intercellular signaling pathways RA and Wnt during pancreatic and intestinal differentiation? (iii) Can we identify rules that predict the genes that will be activated when RA and Wnt-dependent transcription factors bind DNA? By answering these questions, we will have the tools to rewire the retinoic acid and Wnt signaling pathways to promote direct adoption of pancreatic and intestinal progenitor fates from embryonic stem cells, providing a crucial first step to predictive cell therapy.
The ability to replace cells that die or malfunction as a result of disease holds promise to transform treatment of diabetes and digestive diseases. Cell replacement therapy depends upon the ability to make therapeutically relevant cell types de novo, and this proposal aims to further this goal. This proposal aims to establish a predictive model of how cells change fate which will enable computationally guided transformation of cellular identity toward therapeutically relevant cell types, which may enable cell replacement therapy to treat diabetes and digestive diseases.
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| Kang, Daniel; Sherwood, Richard; Barkal, Amira et al. (2017) DNase-capture reveals differential transcription factor binding modalities. PLoS One 12:e0187046 |
| Banerjee, Budhaditya; Sherwood, Richard I (2017) A CRISPR view of gene regulation. Curr Opin Syst Biol 1:1-8 |
| Betancur, Paola A; Abraham, Brian J; Yiu, Ying Y et al. (2017) A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer. Nat Commun 8:14802 |
| Ferreira, Leonardo M R; Meissner, Torsten B; Mikkelsen, Tarjei S et al. (2016) A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface. Proc Natl Acad Sci U S A 113:5364-9 |
| Barkal, Amira A; Srinivasan, Sharanya; Hashimoto, Tatsunori et al. (2016) Cas9 Functionally Opens Chromatin. PLoS One 11:e0152683 |
| Rajagopal, Nisha; Srinivasan, Sharanya; Kooshesh, Kameron et al. (2016) High-throughput mapping of regulatory DNA. Nat Biotechnol 34:167-74 |
| Arbab, Mandana; Sherwood, Richard I (2016) Self-Cloning CRISPR. Curr Protoc Stem Cell Biol 38:5B.5.1-5B.5.16 |
| Hashimoto, Tatsunori; Sherwood, Richard I; Kang, Daniel D et al. (2016) A synergistic DNA logic predicts genome-wide chromatin accessibility. Genome Res 26:1430-1440 |
| Arbab, Mandana; Srinivasan, Sharanya; Hashimoto, Tatsunori et al. (2015) Cloning-free CRISPR. Stem Cell Reports 5:908-917 |
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