Danwei Huangfu: Publications

Select Research Articles (limited to since 2017)

Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions. Luo R, Yan J, Oh JW, Xi W, Shigaki D, Wong W, Cho HS, Murphy D, Cutler R, Rosen BP, Pulecio J, Yang D, Glenn RA, Chen T, Li QV, Vierbuchen T, Sidoli S, Apostolou E, Huangfu D, Beer MA. Nat Genet. 2023 Aug;55(8):1336-1346. doi: 10.1038/s41588-023-01450-7. Epub 2023 Jul 24. [PMID: 37488417]

CRISPR screening uncovers a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction. Yang D, Cho H, Tayyebi Z, Shukla A, Luo R, Dixon G, Ursu V, Stransky S, Tremmel DM, Sackett SD, Koche R, Kaplan SJ, Li QV, Park J, Zhu Z, Rosen BP, Pulecio J, Shi ZD, Bram Y, Schwartz RE, Odorico JS, Sidoli S, Wright CV, Leslie CS, Huangfu D. Nat Cell Biol. 2022 Jul;24(7):1064-1076. doi: 10.1038/s41556-022-00946-4. Epub 2022 Jul 4. [PMID: 35787684]

QSER1 protects DNA methylation valleys from de novo methylation. Dixon G, Pan H, Yang D, Rosen BP, Jashari T, Verma N, Pulecio J, Caspi I, Lee K, Stransky S, Glezer A, Liu C, Rivas M, Kumar R, Lan Y, Torregroza I, He C, Sidoli S, Evans T, Elemento O, Huangfu D. Science. 2021 Apr 9;372(6538):eabd0875. doi: 10.1126/science.abd0875. [PMID: 33833093]

Genome-scale screens identify JNK-JUN signaling as a barrier for pluripotency exit and endoderm differentiation. Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh CL, Yang D, Crespo M, Shukla A, Xiang Q, Dündar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massagué J, Garippa R, Evans T, Beer MA, Huangfu D. Nat Genet. 2019 Jun;51(6):999-1010. doi: 10.1038/s41588-019-0408-9. Epub 2019 May 20. [PMID: 31110351]

TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells. Verma N, Pan H, Doré LC, Shukla A, Li QV, Pelham-Webb B, Teijeiro V, González F, Krivtsov A, Chang CJ, Papapetrou EP, He C, Elemento O, Huangfu D. Nat Genet. 2018 Jan;50(1):83-95. doi: 10.1038/s41588-017-0002-y. Epub 2017 Dec 4.

MLL3 loss drives metastasis by promoting a hybrid epithelial-mesenchymal transition state. Cui J, Zhang C, Lee JE, Bartholdy BA, Yang D, Liu Y, Erler P, Galbo PM Jr, Hodge DQ, Huangfu D, Zheng D, Ge K, Guo W. Nat Cell Biol. 2023 Jan;25(1):145-158. doi: 10.1038/s41556-022-01045-0. Epub 2023 Jan 5. [PMID: 36604594]

A hypomorphic mutation in Pold1 disrupts the coordination of embryo size expansion and morphogenesis during gastrulation. Chen T, Alcorn H, Devbhandari S, Remus D, Lacy E, Huangfu D, Anderson KV. Biol Open. 2022 Aug 15;11(8):bio059307. doi: 10.1242/bio.059307. Epub 2022 Aug 8. [PMID: 35876795]

Abnormal exocrine-endocrine cell cross-talk promotes β-cell dysfunction and loss in MODY8. Kahraman S, Dirice E, Basile G, Diegisser D, Alam J, Johansson BB, Gupta MK, Hu J, Huang L, Soh CL, Huangfu D, Muthuswamy SK, Raeder H, Molven A, Kulkarni RN. Nat Metab. 2022 Jan;4(1):76-89. doi: 10.1038/s42255-021-00516-2. [PMID: 3505863]

Stage-specific regulation of DNA methylation by TET enzymes during human cardiac differentiation. Lan Y, Banks KM, Pan H, Verma N, Dixon GR, Zhou T, Ding B, Elemento O, Chen S, Huangfu D, Evans T. Cell Reports. 2021 Dec 7;37(10):110095. doi: 10.1016/j.celrep.2021.110095. [PMID: 34879277]

Generation of human embryonic stem cell models to exploit the EWSR1-CREB fusion promiscuity as a common pathway of transformation in human tumors.Vanoli F, Meskauskaite B, Herviou L, Mallen W, Sung YS, Fujisawa Y, Zhang L, Simon S, Huangfu D, Jasin M, Antonescu CR. Oncogene. 2021 Aug;40(32):5095-5104. doi: 10.1038/s41388-021-01843-0. [PMID: 34193943]

FOXA2 Is Required for Enhancer Priming during Pancreatic Differentiation. Lee K, Cho H, Rickert RW, Li QV, Pulecio J, Leslie CS, Huangfu D. Cell Reports. 2019;28(2):382-393.e7. 

DICER1 Is Essential for Self-Renewal of Human Embryonic Stem Cells. Teijeiro V, Yang D, Majumdar S, González F, Rickert RW, Xu C, Koche R, Verma N, Lai EC, Huangfu D. Stem Cell Reports. 2018;11(3):616-625. 

Discovery of a drug candidate for GLIS3-associated diabetes. Amin S, Cook B, Zhou T, Ghazizadeh Z, Lis R, Zhang T, Khalaj M, Crespo M, Perera M, Xiang JZ, Zhu Z, Tomishima M, Liu C, Naji A, Evans T, Huangfu D, Chen S. Nat Commun. 2018;9(1):2681.

Genome Editing in hPSCs Reveals GATA6 Haploinsufficiency and a Genetic Interaction with GATA4 in Human Pancreatic Development. Shi ZD, Lee K, Yang D, Amin S, Verma N, Li QV, Zhu Z, Soh CL, Kumar R, Evans T, Chen S, Huangfu D. Cell Stem Cell. 2017;20(5):675-688.e6. 

The p53 Family Coordinates Wnt and Nodal Inputs in Mesendodermal Differentiation of Embryonic Stem Cells. Wang Q, Zou Y, Nowotschin S, Kim SY, Li QV, Soh CL, Su J, Zhang C, Shu W, Xi Q, Huangfu D, Hadjantonakis AK, Massagué J. Cell Stem Cell. 2017;20(1):70-86.

Select Review Articles (limited to since 2017)

Genetic Engineering of Immune Evasive Stem Cell-Derived Islets. Sackett SD, Kaplan SJ, Mitchell SA, Brown ME, Burrack AL, Grey S, Huangfu D, Odorico J.Transpl Int. 2022 Dec 5;35:10817. doi: 10.3389/ti.2022.10817. eCollection 2022. [PMID: 36545154]

Epigenome rewiring in human pluripotent stem cells. Yan J, Huangfu D. Trends Cell Biol. 2022 Mar;32(3):259-271. doi: 10.1016/j.tcb.2021.12.001. [PMID: 34955367]

Enhancer Predictions and Genome-Wide Regulatory Circuits. Beer MA, Shigaki D, Huangfu D. Annu Rev Genomics Hum Genet. 2020 Aug 31;21:37-54. doi: 10.1146/annurev-genom-121719-010946. [PMID: 32443951]

Decoding pluripotency: Genetic screens to interrogate the acquisition, maintenance, and exit of pluripotency. Li QV, Rosen BP, Huangfu D. Wiley Interdiscip Rev Syst Biol Med. 2019:e1464.

Decoding the noncoding genome via large-scale CRISPR screens. Shukla A, Huangfu D. Curr Opin Genet Dev. 2018;52:70-76.

CRISPR/Cas9-Based Engineering of the Epigenome. Pulecio J, Verma N, Mejía-Ramírez E, Huangfu D, Raya A. Cell Stem Cell. 2017;21(4):431-447. Review.