Select Research Articles Since 2013

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. [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]

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

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;51(6):999-1010.

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;50(1):83-95.

 

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 Rep. 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]

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.

Genome Editing of Lineage Determinants in Human Pluripotent Stem Cells Reveals Mechanisms of Pancreatic Development and Diabetes. Zhu Z, Li QV, Lee K, Rosen BP, González F, Soh CL, Huangfu D. Cell Stem Cell. 2016;18(6):755-68. 

A CRISPR/Cas-Mediated Selection-free Knockin Strategy in Human Embryonic Stem Cells. Zhu Z, Verma N, González F, Shi ZD, Huangfu D. Stem Cell Reports. 2015;4(6):1103-11. 

Functional analysis of a chromosomal deletion associated with myelodysplastic syndromes using isogenic human induced pluripotent stem cells. Kotini A. G., Chang C. J., Boussaad I., Delrow J. J., Dolezal E. K., Nagulapally A. B., … & Papapetrou E. P. (2015). Nature Biotechnol. 2015;33(6):646-55. 

The iCRISPR platform for rapid genome editing in human pluripotent stem cells. González F, Zhu Z, Shi ZD, Lelli K, Verma N, Li QV, Huangfu D. Cell Stem Cell. 2014;15(2):215-226.

Homologous recombination DNA repair genes play a critical role in reprogramming to a pluripotent state. Gonzalez F, Georgieva D, Vanoli F, Shi Z-D, Stadtfeld M, Ludwig T, Jasin M, Huangfu D. Cell Reports 2013;3(3):651-660.

 

Select Reviewed Articles since 2013

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.

Human pluripotent stem cells: an emerging model in developmental biology. Zhu Z, Huangfu D. Development. Review. 2013;140(4):705-717.