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
Cytotoxic innate lymphoid cells sense cancer cell-expressed interleukin-15 to suppress human and murine malignancies. Kansler ER, Dadi S, Krishna C, Nixon BG, Stamatiades EG, Liu M, Kuo F, Zhang J, Zhang X, Capistrano K, Blum KA, Weiss K, Kedl RM, Cui G, Ikuta K, Chan TA, Leslie CS, Hakimi AA, Li MO.Nat Immunol. 2022 Jun;23(6):904-915. doi: 10.1038/s41590-022-01213-2. Epub 2022 May 26.PMID: 35618834
Globin vector regulatory elements are active in early hematopoietic progenitor cells. Cabriolu A, Odak A, Zamparo L, Yuan H, Leslie CS, Sadelain M.Mol Ther. 2022 Jun 1;30(6):2199-2209. doi: 10.1016/j.ymthe.2022.02.028. Epub 2022 Mar 2.PMID: 35247584
Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants. Sánchez-Rivera FJ, Diaz BJ, Kastenhuber ER, Schmidt H, Katti A, Kennedy M, Tem V, Ho YJ, Leibold J, Paffenholz SV, Barriga FM, Chu K, Goswami S, Wuest AN, Simon JM, Tsanov KM, Chakravarty D, Zhang H, Leslie CS, Lowe SW, Dow LE.Nat Biotechnol. 2022 Jun;40(6):862-873. doi: 10.1038/s41587-021-01172-3. Epub 2022 Feb 14.PMID: 35165384
Programme of self-reactive innate-like T cell-mediated cancer immunity. Chou C, Zhang X, Krishna C, Nixon BG, Dadi S, Capistrano KJ, Kansler ER, Steele M, Han J, Shyu A, Zhang J, Stamatiades EG, Liu M, Li S, Do MH, Edwards C, Kang DS, Chen CT, Wei IH, Pappou EP, Weiser MR, Garcia-Aguilar J, Smith JJ, Leslie CS, Li MO.Nature. 2022 May;605(7908):139-145. doi: 10.1038/s41586-022-04632-1. Epub 2022 Apr 20.PMID: 35444279
Chromatin interaction-aware gene regulatory modeling with graph attention networks. Karbalayghareh A, Sahin M, Leslie CS.Genome Res. 2022 May;32(5):930-944. doi: 10.1101/gr.275870.121. Epub 2022 Apr 8.PMID: 35396274
Cytotoxic granzyme C-expressing ILC1s contribute to antitumor immunity and neonatal autoimmunity. Nixon BG, Chou C, Krishna C, Dadi S, Michel AO, Cornish AE, Kansler ER, Do MH, Wang X, Capistrano KJ, Rudensky AY, Leslie CS, Li MO.Sci Immunol. 2022 Apr 8;7(70):eabi8642. doi: 10.1126/sciimmunol.abi8642. Epub 2022 Apr 8.PMID: 35394814
Single-Cell Transcriptional Profiling Reveals Signatures of Helper, Effector, and Regulatory MAIT Cells during Homeostasis and Activation. Vorkas CK, Krishna C, Li K, Aubé J, Fitzgerald DW, Mazutis L, Leslie CS, Glickman MS.J Immunol. 2022 Mar 1;208(5):1042-1056. doi: 10.4049/jimmunol.2100522. Epub 2022 Feb 11.PMID: 35149530
SETD2 loss perturbs the kidney cancer epigenetic landscape to promote metastasis and engenders actionable dependencies on histone chaperone complexes. Xie Y, Sahin M, Sinha S, Wang Y, Nargund AM, Lyu Y, Han S, Dong Y, Hsieh JJ, Leslie CS, Cheng EH.Nat Cancer. 2022 Feb;3(2):188-202. doi: 10.1038/s43018-021-00316-3. Epub 2022 Feb 3.PMID: 35115713
Hierarchical regulation of the resting and activated T cell epigenome by major transcription factor families. Zhong Y, Walker SK, Pritykin Y, Leslie CS, Rudensky AY, van der Veeken J.Nat Immunol. 2022 Jan;23(1):122-134. doi: 10.1038/s41590-021-01086-x. Epub 2021 Dec 22.PMID: 34937932
HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. Sahin M, Wong W, Zhan Y, Van Deynze K, Koche R, Leslie CS.Nat Commun. 2021 Jun 7;12(1):3366. doi: 10.1038/s41467-021-23749-x.PMID: 34099725
A unified atlas of CD8 T cell dysfunctional states in cancer and infection. Pritykin Y, van der Veeken J, Pine AR, Zhong Y, Sahin M, Mazutis L, Pe’er D, Rudensky AY, Leslie CS.Mol Cell. 2021 Jun 3;81(11):2477-2493.e10. doi: 10.1016/j.molcel.2021.03.045. Epub 2021 Apr 22.PMID: 33891860
Pancreatic cancer prognosis is predicted by an ATAC-array technology for assessing chromatin accessibility. Dhara S, Chhangawala S, Chintalapudi H, Askan G, Aveson V, Massa AL, Zhang L, Torres D, Makohon-Moore AP, Lecomte N, Melchor JP, Bermeo J, Cardenas A 3rd, Sinha S, Glassman D, Nicolle R, Moffitt R, Yu KH, Leppanen S, Laderman S, Curry B, Gui J, Balachandran VP, Iacobuzio-Donahue C, Chandwani R, Leslie CS, Leach SD.Nat Commun. 2021 May 24;12(1):3044. doi: 10.1038/s41467-021-23237-2.PMID: 34031415
Glycolytic ATP fuels phosphoinositide 3-kinase signaling to support effector T helper 17 cell responses. Xu K, Yin N, Peng M, Stamatiades EG, Chhangawala S, Shyu A, Li P, Zhang X, Do MH, Capistrano KJ, Chou C, Leslie CS, Li MO.Immunity. 2021 May 11;54(5):976-987.e7. doi: 10.1016/j.immuni.2021.04.008.PMID: 33979589
Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy. Krishna C, DiNatale RG, Kuo F, Srivastava RM, Vuong L, Chowell D, Gupta S, Vanderbilt C, Purohit TA, Liu M, Kansler E, Nixon BG, Chen YB, Makarov V, Blum KA, Attalla K, Weng S, Salmans ML, Golkaram M, Liu L, Zhang S, Vijayaraghavan R, Pawlowski T, Reuter V, Carlo MI, Voss MH, Coleman J, Russo P, Motzer RJ, Li MO, Leslie CS, Chan TA, Hakimi AA.Cancer Cell. 2021 May 10;39(5):662-677.e6. doi: 10.1016/j.ccell.2021.03.007. Epub 2021 Apr 15.PMID: 33861994
FXR mediates T cell-intrinsic responses to reduced feeding during infection. Campbell C, Marchildon F, Michaels AJ, Takemoto N, van der Veeken J, Schizas M, Pritykin Y, Leslie CS, Intlekofer AM, Cohen P, Rudensky AY.Proc Natl Acad Sci U S A. 2020 Dec 29;117(52):33446-33454. doi: 10.1073/pnas.2020619117. Epub 2020 Dec 14.PMID: 33318189
The Transcription Factor Foxp3 Shapes Regulatory T Cell Identity by Tuning the Activity of trans-Acting Intermediaries. van der Veeken J, Glasner A, Zhong Y, Hu W, Wang ZM, Bou-Puerto R, Charbonnier LM, Chatila TA, Leslie CS, Rudensky AY.Immunity. 2020 Nov 17;53(5):971-984.e5. doi: 10.1016/j.immuni.2020.10.010. Epub 2020 Nov 10.PMID: 33176163
High-Resolution In Vivo Identification of miRNA Targets by Halo-Enhanced Ago2 Pull-Down. Li X, Pritykin Y, Concepcion CP, Lu Y, La Rocca G, Zhang M, King B, Cook PJ, Au YW, Popow O, Paulo JA, Otis HG, Mastroleo C, Ogrodowski P, Schreiner R, Haigis KM, Betel D, Leslie CS, Ventura A.Mol Cell. 2020 Jul 2;79(1):167-179.e11. doi: 10.1016/j.molcel.2020.05.009. Epub 2020 Jun 3.PMID: 32497496
Acute Myeloid Leukemia iPSCs Reveal a Role for RUNX1 in the Maintenance of Human Leukemia Stem Cells. Wesely J, Kotini AG, Izzo F, Luo H, Yuan H, Sun J, Georgomanoli M, Zviran A, Deslauriers AG, Dusaj N, Nimer SD, Leslie C, Landau DA, Kharas MG, Papapetrou EP.Cell Rep. 2020 Jun 2;31(9):107688. doi: 10.1016/j.celrep.2020.107688.PMID: 32492433
HyperTRIBE uncovers increased MUSASHI-2 RNA binding activity and differential regulation in leukemic stem cells. Nguyen DTT, Lu Y, Chu KL, Yang X, Park SM, Choo ZN, Chin CR, Prieto C, Schurer A, Barin E, Savino AM, Gourkanti S, Patel P, Vu LP, Leslie CS, Kharas MG.Nat Commun. 2020 Apr 24;11(1):2026. doi: 10.1038/s41467-020-15814-8.PMID: 32332729
ARID1A determines luminal identity and therapeutic response in estrogen-receptor-positive breast cancer. Xu G, Chhangawala S, Cocco E, Razavi P, Cai Y, Otto JE, Ferrando L, Selenica P, Ladewig E, Chan C, Da Cruz Paula A, Witkin M, Cheng Y, Park J, Serna-Tamayo C, Zhao H, Wu F, Sallaku M, Qu X, Zhao A, Collings CK, D’Avino AR, Jhaveri K, Koche R, Levine RL, Reis-Filho JS, Kadoch C, Scaltriti M, Leslie CS, Baselga J, Toska E.Nat Genet. 2020 Feb;52(2):198-207. doi: 10.1038/s41588-019-0554-0. Epub 2020 Jan 13.PMID: 31932695
Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity. Brown CC, Gudjonson H, Pritykin Y, Deep D, Lavallée VP, Mendoza A, Fromme R, Mazutis L, Ariyan C, Leslie C, Pe’er D, Rudensky AY.Cell. 2019 Oct 31;179(4):846-863.e24. doi: 10.1016/j.cell.2019.09.035. Epub 2019 Oct 24.PMID: 31668803
Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers. Osmanbeyoglu HU, Shimizu F, Rynne-Vidal A, Alonso-Curbelo D, Chen HA, Wen HY, Yeung TL, Jelinic P, Razavi P, Lowe SW, Mok SC, Chiosis G, Levine DA, Leslie CS.Nat Commun. 2019 Sep 25;10(1):4369. doi: 10.1038/s41467-019-12291-6.PMID: 31554806
BindSpace decodes transcription factor binding signals by large-scale sequence embedding. Yuan H, Kshirsagar M, Zamparo L, Lu Y, Leslie CS.Nat Methods. 2019 Sep;16(9):858-861. doi: 10.1038/s41592-019-0511-y. Epub 2019 Aug 12.PMID: 31406384
Mouse cytomegalovirus-experienced ILC1s acquire a memory response dependent on the viral glycoprotein m12. Weizman OE, Song E, Adams NM, Hildreth AD, Riggan L, Krishna C, Aguilar OA, Leslie CS, Carlyle JR, Sun JC, O’Sullivan TE.Nat Immunol. 2019 Aug;20(8):1004-1011. doi: 10.1038/s41590-019-0430-1. Epub 2019 Jul 1.PMID: 31263280
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 Jul 9;28(2):382-393.e7. doi: 10.1016/j.celrep.2019.06.034.PMID: 31291575
FOXA1 mutations alter pioneering activity, differentiation and prostate cancer phenotypes. Adams EJ, Karthaus WR, Hoover E, Liu D, Gruet A, Zhang Z, Cho H, DiLoreto R, Chhangawala S, Liu Y, Watson PA, Davicioni E, Sboner A, Barbieri CE, Bose R, Leslie CS, Sawyers CL.Nature. 2019 Jul;571(7765):408-412. doi: 10.1038/s41586-019-1318-9. Epub 2019 Jun 26.PMID: 31243370
Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia. Minuesa G, Albanese SK, Xie W, Kazansky Y, Worroll D, Chow A, Schurer A, Park SM, Rotsides CZ, Taggart J, Rizzi A, Naden LN, Chou T, Gourkanti S, Cappel D, Passarelli MC, Fairchild L, Adura C, Glickman JF, Schulman J, Famulare C, Patel M, Eibl JK, Ross GM, Bhattacharya S, Tan DS, Leslie CS, Beuming T, Patel DJ, Goldgur Y, Chodera JD, Kharas MG.Nat Commun. 2019 Jun 19;10(1):2691. doi: 10.1038/s41467-019-10523-3.PMID: 31217428
Natural Genetic Variation Reveals Key Features of Epigenetic and Transcriptional Memory in Virus-Specific CD8 T Cells. van der Veeken J, Zhong Y, Sharma R, Mazutis L, Dao P, Pe’er D, Leslie CS, Rudensky AY.Immunity. 2019 May 21;50(5):1202-1217.e7. doi: 10.1016/j.immuni.2019.03.031. Epub 2019 Apr 23.PMID: 31027997
PI3K Inhibition Activates SGK1 via a Feedback Loop to Promote Chromatin-Based Regulation of ER-Dependent Gene Expression. Toska E, Castel P, Chhangawala S, Arruabarrena-Aristorena A, Chan C, Hristidis VC, Cocco E, Sallaku M, Xu G, Park J, Minuesa G, Shifman SG, Socci ND, Koche R, Leslie CS, Scaltriti M, Baselga J.Cell Rep. 2019 Apr 2;27(1):294-306.e5. doi: 10.1016/j.celrep.2019.02.111.PMID: 30943409
Transcription factor Foxp1 regulates Foxp3 chromatin binding and coordinates regulatory T cell function. Konopacki C, Pritykin Y, Rubtsov Y, Leslie CS, Rudensky AY.Nat Immunol. 2019 Feb;20(2):232-242. doi: 10.1038/s41590-018-0291-z. Epub 2019 Jan 14.PMID: 30643266
IKZF2 Drives Leukemia Stem Cell Self-Renewal and Inhibits Myeloid Differentiation. Park SM, Cho H, Thornton AM, Barlowe TS, Chou T, Chhangawala S, Fairchild L, Taggart J, Chow A, Schurer A, Gruet A, Witkin MD, Kim JH, Shevach EM, Krivtsov A, Armstrong SA, Leslie C, Kharas MG.Cell Stem Cell. 2019 Jan 3;24(1):153-165.e7. doi: 10.1016/j.stem.2018.10.016. Epub 2018 Nov 21.PMID: 30472158
The effect of cellular context on miR-155-mediated gene regulation in four major immune cell types. Hsin JP, Lu Y, Loeb GB, Leslie CS, Rudensky AY.Nat Immunol. 2018 Oct;19(10):1137-1145. doi: 10.1038/s41590-018-0208-x. Epub 2018 Sep 17.PMID: 30224821
Widespread intronic polyadenylation inactivates tumour suppressor genes in leukaemia. Lee SH, Singh I, Tisdale S, Abdel-Wahab O, Leslie CS, Mayr C.Nature. 2018 Sep;561(7721):127-131. doi: 10.1038/s41586-018-0465-8. Epub 2018 Aug 27.PMID: 30150773
Epigenetic control of innate and adaptive immune memory. Lau CM, Adams NM, Geary CD, Weizman OE, Rapp M, Pritykin Y, Leslie CS, Sun JC.Nat Immunol. 2018 Sep;19(9):963-972. doi: 10.1038/s41590-018-0176-1. Epub 2018 Aug 6.PMID: 30082830
Non-redundant ISGF3 Components Promote NK Cell Survival in an Auto-regulatory Manner during Viral Infection. Geary CD, Krishna C, Lau CM, Adams NM, Gearty SV, Pritykin Y, Thomsen AR, Leslie CS, Sun JC.Cell Rep. 2018 Aug 21;24(8):1949-1957.e6. doi: 10.1016/j.celrep.2018.07.060.PMID: 30134157
Widespread intronic polyadenylation diversifies immune cell transcriptomes. Singh I, Lee SH, Sperling AS, Samur MK, Tai YT, Fulciniti M, Munshi NC, Mayr C, Leslie CS.Nat Commun. 2018 Apr 30;9(1):1716. doi: 10.1038/s41467-018-04112-z. [PMID: 29712909]
ILC1 Confer Early Host Protection at Initial Sites of Viral Infection. Weizman OE, Adams NM, Schuster IS, Krishna C, Pritykin Y, Lau C, Degli-Esposti MA, Leslie CS, Sun JC, O’Sullivan TE.Cell. 2017 Nov 2;171(4):795-808.e12. doi: 10.1016/j.cell.2017.09.052. Epub 2017 Oct 19. [PMID: 29056343]
Ets transcription factor GABP controls T cell homeostasis and immunity. Luo CT, Osmanbeyoglu HU, Do MH, Bivona MR, Toure A, Kang D, Xie Y, Leslie CS, Li MO. Nat Commun. 2017 Oct 20;8(1):1062. doi: 10.1038/s41467-017-01020-6.
Functional screen of MSI2 interactors identifies an essential role for SYNCRIP in myeloid leukemia stem cells. Vu LP, Prieto C, Amin EM, Chhangawala S, Krivtsov A, Calvo-Vidal MN, Chou T, Chow A, Minuesa G, Park SM, Barlowe TS, Taggart J, Tivnan P, Deering RP, Chu LP, Kwon JA, Meydan C, Perales-Paton J, Arshi A, Gönen M, Famulare C, Patel M, Paietta E, Tallman MS, Lu Y, Glass J, Garret-Bakelman FE, Melnick A, Levine R, Al-Shahrour F, Järås M, Hacohen N, Hwang A, Garippa R, Lengner CJ, Armstrong SA, Cerchietti L, Cowley GS, Root D, Doench J, Leslie C, Ebert BL, Kharas MG.Nat Genet. 2017 Jun;49(6):866-875. doi: 10.1038/ng.3854. Epub 2017 Apr 24.PMID: 28436985
Chromatin states define tumour-specific T cell dysfunction and reprogramming. Philip M, Fairchild L, Sun L, Horste EL, Camara S, Shakiba M, Scott AC, Viale A, Lauer P, Merghoub T, Hellmann MD, Wolchok JD, Leslie CS, Schietinger A. Nature. 2017 May 25;545(7655):452-456. doi: 10.1038/nature22367. Epub 2017 May 17.
An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data. Carty M, Zamparo L, Sahin M, González A, Pelossof R, Elemento O, Leslie CS. Nat Commun. 2017 May 17;8:15454. doi: 10.1038/ncomms15454.
PI3K pathway regulates ER-dependent transcription in breast cancer through the epigenetic regulator KMT2D. Toska E, Osmanbeyoglu HU, Castel P, Chan C, Hendrickson RC, Elkabets M, Dickler MN, Scaltriti M, Leslie CS, Armstrong SA, Baselga J. Science. 2017 Mar 24;355(6331):1324-1330. doi: 10.1126/science.aah6893.
The SWI/SNF Protein PBRM1 Restrains VHL-Loss-Driven Clear Cell Renal Cell Carcinoma. Nargund AM, Pham CG, Dong Y, Wang PI, Osmangeyoglu HU, Xie Y, Aras O, Han S, Oyama T, Takeda S, Ray CE, Dong Z, Berge M, Hakimi AA, Monette S, Lekaye CL, Koutcher JA, Leslie CS, Creighton CJ, Weinhold N, Lee W, Tickoo SK, Wang Z, Cheng EH, Hsieh JJ.Cell Rep. 2017 Mar 21;18(12):2893-2906. doi: 10.1016/j.celrep.2017.02.074.PMID: 28329682
GuideScan software for improved single and paired CRISPR guide RNA design. Perez AR, Pritykin Y, Vidigal JA, Chhangawala S, Zamparo L, Leslie CS, Ventura A. Nat Biotechnol. 2017 Apr;35(4):347-349. doi: 10.1038/nbt.3804. Epub 2017 Mar 6.
Prediction of potent shRNAs with a sequential classification algorithm. Pelossof R, Fairchild L, Huang CH, Widmer C, Sreedharan VT, Sinha N, Lai DY, Guan Y, Premsrirut PK, Tschaharganeh DF, Hoffmann T, Thapar V, Xiang Q, Garippa RJ, Rätsch G, Zuber J, Lowe SW, Leslie CS, Fellmann C. Nat Biotechnol. 2017 Apr;35(4):350-353. doi: 10.1038/nbt.3807. Epub 2017 Mar 6.
Pancancer modelling predicts the context-specific impact of somatic mutations on transcriptional programs. Osmanbeyoglu HU, Toska E, Chan C, Baselga J, Leslie CS. Nat Commun. 2017 Jan 31;8:14249. doi: 10.1038/ncomms14249.
Aerobic glycolysis promotes T helper 1 cell differentiation through an epigenetic mechanism. Peng M, Yin N, Chhangawala S, Xu K, Leslie CS, Li MO. Science. 2016 Oct 28;354(6311):481-484. Epub 2016 Sep 29.
Multitask learning improves prediction of cancer drug sensitivity. Yuan H, Paskov I, Paskov H, González AJ, Leslie CS.Sci Rep. 2016 Aug 23;6:31619. doi: 10.1038/srep31619.PMID: 27550087