2024

Cassandri M, Porrazzo A, Pomella S, Noce B, Zwergel C, Aiello FA, Vulcano F, Milazzo L, Camero S, Pajalunga D, Spada M, Manzi V, Gravina GL, Codenotti S, Piccione M, Tomaciello M, Signore M, Barillari G, Marchese C, Fanzani A, De Angelis B, Quintarelli C, Vakoc CR, Chen EY, Megiorni F, Locatelli F, Valente S, Mai A, Rota R, Marampon F. HDAC3 genetic and pharmacologic inhibition radiosensitizes fusion positive rhabdomyosarcoma by promoting DNA double-strand breaks. Cell Death Discov. 2024 Aug 6;10(1):351. 
 
Klingbeil O, Skopelitis D, Tonelli C, Yoshimoto T, Alpsoy A, Panepinto MC, Minicozzi F, Merrill JR, Cafiero AM, Aggarwal D, Russo S, Ha T, Demerdash OE, Wee TL, Spector DL, Lyons SK, Tuveson DA, Cifani P, Vakoc CR. MARK2/MARK3 kinases are catalytic co-dependencies of YAP/TAZ in human cancer. Cancer Discov. 2024 Jul 26. doi: 10.1158/2159-8290.CD-23-1529. Online ahead of print.
 
Duplaquet L, So K, Ying AW, Pal Choudhuri S, Li X, Xu GD, Li Y, Qiu X, Li R, Singh S, Wu XS, Hamilton S, Chien VD, Liu Q, Qi J, Somerville TDD, Heiling HM, Mazzola E, Lee Y, Zoller T, Vakoc CR, Doench JG, Forrester WC, Abrams T, Long HW, Niederst MJ, Drapkin BJ, Kadoch C, Oser MG. Mammalian SWI/SNF complex activity regulates POU2F3 and constitutes a targetable dependency in small cell lung cancer. Cancer Cell. 2024 Aug 12;42(8):1352-1369.e13. 
 
He T, Xiao L, Qiao Y, Klingbeil O, Young E, Wu XS, Mannan R, Mahapatra S, Redin E, Cho H, Bao Y, Kandarpa M, Ching-Yi Tien J, Wang X, Eyunni S, Zheng Y, Kim N, Zheng H, Hou S, Su F, Miner SJ, Mehra R, Cao X, Abbineni C, Samajdar S, Ramachandra M, Dhanasekaran SM, Talpaz M, Parolia A, Rudin CM, Vakoc CR, Chinnaiyan AM. Targeting the mSWI/SNF complex in POU2F-POU2AF transcription factor-driven malignancies. Cancer Cell. 2024 Aug 12;42(8):1336-1351.e9.
 
Maia-Silva D, Cunniff PJ, Schier AC, Skopelitis D, Trousdell MC, Moresco P, Gao Y, Kechejian V, He XY, Sahin Y, Wan L, Alpsoy A, Liverpool J, Krainer AR, Egeblad M, Spector DL, Fearon DT, Dos Santos CO, Taatjes DJ, Vakoc CR. Interaction between MED12 and ΔNp63 activates basal identity in pancreatic ductal adenocarcinoma. Nat Genet. 2024 Jul;56(7):1377-1385.
 
Zhang X, Duan S, Apostolou PE, Wu X, Watanabe J, Gallitto M, Barron T, Taylor KR, Woo PJ, Hua X, Zhou H, Wei HJ, McQuillan N, Kang KD, Friedman GK, Canoll PD, Chang K, Wu CC, Hashizume R, Vakoc CR, Monje M, McKhann GM 2nd, Gogos JA, Zhang Z. CHD2 Regulates Neuron-Glioma Interactions in Pediatric Glioma. Cancer Discov. 2024 Sep 4;14(9):1732-1754. 
 
He XY, Gao Y, Ng D, Michalopoulou E, George S, Adrover JM, Sun L, Albrengues J, Daßler-Plenker J, Han X, Wan L, Wu XS, Shui LS, Huang YH, Liu B, Su C, Spector DL, Vakoc CR, Van Aelst L, Egeblad M. Chronic stress increases metastasis via neutrophil-mediated changes to the microenvironment. Cancer Cell. 2024 Mar 11;42(3):474-486.e12. 
 
Gao Y, Vakoc CR. Therapeutic index of targeting select chromatin complexes in human cancer patients. Curr Opin Genet Dev. 2024 Apr;85:102162. 
 
Alpsoy A, Wu XS, Pal S, Klingbeil O, Kumar P, El Demerdash O, Nalbant B, Vakoc CR. IκBζ is a dual-use coactivator of NF-κB and POU transcription factors. Mol Cell. 2024 Mar 21;84(6):1149-1157.e7. 
 
Tonelli C, Yordanov GN, Hao Y, Deschênes A, Hinds J, Belleau P, Klingbeil O, Brosnan E, Doshi A, Park Y, Hruban RH, Vakoc CR, Dobin A, Preall J, Tuveson DA. A mucus production programme promotes classical pancreatic ductal adenocarcinoma. Gut. 2024 May 10;73(6):941-954. 

Xu J, Roe JS, Lee E, Tonelli C, Ji KY, Younis OW, Somervile TDD, Yao M, Milazzo JP, Tiriac H, Kolarzyk AM, Lee E, Grem JL, Lazenby AJ, Grunkemeyer JA, Hollingsworth MA, Grandgenett PM, Borowsky AD, Park Y, Vakoc CR, Tuveson DA, Hwang CI. Engrailed-1 Promotes Pancreatic Cancer Metastasis. Adv Sci (Weinh). 2024 Feb;11(6):e2308537. doi: 10.1002/advs.202308537. 

 

2023

Xu J, Roe JS, Lee E, Tonelli C, Ji KY, Younis OW, Somervile TDD, Yao M, Milazzo JP, Tiriac H, Kolarzyk AM, Lee E, Grem JL, Lazenby AJ, Grunkemeyer JA, Hollingsworth MA, Grandgenett PM, Borowsky AD, Park Y, Vakoc CR, Tuveson DA, Hwang CI. Engrailed-1 Promotes Pancreatic Cancer Metastasis. Adv Sci (Weinh). e2308537 (2023).

Pomella S, Cassandri M, D’Archivio L, Porrazzo A, Cossetti C, Phelps D, Perrone C, Pezzella M, Cardinale A, Wachtel M, Aloisi S, Milewski D, Colletti M, Sreenivas P, Walters ZS, Barillari G, Di Giannatale A, Milano GM, De Stefanis C, Alaggio R, Rodriguez-Rodriguez S, Carlesso N, Vakoc CR, Velardi E, Schafer BW, Guccione E, Gatz SA, Wasti A, Yohe M, Ignatius M, Quintarelli C, Shipley J, Miele L, Khan J, Houghton PJ, Marampon F, Gryder BE, De Angelis B, Locatelli F, Rota R. MYOD-SKP2 axis boosts tumorigenesis in fusion negative rhabdomyosarcoma by preventing differentiation through p57Kip2 targeting. Nat Commun. 14(1):8373 (2023). 
 
Maia-Silva D, Schier AC, Skopelitis D, Kechejian V, Alpsoy A, Liverpool J, Taatjes DJ, Vakoc CR. Marker-based CRISPR screening reveals a MED12-p63 interaction that activates basal identity in pancreatic ductal adenocarcinoma. bioRxiv. doi: 10.1101/2023.10.24.563848 (2023).

Sroka MW, Skopelitis D, Vermunt MW, Preall JB, El Demerdash O, de Almeida LMN, Chang K, Utama R, Gryder B, Caligiuri G, Ren D, Nalbant B, Milazzo JP, Tuveson DA, Dobin A, Hiebert SW, Stengel KR, Mantovani R, Khan J, Kohli RM, Shi J, Blobel GA, Vakoc CR. Myo-differentiation reporter screen reveals NF-Y as an activator of PAX3-FOXO1 in rhabdomyosarcoma.Proc Natl Acad Sci U S A. 120(36):e2303859120 (2023).

Li BE, Li GY, Cai W, Zhu Q, Seruggia D, Fujiwara Y, Vakoc CR, Orkin SH. In vivo CRISPR/Cas9 screening identifies Pbrm1 as a regulator of myeloid leukemia development in mice. Blood Adv. 7(18):5281-5293 (2023).

Wu XS, Vakoc CR. Made to order tuft cells by an OCA-T1 isoform switch. Sci Immunol. 8(83):eadh3123 (2023).

Hur SK, Somerville TDD, Wu XS, Maia-Silva D, Demerdash OE, Tuveson DA, Notta F, Vakoc CR.p73 activates transcriptional signatures of basal lineage identity and ciliogenesis in pancreatic ductal adenocarcinoma. bioRxiv. doi: 10.1101/2023.04.20.537667 (2023).

Fiskus W, Mill CP, Birdwell C, Davis JA, Das K, Boettcher S, Kadia TM, DiNardo CD, Takahashi K, Loghavi S, Soth MJ, Heffernan T, McGeehan GM, Ruan X, Su X, Vakoc CR, Daver N, Bhalla KN.Targeting of epigenetic co-dependencies enhances anti-AML efficacy of Menin inhibitor in AML with MLL1-r or mutant NPM1. Blood Cancer J. 13(1):53 (2023).
Gao Y, He XY, Wu XS, Huang YH, Toneyan S, Ha T, Ipsaro JJ, Koo PK, Joshua-Tor L, Bailey KM, Egeblad M, Vakoc CR.ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation. Nat Cell Biol. 25(2):298-308 (2023).
Sun X, Klingbeil O, Lu B, Wu C, Ballon C, Ouyang M, Wu XS, Jin Y, Hwangbo Y, Huang YH, Somerville TDD, Chang K, Park J, Chung T, Lyons SK, Shi J, Vogel H, Schulder M, Vakoc CR, Mills AA.BRD8 maintains glioblastoma by epigenetic reprogramming of the p53 network. Nature. 613(7942):195-202 (2023).

2022

Mo Y, Duan S, Zhang X, Hua X, Zhou H, Wei HJ, Watanabe J, McQuillan N, Su Z, Gu W, Wu CC, Vakoc CR, Hashizume R, Chang K, Zhang Z. Epigenome Programming by H3.3K27M Mutation Creates a Dependence of Pediatric Glioma on SMARCA4. Cancer Discov. 12(12):2906-2929 (2022).

Xiong X, Yang C, He WQ, Yu J, Xin Y, Zhang X, Huang R, Ma H, Xu S, Li Z, Ma J, Xu L, Wang Q, Ren K, Wu XS, Vakoc CR, Zhong J, Zhong G, Zhu X, Song Y, Ruan HB, Wang Q. Sirtuin 6 maintains epithelial STAT6 activity to support intestinal tuft cell development and type 2 immunity. Nat Commun. 13(1):5192 (2022).

Doepner M, Lee I, Natale CA, Brathwaite R, Venkat S, Kim SH, Wei Y, Vakoc CR, Capell BC, Katzenellenbogen JA, Katzenellenbogen BS, Feigin ME, Ridky TW. Endogenous DOPA inhibits melanoma through suppression of CHRM1 signaling. Sci Adv. 8(35):eabn4007 (2022).

Orstad G, Fort G, Parnell TJ, Jones A, Stubben C, Lohman B, Gillis KL, Orellana W, Tariq R, Klingbeil O, Kaestner K, Vakoc CR, Spike BT, Snyder EL.FoxA1 and FoxA2 control growth and cellular identity in NKX2-1-positive lung adenocarcinoma. Dev Cell. 57(15):1866-1882.e10 (2022).
 
Wu XS, He XY, Ipsaro JJ, Huang YH, Preall JB, Ng D, Shue YT, Sage J, Egeblad M, Joshua-Tor L, Vakoc CR. OCA-T1 and OCA-T2 are coactivators of POU2F3 in the tuft cell lineage. Nature. 607(7917):169-175 (2022).
 
Li R, Klingbeil O, Monducci D, Young MJ, Rodriguez DJ, Bayyat Z, Dempster JM, Kesar D, Yang X, Zamanighomi M, Vakoc CR, Ito T, Sellers WR.Comparative optimization of combinatorial CRISPR screens. Nat Commun. 13(1):2469 (2022).
 
Bharathy N, Cleary MM, Kim JA, Nagamori K, Crawford KA, Wang E, Saha D, Settelmeyer TP, Purohit R, Skopelitis D, Chang K, Doran JA, Kirschbaum CW, Bharathy S, Crews DW, Randolph ME, Karnezis AN, Hudson-Price L, Dhawan J, Michalek JE, Ciulli A, Vakoc CR, Keller C. SMARCA4 biology in alveolar rhabdomyosarcoma. Oncogene. 41(11):1647-1656 (2022).
 
Polyanskaya SA, Moreno RY, Lu B, Feng R, Yao Y, Irani S, Klingbeil O, Yang Z, Wei Y, Demerdash OE, Benjamin LA, Weiss MJ, Zhang YJ, Vakoc CR. SCP4-STK35/PDIK1L complex is a dual phospho-catalytic signaling dependency in acute myeloid leukemia. Cell Rep. 38(2):110233 (2022).

2021

2020

Miyabayashi K, Baker LA, Deschênes A, Traub B, Caligiuri G, Plenker D, Alagesan B, Belleau P, Li S, Kendall J, Jang GH, Kawaguchi RK, Somerville TDD, Tiriac H, Hwang CI, Burkhart RA, Roberts NJ, Wood LD, Hruban RH, Gillis J, Krasnitz A, Vakoc CR, Wigler M, Notta F, Gallinger S, Park Y, Tuveson DA. Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes. Cancer Discov. 10(10):1566-1589 (2020).

Oni TE, Biffi G, Baker LA, Hao Y, Tonelli C, Somerville TDD, Deschênes A, Belleau P, Hwang CI, Sánchez-Rivera FJ, Cox H, Brosnan E, Doshi A, Lumia RP, Khaledi K, Park Y, Trotman LC, Lowe SW, Krasnitz A, Vakoc CR, Tuveson DA. SOAT1 promotes mevalonate pathway dependency in pancreatic cancer. J Exp Med. 217(9):e20192389 (2020).

Wu XS, Vakoc CR. A pliable ERα cistrome evades therapy. Nat Cell Biol. 22(6):619-620 (2020).

Gryder BE, Wachtel M, Chang K, El Demerdash O, Aboreden NG, Mohammed W, Ewert W, Pomella S, Rota R, Wei JS, Song Y, Stanton BZ, Schäfer B, Vakoc CR, Khan J. Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage. iScience.23(5):101103, (2020).

Somerville TDD, Xu Y, Wu XS, Maia-Silva D, Hur SK, de Almeida LMN, Preall JB, Koo PK, Vakoc CR. ZBED2 is an antagonist of interferon regulatory factor 1 and modifies cell identity in pancreatic cancer. Proc Natl Acad Sci U S A. 117(21):11471-11482 (2020).

Somerville TD, Biffi G, Daßler-Plenker J, Hur SK, He XY, Vance KE, Miyabayashi K, Xu Y, Maia-Silva D, Klingbeil O, Demerdash OE, Preall JB, Hollingsworth MA, Egeblad M, Tuveson DA, Vakoc CR. Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation. Elife. 9:e53381 (2020).

Poirier JT, George J, Owonikoko TK, Berns A, Brambilla E, Byers LA, Carbone D, Chen HJ, Christensen CL, Dive C, Farago AF, Govindan R, Hann C, Hellmann MD, Horn L, Johnson JE, Ju YS, Kang S, Krasnow M, Lee J, Lee SH, Lehman J, Lok B, Lovly C, MacPherson D, McFadden D, Minna J, Oser M, Park K, Park KS, Pommier Y, Quaranta V, Ready N, Sage J, Scagliotti G, Sos ML, Sutherland KD, Travis WD, Vakoc CR, Wait SJ, Wistuba I, Wong KK, Zhang H, Daigneault J, Wiens J, Rudin CM, Oliver TG. New Approaches to SCLC Therapy: From the Laboratory to the Clinic. J Thorac Oncol. 15(4):520-540 (2020).

Tarumoto Y, Lin S, Wang J, Milazzo JP, Xu Y, Lu B, Yang Z, Wei Y, Polyanskaya S, Wunderlich M, Gray NS, Stegmaier K, Vakoc CR. Salt-Inducible Kinase inhibition suppresses acute myeloid leukemia progression in vivo. Blood. 135(1):56-70 (2020).

2019

Foronda M, Tarumoto Y, Schatoff EM, Leach BI, Diaz BJ, Zimmerman J, Goswami S, Shusterman M, Vakoc CR, Dow LE. Tankyrase inhibition sensitizes cells to CDK4 blockade. PLoS One. 14(12):e0226645 (2019).

Gryder BE, Pomella S, Sayers C, Wu XS, Song Y, Chiarella AM, Bagchi S, Chou HC, Sinniah RS, Walton A, Wen X, Rota R, Hathaway NA, Zhao K, Chen J, Vakoc CR, Shern JF, Stanton BZ, Khan J. Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma. Nat Genet.51(12):1714-1722 (2019).

Caiado F, Maia-Silva D, Jardim C, Schmolka N, Carvalho T, Reforço C, Faria R, Kolundzija B, Simões AE, Baubec T, Vakoc CR, da Silva MG, Manz MG, Schumacher TN, Norell H, Silva-Santos B. Lineage tracing of acute myeloid leukemia reveals the impact of hypomethylating agents on chemoresistance selection. Nat Commun. 1;10(1):4986 (2019).

Li F, Deng Z, Zhang L, Wu C, Jin Y, Hwang I, Vladimirova O, Xu L, Yang L, Lu B, Dheekollu J, Li JY, Feng H, Hu J, Vakoc CR, Ying H, Paik J, Lieberman PM, Zheng H. ATRX loss induces telomere dysfunction and necessitates induction of alternative lengthening of telomeres during human cell immortalization. EMBO J. e96659 (2019).

Ehrenhöfer-Wölfer K, Puchner T, Schwarz C, Rippka J, Blaha-Ostermann S, Strobl U, Hörmann A, Bader G, Kornigg S, Zahn S, Sommergruber W, Schweifer N, Zichner T, Schlattl A, Neumüller RA, Shi J, Vakoc CR, Kögl M, Petronczki M, Kraut N, Pearson MA, Wöhrle S. SMARCA2-deficiency confers sensitivity to targeted inhibition of SMARCA4 in esophageal squamous cell carcinoma cell lines. Sci Rep. 9(1):11661 (2019).

Böttcher J, Dilworth D, Reiser U, Neumüller RA, Schleicher M, Petronczki M, Zeeb M, Mischerikow N, Allali-Hassani A, Szewczyk MM, Li F, Kennedy S, Vedadi M, Barsyte-Lovejoy D, Brown PJ, Huber KVM, Rogers CM, Wells CI, Fedorov O, Rumpel K, Zoephel A, Mayer M, Wunberg T, Böse D, Zahn S, Arnhof H, Berger H, Reiser C, Hörmann A, Krammer T, Corcokovic M, Sharps B, Winkler S, Häring D, Cockcroft XL, Fuchs JE, Müllauer B, Weiss-Puxbaum A, Gerstberger T, Boehmelt G, Vakoc CR, Arrowsmith CH, Pearson M, McConnell DB. Fragment-based discovery of a chemical probe for the PWWP1 domain of NSD3. Nat Chem Biol. 15(8):822-829 (2019).

Yohe ME, Heske CM, Stewart E, Adamson PC, Ahmed N, Antonescu CR, Chen E, Collins N, Ehrlich A, Galindo RL, Gryder BE, Hahn H, Hammond S, Hatley ME, Hawkins DS, Hayes MN, Hayes-Jordan A, Helman LJ, Hettmer S, Ignatius MS, Keller C, Khan J, Kirsch DG, Linardic CM, Lupo PJ, Rota R, Shern JF, Shipley J, Sindiri S, Tapscott SJ, Vakoc CR, Wexler LH, Langenau DM. Insights into pediatric rhabdomyosarcoma research: Challenges and goals. Pediatr Blood Cancer. 66(10):e27869 (2019).

Bell CC, Fennell KA, Chan YC, Rambow F, Yeung MM, Vassiliadis D, Lara L, Yeh P, Martelotto LG, Rogiers A, Kremer BE, Barbash O, Mohammad HP, Johanson TM, Burr ML, Dhar A, Karpinich N, Tian L, Tyler DS, MacPherson L, Shi J, Pinnawala N, Yew Fong C, Papenfuss AT, Grimmond SM, Dawson SJ, Allan RS, Kruger RG, Vakoc CR, Goode DL, Naik SH, Gilan O, Lam EYN, Marine JC, Prinjha RK, Dawson MA. Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia. Nat Commun. 10(1):2723 (2019).

Lan X, Khandros E, Huang P, Peslak SA, Bhardwaj SK, Grevet JD, Abdulmalik O, Wang H, Keller CA, Giardine B, Baeza J, Duffner ER, El Demerdash O, Wu XS, Vakoc CR, Garcia BA, Hardison RC, Shi J, Blobel GA. The E3 ligase adaptor molecule SPOP regulates fetal hemoglobin levels in adult erythroid cells. Blood Adv. 3(10):1586-1597 (2019).

Bharathy N, Berlow NE, Wang E, Abraham J, Settelmeyer TP, Hooper JE, Svalina MN, Bajwa Z, Goros MW, Hernandez BS, Wolff JE, Pal R, Davies AM, Ashok A, Bushby D, Mancini M, Noakes C, Goodwin NC, Ordentlich P, Keck J, Hawkins DS, Rudzinski ER, Mansoor A, Perkins TJ, Vakoc CR, Michalek JE, Keller C. Preclinical rationale for entinostat in embryonal rhabdomyosarcoma. Skelet Muscle. 9(1):12 (2019).

Rudin CM, Poirier JT, Byers LA, Dive C, Dowlati A, George J, Heymach JV, Johnson JE, Lehman JM, MacPherson D, Massion PP, Minna JD, Oliver TG, Quaranta V, Sage J, Thomas RK, Vakoc CR, Gazdar AF.Molecular subtypes of small cell lung cancer: a synthesis of human and mouse model data. Nat Rev Cancer. 19(5):289-297 (2019)

Aho ER, Wang J, Gogliotti RD, Howard GC, Phan J, Acharya P, Macdonald JD, Cheng K, Lorey SL, Lu B, Wenzel S, Foshage AM, Alvarado J, Wang F, Shaw JG, Zhao B, Weissmiller AM, Thomas LR, Vakoc CR, Hall MD, Hiebert SW, Liu Q, Stauffer SR, Fesik SW, Tansey WP. Displacement of WDR5 from Chromatin by a WIN Site Inhibitor with Picomolar Affinity. Cell Rep. 26(11):2916-2928.e13 (2019).

2018

Lu B, Klingbeil O, Tarumoto Y, Somerville TDD, Huang YH, Wei Y, Wai DC, Low JKK, Milazzo JP, Wu XS, Cao Z, Yan X, Demerdash OE, Huang G, Mackay JP, Kinney JB, Shi J, Vakoc CR. A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence. Cancer Cell. 34(6):970-981 (2018).

Bharathy N, Berlow NE, Wang E, Abraham J, Settelmeyer TP, Hooper JE, Svalina MN, Ishikawa Y, Zientek K, Bajwa Z, Goros MW, Hernandez BS, Wolff JE, Rudek MA, Xu L, Anders NM, Pal R, Harrold AP, Davies AM, Ashok A, Bushby D, Mancini M, Noakes C, Goodwin NC, Ordentlich P, Keck J, Hawkins DS, Rudzinski ER, Chatterjee B, Bächinger HP, Barr FG, Liddle J, Garcia BA, Mansoor A, Perkins TJ, Vakoc CR, Michalek JE, Keller C. The HDAC3-SMARCA4-miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma. Sci Signal. 11(557) (2018).

Brien GL, Remillard D, Shi J, Hemming ML, Chabon J, Wynne K, Dillon ET, Cagney G, Van Mierlo G, Baltissen MP, Vermeulen M, Qi J, Fröhling S, Gray NS, Bradner JE, Vakoc CR, Armstrong SA. Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma. Elife. 7. pii: e41305.

Somerville TDD, Xu Y, Miyabayashi K, Tiriac H, Cleary CR, Maia-Silva D, Milazzo JP, Tuveson DA, Vakoc CR. TP63-Mediated Enhancer Reprogramming Drives the Squamous Subtype of Pancreatic Ductal Adenocarcinoma. Cell Rep. 25(7):1741-1755.e7 (2018).

Vakoc CR, Kentsis A. Disabling an oncogenic transcription factor by targeting of control kinases. Oncotarget. 9(64):32276-32277 (2018).

Hörmann A, Hopfgartner B, Köcher T, Corcokovic M, Krammer T, Reiser C, Bader G, Shi J, Ehrenhöfer K, Wöhrle S, Schweifer N, Vakoc CR, Kraut N, Pearson M, Petronczki M, Neumüller RA. RIOK1 kinase activity is required for cell survival irrespective of MTAP status. Oncotarget.  9(47):28625-28637 (2018).

Zafra MP, Schatoff EM, Katti A, Foronda M, Breinig M, Schweitzer AY, Simon A, Han T, Goswami S, Montgomery E, Thibado J, Kastenhuber ER, Sánchez-Rivera FJ, Shi J, Vakoc CR, Lowe SW, Tschaharganeh DF, Dow LE. Optimized base editors enable efficient editing in cells, organoids and mice. Nat Biotechnol. 36(9):888-893 (2018).

Huang YH, Klingbeil O, He XY, Wu XS, Arun G, Lu B, Somerville TDD, Milazzo JP, Wilkinson JE, Demerdash OE, Spector DL, Egeblad M, Shi J, Vakoc CR. POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer. Genes Dev. 32(13-14):915-928 (2018).

Tiriac H, Belleau P, Engle DD, Plenker D, Deschênes A, Somerville T, Froeling FEM, Burkhart RA, Denroche RE, Jang GH, Miyabayashi K, Young CM, Patel H, Ma M, LaComb JF, Palmaira RLD, Javed AA, Huynh JA, Johnson M, Arora K, Robine N, Shah M, Sanghvi R, Goetz AB, Lowder CY, Martello L, Driehuis E, Lecomte N, Askan G, Iacobuzio-Donahue CA, Clevers H, Wood LD, Hruban RH, Thompson ED, Aguirre AJ, Wolpin BM, Sasson A, Kim J, Wu M, Bucobo JC, Allen PJ, Sejpal DV, Nealon W, Sullivan JD, Winter JM, Gimotty PA, Grem JL, DiMaio DJ, Buscaglia JM, Grandgenett PM, Brody JR, Hollingsworth MA, O’Kane GM, Notta F, Kim EJ, Crawford JM, Devoe CE, Ocean A, Wolfgang CL, Yu KH, Li E, Vakoc CR, Hubert B, Fischer SE, Wilson JM, Moffitt RA, Knox JJ, Krasnitz A, Gallinger S, Tuveson DA. Organoid profiling identifies common responders to chemotherapy in pancreatic cancer. Cancer Discov. 2018 May 31  [Epub ahead of print]

Skucha A, Ebner J, Schmöllerl J, Roth M, Eder T, César-Razquin A, Stukalov A, Vittori S, Muhar M, Lu B, Aichinger M, Jude J, Müller AC, Győrffy B, Vakoc CR, Valent P, Bennett KL, Zuber J, Superti-Furga G, Grebien F. MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity. Nat Commun. 9(1):1983 (2018).

Wai DCC, Szyszka TN, Campbell AE, Kwong C, Wilkinson-White LE, Silva APG, Low JKK, Kwan AH, Gamsjaeger R, Chalmers JD, Patrick WM, Lu B, Vakoc CR, Blobel GA, Mackay JP. The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators.  J Biol Chem. 293(19):7160-7175 (2018).

Tarumoto Y, Lu B, Somerville TDD, Huang YH, Milazzo JP, Wu XS, Klingbeil O, El Demerdash O, Shi J, Vakoc CR. LKB1, Salt-Inducible Kinases, and MEF2C Are Linked Dependencies in Acute Myeloid Leukemia. Mol Cell. 69(6):1017-1027 (2018).

Banito A, Li X, Laporte AN, Roe JS, Sanchez-Vega F, Huang CH, Dancsok AR, Hatzi K, Chen CC, Tschaharganeh DF, Chandwani R, Tasdemir N, Jones KB, Capecchi MR, Vakoc CR, Schultz N, Ladanyi M, Nielsen TO, Lowe SW. The SS18-SSX Oncoprotein Hijacks KDM2B-PRC1.1 to Drive Synovial Sarcoma. Cancer Cell. 33(3):527-541 (2018).

Bhagwat AS, Lu B, Vakoc CR. Enhancer dysfunction in leukemia. Blood. 131(16):1795-1804 (2018).

Xu Y, Milazzo JP, Somerville TDD, Tarumoto Y, Huang YH, Ostrander EL, Wilkinson JE, Challen GA, Vakoc CR. A TFIID-SAGA Perturbation that Targets MYB and Suppresses Acute Myeloid Leukemia. Cancer Cell. 33(1):13-28 (2018).

2017

Barbieri I, Tzelepis K, Pandolfini L, Shi J, Millán-Zambrano G, Robson SC, Aspris D, Migliori V, Bannister AJ, Han N, De Braekeleer E, Ponstingl H, Hendrick A, Vakoc CR, Vassiliou GS, Kouzarides T. Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control. Nature. 552(7683):126-131 (2017).

Fontanals-Cirera B, Hasson D, Vardabasso C, Di Micco R, Agrawal P, Chowdhury A, Gantz M, de Pablos-Aragoneses A, Morgenstern A, Wu P, Filipescu D, Valle-Garcia D, Darvishian F, Roe JS, Davies MA, Vakoc CR, Hernando E, Bernstein E. Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene. Mol Cell. 68(4):731-744 (2017)

Vakoc CR, Tuveson DA. Soils and Seeds That Initiate Pancreatic Cancer Metastasis. Cancer Discov. 7(10):1067-1068 (2017).

Roe JS, Hwang CI, Somerville TDD, Milazzo JP, Lee EJ, Da Silva B, Maiorino L, Tiriac H, Young CM, Miyabayashi K, Filippini D, Creighton B, Burkhart RA, Buscaglia JM, Kim EJ, Grem JL, Lazenby AJ, Grunkemeyer JA, Hollingsworth MA, Grandgenett PM, Egeblad M, Park Y, Tuveson DA, Vakoc CR. Enhancer Reprogramming Promotes Pancreatic Cancer Metastasis. Cell. 170(5):875-888 (2017).

Lanning BR, Vakoc CR. Single-minded CRISPR screening. Nat Biotechnol. 35(4):339-340 (2017).

Vakoc CR, Tuveson DA. Untangling the genetics from the epigenetics in pancreatic cancer metastasis. Nat Genet. 49(3):323-324 (2017).

Ipsaro JJ, Shen C, Arai E, Xu Y, Kinney JB, Joshua-Tor L, Vakoc CR, Shi J. Rapid generation of drug-resistance alleles at endogenous loci using CRISPR-Cas9 indel mutagenesis. PLoS One. 12(2):e0172177 (2017).

Xu Y, Vakoc CR. Targeting Cancer Cells with BET Bromodomain Inhibitors. Cold Spring Harb Perspect Med. 7(7) (2017).

2016

Roe JS, Vakoc CR. The Essential Transcriptional Function of BRD4 in Acute Myeloid Leukemia. Cold Spring Harb Symp Quant Biol. 81:61-66. (2016).

Oran AR, Adams CM, Zhang XY, Gennaro VJ, Pfeiffer HK, Mellert HS, Seidel HE, Mascioli K, Kaplan J, Gaballa MR, Shen C, Rigoutsos I, King MP, Cotney JL, Arnold JJ, Sharma SD, Martinez-Outschoorn UE, Vakoc CR, Chodosh LA, Thompson JE, Bradner JE, Cameron CE, Shadel GS, Eischen CM, McMahon SB. Multi-focal control of mitochondrial gene expression by oncogenic MYC provides potential therapeutic targets in cancer. Oncotarget. (2016)

Huang YH, Vakoc CR. A Biomarker Harvest from One Thousand Cancer Cell Lines. Cell. 166(3):536-7 (2016).

Somerville TD, Vakoc CR. Modeling the Epigenetic Chain Reaction Downstream of DNMT3A(R882H). Cancer Cell. 30(1):9-10 (2016).

Hohmann AF, Martin LJ, Minder JL, Roe JS, Shi J, Steurer S, Bader G, McConnell D, Pearson M, Gerstberger T, Gottschamel T, Thompson D, Suzuki Y, Koegl M, Vakoc CR. Sensitivity and engineered resistance of myeloid leukemia cells to BRD9 inhibition. Nat Chem Biol. 12(9):672-9 (2016).

Zhang Q, Zeng L, Shen C, Ju Y, Konuma T, Zhao C, Vakoc CR, Zhou MM. Structural Mechanism of Transcriptional Regulator NSD3 Recognition by the ET Domain of BRD4. Structure. 24(7):1201-8 (2016).

Tasdemir N, Banito A, Roe JS, Alonso-Curbelo D, Camiolo M, Tschaharganeh DF, Huang CH, Aksoy O, Bolden JE, Chen CC, Fennell M, Thapar V, Chicas A, Vakoc CR, Lowe SW. BRD4 Connects Enhancer Remodeling to Senescence Immune Surveillance. Cancer Discovery. 6(6):612-29 (2016).

Bhagwat AS, Roe JS, Mok BY, Hohmann AF, Shi J, Vakoc CR. BET Bromodomain Inhibition Releases the Mediator Complex from Select cis-Regulatory Elements. Cell Reports. 15(3):519-30 (2016).

Martin LJ, Koegl M, Bader G, Cockcroft XL, Fedorov O, Fiegen D, Gerstberger T, Hofmann MH, Hohmann AF, Kessler D, Knapp S, Knesl P, Kornigg S, Müller S, Nar H, Rogers C, Rumpel K, Schaaf O, Steurer S, Tallant C, Vakoc CR, Zeeb M, Zoephel A, Pearson M, Boehmelt G, McConnell D. Structure-Based Design of an in Vivo Active Selective BRD9 Inhibitor. J Med Chem. 59(10):4462-75 (2016).

2015

Shen C, Ipsaro JJ, Shi J, Milazzo JP, Wang E, Roe JS, Suzuki Y, Pappin DJ, Joshua-Tor L, Vakoc CR. NSD3-Short Is an Adaptor Protein that Couples BRD4 to the CHD8 Chromatin Remodeler. Molecular Cell. 60(6):847-59 (2015).

Matthews GM, Mehdipour P, Cluse LA, Falkenberg KJ, Wang E, Roth M, Santoro F, Vidacs E, Stanley K, House CM, Rusche JR, Vakoc CR, Zuber J, Minucci S, Johnstone RW. Functional-genetic dissection of HDAC dependencies in mouse lymphoid and myeloid malignancies. Blood. 126(21):2392-403 (2015).

Rathert P, Roth M, Neumann T, Muerdter F, Roe JS, Muhar M, Deswal S, Cerny-Reiterer S, Peter B, Jude J, Hoffmann T, Boryń ŁM, Axelsson E, Schweifer N, Tontsch-Grunt U, Dow LE, Gianni D, Pearson M, Valent P, Stark A, Kraut N, Vakoc CR, Zuber J. Transcriptional plasticity promotes primary and acquired resistance to BET inhibition. Nature. 525(7570):543-7 (2015).

Bhagwat AS, Vakoc CR. Targeting Transcription Factors in Cancer. Trends in Cancer. 1(1): 53-65 (2015).

Roe JS, Mercan F, Rivera K, Pappin DJ,  Vakoc CR. BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia. Molecular Cell. 58(6):1028-39 (2015).

Shi J, Wang E, Milazzo JP, Wang Z, Kinney JB, Vakoc CR. Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nature Biotechnology. 33(6):661-7 (2015).

Wang E, Kawaoka S, Roe JS, Shi J, Hohmann AF, Xu Y, Bhagwat AS, Suzuki Y, Kinney JB, Vakoc CR. The transcriptional cofactor TRIM33 prevents apoptosis in B lymphoblastic leukemia by deactivating a single enhancer. eLife. 4:e06377 (2015).

Yu JR, Tai Y, Jin Y, Hammell MC, Wilkinson JE, Roe JS, Vakoc CR, Van Aelst L. TGF-β/Smad signaling through DOCK4 facilitates lung adenocarcinoma metastasis. Genes and Development. 29(3):250-61 (2015).

Shen C, Vakoc CR. Gain-of-function mutation of chromatin regulators as a tumorigenic mechanism and an opportunity for therapeutic intervention. Curr Opin Oncol. Jan;27(1):57-63 (2015).

2014

Xu Y, Vakoc CR. Brd4 is on the move during inflammation. Trends Cell Biol 24(11):615-6 (2014).

Mazurek A, Park Y, Miething C, Wilkinson JE, Gillis J, Lowe SW, Vakoc CR, Stillman B. Acquired dependence of acute myeloid leukemia on the DEAD-box RNA helicase DDX5. Cell Reports 7(6):1887-99 (2014).

Shi J, Vakoc CR. The mechanisms behind the therapeutic activity of BET bromodomain inhibition. Molecular Cell 54(5): 728-36 (2014).

Hohmann A, Vakoc CR. A rationale to target the SWI/SNF complex for cancer therapy. Trends in Genetics 30(8):356-63 (2014.)

Alpatov R, Lesch BJ, Nakamoto-Kinoshita M, Blanco A, Chen S, Stützer A, Armache KJ, Simon MD, Xu C, Ali M, Murn J, Prisic S, Kutateladze TG, Vakoc CR, Min J, Kingston RE, Fischle W, Warren ST, Page DC, Shi Y. A chromatin-dependent role of the fragile X mental retardation protein FMRP in the DNA damage response. Cell 157(4):869-81 (2014).

Chen C, Liu Y, Rappaport AR, Kitzing T, Schultz N, Zhao Z, Shroff AS, Dickins RA, Vakoc CR, Bradner JE, Stock W, LeBeau MM, Shannon KM, Kogan S, Zuber J, Lowe SW. MLL3 is a haploinsufficient 7q tumor suppressor in acute myeloid leukemia. Cancer Cell 25(5):652-65 (2014).

Vakoc CR, Garcia-Manero G, Look AT. Cancer therapy resistance: chasing epigenetics. Nature Medicine Apr;20(4):340-1 (2014).

Bhagwat AS, Vakoc CR. A new bump in the epigenetic landscape. Molecular Cell 53(6):857-8 (2014).

Roe JS, Vakoc CR. C/EBPα: critical at the origin of leukemic transformation. J Exp Med 211 1-4 (2014).

2013

Shi J, Whyte WA, Zepeda-Mendoza CJ, Milazzo JP, Shen C, Roe JS, Minder JL, Mercan F, Wang E, Eckersley-Maslin MA, Campbell AE, Kawaoka S, Shareef S, Zhu Z, Kendall J, Muhar M, Haslinger C, Yu M, Roeder RG, Wigler MH, Blobel GA, Zuber J, Spector DL, Young RA, Vakoc CR. Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. Genes and Development 27, 2648-62 (2013)

Roe JS, Vakoc CR. Oncogene interference through targeting of chromatin regulators. Cell Cycle 12, 1475-6 (2013)

Shi J*, Wang E*, Zuber J, Rappaport A, Taylor M, Johns C, Lowe SW, Vakoc CR. The Polycomb complex PRC2 supports aberrant self-renewal in a mouse model of MLL-AF9; Nras (G12D) acute myeloid leukemia. Oncogene 32, 930-938 (2013).

Wang E*, Kawaoka S*, Yu M, Shi J, Ni T, Yang W, Shu J, Roeder RG, Vakoc CR. Histone H2B ubiquitin ligase RNF20 is required for MLL-rearranged leukemia. Proc Natl Acad Sci USA. 110, 3901-3906 (2013).

Lovén J, Hoke HA, Lin CY, Lau A, Orlando DA, Vakoc CR, Bradner JE, Lee TI, Young RA. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320-34 (2013).

King B, Trimarchi T, Reavie L, Xu L, Mullenders J, Ntziachristos P, Aranda-Orgilles B, Perez-Garcia A, Shi J, Vakoc C, Sandy P, Shen SS, Ferrando A, Aifantis I. The ubiquitin ligase FBXW7 modulates leukemia-initiating cell activity by regulating MYC stability. Cell. 153(7):1552-66 (2013).

2012

Ernst P, Vakoc CR. WRAD: enabler of the SET1-family of H3K4 methyltransferases. Brief Funct Genomics 11, 217-226 (2012).

Herrmann H, Blatt K, Shi J, Gleixner KV, Cerny-Reiterer S, Mullauer L, Vakoc CR, Sperr WR, Horny HP, Bradner JE, Zuber J, Valent P. Small-molecule inhibition of BRD4 as a new potent approach to eliminate leukemic stem-and progenitor cells in acute myeloid leukemia AML. Oncotarget 3, 1588-1599 (2012).

2011

Zuber J*, Shi J*, Wang E, Rappaport AR, HerrmannH,SisonEA, Magoon D, Qi J, Blatt K, WunderlichM, TaylorMJ, Johns C, Chicas A, Mulloy JC, Kogan SC, Brown P, Valent P,  Bradner JE, Lowe SW, Vakoc CR. RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukemia. Nature 478, 524-528 (2011).

Zuber J, Rappaport AR, Luo W, Wang E, Chen C, Vaseva AV, Shi J, Weissmueller S, TaylorMJ, Weissenboeck M, Graeber TG, Kogan SC, Vakoc CR, Lowe SW. An integrated approach to dissecting oncogene addiction implicates a Myb coordinated self-renewal program as essential for leukemia maintenance. Genes and Development 25, 1628-40 (2011).

Delmore JE, Issa GC, Lemieux ME, Rahl PB, Shi J, Jacobs HM, Kastritis E, Gilpatrick T, Paranal RM, Qi J, Chesi M, Schinzel AC, McKeown MR, Heffernan TP, Vakoc CR, Bergsagel PL, Ghobrial IM, Richardson PG, Young RA, Hahn WC, Anderson KC, Kung AL, Bradner JE, Mitsiades CS. BET Bromodomain Inhibition as a Therapeutic Strategy to Target c-Myc. Cell 146, 904-17 (2011).

2010

Speck NA, Vakoc CR. PAF is in the cabal of MLL1-interacting proteins that promote leukemia. Cancer Cell 17, 531-532 (2010).

2009

Blobel GA, Kadauke S, Wang E, Lau AW, Zuber J, Chou MM, Vakoc CR. A Reconfigured pattern of MLL occupancy within mitotic chromatin promotes rapid transcriptional reactivation following mitotic exit. Molecular Cell 36, 970-983 (2009).

Tripic T, Deng W, Cheng Y, Zhang Y, Vakoc CR, Gregory GD, Hardison RC, Blobel GA. SCL and associated proteins distinguish active from repressive GATA transcription factor complexes. Blood 113, 2191-201 (2009).

Vakoc CR, Wen YW, Johnstone CN, Rustgi AK, Gibbs RA, Blobel GA. Low frequency of MLL3 mutations in colorectal carcinoma. Cancer Genetics and Cytogenetics. 189, 140-1 (2009).

Chou ST, Khandros E, Bailey LC, Nichols KE, Vakoc CR, Yao Y, Huang Z, Crispino JD, Hardison RC, Blobel GA, Weiss MJ. Graded Repression of PU.1/Sfpi1 gene transcription by GATA factors regulates hematopoietic cell fate. Blood 114, 983-94 (2009).

2008

Jing H, Vakoc CR, Mandat S, Wang H,  Zheng X, and Blobel GA. Exchange of GATA Factors Mediates Transitions in Looped Chromatin Organization at a Developmentally Regulated Gene Locus. Molecular Cell 29, 232-242 (2008).

Steger DJ, Lefterova MI, Stonestrom AJ, Schupp M, Zhuo D, Kim J, Chen J, Lazar MA, Blobel GA, and Vakoc CR. DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells. Molecular and Cellular Biology 28, 2825-39 (2008).

2004-2007

Gregory GD, Vakoc CR, Rozovskaia T, Zheng X, Patel S, Nakamura T, Canaani E, and Blobel GA. The ASH1L histone methyltransferase occupies the transcribed region of active mammalian genes. Molecular and Cellular Biology 27, 8466-8479 (2007).

Yao Zeng P, Vakoc CR, Blobel GA, Berger SL. In vivo dual cross-linking for identification of indirect DNA-associated proteins by chromatin immunoprecipitation. Biotechniques 41, 694-698 (2006).

Vakoc CR, Sachdeva MM, Wang H, Blobel GA. A profile of histone lysine methylation across transcribed mammalian chromatin. Molecular and Cellular Biology 26, 9185-9195 (2006).

Lamonica J*, Vakoc CR*, Blobel GA. Acetylation of GATA-1 is required for chromatin occupancy. Blood 108, 3736-3738 (2006). * Equal Contribution

Vakoc CR, Mandat SA, Olenchock BA, Blobel GA. Histone H3 lysine 9 methylation and HP1γ are associated with transcription elongation through mammalian chromatin. Molecular Cell 19, 381-91 (2005).

Hong W, Nakazawa M, Chen YY, Kori R, Vakoc CR, Rakowski C, Blobel GA. FOG-1 recruits the NuRD repressor complex to mediate transcriptional repression by GATA-1. EMBO Journal 24, 2367-78 (2005).

Vakoc CR, Letting DL, Gheldof N, Sawado T, Bender MA, Groudine M, Weiss MJ, Dekker J, Blobel GA. Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Molecular Cell 17, 453-62 (2005)

Welch JJ, Watts JA, Vakoc CR, Yao Y, Wang H, Hardison RC, Blobel GA, Chodosh LA, Weiss MJ. Global regulation of erythroid gene expression by transcription factor GATA-1. Blood 104, 3136-47 (2004).