Cancer Cell Biology Program

The DF/HCC Cancer Cell Biology Program utilizes molecular, biochemical, and cell-based approaches to better understand cancer pathogenesis and to apply this knowledge to cancer therapeutics. The Program facilitates collaborations that funnel basic discoveries into the clinic or mine observations made in the clinic for fundamental discoveries. The Program fosters member collaborations with clinical and translational researchers who bring in-depth knowledge of the clinical features of specific diseases. Members have procured numerous collaborative grants, published a significant number of collaborative papers, and partnered with the clinical investigators and pharmaceutical industry to initiate multiple preclinical studies.

Efforts to achieve the Program’s specific aims are focused on functionalizing the cancer genome, which includes detailed mechanistic studies that build upon the wealth of new genomic information to investigate cancer signaling mechanisms, and the development of new systems-level technologies that enable the analysis of these pathways. Currently, there are more than 100 members of the Cancer Cell Biology Program.

Jovanović B, Temko D, Stevens LE, Seehawer M, Fassl A, Murphy K, Anand J, Garza K, Gulvady A, Qiu X, Harper NW, Daniels VW, Xiao-Yun H, Ge JY, Alečković M, Pyrdol J, Hinohara K, Egri SB, Papanastasiou M, Vadhi R, Font-Tello A, Witwicki R, Peluffo G, Trinh A, Shu S, Diciaccio B, Ekram MB, Subedee A, Herbert ZT, Wucherpfennig KW, Letai AG, Jaffe JD, Sicinski P, Brown M, Dillon D, Long HW, Michor F, Polyak K. Heterogeneity and transcriptional drivers of triple-negative breast cancer. Cell Rep 2023; 42:113564. PubMed
Jiang C, Liu J, He S, Xu W, Huang R, Pan W, Li X, Dai X, Guo J, Zhang T, Inuzuka H, Wang P, Asara JM, Xiao J, Wei W. PRMT1 orchestrates with SAMTOR to govern mTORC1 methionine sensing via Arg-methylation of NPRL2. Cell Metab 2023; 35:2183-2199.e7. PubMed
Devant P, Dong Y, Mintseris J, Ma W, Gygi SP, Wu H, Kagan JC. Structural insights into cytokine cleavage by inflammatory caspase-4. Nature 2023. PubMed
Linder SJ, Bernasocchi T, Martínez-Pastor B, Sullivan KD, Galbraith MD, Lewis CA, Ferrer CM, Boon R, Silveira GG, Cho HM, Vidoudez C, Shroff S, Oliveira-Costa JP, Ross KN, Massri R, Matoba Y, Kim E, Rueda BR, Stott SL, Gottlieb E, Espinosa JM, Mostoslavsky R. Inhibition of the proline metabolism rate-limiting enzyme P5CS allows proliferation of glutamine-restricted cancer cells. Nat Metab 2023. PubMed
Martin BJE, Ablondi EF, Goglia C, Mimoso CA, Espinel-Cabrera PR, Adelman K. Global identification of SWI/SNF targets reveals compensation by EP400. Cell 2023; 186:5290-5307.e26. PubMed
Patil A, Strom AR, Paulo JA, Collings CK, Ruff KM, Shinn MK, Sankar A, Cervantes KS, Wauer T, St Laurent JD, Xu G, Becker LA, Gygi SP, Pappu RV, Brangwynne CP, Kadoch C. A disordered region controls cBAF activity via condensation and partner recruitment. Cell 2023; 186:4936-4955.e26. PubMed
Timms RT, Mena EL, Leng Y, Li MZ, Tchasovnikarova IA, Koren I, Elledge SJ. Defining E3 ligase-substrate relationships through multiplex CRISPR screening. Nat Cell Biol 2023. PubMed
Walsh RM, Rawson S, Schnell HM, Velez B, Rajakumar T, Hanna J. Structure of the preholoproteasome reveals late steps in proteasome core particle biogenesis. Nat Struct Mol Biol 2023. PubMed
Gu X, Nardone C, Kamitaki N, Mao A, Elledge SJ, Greenberg ME. The midnolin-proteasome pathway catches proteins for ubiquitination-independent degradation. Science 2023; 381:eadh5021. PubMed
Lim Y, Tamayo-Orrego L, Schmid E, Tarnauskaite Z, Kochenova OV, Gruar R, Muramatsu S, Lynch L, Schlie AV, Carroll PL, Chistol G, Reijns MAM, Kanemaki MT, Jackson AP, Walter JC. In silico protein interaction screening uncovers DONSON's role in replication initiation. Science 2023; 381:eadi3448. PubMed
Lipper CH, Egan ED, Gabriel KH, Blacklow SC. Structural basis for membrane-proximal proteolysis of substrates by ADAM10. Cell 2023; 186:3632-3641.e10. PubMed

Valencia AM, Sankar A, van der Sluijs PJ, Satterstrom FK, Fu J, Talkowski ME, Vergano SAS, Santen GWE, Kadoch C. Landscape of mSWI/SNF chromatin remodeling complex perturbations in neurodevelopmental disorders. Nat Genet 2023; 55:1400-1412. PubMed
Mitchell MM, Leng Y, Boppana S, Britt WJ, Gutierrez Sanchez LH, Elledge SJ. Signatures of AAV-2 immunity are enriched in children with severe acute hepatitis of unknown etiology. Sci Transl Med 2023; 15:eadh9917. PubMed
Hoetker MS, Yagi M, Di Stefano B, Langerman J, Cristea S, Wong LP, Huebner AJ, Charlton J, Deng W, Haggerty C, Sadreyev RI, Meissner A, Michor F, Plath K, Hochedlinger K. H3K36 methylation maintains cell identity by regulating opposing lineage programmes. Nat Cell Biol 2023; 25:1121-1134. PubMed
Hogstrom JM, Cruz KA, Selfors LM, Ward MN, Mehta TS, Kanarek N, Philips J, Dialani V, Wulf G, Collins LC, Patel JM, Muranen T. Simultaneous isolation of hormone receptor positive breast cancer organoids and fibroblasts reveals stroma-mediated resistance mechanisms. J Biol Chem 2023. PubMed
Zhang T, Xu D, Liu J, Wang M, Duan LJ, Liu M, Meng H, Zhuang Y, Wang H, Wang Y, Lv M, Zhang Z, Hu J, Shi L, Guo R, Xie X, Liu H, Erickson E, Wang Y, Yu W, Dang F, Guan D, Jiang C, Dai X, Inuzuka H, Yan P, Wang J, Babuta M, Lian G, Tu Z, Miao J, Szabo G, Fong GH, Karnoub AE, Lee YR, Pan L, Kaelin WG, Yuan J, Wei W. Prolonged hypoxia alleviates prolyl hydroxylation-mediated suppression of RIPK1 to promote necroptosis and inflammation. Nat Cell Biol 2023. PubMed
Zhang T, Xu D, Trefts E, Lv M, Inuzuka H, Song G, Liu M, Lu J, Liu J, Chu C, Wang M, Wang H, Meng H, Liu H, Zhuang Y, Xie X, Dang F, Guan D, Men Y, Jiang S, Jiang C, Dai X, Liu J, Wang Z, Yan P, Wang J, Tu Z, Babuta M, Erickson E, Hillis AL, Dibble CC, Asara JM, Szabo G, Sicinski P, Miao J, Lee YR, Pan L, Shaw RJ, Yuan J, Wei W. Metabolic orchestration of cell death by AMPK-mediated phosphorylation of RIPK1. Science 2023; 380:1372-1380. PubMed
Lin JR, Chen YA, Campton D, Cooper J, Coy S, Yapp C, Tefft JB, McCarty E, Ligon KL, Rodig SJ, Reese S, George T, Santagata S, Sorger PK. High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers. 2023. PubMed
Guo H, Vuille JA, Wittner BS, Lachtara EM, Hou Y, Lin M, Zhao T, Raman AT, Russell HC, Reeves BA, Pleskow HM, Wu CL, Gnirke A, Meissner A, Efstathiou JA, Lee RJ, Toner M, Aryee MJ, Lawrence MS, Miyamoto DT, Maheswaran S, Haber DA. DNA hypomethylation silences anti-tumor immune genes in early prostate cancer and CTCs. Cell 2023; 186:2765-2782.e28. PubMed
Elias K, Smyczynska U, Stawiski K, Nowicka Z, Webber J, Kaplan J, Landen C, Lubinski J, Mukhopadhyay A, Chakraborty D, Connolly DC, Symecko H, Domchek SM, Garber JE, Konstantinopoulos P, Fendler W, Chowdhury D. Identification of BRCA1/2 mutation female carriers using circulating microRNA profiles. Nat Commun 2023; 14:3350. PubMed
Griffin GK, Booth CAG, Togami K, Chung SS, Ssozi D, Verga JA, Bouyssou JM, Lee YS, Shanmugam V, Hornick JL, LeBoeuf NR, Morgan EA, Bernstein BE, Hovestadt V, van Galen P, Lane AA. Ultraviolet radiation shapes dendritic cell leukaemia transformation in the skin. Nature 2023; 618:834-841. PubMed
Papathanasiou S, Mynhier NA, Liu S, Brunette G, Stokasimov E, Jacob E, Li L, Comenho C, van Steensel B, Buenrostro JD, Zhang CZ, Pellman D. Heritable transcriptional defects from aberrations of nuclear architecture. Nature 2023; 619:184-192. PubMed
Gopal RK, Vantaku VR, Panda A, Reimer B, Rath S, To TL, Fisch AS, Cetinbas M, Livneh M, Calcaterra MJ, Gigliotti BJ, Pierce KA, Clish CB, Dias-Santagata D, Sadow PM, Wirth LJ, Daniels GH, Sadreyev RI, Calvo SE, Parangi S, Mootha VK. Effectors enabling adaptation to mitochondrial complex I loss in Hurthle cell carcinoma. 2023. PubMed
Skinner OS, Blanco-Fernández J, Goodman RP, Kawakami A, Shen H, Kemény LV, Joesch-Cohen L, Rees MG, Roth JA, Fisher DE, Mootha VK, Jourdain AA. Salvage of ribose from uridine or RNA supports glycolysis in nutrient-limited conditions. Nat Metab 2023; 5:765-776. PubMed
Zhang J, Simpson CM, Berner J, Chong HB, Fang J, Ordulu Z, Weiss-Sadan T, Possemato AP, Harry S, Takahashi M, Yang TY, Richter M, Patel H, Smith AE, Carlin AD, Hubertus de Groot AF, Wolf K, Shi L, Wei TY, Dürr BR, Chen NJ, Vornbäumen T, Wichmann NO, Mahamdeh MS, Pooladanda V, Matoba Y, Kumar S, Kim E, Bouberhan S, Oliva E, Rueda BR, Soberman RJ, Bardeesy N, Liau BB, Lawrence M, Stokes MP, Beausoleil SA, Bar-Peled L. Systematic identification of anticancer drug targets reveals a nucleus-to-mitochondria ROS-sensing pathway. Cell 2023; 186:2361-2379.e25. PubMed
Liu J, Bu X, Chu C, Dai X, Asara JM, Sicinski P, Freeman GJ, Wei W. PRMT1 mediated methylation of cGAS suppresses anti-tumor immunity. Nat Commun 2023; 14:2806. PubMed
Jones DTD, Dates AN, Rawson SD, Burruss MM, Lipper CH, Blacklow SC. Tethered agonist activated ADGRF1 structure and signalling analysis reveal basis for G protein coupling. Nat Commun 2023; 14:2490. PubMed
Yao CH, Park JS, Kurmi K, Hu SH, Notarangelo G, Crowley J, Jacobson H, Hui S, Sharpe AH, Haigis MC. Uncoupled glycerol-3-phosphate shuttle in kidney cancer reveals that cytosolic GPD is essential to support lipid synthesis. Mol Cell 2023; 83:1340-1349.e7. PubMed
Bergholz JS, Wang Q, Wang Q, Ramseier M, Prakadan S, Wang W, Fang R, Kabraji S, Zhou Q, Gray GK, Abell-Hart K, Xie S, Guo X, Gu H, Von T, Jiang T, Tang S, Freeman GJ, Kim HJ, Shalek AK, Roberts TM, Zhao JJ. PI3Kβ controls immune evasion in PTEN-deficient breast tumours. Nature 2023; 617:139-146. PubMed
Perurena N, Lock R, Davis RA, Raghavan S, Pilla NF, Ng R, Loi P, Guild CJ, Miller AL, Sicinska E, Cleary JM, Rubinson DA, Wolpin BM, Gray NS, Santagata S, Hahn WC, Morton JP, Sansom OJ, Aguirre AJ, Cichowski K. USP9X mediates an acute adaptive response to MAPK suppression in pancreatic cancer but creates multiple actionable therapeutic vulnerabilities. Cell Rep Med 2023; 4:101007. PubMed
Gungabeesoon J, Gort-Freitas NA, Kiss M, Bolli E, Messemaker M, Siwicki M, Hicham M, Bill R, Koch P, Cianciaruso C, Duval F, Pfirschke C, Mazzola M, Peters S, Homicsko K, Garris C, Weissleder R, Klein AM, Pittet MJ. A neutrophil response linked to tumor control in immunotherapy. Cell 2023; 186:1448-1464.e20. PubMed
Tkacik E, Li K, Gonzalez-Del Pino G, Ha BH, Vinals J, Park E, Beyett TS, Eck MJ. Structure and RAF family kinase isoform selectivity of type II RAF inhibitors tovorafenib and naporafenib. J Biol Chem 2023; 299:104634. PubMed
Chiasson-MacKenzie C, Vitte J, Liu CH, Wright EA, Flynn EA, Stott SL, Giovannini M, McClatchey AI. Cellular mechanisms of heterogeneity in NF2-mutant schwannoma. Nat Commun 2023; 14:1559. PubMed
Liu W, Wang Y, Bozi LHM, Fischer P, Jedrychowski MP, Xiao H, Wu T, Darabedian N, He X, Mills EL, Burger N, Shin S, Reddy A, Sprenger HG, Tran N, Winther S, Hinshaw SM, Shen J, Seo HS, Song K, Xu AZ, Sebastian L, Zhao J, Dhe-Paganon S, Che J, Gygi SP, Arthanari H, Chouchani ET. Lactate regulates cell cycle by remodeling the anaphase promoting complex. Nature 2023. PubMed
Chen JY, Hug C, Reyes J, Tian C, Gerosa L, Fröhlich F, Ponsioen B, Snippert HJG, Spencer SL, Jambhekar A, Sorger PK, Lahav G. Multi-range ERK responses shape the proliferative trajectory of single cells following oncogene induction. Cell Rep 2023; 42:112252. PubMed
Weiss-Sadan T, Ge M, Hayashi M, Gohar M, Yao CH, de Groot A, Harry S, Carlin A, Fischer H, Shi L, Wei TY, Adelmann CH, Wolf K, Vornbäumen T, Dürr BR, Takahashi M, Richter M, Zhang J, Yang TY, Vijay V, Fisher DE, Hata AN, Haigis MC, Mostoslavsky R, Bardeesy N, Papagiannakopoulos T, Bar-Peled L. NRF2 activation induces NADH-reductive stress, providing a metabolic vulnerability in lung cancer. Cell Metab 2023; 35:487-503.e7. PubMed
Darabedian N, Ji W, Fan M, Lin S, Seo HS, Vinogradova EV, Yaron TM, Mills EL, Xiao H, Senkane K, Huntsman EM, Johnson JL, Che J, Cantley LC, Cravatt BF, Dhe-Paganon S, Stegmaier K, Zhang T, Gray NS, Chouchani ET. Depletion of creatine phosphagen energetics with a covalent creatine kinase inhibitor. Nat Chem Biol 2023. PubMed
Matsuda S, Revandkar A, Dubash TD, Ravi A, Wittner BS, Lin M, Morris R, Burr R, Guo H, Seeger K, Szabolcs A, Che D, Nieman L, Getz GA, Ting DT, Lawrence MS, Gainor J, Haber DA, Maheswaran S. TGF-β in the microenvironment induces a physiologically occurring immune-suppressive senescent state. Cell Rep 2023; 42:112129. PubMed
Hunkeler M, Jin CY, Fischer ES. Structures of BIRC6-client complexes provide a mechanism of SMAC-mediated release of caspases. Science 2023; 379:1105-1111. PubMed
Chan WC, Liu X, Magin RS, Girardi NM, Ficarro SB, Hu W, Tarazona Guzman MI, Starnbach CA, Felix A, Adelmant G, Varca AC, Hu B, Bratt AS, DaSilva E, Schauer NJ, Jaen Maisonet I, Dolen EK, Ayala AX, Marto JA, Buhrlage SJ. Accelerating inhibitor discovery for deubiquitinating enzymes. Nat Commun 2023; 14:686. PubMed
Dai X, Jiang C, Jiang Q, Fang L, Yu H, Guo J, Yan P, Chi F, Zhang T, Inuzuka H, Asara JM, Wang P, Guo J, Wei W. AMPK-dependent phosphorylation of the GATOR2 component WDR24 suppresses glucose-mediated mTORC1 activation. Nat Metab 2023; 5:265-276. PubMed
Yu Q, Liu X, Keller MP, Navarrete-Perea J, Zhang T, Fu S, Vaites LP, Shuken SR, Schmid E, Keele GR, Li J, Huttlin EL, Rashan EH, Simcox J, Churchill GA, Schweppe DK, Attie AD, Paulo JA, Gygi SP. Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression. Nat Commun 2023; 14:555. PubMed
Lin JR, Wang S, Coy S, Chen YA, Yapp C, Tyler M, Nariya MK, Heiser CN, Lau KS, Santagata S, Sorger PK. Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer. Cell 2023; 186:363-381.e19. PubMed
Yaneva D, Sparks JL, Donsbach M, Zhao S, Weickert P, Bezalel-Buch R, Stingele J, Walter JC. The FANCJ helicase unfolds DNA-protein crosslinks to promote their repair. Mol Cell 2023; 83:43-56.e10. PubMed
Mitchell DC, Kuljanin M, Li J, Van Vranken JG, Bulloch N, Schweppe DK, Huttlin EL, Gygi SP. A proteome-wide atlas of drug mechanism of action. Nat Biotechnol 2023. PubMed
Cervia LD, Shibue T, Borah AA, Gaeta B, He L, Leung L, Li N, Moyer SM, Shim BH, Dumont N, Gonzalez A, Bick NR, Kazachkova M, Dempster JM, Krill-Burger JM, Piccioni F, Udeshi ND, Olive ME, Carr SA, Root DE, McFarland JM, Vazquez F, Hahn WC. A ubiquitination cascade regulating the integrated stress response and survival in carcinomas. 2022. PubMed
Hosios AM, Wilkinson ME, McNamara MC, Kalafut KC, Torrence ME, Asara JM, Manning BD. mTORC1 regulates a lysosome-dependent adaptive shift in intracellular lipid species. Nat Metab 2022; 4:1792-1811. PubMed
Alečković M, Cristea S, Gil Del Alcazar CR, Yan P, Ding L, Krop ED, Harper NW, Rojas Jimenez E, Lu D, Gulvady AC, Foidart P, Seehawer M, Diciaccio B, Murphy KC, Pyrdol J, Anand J, Garza K, Wucherpfennig KW, Tamimi RM, Michor F, Polyak K. Breast cancer prevention by short-term inhibition of TGFβ signaling. Nat Commun 2022; 13:7558. PubMed
Xiao H, Bozi LHM, Sun Y, Riley CL, Philip VM, Chen M, Li J, Zhang T, Mills EL, Emont MP, Sun W, Reddy A, Garrity R, Long J, Becher T, Vitas LP, Laznik-Bogoslavski D, Ordonez M, Liu X, Chen X, Wang Y, Liu W, Tran N, Liu Y, Zhang Y, Cypess AM, White AP, He Y, Deng R, Schöder H, Paulo JA, Jedrychowski MP, Banks AS, Tseng YH, Cohen P, Tsai LT, Rosen ED, Klein S, Chondronikola M, McAllister FE, Van Bruggen N, Huttlin EL, Spiegelman BM, Churchill GA, Gygi SP, Chouchani ET. Architecture of the outbred brown fat proteome defines regulators of metabolic physiology. Cell 2022. PubMed
Kochenova OV, Mukkavalli S, Raman M, Walter JC. Cooperative assembly of p97 complexes involved in replication termination. Nat Commun 2022; 13:6591. PubMed
Panditharatna E, G Marques J, Wang T, Trissal MC, Liu I, Jiang L, Beck A, Groves A, Dharia NV, Li D, Hoffman SE, Kugener G, Shaw ML, Mire HM, Hack OA, Dempster JM, Lareau C, Dai L, Sigua LH, Quezada MA, Stanton AJ, Wyatt M, Kalani Z, Goodale A, Vazquez F, Piccioni F, Doench JG, Root DE, Anastas JN, Jones KL, Saur Conway A, Stopka S, Regan MS, Liang Y, Seo HS, Song K, Bashyal P, Jerome WP, Mathewson ND, Dhe-Paganon S, Suva ML, Carcaboso AM, Lavarino C, Mora J, Nguyen QD, Ligon KL, Shi Y, Agnihotri S, Agar NYR, Stegmaier K, Stiles CD, Monje M, Golub TR, Qi J, Filbin MG. BAF complex maintains glioma stem cells in pediatric H3K27M-glioma. 2022. PubMed
Wohlrab H, Signoretti S, Rameh LE, DeConti DK, Hansen SH. Mitochondrial transporter expression patterns distinguish tumor from normal tissue and identify cancer subtypes with different survival and metabolism. Sci Rep 2022; 12:17035. PubMed
Prew MS, Adhikary U, Choi DW, Portero EP, Paulo JA, Gowda P, Budhraja A, Opferman JT, Gygi SP, Danial NN, Walensky LD. MCL-1 is a master regulator of cancer dependency on fatty acid oxidation. Cell Rep 2022; 41:111445. PubMed
Notarangelo G, Spinelli JB, Perez EM, Baker GJ, Kurmi K, Elia I, Stopka SA, Baquer G, Lin JR, Golby AJ, Joshi S, Baron HF, Drijvers JM, Georgiev P, Ringel AE, Zaganjor E, McBrayer SK, Sorger PK, Sharpe AH, Wucherpfennig KW, Santagata S, Agar NYR, Suvà ML, Haigis MC. Oncometabolite d-2HG alters T cell metabolism to impair CD8 T cell function. Science 2022; 377:1519-1529. PubMed
Kwon JJ, Hajian B, Bian Y, Young LC, Amor AJ, Fuller JR, Fraley CV, Sykes AM, So J, Pan J, Baker L, Lee SJ, Wheeler DB, Mayhew DL, Persky NS, Yang X, Root DE, Barsotti AM, Stamford AW, Perry CK, Burgin A, McCormick F, Lemke CT, Hahn WC, Aguirre AJ. Structure-function analysis of the SHOC2-MRAS-PP1C holophosphatase complex. Nature 2022. PubMed
Elia I, Rowe JH, Johnson S, Joshi S, Notarangelo G, Kurmi K, Weiss S, Freeman GJ, Sharpe AH, Haigis MC. Tumor cells dictate anti-tumor immune responses by altering pyruvate utilization and succinate signaling in CD8 T cells. Cell Metab 2022; 34:1137-1150.e6. PubMed
Haque F, Freniere C, Ye Q, Mani N, Wilson-Kubalek EM, Ku PI, Milligan RA, Subramanian R. Cytoskeletal regulation of a transcription factor by DNA mimicry via coiled-coil interactions. Nat Cell Biol 2022. PubMed
Yasuhara T, Xing YH, Bauer NC, Lee L, Dong R, Yadav T, Soberman RJ, Rivera MN, Zou L. Condensates induced by transcription inhibition localize active chromatin to nucleoli. Mol Cell 2022. PubMed
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Suski JM, Ratnayeke N, Braun M, Zhang T, Strmiska V, Michowski W, Can G, Simoneau A, Snioch K, Cup M, Sullivan CM, Wu X, Nowacka J, Branigan TB, Pack LR, DeCaprio JA, Geng Y, Zou L, Gygi SP, Walter JC, Meyer T, Sicinski P. CDC7-independent G1/S transition revealed by targeted protein degradation. Nature 2022; 605:357-365. PubMed
Schapiro D, Sokolov A, Yapp C, Chen YA, Muhlich JL, Hess J, Creason AL, Nirmal AJ, Baker GJ, Nariya MK, Lin JR, Maliga Z, Jacobson CA, Hodgman MW, Ruokonen J, Farhi SL, Abbondanza D, McKinley ET, Persson D, Betts C, Sivagnanam S, Regev A, Goecks J, Coffey RJ, Coussens LM, Santagata S, Sorger PK. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nat Methods 2022; 19:311-315. PubMed
Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA, , Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK. MITI minimum information guidelines for highly multiplexed tissue images. Nat Methods 2022; 19:262-267. PubMed
Huang P, Wierbowski BM, Lian T, Chan C, García-Linares S, Jiang J, Salic A. Structural basis for catalyzed assembly of the Sonic hedgehog-Patched1 signaling complex. Dev Cell 2022; 57:670-685.e8. PubMed
Liu J, Tokheim C, Lee JD, Gan W, North BJ, Liu XS, Pandolfi PP, Wei W. Genetic fusions favor tumorigenesis through degron loss in oncogenes. Nat Commun 2021; 12:6704. PubMed
Nirmal AJ, Maliga Z, Vallius T, Quattrochi B, Chen AA, Jacobson CA, Pelletier RJ, Yapp C, Arias-Camison R, Chen YA, Lian CG, Murphy GF, Santagata S, Sorger PK. The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution. 2022. PubMed
Ji Z, Li H, Peterle D, Paulo JA, Ficarro SB, Wales TE, Marto JA, Gygi SP, Engen JR, Rapoport TA. Translocation of polyubiquitinated protein substrates by the hexameric Cdc48 ATPase. Mol Cell 2022; 82:570-584.e8. PubMed
Kim M, Ly SH, Xie Y, Duronio GN, Ford-Roshon D, Hwang JH, Sulahian R, Rennhack JP, So J, Gjoerup O, Talamas JA, Grandclaudon M, Long HW, Doench JG, Sethi NS, Giannakis M, Hahn WC. YAP1 and PRDM14 converge to promote cell survival and tumorigenesis. Dev Cell 2022; 57:212-227.e8. PubMed
Dai X, Zhang X, Yin Q, Hu J, Guo J, Gao Y, Snell AH, Inuzuka H, Wan L, Wei W. Acetylation-dependent regulation of BRAF oncogenic function. Cell Rep 2022; 38:110250. PubMed
Wang Y, Wang M, Djekidel MN, Chen H, Liu D, Alt FW, Zhang Y. eccDNAs are apoptotic products with high innate immunostimulatory activity. Nature 2021; 599:308-314. PubMed
Durbin AD, Wang T, Wimalasena VK, Zimmerman MW, Li D, Dharia NV, Mariani L, Shendy NAM, Nance S, Patel AG, Shao Y, Mundada M, Maxham L, Park PMC, Sigua LH, Morita K, Saur Conway A, Robichaud AL, Perez-Atayde AR, Bikowitz MJ, Quinn TR, Wiest OG, Easton J, Schonbrunn E, Bulyk ML, Abraham BJ, Stegmaier K, Look AT, Qi J. EP300 selectively controls the enhancer landscape of MYCN-amplified neuroblastoma. 2021. PubMed
Shimizu K, Gi M, Suzuki S, North BJ, Watahiki A, Fukumoto S, Asara JM, Tokunaga F, Wei W, Inuzuka H. Interplay between protein acetylation and ubiquitination controls MCL1 protein stability. Cell Rep 2021; 37:109988. PubMed
Dempsey DR, Viennet T, Iwase R, Park E, Henriquez S, Chen Z, Jeliazkov JR, Palanski BA, Phan KL, Coote P, Gray JJ, Eck MJ, Gabelli SB, Arthanari H, Cole PA. The structural basis of PTEN regulation by multi-site phosphorylation. Nat Struct Mol Biol 2021; 28:858-868. PubMed
Guo H, Golczer G, Wittner BS, Langenbucher A, Zachariah M, Dubash TD, Hong X, Comaills V, Burr R, Ebright RY, Horwitz E, Vuille JA, Hajizadeh S, Wiley DF, Reeves BA, Zhang JM, Niederhoffer KL, Lu C, Wesley B, Ho U, Nieman LT, Toner M, Vasudevan S, Zou L, Mostoslavsky R, Maheswaran S, Lawrence MS, Haber DA. NR4A1 regulates expression of immediate early genes, suppressing replication stress in cancer. Mol Cell 2021; 81:4041-4058.e15. PubMed
Papathanasiou S, Markoulaki S, Blaine LJ, Leibowitz ML, Zhang CZ, Jaenisch R, Pellman D. Whole chromosome loss and genomic instability in mouse embryos after CRISPR-Cas9 genome editing. Nat Commun 2021; 12:5855. PubMed
Dang F, Nie L, Zhou J, Shimizu K, Chu C, Wu Z, Fassl A, Ke S, Wang Y, Zhang J, Zhang T, Tu Z, Inuzuka H, Sicinski P, Bass AJ, Wei W. Inhibition of CK1ε potentiates the therapeutic efficacy of CDK4/6 inhibitor in breast cancer. Nat Commun 2021; 12:5386. PubMed
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Cancer Cell Biology Program

Recent Publications

Leadership

Wade Harper, PhD

Raul Mostoslavsky, MD, PhD

Kornelia Polyak, MD, PhD