Cancer Genetics and Epigenetics Program

The DF/HCC Cancer Genetics Program seeks to expand the understanding of the genetic underpinnings of cancer development and to use this information to improve cancer patient care. Its research ranges from basic to translational to clinical.

Areas of particular strength within the Program include analysis of the cancer genome on a broad scale, cancer stem cell studies, functional genomics screens to identify critical oncogenic pathways, GWAS studies for identification of low-risk alleles and studies of functional mechanisms of such alleles, and provision of cancer mutation analyses by CLIA-certified laboratories among DF/HCC institutions. Advancements by the Program’s more than 100 members have impacted cancer research in genetics nationally and internationally.

Iliopoulos O, Iversen AB, Narayan V, Maughan BL, Beckermann KE, Oudard S, Else T, Maranchie JK, Goldberg CM, Fu W, Perini RF, Liu Y, Linehan WM, Srinivasan R, Jonasch E. Belzutifan for patients with von Hippel-Lindau disease-associated CNS haemangioblastomas (LITESPARK-004): a multicentre, single-arm, phase 2 study. Lancet Oncol. 2024. PubMed
Kuru E, Rittichier J, de Puig H, Flores A, Rout S, Han I, Reese AE, Bartlett TM, De Moliner F, Bernier SG, Galpin JD, Marchand J, Bedell W, Robinson-McCarthy L, Ahern CA, Bernhardt TG, Rudner DZ, Collins JJ, Vendrell M, Church GM. Rapid discovery and evolution of nanosensors containing fluorogenic amino acids. Nat Commun 2024; 15:7531. PubMed
Rauh U, Wei G, Serrano-Wu M, Kosmidis G, Kaulfuss S, Siegel F, Thede K, McFarland J, Lemke CT, Werbeck N, Nowak-Reppel K, Pilari S, Menz S, Ocker M, Zhang W, Davis K, Poncet-Montange G, Roth J, Daniels D, Kaushik VK, Hubbard B, Ziegelbauer K, Golub TR. BRD-810 is a highly selective MCL1 inhibitor with optimized in vivo clearance and robust efficacy in solid and hematological tumor models. 2024. PubMed
Achom M, Sadagopan A, Bao C, McBride F, Li J, Konda P, Tourdot RW, Xu Q, Nakhoul M, Gallant DS, Ahmed UA, O'Toole J, Freeman D, Lee GM, Hecht JL, Kauffman EC, Einstein DJ, Choueiri TK, Zhang CZ, Viswanathan SR. A genetic basis for sex differences in Xp11 translocation renal cell carcinoma. Cell 2024. PubMed
Loi P, Schade AE, Rodriguez CL, Krishnan A, Perurena N, Nguyen VTM, Xu Y, Watanabe M, Davis RA, Gardner A, Pilla NF, Mattioli K, Popow O, Gunduz N, Lannagan TRM, Fitzgerald S, Sicinska ET, Lin JR, Tan W, Brais LK, Haigis KM, Giannakis M, Ng K, Santagata S, Helin K, Sansom OJ, Cichowski K. Epigenetic and oncogenic inhibitors cooperatively drive differentiation and kill KRAS-mutant colorectal cancers. 2024. PubMed
Forrest SJ, Gupta H, Ward A, Li YY, Doan D, Al-Ibraheemi A, Alexandrescu S, Bandopadhayay P, Shusterman S, Mullen EA, Collins NB, Chi SN, Wright KD, Kumari P, Mazor T, Ligon KL, Shivdasani P, Manam M, MacConaill LE, Ceca E, Benich SN, London WB, Schilsky RL, Bruinooge SS, Guidry Auvil JM, Cerami E, Rollins BJ, Meyerson ML, Lindeman NI, Johnson BE, Cherniak AD, Church AJ, Janeway KA. Molecular profiling of 888 pediatric tumors informs future precision trials and data-sharing initiatives in pediatric cancer. Nat Commun 2024; 15:5837. PubMed
Ryu J, Barkal S, Yu T, Jankowiak M, Zhou Y, Francoeur M, Phan QV, Li Z, Tognon M, Brown L, Love MI, Bhat V, Lettre G, Ascher DB, Cassa CA, Sherwood RI, Pinello L. Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. Nat Genet 2024; 56:925-937. PubMed
Huang HT, Lumpkin RJ, Tsai RW, Su S, Zhao X, Xiong Y, Chen J, Mageed N, Donovan KA, Fischer ES, Sellers WR. Ubiquitin-specific proximity labeling for the identification of E3 ligase substrates. Nat Chem Biol 2024. PubMed
Lappalainen T, Li YI, Ramachandran S, Gusev A. Genetic and molecular architecture of complex traits. Cell 2024; 187:1059-1075. PubMed
Watson EV, Lee JJ, Gulhan DC, Melloni GEM, Venev SV, Magesh RY, Frederick A, Chiba K, Wooten EC, Naxerova K, Dekker J, Park PJ, Elledge SJ. Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns. Nat Genet 2024. PubMed
Jin H, Gulhan DC, Geiger B, Ben-Isvy D, Geng D, Ljungström V, Park PJ. Accurate and sensitive mutational signature analysis with MuSiCal. Nat Genet 2024; 56:541-552. PubMed

Moqri M, Herzog C, Poganik JR, Ying K, Justice JN, Belsky DW, Higgins-Chen AT, Chen BH, Cohen AA, Fuellen G, Hägg S, Marioni RE, Widschwendter M, Fortney K, Fedichev PO, Zhavoronkov A, Barzilai N, Lasky-Su J, Kiel DP, Kennedy BK, Cummings S, Slagboom PE, Verdin E, Maier AB, Sebastiano V, Snyder MP, Gladyshev VN, Horvath S, Ferrucci L. Validation of biomarkers of aging. Nat Med 2024; 30:360-372. PubMed
Xu J, Liu Y, Yang F, Cao Y, Chen W, Li JSS, Zhang S, Comjean A, Hu Y, Perrimon N. Mechanistic characterization of a Drosophila model of paraneoplastic nephrotic syndrome. Nat Commun 2024; 15:1241. PubMed
Weng C, Yu F, Yang D, Poeschla M, Liggett LA, Jones MG, Qiu X, Wahlster L, Caulier A, Hussmann JA, Schnell A, Yost KE, Koblan LW, Martin-Rufino JD, Min J, Hammond A, Ssozi D, Bueno R, Mallidi H, Kreso A, Escabi J, Rideout WM, Jacks T, Hormoz S, van Galen P, Weissman JS, Sankaran VG. Deciphering cell states and genealogies of human haematopoiesis. Nature 2024; 627:389-398. PubMed
Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sánchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Işik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Götte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS. Structures, functions, and adaptations of the human LINE-1 ORF2 protein. Nature 2023. PubMed
Dezfulian MH, Kula T, Pranzatelli T, Kamitaki N, Meng Q, Khatri B, Perez P, Xu Q, Chang A, Kohlgruber AC, Leng Y, Jupudi AA, Joachims ML, Chiorini JA, Lessard CJ, Darise Farris A, Muthuswamy SK, Warner BM, Elledge SJ. TScan-II: A genome-scale platform for the de novo identification of CD4 T cell epitopes. Cell 2023; 186:5569-5586.e21. PubMed
Huschner F, Głowacka-Walas J, Mills JD, Klonowska K, Lasseter K, Asara JM, Moavero R, Hertzberg C, Weschke B, Riney K, Feucht M, Scholl T, Krsek P, Nabbout R, Jansen AC, Petrák B, van Scheppingen J, Zamecnik J, Iyer A, Anink JJ, Mühlebner A, Mijnsbergen C, Lagae L, Curatolo P, Borkowska J, Sadowski K, Domańska-Pakieła D, Blazejczyk M, Jansen FE, Janson S, Urbanska M, Tempes A, Janssen B, Sijko K, Wojdan K, Jozwiak S, Kotulska K, Lehmann K, Aronica E, Jaworski J, Kwiatkowski DJ. Molecular EPISTOP, a comprehensive multi-omic analysis of blood from Tuberous Sclerosis Complex infants age birth to two years. Nat Commun 2023; 14:7664. PubMed
Hu Y, Salgado Figueroa D, Zhang Z, Veselits M, Bhattacharyya S, Kashiwagi M, Clark MR, Morgan BA, Ay F, Georgopoulos K. Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS. Cell 2023; 186:5269-5289.e22. PubMed
Du H, Yang YC, Liu HJ, Yuan M, Asara JM, Wong KK, Henske EP, Singh M, Kwiatkowski DJ. Bi-steric mTORC1 inhibitors induce apoptotic cell death in tumor models with hyperactivated mTORC1. J Clin Invest 2023. PubMed
Baca SC, Seo JH, Davidsohn MP, Fortunato B, Semaan K, Sotudian S, Lakshminarayanan G, Diossy M, Qiu X, El Zarif T, Savignano H, Canniff J, Madueke I, Saliby RM, Zhang Z, Li R, Jiang Y, Taing L, Awad M, Chau CH, DeCaprio JA, Figg WD, Greten TF, Hata AN, Hodi FS, Hughes ME, Ligon KL, Lin N, Ng K, Oser MG, Meador C, Parsons HA, Pomerantz MM, Rajan A, Ritz J, Thakuria M, Tolaney SM, Wen PY, Long H, Berchuck JE, Szallasi Z, Choueiri TK, Freedman ML. Liquid biopsy epigenomic profiling for cancer subtyping. Nat Med 2023; 29:2737-2741. PubMed
Li L, Bowling S, McGeary SE, Yu Q, Lemke B, Alcedo K, Jia Y, Liu X, Ferreira M, Klein AM, Wang SW, Camargo FD. A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells. Cell 2023; 186:5183-5199.e22. 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
Chang L, Jung NY, Atari A, Rodriguez DJ, Kesar D, Song TY, Rees MG, Ronan M, Li R, Ruiz P, Chaturantabut S, Ito T, van Tienen LM, Tseng YY, Roth JA, Sellers WR. Systematic profiling of conditional pathway activation identifies context-dependent synthetic lethalities. Nat Genet 2023; 55:1709-1720. PubMed
Taylor MS, Wu C, Fridy PC, Zhang SJ, Senussi Y, Wolters JC, Cajuso T, Cheng WC, Heaps JD, Miller BD, Mori K, Cohen L, Jiang H, Molloy KR, Chait BT, Goggins MG, Bhan I, Franses JW, Yang X, Taplin ME, Wang X, Christiani DC, Johnson BE, Meyerson M, Uppaluri R, Egloff AM, Denault EN, Spring LM, Wang TL, Shih IM, Fairman JE, Jung E, Arora KS, Yilmaz OH, Cohen S, Sharova T, Chi G, Norden BL, Song Y, Nieman LT, Pappas L, Parikh AR, Strickland MR, Corcoran RB, Mustelin T, Eng G, Yilmaz OH, Matulonis UA, Skates SJ, Rueda BR, Drapkin R, Klempner SJ, Deshpande V, Ting DT, Rout MP, LaCava J, Walt DR, Burns KH. Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker. 2023. PubMed
Brown DW, Cato LD, Zhao Y, Nandakumar SK, Bao EL, Gardner EJ, Hubbard AK, DePaulis A, Rehling T, Song L, Yu K, Chanock SJ, Perry JRB, Sankaran VG, Machiela MJ. Shared and distinct genetic etiologies for different types of clonal hematopoiesis. Nat Commun 2023; 14:5536. PubMed
Spisak S, Tisza V, Nuzzo PV, Seo JH, Pataki B, Ribli D, Sztupinszki Z, Bell C, Rohanizadegan M, Stillman DR, Alaiwi SA, Bartels AB, Papp M, Shetty A, Abbasi F, Lin X, Lawrenson K, Gayther SA, Pomerantz M, Baca S, Solymosi N, Csabai I, Szallasi Z, Gusev A, Freedman ML. A biallelic multiple nucleotide length polymorphism explains functional causality at 5p15.33 prostate cancer risk locus. Nat Commun 2023; 14:5118. PubMed
Geffen Y, Anand S, Akiyama Y, Yaron TM, Song Y, Johnson JL, Govindan A, Babur Ö, Li Y, Huntsman E, Wang LB, Birger C, Heiman DI, Zhang Q, Miller M, Maruvka YE, Haradhvala NJ, Calinawan A, Belkin S, Kerelsky A, Clauser KR, Krug K, Satpathy S, Payne SH, Mani DR, Gillette MA, Dhanasekaran SM, Thiagarajan M, Mesri M, Rodriguez H, Robles AI, Carr SA, Lazar AJ, Aguet F, Cantley LC, Ding L, Getz G, . Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation. Cell 2023; 186:3945-3967.e26. PubMed
Li Y, Porta-Pardo E, Tokheim C, Bailey MH, Yaron TM, Stathias V, Geffen Y, Imbach KJ, Cao S, Anand S, Akiyama Y, Liu W, Wyczalkowski MA, Song Y, Storrs EP, Wendl MC, Zhang W, Sibai M, Ruiz-Serra V, Liang WW, Terekhanova NV, Rodrigues FM, Clauser KR, Heiman DI, Zhang Q, Aguet F, Calinawan AP, Dhanasekaran SM, Birger C, Satpathy S, Zhou DC, Wang LB, Baral J, Johnson JL, Huntsman EM, Pugliese P, Colaprico A, Iavarone A, Chheda MG, Ricketts CJ, Fenyö D, Payne SH, Rodriguez H, Robles AI, Gillette MA, Kumar-Sinha C, Lazar AJ, Cantley LC, Getz G, Ding L, . Pan-cancer proteogenomics connects oncogenic drivers to functional states. Cell 2023; 186:3921-3944.e25. PubMed
Konda P, Garinet S, Van Allen EM, Viswanathan SR. Genome-guided discovery of cancer therapeutic targets. Cell Rep 2023; 42:112978. PubMed
Moon I, LoPiccolo J, Baca SC, Sholl LM, Kehl KL, Hassett MJ, Liu D, Schrag D, Gusev A. Machine learning for genetics-based classification and treatment response prediction in cancer of unknown primary. Nat Med 2023; 29:2057-2067. PubMed
Wang L, Trasanidis N, Wu T, Dong G, Hu M, Bauer DE, Pinello L. Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics. Nat Methods 2023; 20:1368-1378. PubMed
Isozaki H, Sakhtemani R, Abbasi A, Nikpour N, Stanzione M, Oh S, Langenbucher A, Monroe S, Su W, Cabanos HF, Siddiqui FM, Phan N, Jalili P, Timonina D, Bilton S, Gomez-Caraballo M, Archibald HL, Nangia V, Dionne K, Riley A, Lawlor M, Banwait MK, Cobb RG, Zou L, Dyson NJ, Ott CJ, Benes C, Getz G, Chan CS, Shaw AT, Gainor JF, Lin JJ, Sequist LV, Piotrowska Z, Yeap BY, Engelman JA, Lee JJ, Maruvka YE, Buisson R, Lawrence MS, Hata AN. Therapy-induced APOBEC3A drives evolution of persistent cancer cells. Nature 2023. PubMed
Shui B, Beyett TS, Chen Z, Li X, La Rocca G, Gazlay WM, Eck MJ, Lau KS, Ventura A, Haigis KM. Oncogenic K-Ras suppresses global miRNA function. Mol Cell 2023. PubMed
Qi M, Pang J, Mitsiades I, Lane AA, Rheinbay E. Loss of chromosome Y in primary tumors. Cell 2023. PubMed
Shih J, Sarmashghi S, Zhakula-Kostadinova N, Zhang S, Georgis Y, Hoyt SH, Cuoco MS, Gao GF, Spurr LF, Berger AC, Ha G, Rendo V, Shen H, Meyerson M, Cherniack AD, Taylor AM, Beroukhim R. Cancer aneuploidies are shaped primarily by effects on tumour fitness. Nature 2023. PubMed
Liang J, Yu D, Luo C, Bennett C, Jedrychowski M, Gygi SP, Widlund HR, Puigserver P. Epigenetic suppression of PGC1α (PPARGC1A) causes collateral sensitivity to HMGCR-inhibitors within BRAF-treatment resistant melanomas. Nat Commun 2023; 14:3251. PubMed
Xu C, Xu J, Tang HW, Ericsson M, Weng JH, DiRusso J, Hu Y, Ma W, Asara JM, Perrimon N. A phosphate-sensing organelle regulates phosphate and tissue homeostasis. Nature 2023; 617:798-806. PubMed
Janizek JD, Dincer AB, Celik S, Chen H, Chen W, Naxerova K, Lee SI. Uncovering expression signatures of synergistic drug responses via ensembles of explainable machine-learning models. Nat Biomed Eng 2023; 7:811-829. PubMed
Leshchiner I, Mroz EA, Cha J, Rosebrock D, Spiro O, Bonilla-Velez J, Faquin WC, Lefranc-Torres A, Lin DT, Michaud WA, Getz G, Rocco JW. Inferring early genetic progression in cancers with unobtainable premalignant disease. 2023; 4:550-563. PubMed
Otto JE, Ursu O, Wu AP, Winter EB, Cuoco MS, Ma S, Qian K, Michel BC, Buenrostro JD, Berger B, Regev A, Kadoch C. Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens. Mol Cell 2023; 83:1350-1367.e7. PubMed
Ravi A, Hellmann MD, Arniella MB, Holton M, Freeman SS, Naranbhai V, Stewart C, Leshchiner I, Kim J, Akiyama Y, Griffin AT, Vokes NI, Sakhi M, Kamesan V, Rizvi H, Ricciuti B, Forde PM, Anagnostou V, Riess JW, Gibbons DL, Pennell NA, Velcheti V, Digumarthy SR, Mino-Kenudson M, Califano A, Heymach JV, Herbst RS, Brahmer JR, Schalper KA, Velculescu VE, Henick BS, Rizvi N, Jänne PA, Awad MM, Chow A, Greenbaum BD, Luksza M, Shaw AT, Wolchok J, Hacohen N, Getz G, Gainor JF. Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer. Nat Genet 2023; 55:807-819. PubMed
Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guigó R, Gingeras TR, Gerstein M. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell 2023; 186:1493-1511.e40. PubMed
Battistello E, Hixon KA, Comstock DE, Collings CK, Chen X, Rodriguez Hernaez J, Lee S, Cervantes KS, Hinkley MM, Ntatsoulis K, Cesarano A, Hockemeyer K, Haining WN, Witkowski MT, Qi J, Tsirigos A, Perna F, Aifantis I, Kadoch C. Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion. Mol Cell 2023; 83:1216-1236.e12. PubMed
Liu HJ, Du H, Khabibullin D, Zarei M, Wei K, Freeman GJ, Kwiatkowski DJ, Henske EP. mTORC1 upregulates B7-H3/CD276 to inhibit antitumor T cells and drive tumor immune evasion. Nat Commun 2023; 14:1214. PubMed
Gunn K, Myllykoski M, Cao JZ, Ahmed M, Huang B, Rouaisnel B, Diplas BH, Levitt MM, Looper R, Doench JG, Ligon KL, Kornblum HI, McBrayer SK, Yan H, Duy C, Godley LA, Koivunen P, Losman JA. (R)-2-hydroxyglutarate inhibits KDM5 histone lysine demethylases to drive transformation in IDH-mutant cancers. 2023. PubMed
Najm FJ, DeWeirdt P, Moore MM, Bevill SM, El Farran CA, Macias KA, Hegde M, Waterbury AL, Liau BB, van Galen P, Doench JG, Bernstein BE. Chromatin complex dependencies reveal targeting opportunities in leukemia. Nat Commun 2023; 14:448. PubMed
Nassar AH, Abou Alaiwi S, Baca SC, Adib E, Corona RI, Seo JH, Fonseca MAS, Spisak S, El Zarif T, Tisza V, Braun DA, Du H, He M, Flaifel A, Alchoueiry M, Denize T, Matar SG, Acosta A, Shukla S, Hou Y, Steinharter J, Bouchard G, Berchuck JE, O'Connor E, Bell C, Nuzzo PV, Mary Lee GS, Signoretti S, Hirsch MS, Pomerantz M, Henske E, Gusev A, Lawrenson K, Choueiri TK, Kwiatkowski DJ, Freedman ML. Epigenomic charting and functional annotation of risk loci in renal cell carcinoma. Nat Commun 2023; 14:346. PubMed
Yang JH, Hayano M, Griffin PT, Amorim JA, Bonkowski MS, Apostolides JK, Salfati EL, Blanchette M, Munding EM, Bhakta M, Chew YC, Guo W, Yang X, Maybury-Lewis S, Tian X, Ross JM, Coppotelli G, Meer MV, Rogers-Hammond R, Vera DL, Lu YR, Pippin JW, Creswell ML, Dou Z, Xu C, Mitchell SJ, Das A, O'Connell BL, Thakur S, Kane AE, Su Q, Mohri Y, Nishimura EK, Schaevitz L, Garg N, Balta AM, Rego MA, Gregory-Ksander M, Jakobs TC, Zhong L, Wakimoto H, El Andari J, Grimm D, Mostoslavsky R, Wagers AJ, Tsubota K, Bonasera SJ, Palmeira CM, Seidman JG, Seidman CE, Wolf NS, Kreiling JA, Sedivy JM, Murphy GF, Green RE, Garcia BA, Berger SL, Oberdoerffer P, Shankland SJ, Gladyshev VN, Ksander BR, Pfenning AR, Rajman LA, Sinclair DA. Loss of epigenetic information as a cause of mammalian aging. Cell 2023; 186:305-326.e27. PubMed
Parry EM, Leshchiner I, Guièze R, Johnson C, Tausch E, Parikh SA, Lemvigh C, Broséus J, Hergalant S, Messer C, Utro F, Levovitz C, Rhrissorrakrai K, Li L, Rosebrock D, Yin S, Deng S, Slowik K, Jacobs R, Huang T, Li S, Fell G, Redd R, Lin Z, Knisbacher BA, Livitz D, Schneider C, Ruthen N, Elagina L, Taylor-Weiner A, Persaud B, Martinez A, Fernandes SM, Purroy N, Anandappa AJ, Ma J, Hess J, Rassenti LZ, Kipps TJ, Jain N, Wierda W, Cymbalista F, Feugier P, Kay NE, Livak KJ, Danysh BP, Stewart C, Neuberg D, Davids MS, Brown JR, Parida L, Stilgenbauer S, Getz G, Wu CJ. Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome. Nat Med 2023; 29:158-169. PubMed
Nardone C, Palanski BA, Scott DC, Timms RT, Barber KW, Gu X, Mao A, Leng Y, Watson EV, Schulman BA, Cole PA, Elledge SJ. A central role for regulated protein stability in the control of TFE3 and MITF by nutrients. Mol Cell 2023; 83:57-73.e9. PubMed
Cortes-Ciriano I, Steele CD, Piculell K, Al-Ibraheemi A, Eulo V, Bui MM, Chatzipli A, Dickson BC, Borcherding DC, Feber A, Galor A, Hart J, Jones KB, Jordan JT, Kim RH, Lindsay D, Miller C, Nishida Y, Proszek PZ, Serrano J, Sundby RT, Szymanski JJ, Ullrich NJ, Viskochil D, Wang X, Snuderl M, Park PJ, Flanagan AM, Hirbe AC, Pillay N, Miller DT. Genomic patterns of malignant peripheral nerve sheath tumor (MPNST) evolution correlate with clinical outcome and are detectable in cell-free DNA. 2023. PubMed
Li J, Wang L, Hahn Q, Nowak RP, Viennet T, Orellana EA, Roy Burman SS, Yue H, Hunkeler M, Fontana P, Wu H, Arthanari H, Fischer ES, Gregory RI. Structural basis of regulated mG tRNA modification by METTL1-WDR4. Nature 2023; 613:391-397. PubMed
Yang X, Triboulet R, Liu Q, Sendinc E, Gregory RI. Exon junction complex shapes the mA epitranscriptome. Nat Commun 2022; 13:7904. PubMed
Groha S, Alaiwi SA, Xu W, Naranbhai V, Nassar AH, Bakouny Z, El Zarif T, Saliby RM, Wan G, Rajeh A, Adib E, Nuzzo PV, Schmidt AL, Labaki C, Ricciuti B, Alessi JV, Braun DA, Shukla SA, Keenan TE, Van Allen E, Awad MM, Manos M, Rahma O, Zubiri L, Villani AC, Fairfax B, Hammer C, Khan Z, Reynolds K, Semenov Y, Schrag D, Kehl KL, Freedman ML, Choueiri TK, Gusev A. Germline variants associated with toxicity to immune checkpoint blockade. Nat Med 2022; 28:2584-2591. PubMed
Dutta AK, Alberge JB, Lightbody ED, Boehner CJ, Dunford A, Sklavenitis-Pistofidis R, Mouhieddine TH, Cowan AN, Su NK, Horowitz EM, Barr H, Hevenor L, Beckwith JB, Perry J, Cao A, Lin Z, Kuhr FK, Del Mastro RG, Nadeem O, Greipp PT, Stewart C, Auclair D, Getz G, Ghobrial IM. MinimuMM-seq: Genome sequencing of circulating tumor cells for minimally invasive molecular characterization of multiple myeloma pathology. 2022. PubMed
Boiarsky R, Haradhvala NJ, Alberge JB, Sklavenitis-Pistofidis R, Mouhieddine TH, Zavidij O, Shih MC, Firer D, Miller M, El-Khoury H, Anand SK, Aguet F, Sontag D, Ghobrial IM, Getz G. Single cell characterization of myeloma and its precursor conditions reveals transcriptional signatures of early tumorigenesis. Nat Commun 2022; 13:7040. PubMed
Sklavenitis-Pistofidis R, Aranha MP, Redd RA, Baginska J, Haradhvala NJ, Hallisey M, Dutta AK, Savell A, Varmeh S, Heilpern-Mallory D, Ujwary S, Zavidij O, Aguet F, Su NK, Lightbody ED, Bustoros M, Tahri S, Mouhieddine TH, Wu T, Flechon L, Anand S, Rosenblatt JM, Zonder J, Vredenburgh JJ, Boruchov A, Bhutani M, Usmani SZ, Matous J, Yee AJ, Jakubowiak A, Laubach J, Manier S, Nadeem O, Richardson P, Badros AZ, Mateos MV, Trippa L, Getz G, Ghobrial IM. Immune biomarkers of response to immunotherapy in patients with high-risk smoldering myeloma. Cancer Cell 2022; 40:1358-1373.e8. PubMed
Bondeson DP, Mullin-Bernstein Z, Oliver S, Skipper TA, Atack TC, Bick N, Ching M, Guirguis AA, Kwon J, Langan C, Millson D, Paolella BR, Tran K, Wie SJ, Vazquez F, Tothova Z, Golub TR, Sellers WR, Ianari A. Systematic profiling of conditional degron tag technologies for target validation studies. Nat Commun 2022; 13:5495. PubMed
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Cancer Genetics and Epigenetics Program

Recent Publications

Leadership

Gad Getz, PhD

Cigall Kadoch, PhD

Eliezer Van Allen, MD