All Publications

  • Modeling human adaptive immune responses with tonsil organoids.

    Wagar LE, Salahudeen A, Constantz Cm, Wendel BS, Lyons MM, Mallajosyula V, Jatt LP, Adamska JZ, Blum LK, Guota N, Jackson KJL, Yang F, Roltgen K, Roskin KM, Blaine KM, Meister KD, Ahmad IN, Cortese M, Dora EG, Tucker SN, Sperling AI, Jain A, Davies DH, Felgner PL, Hammer GB, Kim PS, Robinson WH, Boyd SD, Kuo CJ, Davis MM.
    Nat Med. 2021 Jan;27(1):125-135. doi: 10.1038/s41591-020-01145-0.
  • Progenitor identification and SARS-CoV-2 infection in human distal lung organoids.

    Salahudeen AA, Choi SS, Rustagi A, Zhu J, van Unen V, de la O SM, Flynn RA, Margalef-Català M, Santos AJM, Ju J, Batish A, Usui T, Zheng GXY, Edwards CE, Wagar LE, Luca V, Anchang B, Nagendran M, Nguyen K, Hart DJ, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Harbury PB, Glenn JS, Garcia KC, Davis MM, Baric RS, Sabatti C, Amieva MR, Blish CA, Desai TJ, Kuo CJ.
    Nature. 2020 Dec;588(7839):670-675. doi: 10.1038/s41586-020-3014-1.
  • Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing.

    Maynard A, McCoach CE, Rotow JK, Harris L, Haderk F, Kerr DL, Yu EA, Schenk EL, Tan W, Zee A, Tan M, Gui P, Lea T, Wu W, Urisman A, Jones K, Sit R, Kolli PK, Seeley E, Gesthalter Y, Le DD, Yamauchi KA, Naeger DM, Bandyopadhyay S, Shah K, Cech L, Thomas NJ, Gupta A, Gonzalez M, Do H, Tan L, Bacaltos B, Gomez-Sjoberg R, Gubens M, Jahan T, Kratz JR, Jablons D, Neff N, Doebele RC, Weissman J, Blakely CM, Darmanis S, Bivona TG.
    Cell. 2020 Sep 3;182(5):1232-1251.e22. doi: 10.1016/j.cell.2020.07.017.
  • Tumor Microenvironment-Derived NRG1 Promotes Antiandrogen Resistance in Prostate Cancer.

    Zhang Z, Karthaus WR, Lee YS, Gao VR, Wu C, Russo JW, Liu M, Mota JM, Abida W, Linton E, Lee E, Barnes SD, Chen HA, Mao N, Wongvipat J, Choi D, Chen X, Zhao H, Manova-Todorova K, de Stanchina E, Taplin ME, Balk SP, Rathkopf DE, Gopalan A, Carver BS, Mu P, Jiang X, Watson PA, Sawyers CL.
    Cancer Cell. 2020 Aug 10;38(2):279-296.e9. doi: 10.1016/j.ccell.2020.06.005.
  • Identification of PIKfyve kinase as a target in multiple myeloma.

    de Campos CB, Zhu YX, Sepetov N, Romanov S, Bruins LA, Shi CX, Stein CK, Petit JL, Polito AN, Sharik ME, Meermeier EW, Ahmann GJ, Armenta IDL, Kruse J, Bergsagel PL, Chesi M, Meurice N, Braggio E, Stewart AK.
    Haematologica. 2020 Jun;105(6):1641-1649. doi: 10.3324/haematol.2019.222729.
  • "Direct to Drug" screening as a precision medicine tool in multiple myeloma.

    Bonolo de Campos C, Meurice N, Petit JL, Polito AN, Zhu YX, Wang P, Bruins LA, Wang Xuewei, Armenta IDL, Darvish SA, Ahmann GJ, Henderson KJ, Tian S, Kruse JJ, Stewart WM, Larsen JT, Reeder CB, Dingli D, Kapoor P, Kumar SK, Fonseca R, Bergsagel PL, Braggio E, Stewart AK.
    Blood Cancer J. 2020 May 11;10(5):54. doi: 10.1038/s41408-020-0320-7.
  • Serial ctDNA Monitoring to Predict Response to Systemic Therapy in Metastatic Gastrointestinal Cancers.

    PArikh AR, Mojtahed A, Schneider JL, Kanter K, Van Seventer EE, Fetter IJ, Thabet A, Fish MG, Teshome B, Fosbenner K, Nadres B, Shahzade HA, Allen JN, Blaszkowsky LS, Ryan DP, Giantonio B, Goyal L, Nipp RD, Roeland E, Weekes CD, Wo JY, Zhu AX, Dias-Santagata D, Iafrate AJ, Lennerz JK, Hong TS, Siravegna G, Horick N, Clark JW, Corcoran RB.
    Clin Cancer Res. 2020 Apr 15;26(8):1877-1885. doi: 10.1158/1078-0432.CCR-19-3467.
  • MYC dysregulation in the progression of multiple myeloma.

    Misund K, Keane N, Stein CK, Asmann YW, Day G, Welsh S, Van Wier SA, Riggs DL, Ahmann G, Chesi M, Viswanatha DS, Kumar SK, Dispenzieri A, Gonzalez-Calle V, Kyle RA, O'Dwyer M, Rajkumar SV, Kortum KM, Keats JJ, MMRF CoMMpass Network; Fonseca R, Stewart AK, Kuehl WM, Braggio E, Bergsagel PL.
    Leukemia. 2020 Jan;34(1):322-326. doi: 10.1038/s41375-019-0543-4.
  • The Role of Lineage Plasticity in Prostate Cancer Therapy Resistance.

    Beltran H, Hruszkewycz A, Scher HI, Hildesheim J, Isaacs J, Yu EY, Kelly K, Lin D, Dicker A, Arnold J, Hecht T, Wicha M, Sears R, Rowley D, White R, Gulley JL, Lee J, Meco MD, Small EJ, Shen M, Knudsen K, Goodrich DW, Lotan T, Zoubeidi A, Sawyers CL, Rudin CM, Loda M, Thompson T, Rubin MA, Tawab-Amiri A, Dahut W, Nelson PS.
    Clin Cancer Res. 2019 Dec 1;25(23):6916-6924. doi: 10.1158/1078-0432.CCR-19-1423.
  • Myeloid lineage enhancers drive oncogene synergy in CEBPA/CSF3R mutant acute myeloid leukemia.

    Braun TP, Okhovat M, Coblentz C, Carratt SA, Foley A, Schonrock Z, Smith BM, Nevonen K, Davis B, Garcia B, LaTocha D, Weeder BR, Grzadkowski MR, Estabrook JC, Manning HG, Watanabe-Smith K, Jeng S, Smith JL, Leonti AR, Ries RE, McWeeney S, Di Genua C, Drissen R, Nerlov C, Meshinchi S, Carbone L, Druker BJ, Maxson JE.
    Nat Commun. 2019 Nov 29;10(1):5455. doi: 10.1038/s41467-019-13364-2.
  • ClinGen Myeloid Malignancy Variant Curation Expert Panel recommendations for germline RUNX1 variants.

    Luo X, Feurstein S, Mohan S, Porter CC, Jackson SA, Keel S, Chicka M, Brown AL, Kesserwan C, Agarwal A, Luo M, Li Z, Ross JE, Baliakas P, Pineda-Alvarez D, DiNardo CD, Bertuch AA, Mehta N, Vulliamy T, Wang Y, Nichols KE, Malcovati L, Walsh MF, Rawlings LH, McWeeney SK, Soulier J, Raimbault A, Routbort MJ, Zhang L, Ryan G, Speck NA, Plon SE, Wu D, Godley LA.
    Blood Adv. 2019 Oct 22;3(20):2962-2979. doi: 10.1182/bloodadvances.2019000644.
  • A rectal cancer organoid platform to study individual responses to chemoradiation.

    Ganesh K, Wu C, O'Rourke KP, Szeglin BC, Zheng Y, Sauve CEG, Adileh M, Wasserman I, Marco MR, Kim AS, Shady M, Sanchez-Vega F, Karthaus WR, Won HH, Choi SH, Pelossof R, Barlas A, Ntiamoah P, Pappou E, Elghouayel A, Strong JS, Chen CT, Harris JW, Weiser MR, Nash GM, Guillem JG, Wei IH, Kolesnick RN, Veeraraghavan H, Ortiz EJ, Petkovska I, Cercek A, Manova-Todorova KO, Saltz LB, Lavery JA, DeMatteo RP, Massague J, Paty PB, Yaeger R, Chen X, Patil S, Clevers H, Berger MF, Lowe SW, Shia J, Romesser PB, Dow LE, Garcia-Aguilar J, Sawyers CL, Smith JJ.
    Nat Med. 2019 Oct;25(10):1607-1614. doi: 10.1038/s41591-019-0584-2.
  • Genomic landscape of neutrophilic leukemias of ambiguous diagnosis.

    Zhang H, Wilmot B, Bottomly D, Dao KHT, Stevens E, Eide CA, Khanna V, Rofelty A, Savage S, Schultz AR, Long N, White L, Carlos A, Henson R, Lin C, Searles R, Collins RH, DeAngelo DJ, Deininger MW, Dunn T, Hein T, Luskin MR, MEdeiros BC, Oh ST, Pollyea DA, Steensma DP, Stone RM, Druker BJ, McWeeney SK, Maxson JE, Gotlib JR, Tyner JW.
    Blood. 2019 Sep 12;134(11):867-879. doi: 10.1182/blood.2019000611.
  • Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers.

    Parikh AR, Leshchiner I, Elagina L, Goyal L, Levovitz C, Siravegna G, Livitz D, Rhrissorrakrai K, Martin EE, Van Seventer EE, Hanna M, Slowik K, Utro F, Pinto Cj, Wong A, Danysh BP, de la Cruz FF, Fetter IJ, Nadres B, Shahzade HA, Allen JN, Blaszkowsky LS, Clark JW, Giantonio B, Murphy JE, Nipp RD, Roeland E, Ryan DP, Weekes CD, Kwak EL, Faris JE, Wo JY, Aguet F, Dey-Guha I, Hazar-Rethinam M, DIas-Santagata D, Ting DT, Zhu AX, Hong TS, Golub TR, Iafrate AJ, Adalsteinsson VA, Bardelli A, Parida L, Juric D, Getz G, Corcoran RB.
    Nat Med. 2019 Sep;25(9):1415-1421. doi: 10.1038/s41591-019-0561-9.
  • Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers.

    Chatterjee N, Pazarentzos E, Mayekar MK, Gui P, Allegakoen DV, Hrustanovic G, Olivas V, Lin L, Verschueren E, Johnson JR, Hofree M, Yan JJ, Newton BW, Dollen JV, Earnshaw CH, Flanagan J, Chan E, Asthana S, Ideker T, Wu W, Suzuki J, Barad BA, Kirichok Y, Fraser JS, Weiss WA, Krogan NJ, Tulpule A, Sabnis AJ, Bivona TG.
    Cell Rep. 2019 Aug 27;28(9):2317-2330.e8. doi: 10.1016/j.celrep.2019.07.063.
  • Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet.

    Cheng CW, Biton M, Haber AL, Gunduz N, Eng G, Gaynor LT, Tripathi S, Calibasi-Kocal G, Rickelt S, Butty Vl, Moreno-Serrano M, Iqbal AM, Bauer-Rowe KE, Imada S, Ulutas MS, Mylonas C, Whary MT, Levine SS, Basbinar Y, Hynes RO, Mino-Kenudson M, Deshpande V, Boyer LA, Fox JG, Terranova C, Rai K, Piwnica-Worms H, Mihaylova MM, Regev A, Yilmaz OH.
    Cell. 2019 Aug 22;178(5):1115-1131.e15. doi: 10.1016/j.cell.2019.07.048.
  • Genomic correlates of clinical outcome in advanced prostate cancer.

    Abida W, Cyrta J, Heller G, Prandi D, Armenia J, Coleman I, Cieslik M, Benelli M, Robinson D, Van Allen EM, Sboner A, Fedrizzi T, Mosquera JM, Robinson BD, De Sarkar N, Kunju LP, Tomlins S< Wu YM, Rodrigues DN, Loda M, Gopalan A, Reuter VE, Pritchard CC, Mateo J, Bianchini D, Miranda S, Carreira S, Rescigno P, Filipenko J, Vinson J, Montgomery RB, Beltran H, Heath EI, Scher HI, Kantoff PW, Taplin ME, Schultz N, deBono JS, Demichelis F, Nelson PS, Rubin MA, Chinnaiyan AM, Sawyers CL.
    Proc Natl Acad Sci U S A. 2019 Jun 4;116(23):11428-11436. doi: 10.1073/pnas.1902651116.
  • Next-generation characterization of the Cancer Cell Line Encyclopedia.

    Ghandi M, Huang FW, Jane-Valbuena J, Kryukov GV, Lo CC, McDonald 3rd ER, Barretina J, Gelfand ET, Bielski CM, Li H, Hu K, Andreev-Drakhlin AY, Kim J, Hess JM, Haas BJ, Aguet F, Weir BA, Rothberg MV, Paolella BR, Lawrence MS, Akbani R, Lu Y, Tiv HL, Gokhale PC, de Weck A, Mansour AA, Oh C, Shih J, Hadi K, Rosen Y, Bistline J, Venkatesan K, Reddy A, Sonkin D, Liu M, Lehar J, Korn JM, Porter DA, Jones MD, Golji J, Caponigro G, Taylor JE, Dunning CM, Creech AL, Warren AC, McFarland JM, Zamanighomi M, Kauffmann A, Stransky N, Imielinski M, Maruvka YE, Cherniack AD, Tsherniak A, Cazquez F, Jaffe JD, Lane AA, Weinstock DM, Johannessen CM, Morrissey MP, Stegmeier F, Schlegel R, Hahn WC, Getz G, Mills GB, Boehm JS, Golub TR, Garraway LA, Sellers WR.
    Nature. 2019 May;569(7757):503-508. doi: 10.1038/s41586-019-1186-3.
  • Spectrum and functional validation of PSMB5 mutations in multiple myeloma.

    Barrio S, Stühmer T, Da-Viá M, Barrio-Garcia C, Lehners N, Besse A, Cuenca I, Garitano-Trojaola A, Fink S, Leich E, Chatterjee M, Driessen C, Martinez-Lopez J, Rosenwald A, Beckmann R, Bargou RC, Braggio E, Stewart AK, Raab MS, Einsele H, Kortüm KM.
    Leukemia. 2019 Feb;33(2):447-456. doi: 10.1038/s41375-018-0216-8.
  • Clinical resistance to crenolanib in acute myeloid leukemia due to diverse molecular mechanisms.

    Zhang H, Savage S, Schultz AR, Bottomly D, White L, Segerdell E, Wilmot B, McWeeney SK, Eide CA, Nechiporuk T, Carlos A, Henson R, Lin C, Searles R, Ho H, Lam YL, Sweat R, Follit C, Jain V, Lind E, Borthakur G, Garcia-Manero G, Ravandi F, Kantarjian HM, Cortes J, Collins R, Buelow DR, Baker SD, Druker BJ, Tyner JW.
    Nat Commun. 2019 Jan 16;10(1):244.doi: 10.1038/s41467-018-08263-x.
  • Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.

    Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, Lieb DJ, Chen JH, Frederick DT, Barzily-Rokni M, Freeman SS, Reuben A, Hoover PJ, Villani AC, Ivanova E, Portell A, Lizotte PH, Aref AR, Eliane JP, Hammond MR, Vitzthum H, Blackmon SM, Li B, Gopalakrishnan V, Reddy SM, Cooper ZA, Paweletz CP, Barbie DA, Stemmer-Rachamimov AS, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, Hacohen N.
    Cell. 2019 Jan 10;176(1-2):404. doi: 10.1016/j.cell.2018.12.034.
  • Organoid Modeling of the Tumor Immune Microenvironment.

    Neal JT, Li X, Zhu J, Giangarra V, Grzeskowiak CL, Ju J, Liu IH, Chiou SH, Salahudeen AA, Smith AR, Deutsch BC, Liao L, Zemek AJ, Zhao F, Karlsson K, Schultz LM, Metzner TJ, Nadauld LD, Tseng YY, Alkhairy S, Oh C, Keskula P, Mendoza-Villanueva D, De La Vega FM, Kunz PL, Liao JC, Leppert JT, Sunwoo JB, Sabatti C, Boehm JS, Hahn WC, Zheng GXY, Davis MM, Kuo CJ.
    Cell. 2018 Dec 13;175(7):1972-1988.e16. doi: 10.1016/j.cell.2018.11.021.
  • T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.

    Biton M, Haber AL, Rogel N, Burgin G, Beyaz S, Schnell A, Ashenberg O, Su CW, Smillie C, Shekhar K, Chen Z, Wu C, Ordovas-Montane J, Alvarez D, Herbst RH, Zhang M, Tirosh I, Dionne D, Nguyen LT, Xifaras ME, Shalek Ak, von Andrian UH, Graham DB, Rozenblatt-Rosen O, Shi HN, Kuchroo V, Yilmaz OH, Regev A, Xavier RJ.
    Cell. 2018 Nov 15;175(5):1307-1320.e22. doi: 10.1016/j.cell.2018.10.008.
  • Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.

    Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, Lieb DJ, Chen JH, Frederick DT, Barzily-Rokni M, Freeman SS, Reuben A, Hoover PJ, Villani AC, Ivanova E, Portell A, Lizotte PH, Are AR, Eliane JP, Hammond MR, Vitzthum H, Blackmon SM, Li B, Gopalakrishnan V, Reddy SM, Cooper ZA, Paweletz CP, Barbie DA, Stemmer-Rachamimov A, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, Hacohen N.
    Cell. 2018 Nov 1;175(4):998-1013.e20. doi: 10.1016/j.cell.2018.10.038.
  • Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer.

    Rodrigues DN, Rescigno P, Liu D, Yuan W, Carreira S, Lambros MB, Seed G, Mateo J, Riisnaes R, Mullane S, Margolis C, Miao D, Miranda S, Dolling D, Clarke M, Bertan C, Crespo M, Boysen G, Ferreira A, Sharp A, Figueiredo I, Keliher D, Aldubayan S, Burke KP, Sumanasuriya S, Fontes MS, Bianchini D, Zafeiriou Z, Mendes LST, Mouw K, Schweizer MT, Pritchard CC, Salipante S, Taplin ME, Beltran H, Rubin MA, Cieslik M, Robinson D, Heath E, Schultz N, Armenia J, Abida W, Scher H, Lord C, D'Andrea A, Sawyers CL, Chinnaiyan AM, Alimonti A, Nelson PS, Drake CG, Van Allen EM, de Bono JS.
    J Clin Invest. 2018 Nov 1;128(11):5185. doi: 10.1172/JCI125184.
  • Functional genomic landscape of acute myeloid leukaemia.

    Tyner JW, Tognon CE, Bottomly D, Wilmot B, Kurtz SE, Savage SL, Long N, Schultz AR, Traer E, Abel M, Agarwal A, Blucher A, Borate U, Bryant J, Burke R, Carlos A, Carpenter R, Carroll J, Chang BH, Coblentz C, d'Almeida A, Cook R, Danilov A, Dao KHT, Degnin M, Devine D, Dibb J, Edwards 5th DK, Eide CA, English I, Glover J, Henson R, Ho H, Jemal A, Johnson K, Johnson R, Junio B, Kaempf A, Leonard J, Lin C, Liu SQ, Lo P, Loriaux MM, Luty S, Macey T, MacManiman J, Martinez J, Mori M, Nelson D, Nichols C, Peters J, Ramsdill J, Rofelty A, Schuff R, Searles R, Segerdell E, Smith RL, Spurgeon SE, Sweeney T, Thapa A, Visser C, Wagner J, Watanabe-Smith K, Werth K, Wolf J, White L, Yates A, Zhang H, Cogle CR, Collins RH, Connolly DC, Deininger MW, Drusbosky L, Hourigan CS, Jordan CT, Kropf P, Lin TL, Martinez ME, Medeiros BC, Pallapati RR, Pollyea DA, Swords RT, Watts JM, Weir SJ, Wiest DL, Winters RM, McWeeney Sk, Druker BJ.
    Nature. 2018 Oct;562(7728):526-531. doi: 10.1038/s41586-018-0623-z.
  • Patient derived organoids to model rare prostate cancer phenotypes.

    Puca L, Bareja R, Prandi D, Shaw R, Benelli M, Karthaus WR, Hess J, Sigouros M, Donoghue A, Kossai M, Gao D, Cyrta J, Sailer V, Vosoughi A, Pauli C, Churakova Y, Cheung C, Deonarine LD, McNary TJ, Rosati R, Tagawa ST, Nanu DM, Mosquera JM, Sawyers CL, Chen Y, Inghirami G, Rao RA, Grandori C, Elemento O, Sboner A, Demichelis F, Rubin MA, Beltran H.
    Nat Commun. 2018 Jun 19;9(1):2404. doi: 10.1038/s41467-018-04495-z.
  • Blocking IFNAR1 inhibits multiple myeloma-driven Treg expansion and immunosuppression.

    Kawano Y, Zavidij O, Park J, Moschetta M, Kokubun K, Mouhieddine TH, Manier S, Mishima Y, Murakami N, Bustoros M, Pistofidis RS, Reidy M, Shen YJ, Rahmat M, Lukyanchykov P, Karreci ES, Tsukamoto S, Shi J, Takagi S, Huynh D, Sacco A, Tai YT, Chesi M, Bergsagel PL, Roccaro AM, Azzi J, Ghobrial IM.
    J Clin Invest. 2018 Jun 1;128(6):2487-2499. doi: 10.1172/JCI88169. Epub 2018 May 14.
  • The long tail of oncogenic drivers in prostate cancer.

    Armenia J, Wankowicz SAM, Liu D, Gao J, Kundra R, Reznik E, Chatila WK, Chakravarty D, Han GC, Coleman I, Montgomery B, Pritchard C, Morrissey C, Barbieri CE, Beltran H, Sboner A, Zafeiriou Z, Miranda S, Bielski CM, Penson AV, Tolonen C, Huang FW, Robinson D, Wu YM, Lonigro R, Garraway LA, Demichelis F, Kantoff PW, Taplin ME, Abida W, Taylor BS, Scher HI, Nelson PS, de Bono JS, Rubin MA, Sawyers CL, Chinnaiyan AM; PCF/SU2C International Prostate Cancer Dream Team, Schultz N, Van Allen EM.
    Nat Genet. 2018 May;50(5):645-651. doi: 10.1038/s41588-018-0078-z.
  • Antigen-mediated regulation in monoclonal gammopathies and myeloma.

    Nair S, Sng J, Boddupalli CS, Seckinger A, Chesi M, Fulciniti M, Zhang L, Rauniyar N, Lopez M, Neparidze N, Parker T, Munshi NC, Sexton R, Barlogie B, Orlowski R, Bergsagel L, Hose D, Flavell RA, Mistry PK, Meffre E, Dhodapkar MV.
    JCI Insight. 2018 Apr 19;3(8):e98259. doi: 10.1172/jci.insight.98259.
  • Androgen Receptor Pathway-Independent Prostate Cancer Is Sustained through FGF Signaling.

    Bluemn EG, Coleman IM, Lucas JM, Coleman RT, Hernandez-Lopez S, Tharakan R, Bianchi-Frias D, Dumpit RF, Kaipainen A, Corella AN, Yang YC, Nyquist MD, Mostaghel E, Hsieh AC, Zhang X, Corey E, Brown LG, Nguyen HM, Pienta K, Ittmann M, Schweizer M, True LD, Wise D, Rennie PS, Vessella RL, Morrissey C, Nelson PS.
    Cancer Cell. 2017 Oct 9;32(4):474-489.e6. doi: 10.1016/j.ccell.2017.09.003.