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Yu Lab: Publications

2021

  • In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8 T cell fate decisions.
    Huang H, Zhou P, Wei J, Long L, Shi H, Dhungana Y, Chapman NM, Fu G, Saravia J, Raynor JL, Liu S, Palacios G, Wang Y-D, Qian C, Yu J, Chi H#.
    Cell
  • Network-based systems pharmacology identifies heterogeneity in LCK and BCL2 signaling and differential vulnerability of T-cell acute lymphoblastic leukemia to targeted therapy.
    Gocho Y*, Liu J*, Hu J*, Yang W, Dharia NV, Zhang J, Shi H, Du G, John A, Lin T-N, Hunt J, Huang X, Ju B, Rowland L, Shi L, Maxwell D, Smart B, Crews KR, Yang W, Hagiwara K, Zhang Y, Roberts K, Wang H, Jabbour E, Stock W, Eisfelder B, Paietta E, Newman S, Roti G, Litzow M, Easton J, Zhang J, Peng J, Chi H, Pounds S, Relling MV, Inaba H, Zhu X, Kornblau S, Pui C-H, Konopleva M, Teachey D, Mullighan CG, Stegmaier K, Evans WE, Yu J#, Yang JJ#.
    Nature Cancer.
  • Modeling and targeting of erythroleukemia by hematopoietic genome editing.
    Iacobucci I*, Qu C*, Varotto E, Janke L, Yang X, Seth A, Shelat A, Friske J, Fukano R, Yu J, Freeman B, Kennedy J, Sperling A, Zheng R, Wang Y, Jogiraju H, Dickerson K, Turner D, Sarah Morris M, Hollis E, Ghosn N, Haggard G, Lindsley R, L. Ebert B and Mullighan C#
    Blood blood.2020009103.

2020

  • Network Approaches for Dissecting the Immune System.
    Shi H*, Yan K-K*, Ding L, Qian C, Chi H, Yu J#.
    iScience. 23(8):101354. PMID:32717640; PMCID:PMC7390880.
  • Cross-talk between GLI transcription factors and FOXC1 promotes T-cell acute lymphoblastic leukemia dissemination.
    Tosello V, Bongiovanni D, Liu J, Pan Q, Yan KK, Saccomani V, Van Trimpont M, Pizzi M, Mazzoni M, Dei Tos AP, Amadori A, Zanovello P, Van Vlierberghe P, Yu J, Piovan E#.
    Leukemia. PMID:32733009.
  • Akt Inhibition Is Associated With Favorable Immune Profile Changes Within the Tumor Microenvironment of Hormone Receptor Positive, HER2 Negative Breast Cancer.
    Marks DK, Gartrell RD, El Asmar M, Boboila S, Hart T, Lu Y, Pan Q., Yu J, Hibshoosh H, Guo H, Andreopoulou E, Wiechmann L, Crew K, Sparano J, Hershman D, Connolly E, Saenger Y, Kalinsky K.
    Front Oncol. 2020;10:968. Epub 2020/07/03. doi:10.3389/fonc.2020.00968. PubMed PMID:32612958; PMCID:PMC7308467.
  • G3BP1 is a molecular switch that triggers phase separation to assemble stress granules.
    Yang P, Mathieu C, Kolaitis RM, Zhang P, Messing J, Yang Z, Wu J, Li Y, Pan Q, Yu J, Martin E, Mittag T, Kim HJ, Taylor JP.
    Cell (in press)
  • An ABC transporter drives medulloblastoma pathogenesis by regulating Sonic Hedgehog signaling.
    Wijaya J, Vo B, Liu J, Xu B, Wu G, Wang Y, Peng J, Zhang J, Janke L, Orr B, Yu J, Roussel M and Schuetz J.
    Cancer Research
  • Integrative genomic analyses reveal known and novel mechanisms of glucocorticoid resistance in acute lymphoblastic leukemia.
    Autry RJ, Paugh SW, Carter R, Shi L, Liu J, Ferguson D.C., Lau CE, Bonten EJ, Yang W, McCorkle R, Beard JA, Panetta JC, Diedrich JD, Crews KR, Pei D, Coke CJ, Natarajan S, Khatamian A, Karol SE, Lopez-Lopez E, Diouf B, Smith C, Gocho Y, Hagiwara K, Roberts KG, Pounds S, Kornblau SM, Stock W, M.Paietta E, Litzow MR, Inaba H, Mullighan CG, Jeha S, Pui CH, Cheng C, Savic D., Yu J, Gawad C, Relling MV, Yang JJ and Evans WE.
    Nature Cancer (in press)

2019

  • Targeting REGNASE-1 programs long-lived effector T cells for cancer therapy.
    Wei J, Long L, Zheng W, Dhungana Y, Lim SA, Guy C, Wang Y, Wang YD, Qian C, Xu B, KC A, Saravia J, Huang H, Yu J, Doench JG, Geiger TL & Chi H#. (#Corresponding authors)
    Nature, volume 576, pages 471–476
  • LKB1 orchestrates dendritic cell metabolic quiescence and anti-tumor immunity.
    Wang Y, Du X, Wei J, Long L, Tan H, Guy C, Dhungana Y, Qian C, Neale G, Fu YX, Yu J, Peng J, Chi H
    Cell research. 2019
  • Systems immunology: Integrating multi-omics data to infer regulatory networks and hidden drivers of immunity.
    Yu J#, Peng J#, Chi H#. (#Corresponding authors)
    Current Opinion in Systems Biology. 2019.

2018

  • SJARACNe: a scalable software tool for gene network reverse engineering from big data.
    Khatamian A, Paull EO, Califano A#, Yu J#. (#Corresponding authors)
    Bioinformatics. 2018. PMID:30388204.   GitHub

  • Transcription factor activating protein 4 is synthetically lethal and a master regulator of MYCN-amplified neuroblastoma.
    Boboila S, Lopez G, Yu J, Banerjee D, Kadenhe-Chiweshe A, Connolly EP, Kandel JJ, Rajbhandari P, Silva JM, Califano A, Yamashiro DJ.
    Oncogene. 2018. PMID:29880876

  • Hippo/Mst signalling couples metabolic state and immune function of CD8α+ dendritic cells.
    Du X, Wen J, Wang Y, Karmaus PWF, Khatamian A, Tan H, Li Y, Guy C, Nguyen TM, Dhungana Y, Neale G, Peng J, Yu J#, Chi H#. (#Corresponding authors)
    Nature, volume 558, pages 141–145   GitHub

  • Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma.
    Rajbhandari P, Lopez G, Capdevila C, Salvatori B, Yu J, Rodriguez-Barrueco R, Martinez D, Yarmarkovich M, Weichert-Leahey N, Abraham BJ, Alvarez MJ, Iyer A, Harenza JL, Oldridge D, De Preter K, Koster J, Asgharzadeh S, Seeger RC, Wei JS, Khan J, Vandesompele J, Mestdagh P, Versteeg R, Look AT, Young RA, Iavarone A, Lasorella A, Silva JM, Maris JM, Califano A.
    Cancer discovery. 2018; 8(5):582-599. PMID:29510988

  • Bayesian Network to Infer Drug-Induced Apoptosis Circuits from Connectivity Map Data.
    Yu J#, Silva JM. (#Corresponding authors)
    Methods in molecular biology (Clifton, N.J.). 2018; 1783:361-378. PMID:29767372.

2017

  • miR-424(322)/503 is a breast cancer tumor suppressor whose loss promotes resistance to chemotherapy.
    Rodriguez-Barrueco R, Nekritz EA, Bertucci F, Yu J, Sanchez-Garcia F, Zeleke TZ, Gorbatenko A, Birnbaum D, Ezhkova E, Cordon-Cardo C, Finetti P, Llobet-Navas D, Silva JM.
    Genes & development. 2017; 31(6):553-566. PMID:28404630.

2016

2015

  • HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers.
    Putcha P*, Yu J*, Rodriguez-Barrueco R, Saucedo-Cuevas L, Villagrasa P, Murga-Penas E, Quayle SN, Yang M, Castro V, Llobet-Navas D, Birnbaum D, Finetti P, Woodward WA, Bertucci F, Alpaugh ML, Califano A, Silva J. (*Equal contributions)
    Breast cancer research:BCR. 2015; 17(1):149. PMID:26643555.

  • Breast cancer cells respond differentially to modulation of TGFβ2 signaling after exposure to chemotherapy or hypoxia.
    O'Brien SK, Chen L, Zhong W, Armellino D, Yu J, Loreth C, Follettie M, Damelin M.
    Cancer research. 2015; 75(21):4605-16. PMID:26340918.

  • Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers.
    Rodriguez-Barrueco R*, Yu J*, Saucedo-Cuevas LP, Olivan M, Llobet-Navas D, Putcha P, Castro V, Murga-Penas EM, Collazo-Lorduy A, Castillo-Martin M, Alvarez M, Cordon-Cardo C, Kalinsky K, Maurer M, Califano A, Silva JM. (*Equal contributions)
    Genes & development. 2015; 29(15):1631-48. PMID:26227964.

  • Recovering drug-induced apoptosis subnetwork from Connectivity Map data.
    Yu J#, Putcha P, Silva JM#. (#Corresponding authors)
    BioMed research international. 2015; 2015:708563. PMID:25883971.

  • Direct reversal of glucocorticoid resistance by AKT inhibition in acute lymphoblastic leukemia.
    Piovan E*, Yu J*, Tosello V, Herranz D, Ambesi-Impiombato A, Da Silva AC, Sanchez-Martin M, Perez-Garcia A, Rigo I, Castillo M, Indraccolo S, Cross JR, de Stanchina E, Paietta E, Racevskis J, Rowe JM, Tallman MS, Basso G, Meijerink JP, Cordon-Cardo C, Califano A, Ferrando AA. (*Equal contributions)
    Cancer cell. 2013; 24(6):766-76. PMID:24291004.

2013

2009

  • A novel approach to detect differentially expressed genes from count-based digital databases by normalizing with housekeeping genes.
    Lu B*, Yu J*, Xu J, Chen J, Lai M. (*Equal contributions)
    Genomics. 2009; 94(3):211-6. PMID:19446020.