Jiyang Yu, PhD

Yan KK, Condori J, Ma Z, Metais JY, Ju B, Ding L, Dhungana Y, Palmer LE, Langfitt DM, Ferrara F, Throm R, Shi H, Risch I, Bhatara S, Shaner B, Lockey TD, Talleur AC, Easton J, Meagher MM, Puck JM, Cowan MJ, Zhou S, Mamcarz E, Gottschalk S^#, Yu J^#. Integrome signatures of lentiviral gene therapy for SCID-X1 patients. Sci Adv 9(40):eadg9959, 2023. Epub 2023/10/06. doi: 10.1126/sciadv.adg9959. PubMed PMID: 37801507; PMCID: PMC10558130

Su W, Saravia J, Risch I, Rankin S, Guy C, Chapman NM, Shi H, Sun Y, Kc A, Li W, Huang H, Lim SA, Hu H, Wang Y, Liu D, Jiao Y, Chen PC, Soliman H, Yan KK, Zhang J, Vogel P, Liu X, Serrano GE, Beach TG, Yu J, Peng J, Chi H. CXCR6 orchestrates brain CD8(+) T cell residency and limits mouse Alzheimer's disease pathology. Nat Immunol 24(10):1735-47, 2023. Epub 2023/09/08. doi: 10.1038/s41590-023-01604-z. PubMed PMID: 37679549

Dong X, Ding L, Thrasher A, Wang X, Liu J, Pan Q, Rash J, Dhungana Y, Yang X, Risch I, Li Y, Yan L, Rusch M, McLeod C, Yan KK, Peng J, Chi H, Zhang J, Yu J. NetBID2 provides comprehensive hidden driver analysis. Nat Commun 14(1):2581, 2023. Epub 2023/05/05. doi: 10.1038/s41467-023-38335-6. PubMed PMID: 37142594; PMCID: PMC10160099

Zeleke TZ*, Pan Q*, Chiuzan C, Onishi M, Li Y, Tan H, Alvarez MJ, Honan E, Yang M, Chia PL, Mukhopadhyay P, Kelly S, Wu R, Fenn K, Trivedi MS, Accordino M, Crew KD, Hershman DL, Maurer M, Jones S, High A, Peng J, Califano A, Kalinsky K#, Yu J#, Silva J#. Network-based assessment of HDAC6 activity predicts preclinical and clinical responses to the HDAC6 inhibitor ricolinostat in breast cancer. Nat Cancer 2022. Epub 2022/12/31. doi: 10.1038/s43018-022-00489-5. PMID: 36585452 *Co-first author; #Co-corresponding author.

Fan L*, Pan Q*, Yang W, Koo SC, Tian C, Li L, Lu M, Brown A, Ju B, Easton J, Ranganathan S, Shin S, Bondoc A, Yang JJ, Yu J # , Zhu L # . A Developmentally Prometastatic Niche to Hepatoblastoma in Neonatal Liver mediated by the Cxcl1/Cxcr2 Axis. Hepatology 2022. Epub 2022/02/19. doi: 10.1002/hep.32412. PubMed PMID: 35179799. *Co-first author; #Co-corresponding author.

Long L, Wei J, Lim SA, Raynor JL, Shi H, Connelly JP, Wang H, Guy C, Xie B, Chapman NM, Fu G, Wang Y, Huang H, Su W, Saravia J, Risch I, Wang YD, Li Y, Niu M, Dhungana Y, Kc A, Zhou P, Vogel P, Yu J, Pruett-Miller SM, Peng J, Chi H. CRISPR screens unveil signal hubs for nutrient licensing of T cell immunity. Nature 600(7888):308-13, 2021. Epub 2021/11/20. doi: 10.1038/s41586-021-04109-7. PubMed PMID: 34795452; PMCID: 34795452

Gartrell J, Mellado-Largarde M, Clay MR, Bahrami A, Sahr NA, Sykes A, Blankenship K, Hoffmann L, Xie J, Cho HP, Twarog N, Connelly M, Yan KK, Yu J, Porter SN, Pruett-Miller SM, Neale G, Tinkle CL, Federico SM, Stewart EA, Shelat AA. SLFN11 is Widely Expressed in Pediatric Sarcoma and Induces Variable Sensitization to Replicative Stress Caused By DNA-Damaging Agents. Mol Cancer Ther 20(11):2151-65, 2021. Epub 08/21/2021. doi: 10.1158/1535-7163.MCT-21-0089. PubMed PMID: 34413129.

Nekritz EA, Rodriguez-Barrueco R, Yan KK, Davis ML, Werner RL, Devis-Jauregui L, Mukhopadhyay P, Yu J, Llobet-Navas D, Silva J. miR-424/503 modulates Wnt/beta-catenin signaling in the mammary epithelium by targeting LRP6. EMBO reports e53201, 2021. Epub 10/12/2021. doi: 10.15252/embr.202153201. PubMed PMID: 34633138.

Fu G, Guy CS, Wei J, Chapman NM, Palacios G, Long L, Wang Y-D, Qian C, Dhungana Y, Huang H, KC A, Brown SA, Rankin S, Yu J, Jackowski S, Chi H. Reprogramming of phosphatidylethanolamine metabolism selectively governs T follicular helper cell differentiation and humoral immunity. Nature Jul 7, 2021. doi: 10.1038/s41586-021-03692-z. PubMed PMID: 34234346

Zyulina V, Yan KK, Ju B, Schwarzenberger E, Passegger C, Tam-Amersdorfer C, Pan Q, Sconocchia T, Pollack C, Shaner B, Zebisch A, Easton J, Yu J, Silva JM, Strobl H. The miR-424(322)/503 gene cluster regulates pro- versus anti-inflammatory skin DC subset differentiation by modulating TGF-beta signaling. Cell Rep 35(4):109049, 2021. Epub 04/29/2021. doi: 10.1016/j.celrep.2021.109049. PubMed PMID: 33910004.

Shaw TI, Dong L, Tian L, Qian C, Liu Y, Ju B, High A, Kavdia K, Pagala VR, Shaner B, Pei D, Easton J, Janke LJ, Porter SN, Ma X, Cheng C, Pruett-Miller SM, Choi J, Yu J, Peng J, Gu W, Look AT, Downing JR, Zhang J. Integrative network analysis reveals USP7 haploinsufficiency inhibits E-protein activity in pediatric T-lineage acute lymphoblastic leukemia (T-ALL). Scientific Reports 11(1):5154, 2021. Epub 03/06/2021. doi: 10.1038/s41598-021-84647-2. PMID: 33664368; PMCID: PMC7933146.

Luo Z, Dong X, Yu J, Xia Y, Berry KP, Rao R, Xu L, Xue P, Chen T, Lin Y, Yu J, Huang G, Li H, Zhou W, Lu QR. Genomic and Transcriptomic Analyses Reveals ZNF124 as a Critical Regulator in Highly Aggressive Medulloblastomas. Front Cell Dev Biol 9:634056, 2021. Epub 03/09/2021. doi: 10.3389/fcell.2021.634056. PMID: 33681213; PMCID: PMC7930499.

Iacobucci I, Qu C, Varotto E, Janke LJ, Yang X, Seth A, Shelat A, Friske J, Fukano R, Yu J, Freeman BB, Kennedy JA, Sperling AS, Zheng R, Wang Y, Jogiraju H, Dickerson K, Payne-Turner DL, Morris SM, Hollis E, Ghosn NJ, Haggard GE, Lindsley RC, Ebert BL, Mullighan CG. Modeling and targeting of erythroleukemia by hematopoietic genome editing. Blood Epub 01/30/2021. doi: 10.1182/blood.2020009103. PMID: 33512458.

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 YD, Qian C, Yu J, Chi H. In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8(+) T cell fate decisions. Cell 184(5):1245-61 e21, 2021. Epub 2021/02/27. doi: 10.1016/j.cell.2021.02.021. PMID: 33636132.

Gocho Y, Liu J, Hu J, Yang W, Dharia NV, Zhang J, Du G, John A, Lin T-N, Hunt J, Rowland L, Shi L, Maxwell D, Smart B, Crews K, Yang W, Hagiwara K, Zhang Y, Roberts K, Wang H, Jabbour E, Stock W, Eisfelder B, Paietta E, Newman S, Roti G, Litzow M, 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^#. Network-based systems pharmacology identifies heterogeneity in LCK and BCL2 signaling and differential vulnerability of T-cell acute lymphoblastic leukemia to targeted therapy. Nat Cancer. ^#Co-corresponding authors. (Clinical trials are being initiated based on this study).

Shi H, Yan K-K, Ding L, Qian C, Chi H, Yu J. Network Approaches for Dissecting the Immune System. iScience. 23(8):101354, 2020. PMID: 32717640; PMCID: PMC7390880.

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. Cross-talk between GLI transcription factors and FOXC1 promotes T-cell acute lymphoblastic leukemia dissemination. Leukemia. 2020. PMID: 32733009.

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. Akt Inhibition Is Associated With Favorable Immune Profile Changes Within the Tumor Microenvironment of Hormone Receptor Positive, HER2 Negative Breast Cancer. Front Oncol. 10:968,m 2020. Epub 07/03/2020. doi: 10.3389/fonc.2020.00968. PubMed PMID: 32612958; PMCID: PMC7308467.

Autry R, Paugh S, Carter R, Shi L, Liu J, Ferguson D, Lau C, Bonten E, Yang W, McCorkle J, Beard J, Panetta J, Diedrich J, Crews K, Pei D, Coke C, Natarajan S, Khatamian A, Karol S, Lopez-Lopez E, Diouf B, Smith C, Roberts K, Pounds S, Kornblau S, Mullighan C, Jeha S, Pui C, Cheng C, Yang J, Savic D, Yu J, Gawad C, Relling M, Evans WE. Integrative genomic analyses reveal known and novel mechanisms of glucocorticoid resistance in acute lymphoblastic leukemia. Nat Cancer 1(3):329-44, 2020. PMID: 32885175; PMCID: PMC7467080.

Yang P, Mathieu C, Kolaitis RM, Zhang P, Messing J, Yurtsever U, Yang Z, Wu J, Li Y, Pan Q, Yu J, Martin EW, Mittag T, Kim HJ, Taylor JP. G3BP1 Is a Tunable Switch that Triggers Phase Separation to Assemble Stress Granules. Cell. 181(2):325-45 e28, 2020. PMID: 32302571; PMCID: PMC7448383.

Wijaya J, Vo BT, Liu J, Xu B, Wu G, Wang Y, Peng J, Zhang J, Janke LJ, Orr BA, Yu J, Roussel MF, Schuetz JD. An ABC transporter drives the Sonic Hedgehog pathway contributing to medulloblastoma pathogenesis. Cancer research. 80(7):1524-37, 2020. doi: 10.1158/0008-5472.CAN-19-2054. PubMed PMID: 31948942.

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. Targeting REGNASE-1 programs long-lived effector T cells for cancer therapy. Nature 576(7787):471-6., 2019 doi: 10.1038/s41586-019-1821-z. PubMed PMID: 31827283; PMCID: PMC6937596.

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. LKB1 orchestrates dendritic cell metabolic quiescence and anti-tumor immunity. Cell Research 29:391-405; 2019. doi: 10.1038/s41422-019-0157-4. PMID: 30911060

Yu J^#, Peng J^#, Chi H^#. Systems immunology: Integrating multi-omics data to infer regulatory networks and hidden drivers of immunity. Current Opinion in Systems Biology. 15:19-29; 2019. doi: 10.1016/j.coisb.2019.03.003. ^#Co-corresponding authors.

Khatamian A, Paull EO, Califano A^#, Yu J^#. SJARACNe: a scalable software tool for gene network reverse engineering from big data. Bioinformatics 35(12);2165-2166, 2019. PMID: 30388204. ^#Corresponding authors. [GitHub: https://github.com/jyyulab/SJARACNe]

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

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^#. Hippo/Mst signalling couples metabolic state and immune function of CD8α⁺ dendritic cells. Nature 558(7708):141-145, 2018. PMID: 29849151. ^#Corresponding authors. [NetBID GitHub: https://github.com/jyyulab/NetBID]

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. Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma. Cancer discovery 8(5):582-599, 2018. PMID: 29510988.

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

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. miR-424(322)/503 is a breast cancer tumor suppressor whose loss promotes resistance to chemotherapy. Genes & development 31(6):553-566, 2017. PMID: 28404630.

Tosello V, Bordin F, Yu J, Agnusdei V, Indraccolo S, Basso G, Amadori A, Piovan E. Calcineurin and GSK-3 inhibition sensitizes T-cell acute lymphoblastic leukemia cells to apoptosis through X-linked inhibitor of apoptosis protein degradation. Leukemia 30(4):812-22, 2016. PMID: 26648536.

Yu J^#, Silva J^#, Califano A^#. ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling. Bioinformatics (Oxford, England) 32(2):260-7, 2016. PMID: 26415723. ^#Corresponding authors.