Yue Lu, Ph.D.
Department of Epigenetics and Molecular Carcinogenesis, Division of Discovery Science
Present Title & Affiliation
Primary Appointment
Professor, Department of Epigenetics & Molecular Carcinogenesis, Division of Discovery Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
Research Interests
My primary research interest is the design and application of bioinformatics approaches to deciphering biological mechanisms using next-generation sequencing technologies. It includes two major parts:
The first is the collaborative research with wet laboratories to address important biological problems. I have been in collaboration with many labs in and outside MD Anderson in the past several years. In general, most of the projects can be included in the large topic "characterization of genomic, transcriptomic and epigenomic changes in cancer". Specifically, we use exome/targeted high-throughput sequencing for genomic variations (single nucleotide variation, small indels, etc.), RNA-Seq for transcriptome alterations (differential expression, novel transcript identification, etc.), methylation-sequencing (DREAM, bisulfite-sequencing, MeDIP-Seq) for DNA methylation, ChIP-Seq for DNA-binding proteins (nuclear lamina, transcription factors, epigenetic modifiers, etc.) and histone modifications, and then integrate these data to elucidating important molecular mechanisms in cancer development and progression.
The second is the development and implementation of novel computational algorithms. In collaboration with other bioinformaticians, we developed novel methods, for e.g. improvement of the accuracy of RNA-seq, statistical model for the relation of histone marks, sequence error correction and prediction of imprinted genes from deep sequencing. The recent specific topics I'm interested in include: (1) Distribution pattern of epigenetic marks and its effect on biological processes; (2) Bias correction in various NGS technologies; (3) Precise identification of large blocks in ChIP-Seq; and (4) Intra- and inter- platform biological data integration.
From my graduate studies, I'm also very interested in algorithm development of multiple protein sequence alignment.
Education & Training
Degree-Granting Education
| 2008 | Texas A&M University, College Station, Texas, US, Ph.D. in Biochemistry |
| 2002 | Peking University, Beijing, CN, B.S. in Cell Biology & Genetics |
Experience & Service
Academic Appointments
Associate Professor, Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 2018 - 2024
Assistant Professor, Department of Dept. of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 2012 - 2018
Research Scientist, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 2009 - 2012
Data Analyst, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 2008 - 2009
Scientific Programmer, Department of Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 2008 - 2008
Selected Publications
Peer-Reviewed Articles
- Lee J, Chatterjee B, Oh N, Saha D, Lu Y, Bartholomew B, Ishak CA. Introductory Analysis and Validation of CUT&RUN Sequencing Data. J Vis Exp None(214):None, 2024. e-Pub 2024. PMID: 39760380.
- Lyu Y, Kim SJ, Humphrey ES, Nayak R, Guan Y, Liang Q, Kim KH, Tan Y, Dou J, Sun H, Song X, Nagarajan P, Gerner-Mauro KN, Jin K, Liu V, Hassan RH, Johnson ML, Deliu LP, You Y, Sharma A, Pasolli HA, Lu Y, Zhang J, Mohanty V, Chen K, Yang YJ, Chen T, Ge Y. Stem cell activity-coupled suppression of endogenous retrovirus governs adult tissue regeneration. Cell None(None):None, 2024. e-Pub 2024. PMID: 39476839.
- Chen S, Hou J, Jaffery R, Guerrero A, Fu R, Shi L, Zheng N, Bohat R, Egan NA, Yu C, Sharif S, Lu Y, He W, Wang S, Gjuka D, Stone EM, Shah PA, Rodon Ahnert J, Chen T, Liu X, Bedford MT, Xu H, Peng W. MTA-cooperative PRMT5 inhibitors enhance T cell-mediated antitumor activity in MTAP-loss tumors. J Immunother Cancer 12(9), 2024. e-Pub 2024. PMID: 39313308.
- Chen YC, Bhaskara GB, Lu Y, Lin K, Dent SYR. The SAGA acetyltransferase module is required for the maintenance of MAF and MYC oncogenic gene expression programs in multiple myeloma. Genes Dev 38(15-16):738-754, 2024. e-Pub 2024. PMID: 39168636.
- Hardikar S, Ren R, Ying Z, Zhou J, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, Coletta LD, Shen J, Dan J, Zhang X, Cheng X, Chen T. The ICF syndrome protein CDCA7 harbors a unique DNA binding domain that recognizes a CpG dyad in the context of a non-B DNA. Sci Adv 10(34):eadr0036, 2024. e-Pub 2024. PMID: 39178265.
- Saha, D, Animireddy, S, Lee, J, Thommen, A, Murvin, MM, Lu, Y, Calabrese, JM, Bartholomew, B. Enhancer switching in cell lineage priming is linked to eRNA, Brg1’s AT-hook, and SWI/SNF recruitment. Molecular cell 84(10):1855-1869.e5, 2024. e-Pub 2024. PMID: 38593804.
- Figueroa M, Ma H, Alfayez M, Morales-Mantilla DE, Wang F, Lu Y, Estecio M, King KY, Kleinerman ES, Moghaddam SJ, Daver NG, Andreeff M, Konopleva MY, DiNardo CD, Chandra J. Cigarette smoke exposure accelerates AML progression in FLT3-ITD models. Blood Adv None(None):None, 2023. e-Pub 2023. PMID: 37486624.
- Saha D, Hailu S, Hada A, Lee J, Luo J, Ranish JA, Lin YC, Feola K, Persinger J, Jain A, Liu B, Lu Y, Sen P, Bartholomew B. The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming. Nat Commun 14(1):4682, 2023. e-Pub 2023. PMID: 37542049.
- Hussain T, Sanchez K, Crayton J, Saha D, Jeter C, Lu Y, Abba M, Seo R, Noebels JL, Fonken L, Aldaz CM. WWOX P47T partial loss-of-function mutation induces epilepsy, progressive neuroinflammation, and cerebellar degeneration in mice phenocopying human SCAR12. Prog Neurobiol 223(None):102425, 2023. e-Pub 2023. PMID: 36828035.
- Gao G, Hausmann S, Flores NM, Benitez AM, Shen J, Yang X, Person MD, Gayatri S, Cheng D, Lu Y, Liu B, Mazur PK, Bedford MT. The NFIB/CARM1 partnership is a driver in preclinical models of small cell lung cancer. Nat Commun 14(1):363, 2023. e-Pub 2023. PMID: 36690626.
- Stitzlein LM, Gangadharan A, Walsh LM, Nam D, Espejo AB, Singh MM, Patel KH, Lu Y, Su X, Ezhilarasan R, Gumin J, Singh S, Sulman E, Lang FF, Chandra J. Comparison of pharmacological inhibitors of lysine-specific demethylase 1 in glioblastoma stem cells reveals inhibitor-specific efficacy profiles. Front Neurol 14:1112207, 2023. e-Pub 2023. PMID: 37082446.
- Wang Z, Lu Y, Fornage M, Jiao L, Shen J, Li D, Wei P. Identification of novel susceptibility methylation loci for pancreatic cancer in a two-phase epigenome-wide association study. Epigenetics 17(11):1-16, 2022. e-Pub 2022. PMID: 35030986.
- Darbaniyan F, Zheng H, Kanagal-Shamanna R, Lockyer P, Montalban-Bravo G, Estecio M, Lu Y, Soltysiak KA, Chien KS, Yang H, Sasaki K, Class C, Ganan-Gomez I, Do KA, Garcia-Manero G, Wei Y. Transcriptomic Signatures of Hypomethylating Agent Failure in Myelodysplastic Syndromes and Chronic Myelomonocytic Leukemia. Exp Hematol 115:44-53, 2022. e-Pub 2022. PMID: 36150563.
- Simper MS, Coletta LD, Gaddis S, Lin K, Mikulec CD, Takata T, Tomida MW, Zhang D, Tang DG, Estecio MR, Shen J, Lu Y. Commercial ChIP-Seq Library Preparation Kits Performed Differently for Different Classes of Protein Targets. J Biomol Tech 33(3):None, 2022. e-Pub 2022. PMID: 36910579.
- Li H, Wang Y, Lin K, Venkadakrishnan VB, Bakht M, Shi W, Meng C, Zhang J, Tremble K, Liang X, Song JH, Feng X, Van V, Deng P, Burks JK, Aparicio A, Keyomarsi K, Chen J, Lu Y, Beltran H, Zhao D. CHD1 Promotes Sensitivity to Aurora Kinase Inhibitors by Suppressing Interaction of AURKA with Its Coactivator TPX2. Cancer Res 82(17):3088-3101, 2022. e-Pub 2022. PMID: 35771632.
- Wei Y, Kanagal-Shamanna R, Zheng H, Bao N, Lockyer PP, Class CA, Darbaniyan F, Lu Y, Lin K, Yang H, Montalban-Bravo G, Ganan-Gomez I, Soltysiak KA, Do KA, Colla S, Garcia-Manero G. Cooperation between KDM6B Overexpression and TET2 deficiency in the Pathogenesis of Chronic Myelomonocytic Leukemia. Leukemia 36(8):2097-2107, 2022. e-Pub 2022. PMID: 35697791.
- Meng H, Gonzales NM, Jung SY, Lu Y, Putluri N, Zhu B, Dacso CC, Lonard DM, O'Malley BW. Defining the mammalian coactivation of hepatic 12-h clock and lipid metabolism. Cell Rep 38(10):110491, 2022. e-Pub 2022. PMID: 35263593.
- Van HT, Harkins PR, Patel A, Jain AK, Lu Y, Bedford MT, Santos MA. Methyl-lysine readers PHF20 and PHF20L1 define two distinct gene expression-regulating NSL complexes. J Biol Chem 298(3):101588, 2022. e-Pub 2022. PMID: 35033534.
- Shah VV, Duncan AD, Jiang S, Stratton SA, Allton KL, Yam C, Jain A, Krause PM, Lu Y, Cai S, Tu Y, Zhou X, Zhang X, Jiang Y, Carroll CL, Kang Z, Liu B, Shen J, Gagea M, Manu SM, Huo L, Gilcrease M, Powell RT, Guo L, Stephan C, Davies PJ, Parker-Thornburg J, Lozano G, Behringer RR, Piwnica-Worms H, Chang JT, Moulder SL, Barton MC. Mammary-specific expression of Trim24 establishes a mouse model of human metaplastic breast cancer. Nat Commun 12(1):5389, 2021. e-Pub 2021. PMID: 34508101.
- Kuang X, McAndrew MJ, Mustachio LM, Chen YC, Atanassov BS, Lin K, Lu Y, Shen J, Salinger A, Macatee T, Dent SYR, Koutelou E. Usp22 Overexpression Leads to Aberrant Signal Transduction of Cancer-Related Pathways but Is Not Sufficient to Drive Tumor Formation in Mice. Cancers (Basel) 13(17), 2021. e-Pub 2021. PMID: 34503086.
- Yan L, Gaddis S, Coletta LD, Repass J, Powell KL, Simper MS, Chen Y, Byrom M, Zhong Y, Lin K, Liu B, Lu Y, Shen J, MacLeod MC. ATF3-Induced Mammary Tumors Exhibit Molecular Features of Human Basal-Like Breast Cancer. Int J Mol Sci 22(5), 2021. e-Pub 2021. PMID: 33652981.
- Hu X, Estecio MR, Chen R, Reuben A, Wang L, Fujimoto J, Carrot-Zhang J, McGranahan N, Ying L, Fukuoka J, Chow CW, Pham HHN, Godoy MCB, Carter BW, Behrens C, Zhang J, Antonoff MB, Sepesi B, Lu Y, Pass HI, Kadara H, Scheet P, Vaporciyan AA, Heymach JV, Wistuba II, Lee JJ, Futreal PA, Su D, Issa JJ, Zhang J. Evolution of DNA methylome from precancerous lesions to invasive lung adenocarcinomas. Nat Commun 12(1):687, 2021. e-Pub 2021. PMID: 33514726.
- Farria AT, Plummer JB, Salinger AP, Shen J, Lin K, Lu Y, McBride KM, Koutelou E, Dent SYR. Transcriptional Activation of MYC-Induced Genes by GCN5 Promotes B-cell Lymphomagenesis. Cancer Res 80(24):5543-5553, 2020. e-Pub 2020. PMID: 33168647.
- Veazey KJ, Cheng D, Lin K, Villarreal OD, Gao G, Perez-Oquendo M, Van HT, Stratton SA, Green M, Xu H, Lu Y, Bedford MT, Santos MA. CARM1 inhibition reduces histone acetyltransferase activity causing synthetic lethality in CREBBP/EP300-mutated lymphomas. Leukemia 34(12):3269-3285, 2020. e-Pub 2020. PMID: 32576962.
- Cortez MA, Masrorpour F, Ivan C, Zhang J, Younes AI, Lu Y, Estecio MR, Barsoumian HB, Menon H, Caetano MDS, Ramapriyan R, Schoenhals JE, Wang X, Skoulidis F, Wasley MD, Calin G, Hwu P, Welsh JW. Bone morphogenetic protein 7 promotes resistance to immunotherapy. Nat Commun 11(1):4840, 2020. e-Pub 2020. PMID: 32973129.
- Kumar J, Kaur G, Ren R, Lu Y, Lin K, Li J, Huang Y, Patel A, Barton MC, Macfarlan T, Zhang X, Cheng X. KRAB domain of ZFP568 disrupts TRIM28-mediated abnormal interactions in cancer cells. NAR Cancer 2(2):zcaa007, 2020. e-Pub 2020. PMID: 32743551.
- Li Q, Liu B, Chao HP, Ji Y, Lu Y, Mehmood R, Jeter C, Chen T, Moore JR, Li W, Liu C, Rycaj K, Tracz A, Kirk J, Calhoun-Davis T, Xiong J, Deng Q, Huang J, Foster BA, Gokhale A, Chen X, Tang DG. LRIG1 is a pleiotropic androgen receptor-regulated feedback tumor suppressor in prostate cancer. Nat Commun 10(1):5494, 2019. e-Pub 2019. PMID: 31792211.
- Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, Zhang X, Chen T, Cheng X. Structural basis of specific DNA binding by the transcription factor ZBTB24. Nucleic Acids Res 47(16):8388-8398, 2019. e-Pub 2019. PMID: 31226215.
- Chao HP, Chen Y, Takata Y, Tomida MW, Lin K, Kirk JS, Simper MS, Mikulec CD, Rundhaug JE, Fischer SM, Chen T, Tang DG, Lu Y, Shen J. Systematic evaluation of RNA-Seq preparation protocol performance. BMC Genomics 20(1):571, 2019. e-Pub 2019. PMID: 31296163.
- Sinha KM, Bagheri-Yarmand R, Lahiri S, Lu Y, Zhang M, Amra S, Rizvi Y, Wan X, Navone N, Ozpolat B, Logothetis C, Gagel RF, Huard J. Oncogenic and osteolytic functions of histone demethylase NO66 in castration-resistant prostate cancer. Oncogene 38(25):5038-5049, 2019. e-Pub 2019. PMID: 30858546.
- Bagheri-Yarmand R, Sinha KM, Li L, Lu Y, Cote GJ, Sherman SI, Gagel RF. Combinations of Tyrosine Kinase Inhibitor and ERAD Inhibitor Promote Oxidative Stress-Induced Apoptosis through ATF4 and KLF9 in Medullary Thyroid Cancer. Mol Cancer Res 17(3):751-760, 2019. e-Pub 2019. PMID: 30552230.
- Koutelou E, Wang L, Schibler AC, Chao HP, Kuang X, Lin K, Lu Y, Shen J, Jeter CR, Salinger A, Wilson M, Chen YC, Atanassov BS, Tang DG, Dent SYR. USP22 controls multiple signaling pathways that are essential for vasculature formation in the mouse placenta. Development 146(4), 2019. e-Pub 2019. PMID: 30718289.
- Veland N, Lu Y, Hardikar S, Gaddis S, Zeng Y, Liu B, Estecio MR, Takata Y, Lin K, Tomida MW, Shen J, Saha D, Gowher H, Zhao H, Chen T. DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells. Nucleic Acids Res 47(1):152-167, 2019. e-Pub 2019. PMID: 30321403.
- Bao J, Di Lorenzo A, Lin K, Lu Y, Zhong Y, Sebastian MM, Muller WJ, Yang Y, Bedford MT. Mouse Models of Overexpression Reveal Distinct Oncogenic Roles for Different Type I Protein Arginine Methyltransferases. Cancer Res 79(1):21-32, 2019. e-Pub 2019. PMID: 30352814.
- Das P, Veazey KJ, Van HT, Kaushik S, Lin K, Lu Y, Ishii M, Kikuta J, Ge K, Nussenzweig A, Santos MA. Histone methylation regulator PTIP is required to maintain normal and leukemic bone marrow niches. Proc Natl Acad Sci U S A 115(43):E10137-E10146, 2018. e-Pub 2018. PMID: 30297393.
- Cheng D, Vemulapalli V, Lu Y, Shen J, Aoyagi S, Fry CJ, Yang Y, Foulds CE, Stossi F, Treviño LS, Mancini MA, O'Malley BW, Walker CL, Boyer TG, Bedford MT. CARM1 methylates MED12 to regulate its RNA-binding ability. Life Sci Alliance 1(5):e201800117, 2018. e-Pub 2018. PMID: 30456381.
- Wei Y, Zheng H, Bao N, Jiang S, Bueso-Ramos CE, Khoury J, Class C, Lu Y, Lin K, Yang H, Ganan-Gomez I, Starczynowski DT, Do KA, Colla S, Garcia-Manero G. KDM6B overexpression activates innate immune signaling and impairs hematopoiesis in mice. Blood Adv 2(19):2491-2504, 2018. e-Pub 2018. PMID: 30275007.
- Li Q, Deng Q, Chao HP, Liu X, Lu Y, Lin K, Liu B, Tang GW, Zhang D, Tracz A, Jeter C, Rycaj K, Calhoun-Davis T, Huang J, Rubin MA, Beltran H, Shen J, Chatta G, Puzanov I, Mohler JL, Wang J, Zhao R, Kirk J, Chen X, Tang DG. Linking prostate cancer cell AR heterogeneity to distinct castration and enzalutamide responses. Nat Commun 9(1):3600, 2018. e-Pub 2018. PMID: 30190514.
- Bao J, Perez CJ, Kim J, Zhang H, Murphy CJ, Hamidi T, Jaubert J, Platt CD, Chou J, Deng M, Zhou MH, Huang Y, Gaitán-Peñas H, Guénet JL, Lin K, Lu Y, Chen T, Bedford MT, Dent SY, Richburg JH, Estévez R, Pan HL, Geha RS, Shi Q, Benavides F. Deficient LRRC8A-dependent volume-regulated anion channel activity is associated with male infertility in mice. JCI Insight 3(16):None, 2018. e-Pub 2018. PMID: 30135305.
- Bao J, Rousseaux S, Shen J, Lin K, Lu Y, Bedford MT. The arginine methyltransferase CARM1 represses p300•ACT•CREMτ activity and is required for spermiogenesis. Nucleic Acids Res 46(9):4327-4343, 2018. e-Pub 2018. PMID: 29659998.
- Wood RD, Manandhar M, Lowery M, Boulware KS, Lin K, Lu Y. Response to "XPA is primarily cytoplasmic but is transported into the nucleus upon UV damage". DNA Repair (Amst) 62:30-31, 2018. e-Pub 2018. PMID: 29337160.
- Kaushik S, Liu F, Veazey KJ, Gao G, Das P, Neves LF, Lin K, Zhong Y, Lu Y, Giuliani V, Bedford MT, Nimer SD, Santos MA. Genetic deletion or small molecule inhibition of the arginine methyltransferase PRMT5 exhibit anti-tumoral activity in mouse models of MLL-rearranged AML. Leukemia 32(2):499-509, 2018. e-Pub 2018. PMID: 28663579.
- Wang L, Koutelou E, Hirsch C, McCarthy R, Schibler A, Lin K, Lu Y, Jeter C, Shen J, Barton MC, Dent SYR. GCN5 Regulates FGF Signaling and Activates Selective MYC Target Genes during Early Embryoid Body Differentiation. Stem Cell Reports 10(1):287-299, 2018. e-Pub 2018. PMID: 29249668.
- Zhang D, Jeter C, Gong S, Tracz A, Lu Y, Shen J, Tang DG. Histone 2B-GFP Label-Retaining Prostate Luminal Cells Possess Progenitor Cell Properties and Are Intrinsically Resistant to Castration. Stem Cell Reports 10(1):228-242, 2018. e-Pub 2018. PMID: 29276153.
- Jelinek J, Lee JT, Cesaroni M, Madzo J, Liang S, Lu Y, Issa JJ. Digital Restriction Enzyme Analysis of Methylation (DREAM). Methods Mol Biol 1708:247-265, 2018. e-Pub 2018. PMID: 29224148.
- Napierala JS, Li Y, Lu Y, Lin K, Hauser LA, Lynch DR, Napierala M. Comprehensive analysis of gene expression patterns in Friedreich's ataxia fibroblasts by RNA sequencing reveals altered levels of protein synthesis factors and solute carriers. Dis Model Mech 10(11):1353-1369, 2017. e-Pub 2017. PMID: 29125828.
- Kelly AD, Kroeger H, Yamazaki J, Taby R, Neumann F, Yu S, Lee JT, Patel B, Li Y, He R, Liang S, Lu Y, Cesaroni M, Pierce SA, Kornblau SM, Bueso-Ramos CE, Ravandi F, Kantarjian HM, Jelinek J, Issa JP. A CpG island methylator phenotype in acute myeloid leukemia independent of IDH mutations and associated with a favorable outcome. Leukemia None(None):None, 2017. e-Pub 2017. PMID: 28074068.
- Li M, Radvanyi L, Yin B, Li J, Chivukula R, Lin K, Lu Y, Shen J, Chang DZ, Li D, Johanning GL, Wang-Johanning F. Down-regulation of human endogenous retrovirus type K (HERV-K) viral env RNA in pancreatic cancer cells decreases cell proliferation and tumor growth. Clin Cancer Res 23(19):5892-5911, 2017. e-Pub 2017. PMID: 28679769.
- Maegawa S, Lu Y, Tahara T, Lee JT, Madzo J, Liang S, Jelinek J, Colman RJ, Issa JJ. Caloric restriction delays age-related methylation drift. Nat Commun 8(1):539, 2017. e-Pub 2017. PMID: 28912502.
- Manandhar M, Lowery MG, Boulware KS, Lin KH, Lu Y, Wood RD. Transcriptional consequences of XPA disruption in human cell lines. DNA Repair (Amst) 57:76-90, 2017. e-Pub 2017. PMID: 28704716.
- Mao Y, Shen J, Lu Y, Lin K, Wang H, Li Y, Chang P, Walker MG, Li D. RNA sequencing analyses reveal novel differentially expressed genes and pathways in pancreatic cancer. Oncotarget 8(26):42537-42547, 2017. e-Pub 2017. PMID: 28418924.
- Takata KI, Reh S, Yousefzadeh MJ, Zelazowski MJ, Bhetawal S, Trono D, Lowery MG, Sandoval M, Takata Y, Lu Y, Lin K, Shen J, Kusewitt DF, McBride KM, Cole F, Wood RD. Analysis of DNA polymerase ν function in meiotic recombination, immunoglobulin class-switching, and DNA damage tolerance. PLoS Genet 13(6):e1006818, 2017. e-Pub 2017. PMID: 28570559.
- Zhang D, Lin K, Lu Y, Rycaj K, Zhong Y, Chao HP, Calhoun-Davis T, Shen J, Tang DG. Developing a Novel Two-Dimensional Culture System to Enrich Human Prostate Luminal Progenitors that Can Function as a Cell of Origin for Prostate Cancer. Stem Cells Transl Med 6(3):748-760, 2017. e-Pub 2017. PMID: 28297567.
- Liu C, Liu R, Zhang D, Deng Q, Liu B, Chao HP, Rycaj K, Takata Y, Lin K, Lu Y, Zhong Y, Krolewski J, Shen J, Tang DG. MicroRNA-141 suppresses prostate cancer stem cells and metastasis by targeting a cohort of pro-metastasis genes. Nat Commun 8:14270, 2017. e-Pub 2017. PMID: 28112170.
- Zhou F, Li M, Wei Y, Lin K, Lu Y, Shen J, Johanning GL, Wang-Johanning F. Activation of HERV-K Env protein is essential for tumorigenesis and metastasis of breast cancer cells. Oncotarget 7(51):84093-84117, 2016. e-Pub 2016. PMID: 27557521.
- Malouf GG, Su X, Zhang J, Creighton CJ, Ho TH, Lu Y, Raynal NJ, Karam JA, Tamboli P, Allanick F, Mouawad R, Spano JP, Khayat D, Wood CG, Jelinek J, Tannir NM. DNA Methylation Signature Reveals Cell Ontogeny of Renal Cell Carcinomas. Clin Cancer Res 22(24):6236-6246, 2016. e-Pub 2016. PMID: 27256309.
- Liu C, Eng C, Shen J, Lu Y, Takata Y, Mehdizadeh A, Chang GJ, Rodriguez-Bigas MA, Li Y, Chang P, Mao Y, Hassan MM, Wang F, Li D. Serum exosomal miR-4772-3p is a predictor of tumor recurrence in stage II and III colon cancer. Oncotarget 7(46):76250-76260, 2016. e-Pub 2016. PMID: 27788488.
- Klein BJ, Wang X, Cui G, Yuan C, Botuyan MV, Lin K, Lu Y, Wang X, Zhao Y, Bruns CJ, Mer G, Shi X, Kutateladze TG. PHF20 Readers Link Methylation of Histone H3K4 and p53 with H4K16 Acetylation. Cell Rep 17(4):1158-1170, 2016. e-Pub 2016. PMID: 27760318.
- Chen X, Li Q, Liu X, Liu C, Liu R, Rycaj K, Zhang D, Liu B, Jeter C, Calhoun-Davis T, Lin K, Lu Y, Chao HP, Shen J, Tang DG. Defining a population of stem-like human prostate cancer cells that can generate and propagate castration-resistant prostate cancer (CRPC). Clin Cancer Res 22(17):4505-16, 2016. e-Pub 2016. PMID: 27060154.
- Abba MC, Zhong Y, Lee J, Kil H, Lu Y, Takata Y, Simper MS, Gaddis S, Shen J, Aldaz CM. DMBA induced mouse mammary tumors display high incidence of activating Pik3caH1047 and loss of function Pten mutations. Oncotarget None(None):None, 2016. e-Pub 2016. PMID: 27588403.
- Atanassov BS, Mohan RD, Lan X, Kuang X, Lu Y, Lin K, McIvor E, Li W, Zhang Y, Florens L, Byrum SD, Mackintosh SG, Calhoun-Davis T, Koutelou E, Wang L, Tang DG, Tackett AJ, Washburn MP, Workman JL, Dent SY. ATXN7L3 and ENY2 Coordinate Activity of Multiple H2B Deubiquitinases Important for Cellular Proliferation and Tumor Growth. Mol Cell 62(4):558-71, 2016. e-Pub 2016. PMID: 27132940.
- Schibler A, Koutelou E, Tomida J, Wilson-Pham M, Wang L, Lu Y, Cabrera AP, Chosed RJ, Li W, Li B, Shi X, Wood RD, Dent SY. Histone H3K4 methylation regulates deactivation of the spindle assembly checkpoint through direct binding of Mad2. Genes Dev 30(10):1187-97, 2016. e-Pub 2016. PMID: 27198228.
- Kim J, Zhao H, Dan J, Kim S, Hardikar S, Hollowell D, Lin K, Lu Y, Takata Y, Shen J, Chen T. Maternal Setdb1 Is Required for Meiotic Progression and Preimplantation Development in Mouse. PLoS Genet 12(4):e1005970, 2016. e-Pub 2016. PMID: 27070551.
- Jeter CR, Liu B, Lu Y, Chao HP, Zhang D, Liu X, Chen X, Li Q, Rycaj K, Calhoun-Davis T, Yan L, Hu Q, Wang J, Shen J, Liu S, Tang DG. NANOG reprograms prostate cancer cells to castration resistance via dynamically repressing and engaging the AR/FOXA1 signaling axis. Cell Discov 2:16041, 2016. e-Pub 2016. PMID: 27867534.
- Zhang D, Park D, Zhong Y, Lu Y, Rycaj K, Gong S, Chen X, Liu X, Chao HP, Whitney P, Calhoun-Davis T, Takata Y, Shen J, Iyer VR, Tang DG. Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer. Nat Commun 7:10798, 2016. e-Pub 2016. PMID: 26924072.
- Li Y, Lu Y, Polak U, Lin K, Shen J, Farmer J, Seyer L, Bhalla AD, Rozwadowska N, Lynch DR, Butler JS, Napierala M. Expanded GAA repeats impede transcription elongation through the FXN gene and induce transcriptional silencing that is restricted to the FXN locus. Hum Mol Genet 24(24):6932-43, 2015. e-Pub 2015. PMID: 26401053.
- Abba MC, Gong T, Lu Y, Lee J, Zhong Y, Lacunza E, Butti M, Takata Y, Gaddis S, Shen J, Estecio MR, Sahin AA, Aldaz CM. A Molecular Portrait of High-Grade Ductal Carcinoma In Situ. Cancer Res 75(18):3980-90, 2015. e-Pub 2015. PMID: 26249178.
- Rolyan H, Tyurina YY, Hernandez M, Amoscato AA, Sparvero LJ, Nmezi BC, Lu Y, Estécio MR, Lin K, Chen J, He RR, Gong P, Rigatti LH, Dupree J, Bayir H, Kagan VE, Casaccia P, Padiath QS. Defects of Lipid Synthesis Are Linked to the Age-Dependent Demyelination Caused by Lamin B1 Overexpression. J Neurosci 35(34):12002-17, 2015. e-Pub 2015. PMID: 26311780.
- Yamazaki J, Jelinek J, Lu Y, Cesaroni M, Madzo J, Neumann F, He R, Taby R, Vasanthakumar A, Macrae T, Ostler KR, Kantarjian HM, Liang S, Estecio MR, Godley LA, Issa JP. TET2 mutations affect non-CpG island DNA methylation at enhancers and transcription factor binding sites in chronic myelomonocytic leukemia. Cancer Res 75(14):2833-43, 2015. e-Pub 2015. PMID: 25972343.
- Mallampati S, Leng X, Ma H, Zeng J, Li J, Wang H, Lin K, Lu Y, Yang Y, Sun B, Gong Y, Lee JS, Konopleva M, Andreeff M, Arlinghaus RB, Cai Z, Fang B, Shen H, Han X, Hirsch-Ginsberg CF, Gao X, Paranjape AN, Mani SA, Clise-Dwyer K, Sun X. Tyrosine kinase inhibitors induce mesenchymal stem cell-mediated resistance in BCR-ABL+ acute lymphoblastic leukemia. Blood 125(19):2968-73, 2015. e-Pub 2015. PMID: 25712988.
- Qin T, Si J, Raynal NJ, Wang X, Gharibyan V, Ahmed S, Hu X, Jin C, Lu Y, Shu J, Estecio MR, Jelinek J, Issa JP. Epigenetic synergy between decitabine and platinum derivatives. Clin Epigenetics 7(1):97, 2015. e-Pub 2015. PMID: 26366234.
- Kim J, Singh AK, Takata Y, Lin K, Shen J, Lu Y, Kerenyi MA, Orkin SH, Chen T. LSD1 is essential for oocyte meiotic progression by regulating CDC25B expression in mice. Nat Commun 6:10116, 2015. e-Pub 2015. PMID: 26626423.
- Malouf GG, Tahara T, Paradis V, Fabre M, Guettier C, Yamazaki J, Long H, Lu Y, Raynal NJ, Jelinek J, Mouawad R, Khayat D, Brugières L, Raymond E, Issa JP. Methylome sequencing for fibrolamellar hepatocellular carcinoma depicts distinctive features. Epigenetics 10(9):872-81, 2015. e-Pub 2015. PMID: 26224146.
- Simper MS, Rundhaug JE, Mikulec C, Bowen R, Shen J, Lu Y, Lin K, Surh I, Fischer SM. The tumor promoting activity of the EP4 receptor for prostaglandin E2 in murine skin. Mol Oncol 8(8):1626-39, 2014. e-Pub 2014. PMID: 25034079.
- Raymond A, Liu B, Liang H, Wei C, Guindani M, Lu Y, Liang S, St John LS, Molldrem J, Nagarajan L. A role for BMP-induced homeobox gene MIXL1 in acute myelogenous leukemia and identification of type I BMP receptor as a potential target for therapy. Oncotarget 5(24):12675-93, 2014. e-Pub 2014. PMID: 25544748.
- Jin Q, Zhuang L, Lai B, Wang C, Li W, Dolan B, Lu Y, Wang Z, Zhao K, Peng W, Dent SY, Ge K. Gcn5 and PCAF negatively regulate interferon-β production through HAT-independent inhibition of TBK1. EMBO Rep 15(11):1192-201, 2014. e-Pub 2014. PMID: 25269644.
- Ma H, Mallampati S, Lu Y, Sun B, Wang E, Leng X, Gong Y, Shen H, Yin CC, Jones D, Amin HM, You MJ, Zweidler-McKay P, Ma Y, Kantarjian HM, Arlinghaus RB, Glassman A, Sun X. The Sox4/Tcf7l1 axis promotes progression of BCR-ABL-positive acute lymphoblastic leukemia. Haematologica 99(10):1591-8, 2014. e-Pub 2014. PMID: 24997151.
- Mallampati S, Sun B, Lu Y, Ma H, Gong Y, Wang D, Lee JS, Lin K, Sun X. Integrated genetic approaches identify the molecular mechanisms of Sox4 in early B-cell development: intricate roles for RAG1/2 and CK1ε. Blood 123(26):4064-76, 2014. e-Pub 2014. PMID: 24786772.
- Maegawa S, Gough SM, Watanabe-Okochi N, Lu Y, Zhang N, Castoro RJ, Estecio MR, Jelinek J, Liang S, Kitamura T, Aplan PD, Issa JP. Age-related epigenetic drift in the pathogenesis of MDS and AML. Genome Res 24(4):580-91, 2014. e-Pub 2014. PMID: 24414704.
- Yang Y, McBride KM, Hensley S, Lu Y, Chedin F, Bedford MT. Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R loop accumulation. Mol Cell 53(3):484-97, 2014. e-Pub 2014. PMID: 24507716.
- Jin C, Lu Y, Jelinek J, Liang S, Estecio MR, Barton MC, Issa JP. TET1 is a maintenance DNA demethylase that prevents methylation spreading in differentiated cells. Nucleic Acids Res 42(11):6956-71, 2014. e-Pub 2014. PMID: 24875481.
- Oh CD, Lu Y, Liang S, Mori-Akiyama Y, Chen D, de Crombrugghe B, Yasuda H. SOX9 regulates multiple genes in chondrocytes, including genes encoding ECM proteins, ECM modification enzymes, receptors, and transporters. PLoS One 9(9):e107577, 2014. e-Pub 2014. PMID: 25229425.
- Chen K, Wilson MA, Hirsch C, Watson A, Liang S, Lu Y, Li W, Dent SY. Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor. Genome Res 23(2):312-22, 2013. e-Pub 2013. PMID: 23124522.
- Gururaj AE, Gibson L, Panchabhai S, Bai M, Manyam G, Lu Y, Latha K, Rojas ML, Hwang Y, Liang S, Bogler O. Access to the Nucleus and Functional Association with c-Myc Is Required for the Full Oncogenic Potential of ∆EGFR/EGFRvIII. J Biol Chem 288(5):3428-38, 2013. e-Pub 2013. PMID: 23250739.
- Yamazaki J, Estecio MR, Lu Y, Long H, Malouf GG, Graber D, Huo Y, Ramagli L, Liang S, Kornblau SM, Jelinek J, Issa JP. The epigenome of AML stem and progenitor cells. Epigenetics 8(1):92-104, 2013. e-Pub 2013. PMID: 23249680.
- Malouf GG, Taube JH, Lu Y, Roysarkar T, Panjarian S, Estecio MR, Jelinek J, Yamazaki J, Raynal NJ, Long H, Tahara T, Tinnirello A, Ramachandran P, Zhang XY, Liang S, Mani SA, Issa JP. Architecture of epigenetic reprogramming following Twist1-mediated epithelial-mesenchymal transition. Genome Biol 14(12):R144, 2013. e-Pub 2013. PMID: 24367927.
- Mitra R, Muller P, Liang S, Lu Y, Ji Y. A Bayesian Graphical Model for ChIP-Seq Data on Histone Modifications. Journal of the American Statistical Association, 2013. e-Pub 2013. PMID: None.
- Jelinek J, Liang S, Lu Y, He R, Ramagli LS, Shpall EJ, Estecio MR, Issa JP. Conserved DNA methylation patterns in healthy blood cells and extensive changes in leukemia measured by a new quantitative technique. Epigenetics 7(12):1368-78, 2012. e-Pub 2012. PMID: 23075513.
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Grant & Contract Support
| Title: | Determine the Role of Histone Methyltransferase ASH1L in Metastatic Prostate Cancer |
| Funding Source: | NIH |
| Role: | Co-I |
| Title: | Novel Epigenetic Determinant in Metastatic Prostate Cancer |
| Funding Source: | Department of Defense (DOD) |
| Role: | Co-I |
| Title: | Role of PRMT7 in Genomic Imprinting |
| Funding Source: | NIH/NIGMS |
| Role: | Co-I |
| Title: | Transcriptional enhancer regulation by MLL3/4 in blood cell differentiation |
| Funding Source: | NIH |
| Role: | Co-I |
| Title: | Investigating the Role of BCL11A in AML Differentiation Blockade and Stem Cell Maintenance |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| Title: | Deciphering cellular and circuit mechanisms underlying WWOX-related hereditary ataxia |
| Funding Source: | US Department of Defense |
| Role: | Co-I |
| Title: | Determining Clinical Relevant Organ Specific Relative Biological Effectiveness (RBE) of Protons in Lung Cancer |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| Title: | Personalized Cardio-Oncology through Blood and Digital Biomarker Monitoring of Cardiovascular Risk in Thoracic Radiotherapy |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| Title: | Elucidating the role of the nuclear lamina in Alzheimer’s Disease |
| Funding Source: | NIH |
| Role: | Co-I |
| Title: | Linking genome variation to transcriptional network dynamics in human B cells |
| Funding Source: | NIH/NHGRI |
| Role: | Co-I |
| Title: | Study of PRMT6 in Small Cell Lung Cancer |
| Funding Source: | Internal, DRP Lung Spore |
| Role: | Co-I |
| Title: | TWIST1 post-translational modification crosstalk in EMT |
| Funding Source: | National Science Foundation (NSF) |
| Role: | Co-I |
| Title: | Systems approach for PARP-based novel combination therapy in ovarian cancer |
| Funding Source: | Ovarian Cancer Research Alliance |
| Role: | Co-I |
| Title: | Exploring Antisense Oligonucleotides as a potential therapy for Autosomal Dominant Leukodystrophy |
| Funding Source: | NIH/IGNITE |
| Role: | Co-I |
| Title: | Regulation of chromatin organization and dynamics by INO80 |
| Funding Source: | NIH/NIGMS |
| Role: | Co-I |
| Title: | Defining USP22 Functions During Mammalian Development |
| Funding Source: | NIH/NIGMS |
| Role: | Co-I |
| Title: | Epigenetic Regulation by CHD7 in Colon Cancer |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| Title: | The University of Texas MD Anderson Cancer Center Science Park Next-Generation Sequencing Facility |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Collaborator |
| Title: | Modeling ICF syndrome in mice: Role of Zbtb24 in DNA methylation and antibody production |
| Funding Source: | NIH/NIAID |
| Role: | Co-I |
| Title: | Elucidating mechanisms involved in Lamin B1 mediated demyelination |
| Funding Source: | NIH/NINDS |
| Role: | Co-I |
| Title: | MDS Clinical Research Consortium |
| Funding Source: | Aplastic Anemia & MDS International Foundation supported by the Evans Foundation |
| Role: | Co-I |
| Title: | Role of Histone H3K9 Methyltransferase Eset in Intestinal Stem Cells |
| Funding Source: | NIH/NIDDK |
| Role: | Co-I |
| Title: | The interplay between the chromatin remodeler INO80 and histone variant H2A.Z |
| Funding Source: | NIH/NIGMS |
| Role: | Co-I |
| Title: | Functions of Mammalian Histone Modifiers |
| Funding Source: | NIH/NIGMS |
| Role: | Co-I |
| Title: | Studying the role of the nuclear lamina in age dependent demyelination |
| Funding Source: | NIH/NIAID |
| Role: | Co-I |
| Title: | Functional study of the chromodomain protein CHD7 in colorectal cancer |
| Funding Source: | UT MD Anderson Cancer Center |
| Role: | Co-I |
| Title: | Molecular Oncogenesis of Nanog in Castration-Resistant Prostate Cancer |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-I |
| Title: | The University of Texas MD Anderson Cancer Center Science Park Next-Generation Sequencing Facility |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Collaborator |
| Title: | The Role of the Nuclear Lamina in Chromatin Organization and Gene Expression in Normal and Tumor Cells |
| Funding Source: | NIH/NCI |
| Role: | Collaborator |
| Title: | Targeting a bacterial enzyme-domain in Acute Myeloid Leukemia |
| Funding Source: | American Cancer Society |
| Role: | Co-I |
| Title: | Role of NLRP5 in Epigenetic Reprogramming During Early Embryogenesis |
| Funding Source: | NIH |
| Role: | Co-I |
| Title: | Neurovascular uncoupling and mitigation in pediatric high-grade gliomas |
| Funding Source: | UT Austin/UT MDA Strategic Collaboration |
| Role: | Co-I |
| Title: | Determining organ-specific relative biological effectiveness (RBE) of proton radiation using clinical data from prospective trials |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | Elucidating the role of the nuclear lamina in Alzheimer’s Disease |
| Funding Source: | NIH |
| Role: | Co-I |
| Title: | Targeting Staphylococcal Nuclease and Tudor Domain Containing 1 (SND1) in Acute Myeloid Leukemia |
| Funding Source: | Elsa U. Pardee Foundation |
| Role: | Co-I |
| Title: | Cellular and Circuit Mechanisms of WWOX-related Neurodevelopmental Disorders |
| Funding Source: | Baylor College of Medicine/NIH |
| Role: | PI |
| Title: | Design and testing of personalized Therapy for AML based on toobacco use |
| Funding Source: | NIH |
| Role: | Co-I |
| Title: | Determine the Role of Histone Methyltransferase ASH1L in Metastatic Niche |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-I |
| Title: | Understanding and mitigating effects of combustible and non-combustible tobacco use in high risk AML patients |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-I |
| Title: | Understanding poor treatment outcomes conferred by cigarette smoking in acute leukemia |
| Funding Source: | Department of Defense (DOD) |
| Role: | Co-I |
| Title: | Determine the Role of Histone Methyltransferase ASH1L in Metastatic Prostate Cancer |
| Funding Source: | NIH |
| Role: | Co-I |
| Title: | SWI/SNF, RNA polymerase directionality/pausing and cancer |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Collaborator |
Patient Reviews
CV information above last modified February 19, 2025