Xiaoqing Yu, PhD

Studying the immune-tumor interaction across cancer types and building predictive models for patients’ response to immunotherapy; and 2) Statistical and bioinformatics methods development to identify aberrant methylation patterns in tumors using bisulfite sequencing data.

Associations

• Biostatistics and Bioinformatics
• Genitourinary Oncology
• Immuno-Oncology Program

Education & Training

Graduate:

• Case Western University, PhD - Biostatistics and Epidemiology

Dr. Yu brings both experience in methodology development and collaborative research in bioinformatics, biostatistics and genomics. Her particular areas of research focus and interest include: 1) Studying the immune-tumor interaction across cancer types and building predictive models for patients’ response to immunotherapy; and 2) Statistical and bioinformatics methods development to identify aberrant methylation patterns in tumors using bisulfite sequencing data. Through her research experience she is poised to make significant contributions to addressing complex questions in cancer research by applying and developing modern statistical, bioinformatics and computational methods.

• Ibrahim ML, Zheng H, Barlow ML, Latif Y, Chen Z, Yu X, Beg AA. Histone Deacetylase Inhibitors Directly Modulate T Cell Gene Expression and Signaling and Promote Development of Effector-Exhausted T Cells in Murine Tumors. J Immunol. 2024 Feb.212(4):737-747. Pubmedid: 38169329. Pmcid: PMC10872871.
• Harro CM, Sprenger KB, Chaurio RA, Powers JJ, Innamarato P, Anadon CM, Zhang Y, Biswas S, Mandal G, Mine JA, Cortina C, Nagy MZ, Martin AL, Handley KF, Borjas GJ, Chen PL, Pinilla-Ibarz J, Sokol L, Yu X, Conejo-Garcia JR. Sézary syndrome originates from heavily mutated hematopoietic progenitors. Blood Adv. 2023 Sep.7(18):5586-5602. Pubmedid: 37531660. Pmcid: PMC10514084.
• Hall MS, Teer JK, Yu X, Branthoover H, Snedal S, Rodriguez-Valentin M, Nagle L, Scott E, Schachner B, Innamarato P, Hall AM, Blauvelt J, Rich CJ, Richards AD, Ceccarelli J, Langer TJ, Yoder SJ, Beatty MS, Cox CA, Messina JL, Abate-Daga D, Mule JJ, Mullinax JE, Sarnaik AA, Pilon-Thomas S. Neoantigen-specific CD4+ tumor-infiltrating lymphocytes are potent effectors identified within adoptive cell therapy products for metastatic melanoma patients. J Immunother Cancer. 2023 Oct.11(10). Pubmedid: 37802604. Pmcid: PMC10565316.
• Biswas S, Mandal G, Anadon CM, Chaurio RA, Lopez-Bailon LU, Nagy MZ, Mine JA, Hänggi K, Sprenger KB, Innamarato P, Harro CM, Powers JJ, Johnson J, Fang B, Eysha M, Nan X, Li R, Perez BA, Curiel TJ, Yu X, Rodriguez PC, Conejo-Garcia JR. Targeting intracellular oncoproteins with dimeric IgA promotes expulsion from the cytoplasm and immune-mediated control of epithelial cancers. Immunity. 2023 Nov.56(11):2570-2583.e6. Pubmedid: 37909039. Pmcid: PMC10703011.
• Li T, Patel KB, Yu X, Yao S, Wang L, Chung CH, Wang X. Unveiling targeted cell-free DNA methylation regions through paired methylome analysis of tumor and normal tissues. bioRxiv. 2023 Jun. Pubmedid: 37425680. Pmcid: PMC10327111.
• Handley KF, Mehta S, Martin AL, Biswas S, Maharaj K, Nagy MZ, Mine JA, Cortina C, Yu X, Sprenger K, Mandal G, Innamarato P, Powers JJ, Harro CM, Chaurio RA, Anadon CM, Shahzad MM, Flores I, Conejo-Garcia JR. Actionable spontaneous antibody responses antagonize malignant progression in ovarian carcinoma. Gynecol Oncol. 2023 Jun.173:114-121. Pubmedid: 37121178.
• Kimmel GJ, Beck RJ, Yu X, Veith T, Bakhoum S, Altrock PM, Andor N. Intra-tumor heterogeneity, turnover rate and karyotype space shape susceptibility to missegregation-induced extinction. PLoS Comput Biol. 2023 Jan.19(1):e1010815. Pubmedid: 36689467. Pmcid: PMC9917311.
• Maurin M, Ranjouri M, Megino-Luque C, Newberg JY, Du D, Martin K, Miner RE, Prater MS, Wee DKB, Centeno B, Pruett-Miller SM, Stewart P, Fleming JB, Yu X, Bravo-Cordero JJ, Guccione E, Black MA, Mann KM. RBFOX2 deregulation promotes pancreatic cancer progression and metastasis through alternative splicing. Nat Commun. 2023 Dec.14(1):8444. Pubmedid: 38114498. Pmcid: PMC10730836.
• Zheng H, Yu X, Ibrahim ML, Foresman D, Xie M, Johnson JO, Boyle TA, Ruffell B, Perez BA, Antonia SJ, Ready N, Saltos AN, Cantwell MJ, Beg AA. Combination IFNβ and Membrane-Stable CD40L Maximize Tumor Dendritic Cell Activation and Lymph Node Trafficking to Elicit Systemic T-cell Immunity. Cancer Immunol Res. 2023 Apr.11(4):466-485. Pubmedid: 36757308. Pmcid: PMC10165690.
• Eschrich SA, Yu X, Teer JK. Fast all versus all genotype comparison using DNA/RNA sequencing data: method and workflow. BMC Bioinformatics. 2023 Apr.24(1):164. Pubmedid: 37095442. Pmcid: PMC10124007.
• Xu X, Wang K, Vera O, Verma A, Jasani N, Bok I, Elemento O, Du D, Yu X, Karreth FA. Gain of Chromosome 1q Perturbs a Competitive Endogenous RNA Network to Promote Melanoma Metastasis. Cancer Res. 2022 Sep.82(17):3016-3031. Pubmedid: 36052492. Pmcid: PMC9971359.
• Anadon CM, Zhang C, Wang X, Cen L, Conejo-Garcia JR, Yu X. Protocol for the isolation of CD8+ tumor-infiltrating lymphocytes from human tumors and their characterization by single-cell immune profiling and multiome. STAR Protoc. 2022 Sep.3(3):101649. Pubmedid: 36065294. Pmcid: PMC9440482.
• Anadon CM, Yu X, Hänggi K, Biswas S, Chaurio RA, Martin A, Payne KK, Mandal G, Innamarato P, Harro CM, Mine JA, Sprenger KB, Cortina C, Powers JJ, Costich TL, Perez BA, Gatenbee CD, Prabhakaran S, Marchion D, Heemskerk MHM, Curiel TJ, Anderson AR, Wenham RM, Rodriguez PC, Conejo-Garcia JR. Ovarian cancer immunogenicity is governed by a narrow subset of progenitor tissue-resident memory T cells. Cancer Cell. 2022 May.40(5):545-557.e13. Pubmedid: 35427494. Pmcid: PMC9096229.
• Yu X, Cen L, Chen YA, Markowitz J, Shaw TI, Tsai KY, Conejo-Garcia JR, Wang X. Tumor Expression Quantitative Trait Methylation Screening Reveals Distinct CpG Panels for Deconvolving Cancer Immune Signatures. Cancer Res. 2022 May.82(9):1724-1735. Pubmedid: 35176128. Pmcid: PMC9064917.
• Mandal G, Biswas S, Anadon CM, Yu X, Gatenbee CD, Prabhakaran S, Payne KK, Chaurio RA, Martin A, Innamarato P, Moran C, Powers JJ, Harro CM, Mine JA, Sprenger KB, Rigolizzo KE, Wang X, Curiel TJ, Rodriguez PC, Anderson ARA, Saglam O, Conejo-Garcia JR. IgA-Dominated Humoral Immune Responses Govern Patients' Outcome in Endometrial Cancer. Cancer Res. 2022 Mar.82(5):859-871. Pubmedid: 34949671. Pmcid: PMC8898267.
• Nakamura K, Reid BM, Chen A, Chen Z, Goode EL, Permuth JB, Teer JK, Tyrer J, Yu X, Kanetsky PA, Pharoah PD, Gayther SA, Sellers TA, Lawrenson K, Karreth FA. Functional analysis of the 1p34.3 risk locus implicates GNL2 in high-grade serous ovarian cancer. Am J Hum Genet. 2022 Jan.109(1):116-135. Pubmedid: 34965383. Pmcid: PMC8764204.
• Chaurio RA, Anadon CM, Lee Costich T, Payne KK, Biswas S, Harro CM, Moran C, Ortiz AC, Cortina C, Rigolizzo KE, Sprenger KB, Mine JA, Innamarato P, Mandal G, Powers JJ, Martin A, Wang Z, Mehta S, Perez BA, Li R, Robinson J, Kroeger JL, Curiel TJ, Yu X, Rodriguez PC, Conejo-Garcia JR. TGF-β-mediated silencing of genomic organizer SATB1 promotes Tfh cell differentiation and formation of intra-tumoral tertiary lymphoid structures. Immunity. 2022 Jan.55(1):115-128.e9. Pubmedid: 35021053. Pmcid: PMC8852221.
• El-Kenawi A, Dominguez-Viqueira W, Liu M, Awasthi S, Abraham-Miranda J, Keske A, Steiner KK, Noel L, Serna AN, Dhillon J, Gillies RJ, Yu X, Koomen JM, Yamoah K, Gatenby RA, Ruffell B. Macrophage-Derived Cholesterol Contributes to Therapeutic Resistance in Prostate Cancer. Cancer Res. 2021 Nov.81(21):5477-5490. Pubmedid: 34301759. Pmcid: PMC8563406.
• Biswas S, Mandal G, Payne KK, Anadon CM, Gatenbee CD, Chaurio RA, Costich TL, Moran C, Harro CM, Rigolizzo KE, Mine JA, Trillo-Tinoco J, Sasamoto N, Terry KL, Marchion D, Buras A, Wenham RM, Yu X, Townsend MK, Tworoger SS, Rodriguez PC, Anderson AR, Conejo-Garcia JR. IgA transcytosis and antigen recognition govern ovarian cancer immunity. Nature. 2021 Mar.591(7850):464-470. Pubmedid: 33536615. Pmcid: PMC7969354.
• Yun S, Vincelette ND, Yu X, Watson GW, Fernandez MR, Yang C, Hitosugi T, Cheng CH, Freischel AR, Zhang L, Li W, Hou H, Schaub FX, Vedder AR, Cen L, McGraw KL, Moon J, Murphy DJ, Ballabio A, Kaufmann SH, Berglund AE, Cleveland JL. TFEB links MYC signaling to epigenetic control of myeloid differentiation and acute myeloid leukemia. Blood Cancer Discov. 2021 Mar.2(2):162-185. Pubmedid: 33860275. Pmcid: PMC8043621.
• de Mingo Pulido Á, Hänggi K, Celias DP, Gardner A, Li J, Batista-Bittencourt B, Mohamed E, Trillo-Tinoco J, Osunmakinde O, Peña R, Onimus A, Kaisho T, Kaufmann J, McEachern K, Soliman H, Luca VC, Rodriguez PC, Yu X, Ruffell B. The inhibitory receptor TIM-3 limits activation of the cGAS-STING pathway in intra-tumoral dendritic cells by suppressing extracellular DNA uptake. Immunity. 2021 Jun.54(6):1154-1167.e7. Pubmedid: 33979578. Pmcid: PMC8192496.
• Smalley I, Chen Z, Phadke MS, Li J, Yu X, Wyatt C, Evernden B, Messina JL, Sarnaik A, Sondak VK, Zhang C, Law V, Tran N, Etame A, Macaulay RJB, Eroglu Z, Forsyth PA, Rodriguez PC, Chen YA, Smalley KSM. Single-Cell Characterization of the Immune Microenvironment of Melanoma Brain and Leptomeningeal Metastases. Clin Cancer Res. 2021 Jul.27(14):4109-4125. Pubmedid: 34035069. Pmcid: PMC8282775.
• Wilson CM, Fridley BL, Conejo-Garcia JR, Wang X, Yu X. Wide and deep learning for automatic cell type identification. Comput Struct Biotechnol J. 2021 Jan.19:1052-1062. Pubmedid: 33613870. Pmcid: PMC7878986.
• Harro CM, Perez-Sanz J, Costich TL, Payne KK, Anadon Galindo CM, Chaurio RA, Biswas S, Mandal G, Rigolizzo KE, Sprenger KB, Mine JA, Showe L, Yu X, Liu K, Rodriguez PC, Pinilla-Ibarz J, Sokol L, Conejo-Garcia JR. Methyltransferase inhibitors restore SATB1 protective activity against cutaneous T cell lymphoma in mice. J Clin Invest. 2021 Feb.131(3). Pubmedid: 33270606. Pmcid: PMC7843215.
• Yu X, Abbas-Aghababazadeh F, Chen YA, Fridley BL. Statistical and Bioinformatics Analysis of Data from Bulk and Single-Cell RNA Sequencing Experiments. Methods Mol Biol. 2020 Sep.2194:143-175. Pubmedid: 32926366. Pmcid: PMC7771369.
• Wang X, Yu X, Krauthammer M, Hugo W, Duan C, Kanetsky PA, Teer JK, Thompson ZJ, Kalos D, Tsai KY, Smalley KSM, Sondak VK, Chen YA, Conejo-Garcia JR. The Association of MUC16 Mutation with Tumor Mutation Burden and Its Prognostic Implications in Cutaneous Melanoma. Cancer Epidemiol Biomarkers Prev. 2020 Sep.29(9):1792-1799. Pubmedid: 32611582. Pmcid: PMC7483810.
• Yu X, Chen YA, Conejo-Garcia JR, Chung CH, Wang X. Estimation of immune cell content in tumor using single-cell RNA-seq reference data. BMC Cancer. 2019 Jul.19(1):715. Pubmedid: 31324168. Pmcid: PMC6642583.
• Li Q, Yu X, Chaudhary R, Slebos RJC, Chung CH, Wang X. lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNA. BMC Genomics. 2019 Jul.20(1):539. Pubmedid: 31266446. Pmcid: PMC6604377.
• Biswas S, Mandal G, Roy Chowdhury S, Purohit S, Payne KK, Anadon C, Gupta A, Swanson P, Yu X, Conejo-Garcia JR, Bhattacharyya A. Exosomes Produced by Mesenchymal Stem Cells Drive Differentiation of Myeloid Cells into Immunosuppressive M2-Polarized Macrophages in Breast Cancer. J Immunol. 2019 Dec.203(12):3447-3460. Pubmedid: 31704881. Pmcid: PMC6994919.
• Wilson CM, Li K, Yu X, Kuan PF, Wang X. Multiple-kernel learning for genomic data mining and prediction. BMC Bioinformatics. 2019 Aug.20(1):426. Pubmedid: 31416413. Pmcid: PMC6694479.
• Rauniyar N, Yu X, Cantley J, Voss EZ, Belcher J, Colangelo CM, Stone KL, Dahl N, Parikh C, Lam TT, Cantley LG. Quantification of Urinary Protein Biomarkers of Autosomal Dominant Polycystic Kidney Disease by Parallel Reaction Monitoring. Proteom Clin Appl. 2018 Sep.12(5):e1700157. Pubmedid: 29573172. Pmcid: PMC6736530.
• Chorzalska A, Ahsan N, Rao RSP, Roder K, Yu X, Morgan J, Tepper A, Hines S, Zhang P, Treaba DO, Zhao TC, Olszewski AJ, Reagan JL, Liang O, Gruppuso PA, Dubielecka PM. Overexpression of Tpl2 is linked to imatinib resistance and activation of MEK-ERK and NF-κB pathways in a model of chronic myeloid leukemia. Mol Oncol. 2018 May.12(5):630-647. Pubmedid: 29485707. Pmcid: PMC5928369.
• Yu X, Wang X. Tumor immunity landscape in non-small cell lung cancer. PeerJ. 2018 Mar.6:e4546. Pubmedid: 29593943. Pmcid: PMC5868477.
• Villarroel-Espindola F, Yu X, Datar I, Mani N, Sanmamed MF, Velcheti V, Syrigos KN, Toki MI, Zhao H, Chen L, Herbst RS, Schalper KA. Spatially Resolved and Quantitative Analysis of VISTA/PD-1H as a Novel Immunotherapy Target in Human Non-Small Cell Lung Cancer. Clin Cancer Res. 2018 Apr.24(7):1562-1573. Pubmedid: 29203588. Pmcid: PMC5884702.
• Charkoftaki G, Chen Y, Han M, Sandoval M, Yu X, Zhao H, Orlicky DJ, Thompson DC, Vasiliou V. Transcriptomic analysis and plasma metabolomics in Aldh16a1-null mice reveals a potential role of ALDH16A1 in renal function. Chem Biol Interact. 2017 Oct.276:15-22. Pubmedid: 28254523. Pmcid: PMC5725231.
• Chorzalska A, Kim JF, Roder K, Tepper A, Ahsan N, Rao RSP, Olszewski AJ, Yu X, Terentyev D, Morgan J, Treaba DO, Zhao TC, Liang O, Gruppuso PA, Dubielecka PM. Long-Term Exposure to Imatinib Mesylate Downregulates Hippo Pathway and Activates YAP in a Model of Chronic Myelogenous Leukemia. Stem Cells Dev. 2017 May.26(9):656-677. Pubmedid: 28103766. Pmcid: PMC5421616.
• Goffredo M, Santoro N, Tricò D, Giannini C, D'Adamo E, Zhao H, Peng G, Yu X, Lam TT, Pierpont B, Caprio S, Herzog RI. A Branched-Chain Amino Acid-Related Metabolic Signature Characterizes Obese Adolescents with Non-Alcoholic Fatty Liver Disease. Nutrients. 2017 Jun.9(7). Pubmedid: 28640216. Pmcid: PMC5537762.
• Heit C, Marshall S, Singh S, Yu X, Charkoftaki G, Zhao H, Orlicky DJ, Fritz KS, Thompson DC, Vasiliou V. Catalase deletion promotes prediabetic phenotype in mice. Free Radical Bio Med. 2017 Feb.103:48-56. Pubmedid: 27939935. Pmcid: PMC5513671.
• Johnson RM, Bergmann KR, Manaloor JJ, Yu X, Slaven JE, Kharbanda AB. Pediatric Kawasaki Disease and Adult Human Immunodeficiency Virus Kawasaki-Like Syndrome Are Likely the Same Malady. Open Forum Infect Dis. 2016 Sep.3(3):ofw160. Pubmedid: 27704015. Pmcid: PMC5047405.
• Li N, Subrahmanyan L, Smith E, Yu X, Zaidi S, Choi M, Mane S, Nelson-Williams C, Behjati M, Kazemi M, Hashemi M, Fathzadeh M, Narayanan A, Tian L, Montazeri F, Mani M, Begleiter ML, Coon BG, Lynch HT, Olson EN, Zhao H, Ruland J, Lifton RP, Mani A. Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus. Am J Hum Genet. 2016 Oct.99(4):1000. Pubmedid: 27716515. Pmcid: PMC5065682.
• Delpech JC, Wei L, Hao J, Yu X, Madore C, Butovsky O, Kaffman A. Early life stress perturbs the maturation of microglia in the developing hippocampus. Brain Behav Immun. 2016 Oct.57:79-93. Pubmedid: 27301858. Pmcid: PMC5010940.
• Wang X, Chen M, Yu X, Pornputtapong N, Chen H, Zhang NR, Powers RS, Krauthammer M. Global copy number profiling of cancer genomes. Bioinformatics. 2016 Mar.32(6):926-928. Pubmedid: 26576652. Pmcid: PMC4907391.
• Yu X, Sun S. HMM-DM: identifying differentially methylated regions using a hidden Markov model. Stat Appl Genet Mol Biol. 2016 Mar.15(1):69-81. Pubmedid: 26887041.
• Sun S, Yu X. HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher's exact test. Stat Appl Genet Mol Biol. 2016 Mar.15(1):55-67. Pubmedid: 26854292.
• Li N, Subrahmanyan L, Smith E, Yu X, Zaidi S, Choi M, Mane S, Nelson-Williams C, Bahjati M, Kazemi M, Hashemi M, Fathzadeh M, Narayanan A, Tian L, Montazeri F, Mani M, Begleiter ML, Coon BG, Lynch HT, Olson EN, Zhao H, Ruland J, Lifton RP, Mani A. Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus. Am J Hum Genet. 2016 Jun.98(6):1082-1091. Pubmedid: 27181681. Pmcid: PMC4908195.
• Yao J, Leng L, Sauler M, Fu W, Zheng J, Zhang Y, Du X, Yu X, Lee P, Bucala R. Transcription factor ICBP90 regulates the MIF promoter and immune susceptibility locus. J Clin Invest. 2016 Feb.126(2):732-744. Pubmedid: 26752645. Pmcid: PMC4731159.
• Dong J, Yu X, Porter DW, Battelli LA, Kashon ML, Ma Q. Common and distinct mechanisms of induced pulmonary fibrosis by particulate and soluble chemical fibrogenic agents. Arch Toxicol. 2016 Feb.90(2):385-402. Pubmedid: 26345256. Pmcid: PMC4749430.
• Yu X, Sun S. Comparing five statistical methods of differential methylation identification using bisulfite sequencing data. Stat Appl Genet Mol Biol. 2016 Apr.15(2):173-191. Pubmedid: 26910753.
• Wang X, Yu X, Zhu W, McCombie WR, Antoniou E, Powers RS, Davidson NO, Li E, Williams J. A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing. Bioinformatics. 2015 Jun.31(12):2040-2042. Pubmedid: 25681254. Pmcid: PMC4481698.
• Yu X, Sun S. Comparing a few SNP calling algorithms using low-coverage sequencing data. BMC Bioinformatics. 2013 Sep.14:274. Pubmedid: 24044377. Pmcid: PMC3848615.
• Sun S, Noviski A, Yu X. MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment. BMC Bioinformatics. 2013 Aug.14:259. Pubmedid: 23968174. Pmcid: PMC3765750.
• Yu X, Guda K, Willis J, Veigl M, Wang Z, Markowitz S, Adams MD, Sun S. How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?. BioData Min. 2012 Jun.5(1):6. Pubmedid: 22709551. Pmcid: PMC3414812.
• Adams MD, Veigl ML, Wang Z, Molyneux N, Sun S, Guda K, Yu X, Markowitz SD, Willis J. Global mutational profiling of formalin-fixed human colon cancers from a pathology archive. Mod Pathol. 2012 Dec.25(12):1599-1608. Pubmedid: 22878650. Pmcid: PMC3697090.
• Xu P, Lu J, Li Z, Yu X, Chen L, Xu T. Aggregation of STIM1 underneath the plasma membrane induces clustering of Orai1. Biochem Bioph Res Co. 2006 Dec.350(4):969-976. Pubmedid: 17045966.

• Title: Investigation of the immune architecture of immunotherapy resistant clear cell renal cell carcinoma leveraging spatial transcriptomics
  Sponsor: Moffitt Cancer Center
  PI: Manley, B., CO-PI: Yu, X.
• Title: Optimizing single cell sequencing to elucidate the relationship between response to brexucabtagene autoleucel (brexu-cel)and cellular determinants of exhaustion
  Sponsor: Kite Pharma
  PI: Shah, B., CO-PI: Yu, X., CO-PI: Locke, F.
• Title: Analytical Tools for Studying the Tumor Microenvironment Leveraging Spatial Transcriptomics
  Sponsor: Nat Institutes of Health
  PI (Contact): Yu, X.