WANG, Xin

Dr WANG, Xin (王鑫)

Adjunct Professor

PhD (Cambridge)

Postdoc (Harvard)

  • 1B-102, 1/F, Block 1, To Yuen Building
  • +852 3442-2367
  • +852 3442-0549
  • CityU Scholars
  • Lab Website
  • Cancer genomics • Prognostic and predictive biomarkers • Regulatory networks • Therapeutic targets • Bioinformatic tools

Dr Wang is a computational biologist. He was trained as a computer scientist initially in China. Impressed by the beauty of Life Sciences and importance of cancer research, he decided to dedicate to the interdisciplinary field of computational biology. Dr Wang pursued his PhD at the University of Cambridge Department of Oncology and Cancer Research UK Cambridge Institute, where his research was concerned with how to infer intracellular signalling pathways from phenotyping screens. In collaboration with experimental oncologists, he also identified three molecularly distinct colon cancer subtypes using an unsupervised classification approach. From 2013 to 2015, Dr Wang did his postdoc training at Harvard Medical School Department of Biomedical Informatics, where he learned advanced techniques in next-generation sequencing data analysis. Dr Wang joined Department of Biomedical Sciences at City University of Hong Kong in Mar 2015, and was promoted to associated professor with tenure in July 2019.

Research Interest

Dr Wang’s major research interest is to better understand the biology underlying cancer using quantitative approaches, with a focus on the following fields:

Cancer Bioinformatics: We have been developing novel methodologies using bioinformatics, systems biology, machine learning and artificial intelligence for integrative analysis of (multi-)omics data (e.g., Sem Cancer Biol 2019, Oncogenesis 2019, Medicine in Omics 2021). Focusing on major malignancies, we are especially interested in multi-omic molecular subtyping followed by comprehensive molecular, histopathological, immunological and clinical characterizations as well as clinical implementations (e.g., Nat Med 2013, Nat Med 2015, Oncogene 2016, Oncogene 2019).

Cancer Biology: We are specialized in leveraging the power of data mining from large-scale, high-throughput public data sets to discovery key regulatory mechanisms followed by in silico and in-house experimental validations (e.g., npj Precis Oncol 2019, BIBM 2021). In collaboration with molecular biologists and experimental oncologists, we have been working on elucidating the genetic and epigenetic regulatory mechanisms underlying cancer development and metastasis (e.g., Genes & Dev 2015, Hepatology 2019, Nat Comm 2021).

Biomarker Development: We have been developing integrated workflows for genome-wide identification of tissue, cell-free and exosome biomarkers for precision medicine (e.g., The Royal Society of Chemistry 2020, Sem Cancer Biol 2021). Together with clinicians, we have been dedicating to multi-centre preclinical and clinical studies about biomarkers for cancer early detection, prognosis, therapeutic response and disease monitoring (e.g., Clin Cancer Res 2018, Gastroenterology 2019, Ann Surg 2019, Sci Adv 2020).

Selected Publications

( co-first author; * co-corresponding author)

  1. Kandimalla R, Wang W, Yu F, Zhou N, Gao F, Spillman M, Moukova L, Slaby O, Salhia B, Zhou S*, Wang X*, Goel A*, OCaMIR – A noninvasive, diagnostic signature for early stage ovarian cancer: a multi-cohort retrospective and prospective study, Clinical Cancer Research 2021, doi:10.1158/1078-0432.CCR-21-0267
  2. Huang H, Hu J, Maryam A, Huang Q, Zhang Y, Ramakrishnan S, Li J, Ma VW, Cheuk W, So GYK, Wang W, Cho WCS, Zhang L, Chan M, Wang X*, Chin YR*, Defining super-enhancer landscape in triple-negative breast cancer by multi-omic profiling, Nature Communications 2021, 12:1–16.
  3. Chen Y, Wu T, Zhu Z, Huang H, Zhang L, Goel A, Yang M, Wang X*, An integrated workflow for biomarker development using microRNAs in extracellular vesicles for cancer precision medicine. Seminars in Cancer Biology 2021, doi:10.1016/j.semcancer.2021.03.011
  4. Xie K, Wang Z, Qi L, Zhao X, Wang Y, Qu J, Huang L, Zhang W, Yang Y*, Wang X*, Shi P*, Profiling MicroRNAs with Associated Spatial Dynamics in Acute Tissue Slices, ACS Nano 2021. doi:10.1021/acsnano.0c09676
  5. Shao X, Tan M, Xie Y, Wang T, Huang H, Zhang Y, Liu J, Zhang W, Wang X*, Deng X*, An integrated network of virulence-associated transcriptional regulators in Pseudomonas syringae, Cell Reports 2021, 34:108920.
  6. Zhang Y, Zhu L, Wang X*, NEM-Tar: a probabilistic graphical model for cancer regulatory network inference and prioritization of potential therapeutic targets from multi-omics data, Frontiers in Genetics 2021;12: 540.
  7. Chen S, Zhu Z, Yang X, Liu L, He Y, Yang M, Guan X, Wang X*, Yun J*, Cleavage and Polyadenylation Specific Factor 1 Promotes Tumor Progression via Alternative Polyadenylation and Splicing in Hepatocellular Carcinoma. Frontiers in Cell and Developmental Biology 2021;9: 340.
  8. Feng Z, Zhou F, Tan M, Wang T, Chen Y, Xu W, Li B, Wang X*, Deng X*, He M*, Targeting m6A Modification Inhibits Herpes Virus 1 Infection, Genes & Diseases 2021. doi:10.1016/j.gendis.2021.02.004
  9. Yang Z, Wang W, Zhao L, Wang X, Gimple RC, Xu L, Wang Y*, Rich JN*, Zhou S*, Plasma Cells Shape the Mesenchymal Identity of Ovarian Cancers through Transfer of Exosome-Derived microRNAs, Science Advances 2021, 7(9):eabb0737
  10. Du Y, Yan Y, Xie S, Huang H, Wang X, Ng R, Zhou MM, Qian C, Structural Mechanism of Bivalent Histone H3K4me3K9me3 Recognition by the Spindlin1/C11orf84 Complex in rRNA Transcription Activation, Nature Communications 2021, 12: 949.
  11. Qi L, Ke J, Yu Z, Cao Y, Lai Y, Chen Y, Gao F*, Wang X*, Identification of prognostic spatial organization features in colorectal cancer microenvironment using deep learning on histopathology images. Medicine in Omics. 2021; 100008.
  12. Shao X, Xie Y, Zhang Y, Liu J, Ding Y, Wu M, Wang X, Deng X, Novel therapeutic strategies for treating Pseudomonas aeruginosa infection. Expert Opin Drug Discov. 2020;15: 1403–1423.
  13. Huang S, Choi MH, Huang H, Wang X, Chang YC, Kim JY, Demyelination regulates the circadian transcription factor BMAL1 to signal adult neural stem cells to initiate oligodendrogenesis, Cell Reports 2020, 33: 108394.
  14. Zhu Z, Han G, Huang H, He L, Chen Y, Ke J, Gao F, Vermeulen L, Wang X*, book chapter, Genome-wide discovery of microRNA biomarkers for cancer precision medicine, In Detection Methods in Precision Medicine, Mengsu Yang and Michael Thompson, The Royal Society of Chemistry, 2020
  15. Kan T, Wang W, Ip PP, Zhou S, Wong AS, Wang X, Yang M, Single-cell EMT-related transcriptional analysis revealed intra-cluster heterogeneity of tumor cell clusters in epithelial ovarian cancer ascites, Oncogene 2020, doi:10.1038/s41388-020-1288-2
  16. Hua C, Wang T, Shao X, Xie Y, Huang H, Liu J, Zhang W, Zhang Y, Ding Y, Jiang L, Wang X, Deng X. Pseudomonas syringae dual-function protein Lon switches between virulence and metabolism by acting as both DNA-binding transcriptional regulator and protease in different environments. Environmental Microbiology 2020;22: 2968–2988.
  17. Wan YCE, Liu J, Zhu L, Kang TZE, Zhu X, Lis J, Ishibashi T, Danko CG*, Wang X*, Chan KM*. The H2BG53D oncohistone directly upregulates ANXA3 transcription and enhances cell migration in pancreatic ductal adenocarcinoma. Signal Transduction and Targeted Therapy 2020;5: 106.
  18. Wang Z, Qi L, Yang Y, Lu M, Xie K, Zhao X, Cheung EHC, Wang Y, Jiang X, Zhang W*, Huang L*, Wang X* & Shi P*, High-throughput intracellular biopsy of microRNAs for dissecting the temporal dynamics of cellular heterogeneity, Science Advances 2020, 6: eaba4971.
  19. Wan YCE, Leung TCS, Ding D, Sun X, Liu J, Zhu L, Kang TZE, Yang D, Zhang YC, Zhang J, Qian C, Huen MSY, Li Q, Chow MZY, Zheng Z, Han J, Goel A, Wang X*, Ishibashi T*, Chan KM*. Cancer-associated histone mutation H2BG53D disrupts DNA–histone octamer interaction and promotes oncogenic phenotypes. Signal Transduction and Targeted Therapy 2020;5: 27
  20. Zhang Y, Zhu L, Wang X*. A Network-Based Approach for Identification of Subtype-Specific Master Regulators in Pancreatic Ductal Adenocarcinoma. Genes. 2020;11. doi:10.3390/genes11020155
  21. Dijk F*, Veenstra VL, Soer EC, Dings MPG, Zhao L, Halfwerk JB, Hooijer GK, Damhofer H, Marzano M, Steins A, Waasdorp C, Busch OR, Besselink MG, Tol JA, Welling L, van Rijssen LB, Klompmaker S, Wilmink HW, van Laarhoven HW, Medema JP, Vermeulen L, van Hooff SR, Koster J, Verheij J, van de Vijver MJ, Wang X*, Bijlsma MF*. Unsupervised class discovery in pancreatic ductal adenocarcinoma reveals cell-intrinsic mesenchymal features and high concordance between existing classification systems. Sci Rep 2020;10: 337
  22. Ding X, He M, Chan AWH, Song QX, Sze SC, Chen H, Man MHK, Man K, Chan SL, Lai PBS, Wang X & Wong N. Genomic and Epigenomic Features of Primary and Recurrent Hepatocellular Carcinomas. Gastroenterology 2019, doi:10.1053/j.gastro.2019.09.005
  23. Gao F, Wang W, Tan M, Zhu L, Zhang Y, Fessler E, Vermeulen L* & Wang X*, DeepCC: a novel deep learning-based framework for cancer molecular subtype classification, Oncogenesis 2019, 8:44
  24. Huang H, Shao X, Xie Y, Wang T, Zhang Y, Wang X*, Deng X*, An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa, Nature Communications 2019,10: 2931
  25. Kandimalla R, Gao F, Li Y, Huang H, Ke J, Deng X, Zhao L, Zhou S, Goel A*, and Wang X*, RNAMethyPro: A biologically conserved signature of N6-methyladenosine regulators for predicting survival at pan-cancer level, npj Precision Oncology 2019, 3:13.
  26. Kandimalla R, Ozawa T, Gao F, Wang X*, Goel A* and the T1 Colorectal Cancer Study Group, Gene Expression Signature in Surgical Tissues and Endoscopic Biopsies Identifies High-risk T1 Colorectal Cancers, Gastroenterology 2019, DOI: 10.1053/j.gastro.2019.02.027
  27. Izumi D, Gao F, Toden S, Sonohara F, Kanda M, Ishimoto T, Kodera Y, Wang X*, Baba H and Goel A*, A genome-wide transcriptomic approach identifies a novel gene expression signature for the detection of lymph node metastasis in patients with early stage gastric cancer, EBioMedicine 2019, pii: S2352-3964(19)30063-5
  28. Chen H, Gao F , He M, Ding XF, Wong AM, Sze SC, Yu AC, Sun T, Chan AWH, Wang X*, Wong N*, Long-read RNA Sequencing identifies Novel Splice Variants in Hepatocellular Carcinoma and Tumor‐specific Isoforms, Hepatology 2019; doi:10.1002/hep.30500 (co-corresponding author)
  29. Lin X, Duan X, Jacobs C, Ullmann J, Chan CY, Chen S, Cheng SH, Zhao WN, Poduri A, Wang X*, Haggarty SJ*, Shi P*, High-throughput Brain Activity Mapping and Machine Learning as a Foundation for Systems Neuropharmacology, Nature Communications 2018;9:5142. (co-corresponding author)
  30. Xu Z, Fang P, Xu B, Lu Y, Xiong J, Gao F, Wang X, Fan J, Shi P*, High-throughput Three-dimensional Chemotactic Assays Reveal Steepness-dependent Complexity in Neuronal Sensation to Molecular Gradients, Nature Communications 2018;9: 4745.
  31. Zhao L, Wang W, Xu L, Yi T, Zhao X, Wei Y, Vermeulen L, Goel A, Zhou S* and Wang X*, Integrative network biology analysis identifies miR-508-3p as the determinant for the mesenchymal identity and a strong prognostic biomarker of ovarian cancer, Oncogene 2018, doi:10.1038/s41388-018-0577-5 (co-corresponding author)
  32. He L, Gomes AP, Wang X, Yoon SO, Lee G, Nagiec M, Cho S, Chavez A, Islam T, Yu Y, Asara JM, Kim BY, Blenis J. mTORC1 Promotes Metabolic Reprogramming by the Suppression of GSK3-Dependent Foxk1 Phosphorylation. Molecular Cell 2018, doi:10.1016/j.molcel.2018.04.024
  33. Kandimalla R, Gao F, Matsuyama T, Ishikawa T, Uetake H, Takahashi N, Yamada Y, Becerra C, Kopetz S, Wang X* and Goel A*. Genome-wide discovery and identification of a novel miRNA signature for recurrence prediction in stage II and III colorectal cancer. Clin Cancer Res 2018, doi:10.1158/1078-0432.CCR-17-3236
  34. Wang W, Kandimalla R, Huang H, Zhu L, Li Y, Gao F, Goel A*, Wang X*, Molecular subtyping of colorectal cancer: recent progress, new challenges and emerging opportunities, Seminars in Cancer Biology 2018, doi:10.1016/j.semcancer.2018.05.002
  35. Zhao L, Huang S, Mei S, Yang Z, Xu L, Zhou N, Yang Q, Shen Q, Wang W, Le X, Lau WB, Lau B, Wang X, Yi T, Zhao X, Wei Y, Warner M, Gustafsson JA, Zhou S. Pharmacological activation of estrogen receptor beta augments innate immunity to suppress cancer metastasis. PNAS 2018, 115(16):E3673-E3681
  36. Zhao L, Wang W, Huang S, Yang Z, Xu L, Yang Q, Zhou X, Wang J, Shen Q, Wang C, Le X, Feng M, Zhou N, Lau WB, Lau B, Yao S, Yi T, Wang X, Zhao X, Wei Y and Zhou S. The RNA binding protein SORBS2 suppresses metastatic colonization of ovarian cancer by stabilizing tumor-suppressive immunomodulatory transcripts. Genome Biology 2018, 19(1):35
  37. Sonohara F, Gao F, Iwata N, Kanda M, Koike M, Takahashi N, Yamada Y, Kodera Y, Wang X*, Goel A*, Genome-wide Discovery of a Novel Gene-expression Signature for the Identification of Lymph Node Metastasis in Esophageal Squamous Cell Carcinoma, Annals of Surgery 2017, doi:10.1097/SLA.0000000000002622
  38. Xu Z, Wang W, Ren Y, Zhang W, Fang P, Huang L, Wang X and Shi P. Regeneration of cortical tissue from brain injury by implantation of defined molecular gradient of semaphorin 3A. Biomaterials 2018;157: 125-135, doi: 10.1016/j.biomaterials.2017.12.010
  39. Linnekamp JF, van Hooff SR, Prasetyanti PR, Kandimalla R, Buikhuisen JY, Fessler E, Ramesh P, Lee KAST, van Bochove GGW, de Jong JH, Cameron K, van Leersum R, Rodermond HM, Franitza M, Nürnberg P, Mangiapane LR, Wang X, Clevers H, Vermeulen L, Stassi G and Medema JP, Consensus Molecular Subtypes of colorectal cancer are recapitulated in in vitro and in vivo models, Cell Death and Differentiation 2018, doi:10.1038/s41418-017-0011-5
  40. Ozawa T, Kandimalla R, Gao F, Nozawa H, Hata K, Nagata H, Okada S, Izumi D, Baba H, Fleshman J, Wang X, Watanabe T, Goel A, A microRNA Signature Associated With Metastasis of T1 Colorectal Tumors to Lymph Nodes, Gastroenterology 2017, doi: 10.1053/j.gastro.2017.11.275
  41. Wang Y, Lin X, Chen X, Chen X, Xu Z, Zhang W, Liao Q, Duan X, Wang X, Liu M, Wang F, He J & Shi P, Tetherless near-infrared control of brain activity in behaving animals using fully implantable upconversion microdevices, Biomaterials 2017, 142, 136-148, doi: 10.1016/j.biomaterials.2017.07.017
  42. Yu VWC, Yusuf RZ, Oki T, Wu J, Saez B, Wang X, Cook C, Baryawno N, Ziller MJ, Lee E, Gu H, Meissner A, Lin CP, Kharchenko PV, Scadden DT, Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells, Cell 2016, 167(5):1310-1322
  43. Trinh A, Trumpi K, De Sousa E Melo F, Wang X, de Jong JH, Fessler E, Kuppen PJK, Reimers MS, Swets M, Koopman M, Nagtegaal I, Jansen M, Hooijer GKJ, Offerhaus GJ, Kranenburg O, Punt CJ, Medema JP, Markowetz F, Vermeulen L, Practical and Robust Identification of Molecular Subtypes in Colorectal Cancer by Immunohistochemistry, Clinical Cancer Research 2016, doi: 10.1158/1078-0432.CCR-16-0680
  44. Fessler E, Drost J, van Hooff SR, Linnekamp JF, Wang X, Jansen M, De Sousa E Melo F, Prasetyanti PR, IJspeert JEG, Franitza M, Nürnberg P, van Noesel CJM, Dekker E, Vermeulen L, Clevers H, and Medem JP, TGFβ signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype, EMBO Molecular Medicine 2016, 8(7): 745–760, doi: 10.15252/emmm.201606184
  45. Fessler E, Jansen M, De Sousa E Melo F, Zhao L, Prasetyanti PR, Rodermond H, Kandimalla R, Linnekamp JF, Franitza M, van Hooff SR, de Jong JH, Oppeneer SC, van Noesel CJM, Dekker E, Stassi G, Wang X*, Medema JP*, and Vermeulen L*, A multidimensional network approach reveals microRNAs as determinants of the mesenchymal colorectal cancer subtype, Oncogene 2016, doi: 10.1038/onc.2016.134 (co-corresponding author)
  46. Masuda T, Wang X, Maeda M, Canver MC, Sher F, Funnell APW, Fisher C, Suciu M, Martyn GE, Norton LJ, Zhu C, Kurita R, Nakamura Y, Xu J, Higgs DR, Crossley M, Bauer DE, Orkin SH, Kharchenko PV, Maeda T, Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin, Science 2016, 351(6270):285-289
  47. Guinney J, Dienstmann R, Wang X, de Reyniès A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, Bot BM, Morris JS, Simon IM, Gerster S, Fessler E, De Sousa E Melo F, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam GC, Broom B, Boige V, Perez-Villamil B, Laderas T, Salazar R, Gray JW, Hanahan D, Tabernero J, Bernards R, Friend SH, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L & Sabine Tejpar, The consensus molecular subtypes of colorectal cancer, Nature Medicine 2015, 10.1038/nm.3967
  48. Alekseyenko AA, Walsh EM, Wang X, Grayson AR, Hsi PT, Kharchenko PV, Kuroda MI, and French CA, The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains, Genes Dev 2015, 29: 1507-1523
  49. Wang X and Markowetz F, "Joining the dots–network analysis of gene perturbation data", book chapter, In Systems Genetics: linking phenotype and genotype, Markowetz F and Boutros M, Cambridge University Press, 2015
  50. Sadanandam A, Wang X, Felipe de Sousa E, Gray JW, Vermeulen L, Hanahan D, & Medema JP, Reconciliation of classification systems defining molecular subtypes of colorectal cancer, Cell Cycle 2014, 13(3): 353-357
  51. De Sousa E Mello, F, Wang X, Jansen M, Fessler E, Trinh A, et al., Poor prognosis colon cancer is defined by a distinct molecular subtype and develops from serrated precursor lesions, Nature Medicine 2013, 19(5): 614-618
  52. Wang X, Yuan K, Hellmayr C, Liu W and Markowetz F, Reconstructing evolving signaling networks by hidden Markov nested effects models, Annals of Applied Statistics 2014, 8(1): 448-480
  53. Mulder KW, Wang X, Escriu C, Ito Y, Schwarz RF, Gillis J, et al., Diverse epigenetic strategies interact to control epidermal differentiation. Nature Cell Biology 2012, 14(7):753-763
  54. Wang X, Castro MA, Mulder KW and Markowetz F, Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations. PLoS Computational Biology 2012, 8(6):e1002566
  55. Castro MA, Wang X, Fletcher M, Ponder BAJ, Meyer KB, Markowetz F, RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations, Genome Biology 2012, 13:R29
  56. Wang X, Terfve C, Rose JC, Markowetz F, HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens. Bioinformatics 2011, 27(6):879

5 November 2021

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