Zigui CHEN

Professor Zigui CHEN

B.Sc., Ph.D.
Associate Professor,
Department of Microbiology,
Faculty of Medicine, The Chinese University of Hong Kong
Honorary Associate Professor,
Faculty of Dentistry, The University of Hong Kong

Member,
Papillomaviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV)

Scientific Advisor,
Papillomavirus Episteme (PaVE), NIAID/NIH

Professor Zigui CHEN

zigui.chen@cuhk.edu.hk

Research

ORCID: orcid.org/0000-0002-8577-1298

ResearchGate: https://www.researchgate.net/profile/Zigui-Chen-2

Research interest
Microbial evolution and bioinformatics
Using big dataset and bioinformatics to elucidate the community dynamics and host-microorganism interaction of human microbiome, mycobiome and virome.
Human micro-pathogens in cancer
Using molecular evolution and in-vitro cell models to understand the genomics diversity and carcinogenic potential of human papillomaviruses (HPV) and human microbiome in cervical cancer and head and neck squamous cell carcinoma.
Emerging respiratory tract infection
Using bioinformatics and omics approaches to study the molecular genomics, epidemiology and pathogenesis of emerging respiratory infections including COVID-19, seasonal influenza, and bacterial pneumonia.

Understanding evolution of disease-causing microorganisms is the foundation of what we know about genetic basis, gene origins, and the adaptation of pathogens to a changing environment. It helps us solve biological problems that impact our health. Our group devotes to the studies of human microbial and viral evolution, genomics and epigenetics using analytic tools of systems biology and advanced bioinformatics pipeline. We have collaborated with several scientists and made fruitful contributions to identifying the genetic heterogeneity of human papillomaviruses (HPVs) causing cervical cancer. With the quick facilitation of Next-Generation Sequencing (NGS) and big dataset analysis, we are expanding our research interests in the complex ecological community of human microbiome interacting with human cancers and disease outcomes. Our mission is to develop and apply evolutionary and bioinformatics approaches to characterize and interpret the host-pathogen causality.
Postgraduate students
Information for Postgraduate Study in Department of Microbiology
Our Team
Staff
Student
Research Experience
5/2021 – currentAssociate Professor
Department of Microbiology, The Chinese University of Hong Kong
5/2015 – 4/2021 Assistant Professor
Department of Microbiology, The Chinese University of Hong Kong
7/2009 – 4/2015Instructor (Research Assistant Professor)
Department of Paediatrics, Albert Einstein College of Medicine, NY, USA
9/2002 – 6/2009Research Associate
Department of Microbiology and Immunology, Albert Einstein College of Medicine, NY, USA
9/1997 – 7/2002PhD, Ocean University of China
9/1993 – 7/1997Bachelor, Ocean University of China
Grants
Association between oral microbiome, HPV and human epigenetic events in head and neck squamous cell carcinoma
General Research Fund (GRF) / University Grants Committee (Hong Kong)
Principle Investigator
Evolutionary dynamics and genetic basis of carcinogenicity of primate papillomaviruses
Early Career Scheme (ECS) / University Grants Committee (Hong Kong)
Principle Investigator
Characterization of Genomic and Functional Features of Human Microbiome Associated with Oral Cavity Squamous Cell Carcinoma Using Multi-Omics Approaches
Health and Medical Research Fund (HMRF) / Food and Health Bureau (Hong Kong)
Principle Investigator
Genetic and Epigenetic Abnormalities Associated with Dysbiosis of the Human Microbiota in Esophageal Squamous Cell Carcinoma (ESCC)
Health and Medical Research Fund (HMRF) / Food and Health Bureau (Hong Kong)
Principle Investigator
Origin and evolutionary adaptation of the carcinogenicity of human papillomaviruses: evaluation of human and non-human primate PV E6 and E7 oncogenes interacting with host proteomes
National Science Foundation of China (NSFC)
Principle Investigator
Multi-modal Approaches to Determine Digital Clinical Phenotyping, Novel Proteomic Biomarkers, and Microbiota-host Responses of REM Sleep Behavior Disorder, a Prodromal Stage of Alpha-synucleinopathy Neurodegeneration, in a Prospective Family Cohort
Collaborative Research Fund (CRF) / University Grants Committee (Hong Kong)
Co-Principle Investigator
The association between human papillomavirus (HPV) E6 oncoprotein and Aurora B in carcinogenesis – a potential horizon for therapeutic intervention
General Research Fund (GRF) / University Grants Committee (Hong Kong)
Co-Investigator
Early biomarkers in SARS-CoV-2 infection: correlation with short/medium/long-term clinical outcomes, and implications on acute patient management and long-term medical and health care
Health and Medical Research Fund (HMRF) / Food and Health Bureau (Hong Kong)
Co-Investigator
Characterizing whole genome stability of the novel coronavirus SARS-CoV-2
Health and Medical Research Fund (HMRF) / Food and Health Bureau (Hong Kong)
Co-Investigator
Publications (Selected publications relevance to viruses and microbiota)

  1. Cheung MK, Leung TF, Tam WH, Leung ASY, Chan OM, Ng RWY, Yau JWK, Yuen LY, Tong SLY, Ho WCS, Yeung ACM, Chen Z*, Chan PKS. Development of the early-life gut microbiome and associations with eczema in a prospective Chinese cohort. mSystems. 2023:e0052123. Epub 20230830. doi: 10.1128/msystems.00521-23. PubMed PMID: 37646516.
  2. Zhu H, Yip HC, Cheung MK, Chan HC, Ng C, Lau EHL, Yeung ZWC, Wong EWY, Leung L, Qu X, Wang D, Cai L, Chan PKS, Chan JYK, Chen Z*. Convergent dysbiosis of upper aerodigestive microbiota between patients with esophageal and oral cavity squamous cell carcinoma. Int J Cancer. 2023;152(9):1903-15. doi: 10.1002/ijc.34460.
  3. Chan JYK, Cheung MK, Lan L, Ng C, Lau EHL, Yeung ZWC, Wong EWY, Leung L, Qu X, Cai L, Zhu H, Boon SS, Burk RD, Chan PKS, Chen Z*. Characterization of oral microbiota in HPV and non-HPV head and neck squamous cell carcinoma and its association with patient outcomes. Oral Oncol. 2022;135:106245. doi: 10.1016/j.oraloncology.2022.106245.
  4. Long T, Burk RD, Chan PKS, Chen Z*. Non-Human Primate Papillomavirus E6-Mediated p53 Degradation Reveals Ancient Evolutionary Adaptation of Carcinogenic Phenotype to Host Niche. PLoS Pathog. 2022;18(3):e1010444. doi: 10.1371/journal.ppat.1010444.
  5. Chen Z, Ng RWY, Lui G, Ling L, Chow C, Yeung ACM, Boon SS, Wang MH, Chan KCC, Chan RWY, Hui DSC, Chan PKS. Profiling of SARS-CoV-2 subgenomic RNAs in clinical specimens. Microbiol Spectr. 2022:e0018222. doi: 10.1128/spectrum.00182-22.
  6. Cheung MK, Chan JYK, Wong MCS, Wong PY, Lei P, Cai L, Lan L, Ho WCS, Yeung ACM, Chan PKS, Chen Z*. Determinants and Interactions of Oral Bacterial and Fungal Microbiota in Healthy Chinese Adults. Microbiol Spectr. 2022:e0241021. doi: 10.1128/spectrum.02410-21.
  7. Boon SS, Xia C, Wang MH, Yip KL, Luk HY, Li S, Ng RWY, Lai CKC, Chan PKS, Chen Z*. Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. mBio. 2021;12(5):e0268721. doi: 10.1128/mBio.02687-21.
  8. Chan JYK, Ng CWK, Lan L, Fung S, Li JW, Cai L, Lei P, Mou Q, Meehan K, Lau EHL, Yeung Z, Chan KCA, Wong EWY, Chan PKS, Chen Z*. Restoration of the Oral Microbiota After Surgery for Head and Neck Squamous Cell Carcinoma Is Associated With Patient Outcomes. Front Oncol. 2021;11:737843. doi: 10.3389/fonc.2021.737843.
  9. Chen Z, Chong KC, Wong MCS, Boon SS, Huang J, Wang MH, Ng RWY, Lai CKC, Chan PKS. A global analysis of replacement of genetic variants of SARS-CoV-2 in association with containment capacity and changes in disease severity. Clin Microbiol Infect. 2021. doi: 10.1016/j.cmi.2021.01.018.
  10. Chen Z*, Wong PY, Ng CWK, Lan L, Fung S, Li JW, Cai L, Lei P, Mou Q, Wong SH, Wu WKK, Li RJ, Meehan K, Lui VWY, Chow C, Lo KW, Chan ABW, Boon SS, Lau EHL, Yeung Z, Chan KCA, Wong EWY, Cheng ASL, Yu J, Chan PKS, Chan JYK. The Intersection between Oral Microbiota, Host Gene Methylation and Patient Outcomes in Head and Neck Squamous Cell Carcinoma. Cancers (Basel). 2020;12(11). doi: 10.3390/cancers12113425.
  11. Yeoh YK, Chen Z, Wong MCS, Hui M, Yu J, Ng SC, Sung JJY, Chan FKL, Chan PKS. Southern Chinese populations harbour non-nucleatum Fusobacteria possessing homologues of the colorectal cancer-associated FadA virulence factor. Gut. 2020;69(11):1998-2007. doi: 10.1136/gutjnl-2019-319635.
  12. Chen Z*, Long T, Wong PY, Ho WCS, Burk RD, Chan PKS. Non-human Primate Papillomaviruses Share Similar Evolutionary Histories and Niche Adaptation as the Human Counterparts. Front Microbiol. 2019;10(2093):2093. doi: 10.3389/fmicb.2019.02093.
  13. Chen Z*, Hui PC, Hui M, Yeoh YK, Wong PY, Chan MCW, Wong MCS, Ng SC, Chan FKL, Chan PKS. Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling. mSystems. 2019;4(1). doi: 10.1128/mSystems.00271-18.
  14. Chen Z*, DeSalle R, Schiffman M, Herrero R, Wood CE, Ruiz JC, Clifford GM, Chan PKS, Burk RD. Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans. PLoS Pathog. 2018;14(11):e1007352. doi: 10.1371/journal.ppat.1007352.
  15. Wong MCS, Vlantis AC, Liang M, Wong PY, Ho WCS, Boon SS, Sze RKH, Leung C, Chan PKS, Chen Z*. Prevalence and Epidemiologic Profile of Oral Infection with Alpha, Beta, and Gamma Papillomaviruses in an Asian Chinese Population. J Infect Dis. 2018;218(3):388-97. doi: 10.1093/infdis/jiy160.
  16. Goldman DL, Chen Z#, Shankar V, Tyberg M, Vicencio A, Burk R. Lower airway microbiota and mycobiota in children with severe asthma. J Allergy Clin Immunol. 2018;141(2):808-11 e7. doi: 10.1016/j.jaci.2017.09.018.
  17. Chen Z, Ho WCS, Boon SS, Law PTY, Chan MCW, DeSalle R, Burk RD, Chan PKS. Ancient Evolution and Dispersion of Human Papillomavirus 58 Variants. J Virol. 2017;91(21). doi: 10.1128/JVI.01285-17.
  18. The Cancer Genome Atlas Research Network. Integrated genomic and molecular characterization of cervical cancer. Nature. 2017;543(7645):378-84. doi: 10.1038/nature21386.
  19. Chen Z, DeSalle R, Schiffman M, Herrero R, Burk RD. Evolutionary dynamics of variant genomes of human papillomavirus types 18, 45, and 97. J Virol. 2009;83(3):1443-55. doi: 10.1128/JVI.02068-08.
  20. Wood CE, Chen Z, Cline JM, Miller BE, Burk RD. Characterization and experimental transmission of an oncogenic papillomavirus in female macaques. J Virol. 2007;81(12):6339-45. doi: 10.1128/JVI.00233-07.
  21. Chen Z*, Fu L, Herrero R, Schiffman M, Burk RD. Identification of a novel human papillomavirus (HPV97) related to HPV18 and HPV45. Int J Cancer. 2007;121(1):193-8. doi: 10.1002/ijc.22632.
  22. Narechania A, Chen Z, DeSalle R, Burk RD. Phylogenetic incongruence among oncogenic genital alpha human papillomaviruses. J Virol. 2005;79(24):15503-10. doi: 10.1128/JVI.79.24.15503-15510.2005.
  23. Chen Z, Terai M, Fu L, Herrero R, DeSalle R, Burk RD. Diversifying selection in human papillomavirus type 16 lineages based on complete genome analyses. J Virol. 2005;79(11):7014-23. doi: 10.1128/JVI.79.11.7014-7023.2005.

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