Yue Chen, PhD

Associate Professor, Infectious Diseases and Microbiology


2138 Public Health, 130 DeSoto Street, Pittsburgh, PA 15261
R-znvy: pural@cvgg.rqh
Primary Phone: 967-179-0843

Personal Statement

 --- Exploring gut microbiome changes in the early stages of HIV seroconversion. The human gut contains over 1,000 different bacterial species. This microbiome maintains gut mucosal homeostasis. Gut microbial imbalance (dysbiosis) can lead to microbial translocation and chronic inflammation in HIV-infected individuals, further enhancing HIV progression. Our hypothesis is: the gut dysbiosis occurs during HIV infection and enhances development of AIDS. Currently we are measuring the gut microbiome using the fecal samples collected in the MACS during visits 1 through 3 in 1984-1985. This study will reveal the gut microbiome changes in the early stages of HIV seroconversion prior to the implementation of anti-retroviral therapy.  

--- Exploring the role of oral microbiome in HIV pathogenesis. Human oral cavity is home to several million bacteria. The oral microbiome is particularly important to health because it can cause both oral and systemic disease. Oral microbiota in HIV infected individuals plays an important role in initiation and/or enhancement of oral infections. Furthermore, HIV infects oral mucosal tissues and dysregulates oral microbiome. HIV-associated periodontal diseases could lead to microbial translocation and serve as a source of chronic and systemic immune activation, which increases the risk of cardiovascular diseases and pulmonary diseases. 

--In cancer patients, tumor cells are rapidly dividing, constantly releasing tumor DNA into the blood. Recent advances in next-generation sequencing have made it possible to sequence circulating tumor DNA (ctDNA) in blood plasma with high sensitivity and specificity, termed “liquid biopsy”. This will have a key role in clinically assisting early diagnosis, longitudinal analyses of tumor evolution and personalized therapeutic intervention. We hypothesize that there are sufficient ctDNA in the plasma of HIV-1 infected MACS subjects at least 6 months prior to development of AIDS- associated cancers that can be measured and used as biomarkers for early diagnosis and personalized therapeutic intervention of AIDS related cancers. To detect the ctDNA in plasma samples of AIDS- associated cancer patients before and after the cancer diagnosis, longitudinal MACS plasma samples are being used to detect ctDNA via a next-generation sequencing with an Ion AmpliSeq comprehensive cancer panel, which targets 409 tumor suppressor genes and oncogenes frequently cited and frequently mutated in cancer cells. The quantity and evolution of ctDNA will be monitored in plasma DNA. Our eventual goal is to develop a noninvasive method for detecting plasma ctDNA, which assists early diagnosis and personalized therapeutic intervention for AIDS- associated cancers.

---Pennsylvania/MidAtlantic AIDS Education and Training Center (PA/MidAtlantic AETC) provides education, consultation, technical assistance and resource materials of HIV/AIDS/HCV/STD/substance abuse to health care professionals throughout Pennsylvania, Maryland, Virginia, West Virginia, Delaware and District of Columbia. Our effort to educate and train healthcare professionals will increase the providers' capacity to provide high-quality HIV/AIDS care and fight against current opioid epidemics.      


1978-1983 | Dalian Medical University, China | MD, Medicine
1986-1989 | Xian Medical University, China | MS, Pathophysiology
1992-1998 | University o Pittsburgh, PA | PhD,  Virology
1998-1999 | Department of IDM, University of Pittsburgh | Post-doc Fellow


IDM 2023, Microbiology Laboratory
IDM 2003, Host Response to Microbial Infection
IDM 2038, Prevention, Treatment, and Control of Global Infectious Diseases
IDM 2013, Viral Pathogenesis
IDM 2034, Control and Prevention of HIV/AIDS

Selected Publications

Rossi F, Li X, Jacobson L, Levine AJ, Chen Y, Palella FJ, Margolick J, Viscidi R.  (2015).  BK virus capsid antibodies are associated with protection against subsequent development of PML in HIV-infected patients. Virology. 485:467-472. 

Kuniholm MH, Ong E, Hogema BM, Koppelman M, Anastos K, Peters MG, Seaberg EC, Chen Y, Nelson KE, Linnen JM.  (2016). Acute and Chronic Hepatitis E Virus Infection in Human Immunodeficiency Virus-Infected U.S. Women. Hepatology. 63:712-720.

Sankapal S, Gupta P, Ratner D, Ding M, Shen C, Sanyal A, Stolz D, Cu-Uvin
S, Ramratnam B,  Chen Y.  (2016). HIV exposure to epithelial cells in ectocervical and colon tissues induces inflammatory cytokines without tight junction disruption. AIDS Res Hum Retroviruses 32:1054-1066.

Chen Y, Shen C, Guha D, Ding M, Kulich S, Ashimkhanova A, Rinaldo C, Seaberg E, Margolick J, Stosor V, Martínez-Maza O, Gupta P.  (2016). Identification of the transcripts associated with spontaneous HCV clearance in individuals co-infected with HIV and HCV. BMC Infect Dis 16:693.

Sanyal A, Mailliard RB, Rinaldo CR, Ratner D, Ding M, Chen Y, Zerbato JM, Giacobbi NS, Venkatachari NJ, Patterson BK, Chargin A, Sluis-Cremer N, Gupta P.  (2017). Novel assay reveals a large, inducible, replication-competent HIV-1 reservoir in resting CD4+ T cells.  Nature Medicine doi:10.1038/ nm.4347.

Yue  Chen