Yu

Xu Yu, MD

Lab Info:

Principal Investigator:
Xu Yu, MD

Lab Staff:
6 post docs
1 bioinformatician
1 PhD student
3 technicians
Openings: postdoctoral fellow (http://www.nature.com/naturejobs/science/jobs/641345-postdoctoral-fellow-positions-at-mgh-bwh-hms)

Office/Location: 400TS RM758

Phone: (857) 268-7004

Email: xyu@partners.org

Category: Group Leaders, Members

Dr Yu’s laboratory focuses on two major areas of research to investigate molecular and cellular mechanisms involved in immune control of HIV-1. A principal area of our investigations includes the role of dendritic cells and their immunoregulatory functions for generating and fine-tuning adaptive immune responses during HIV-1 infection. These studies focus on how interactions between HLA class I molecules and immunoregulatory MHC class I receptors from the Leukocyte Immunoglobulin Like Receptor (LILR) family determine dendritic cell function, and in this way influence HIV-1 disease outcomes. In addition, our lab centers on the analysis of immunological networks associated with immune control against HIV-1 using systems-biology based approaches. These studies use large-scale, unbiased techniques for generating global pictures of HIV-1 immune defense mechanisms by combining high-throughput genomics, proteomics and transcriptomics techniques with functional immunologic and virologic assays. These two research areas are approached in an interdisciplinary fashion through strategic collaborations with computational biologists, chemical and material scientists, infectious disease physicians and molecular biologists and are designed to contribute to clinical strategies that may increase host resistance against HIV-1.

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Press

  • Dendritic cells of elite controllers able to recognize, mount defense against HIV — MGH News
  • The role of dendritic cells in keeping HIV in check without drugs — Eurek Alert (AAAS)
  • Some people can resist the ravages of HIV – here’s how — New Scientist
  • Dendritic cells may hold key to elite controllers’ immune response — Healio
  • Dendritic cells of elite controllers able to recognize, mount defense against HIV — Medical Xpress

 

 

Major Recent Publications

 

1. Hua S, Vigano S, Tse S, Harrington S, Negron J, Garcia-Broncano P, Resino S, Leal M, Ruiz-Mateos E, Lichterfeld M, Yu XG. Pegylated IFN-α induces NK cell-dependent HIV-1 DNA decline in ART-treated HIV-1/HCV co-infected patients. Clinical Infectious Diseases. 2017. (in press)

 

2. Martin-Gayo E, Cole MB, Kolb KE, Ouyang Z, Cronin J, Kazer SW, Ordovas-Montanes J, Lichterfeld M, Walker BD, Yosef N, Shalek AK, Yu XG. A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers. Genome Biology. 2017. In press.

 

3. Sun X, Hua S, Chen HR, Ouyang Z, Einkauf K, Tse S, Ard K, Ciaranello A, Yawetz S, Sax P, Rosenberg ES, Lichterfeld M, Yu XG. Transcriptional Changes during Naturally Acquired Zika Virus Infection Render Dendritic Cells Highly Conducive to Viral Replication. Cell Reports. 2017. Dec 19 Epub

 

4. Martin-Gayo E, Cronin J, Hickman T, Ouyang Z, Lindqvist M, Kolb KE, Schulze zur Wiesch J, Cubas R, Porichis F, Shalek A, van Lunzen J, Haddad E, Walker BD, Kaufmann D, Lichterfeld M, Yu XG. Circulating CXCR5+CXCR3+PD-1Lo Tfh-like cells in HIV-1 controllers with neutralizing antibody. JCI Insight.2017; 2(2):e89574.

 

5. Viganò S, Negrón JJ, Tse S, Chowdhury FZ,Lichterfeld M, Yu XG. HLA-G+ HIV-1-specific CD8 T cells are associated with HIV-1 immune control. AIDS. 2017; 31(2):207-212.

 

6. Gayo E, Buzon M, Ouyang Z, Hickman T, Cronin J, Pimenova D, Walker BD, Lichterfeld M, Yu XG. Potent cell-intrinsic immune responses in dendritic cells facilitate HIV-1-specific T cell immunity in HIV-1 Elite Controllers. PLoS Pathogens. June 11, 2015. DOI:10.1371/journal.ppat.1004930.

 

7. Vigano S, Negron J, Ouyang Z, Rosenberg ES, Walker BD, Lichterfeld M, Yu XG. Prolonged antiretroviral therapy preserves HIV-1-specific CD8 T cells with stem cell-like properties. J Virol. 2015 May 20. pii: JVI.00789-15. [Epub ahead of print] PMID:25995260

 

8. Bashirova A, Martin-Gayo E, Jones DC, Qi Y, Apps R, Gao X, Burke PS, Taylor CJ, Rogich J, Wolinsky S, Bream JH, Duggal P, Hussain S, Martinson J, Weintrob A, Kirk GD, Fellay J, Buchbinder SP, Goedert JJ, Deeks SG, Pereyra F, Trowsdale J, Lichterfeld M, Telenti A, Walker BD, Allen RL, Carrington M, Yu XG. LILRB2 interaction with HLA class I correlates with control of HIV-1 infection. PLOS Genetics. 2014. Mar 6;10(3):e1004196. PMID: 24603468.

 

9. Li C, Toth I, Zur Wiesch J, Pereyra F, Rychert J, Rosenberg ES, van Lunzen J, Lichterfeld M, Yu XG. Functional characterization of HLA-G+ regulatory T cells in HIV-1 infection. Plos Pathogens 2013 Jan;9(1):e1003140. PMID: 23382678.

 

10. Lichterfeld M, Cung T, Seiss K, Rosenberg ES, Pereyra F, Yu XG. Shelterin dysfunction and p16INK4a-mediated growth inhibition in HIV-1-specific CD8 T cells. J Virol. 2012 May;86(10):5533-40. PMID:22398292.

 

11. Huang J, Al-Mozaini M, Rogich J, Carrington MF, Seiss K, Pereyra F, Lichterfeld M, Yu XG. Systemic inhibition of myeloid dendritic cells by circulating HLA class I molecules in HIV-1 infection. Retrovirology. 2012 Jan 30;9:11. PMID:22289474.

 

12. Huang J, Burke PS, Cung TD, Pereyra F, Toth I, Walker BD, Borges L, Lichterfeld M, Yu XG. Leukocyte immunoglobulin-like receptors maintain unique antigen-presenting properties of circulating myeloid dendritic cells in HIV-1-infected elite controllers. J Virol. 2010;84:9463-71.

 

13. Huang J, Goedert JJ, Sundberg EJ, Cung T, Burke P, Martin MP, Preiss L, Lifson J, Lichterfeld M, Carrington M, Yu XG. HLA-B*35-Px-mediated acceleration of HIV-1 infection by increased inhibitory immunoregulatory impulses. J Exp Med. 2009; 206(13):2959-2966.

 

14. Lichterfeld M*, Mou D*, Cung HT, Williams KL, Waring MT, Huang J, Pereyra F, Trocha A, Freeman GJ, Rosenberg ES, Walker BD, Yu XG. Telomerase activity of HIV-1-specific CD8+ T cells: Constitutive upregulation in controllers and selective increase by blockade of PD ligand 1 in progressors. Blood, prepublished online August 26, 2008; DOI 10.1182/blood-2008-01-135442.

 

15. Lichterfeld M*, Kavanagh D*, Williams KL, Mosa B, Mui S, Miura T, Allgaier R, Pereyra F, Trocha A, Feeney M, Gandhi R, Rosenberg E, Altfeld M, Allen T, Allen R, Walker B, Sundberg E, Yu XG. A Viral CTL escape mutation leading to ILT4-mediated functional inhibition of myelomonocytic cells. J Exp Med. 2007; 204(12):2813-24.

 

More Publications

Current Members

navin

Fatema (Navin) Chowdhury | fchowdhury@partners.org

Navin joined Dr. Yu’s and Dr. Lichterfeld’s groups in August of 2014 as a Research Fellow. She received her PhD in Immunology at UT Southwestern Medical Center, where she studied how innate cytokines regulate CD8+ T cell function. She is interested in infectious diseases in the context of global health and will study immune response to HIV-1. A native of Bangladesh, Navin grew up in the beautiful tea gardens of Srimongol and developed a love for the wilderness. She loves to travel around the world in search of culture and cuisine.

 


Xiaoming Sun | xsun16@mgh.harvard.edu

Xiaoming joined Dr. Yu’s group as a Research Fellow in July 2015. He received his PhD in Immunology in 2014 at Kumamoto University, under the mentorship of Dr. Masafumi Takiguchi, where he studied HIV-1 escape mutations and CD8 Cytotoxic T lymphocytes. After his PhD studies, he moved to Boston to join Dr. Yu’s group where he studies immune response to ZIKA virus, as well as HIV-1 immune defense in Elite Controllers using a system immunology approach. When not in lab, he serves as vice-president of the Massachusetts General Hospital Chinese Scientists and Staff Association (MGH-CSSA). Additionally, he enjoys photography, reading, and spending time with his family and friends.

 

Guinevere (Guin) Lee | klee54@mgh.harvard.edu

Guinevere (Guin) received her PhD in HIV genotypic drug resistance and tropism inferences from the University of British Columbia in Vancouver, Canada. She is fascinated by the intrahost genetic diversity of HIV, and dreams to understand more about its impact on clinical outcomes. She joined Dr. Yu’s and Dr. Lichterfeld’s labs in August 2015 as a postdoctoral fellow to specifically study HIV reservoir(s) in different immune cell types using HIV nucleotide sequence diversity as markers. When not in the lab, Guin enjoys scuba diving, traveling, creating music, and audio processing. She is also a big fan of anime.

 

Stephane Hua | shua4@mgh.harvard.edu

Stephane joined Dr. Yu’s group in September 2015 as a Research Fellow. He received his PhD in immunology at INSERM U1012 in France under the supervision of Dr. Alain Venet and has characterized different subsets of HIV-specific CD8+ T cells in HIV infected patients. He is now investigating the effect of type I interferon in the immune response in HCV/HIV coinfected patients and in HIV infected patients. When not at work, he enjoys visiting new places, watching and playing sports (football, badminton) and watching movies.

 

Pilar Garcia Broncano | pgarciabroncano@mgh.harvard.edu

Pilar received her PhD in 2017 at the Complutense University of Madrid, where she studied immune cell dysfunction and hyperactivation in HIV/HCV coinfected patients, as well as the in vitro and in vivo activity of nanoparticles against HIV-1 and HSV-2 infections to prevent their transmission in humans as a topical microbicide. She joined Dr. Yu’s and Dr. Lichterfeld’s labs in January 2016 as a visiting PhD student to study possible alterations in the HIV reservoir due to HCV treatment using HIV full genome sequencing in HIV/HCV coinfected patients. She returned to the lab in October 2016, as a Graduate Research Assistant while completing her PhD studies. She is currently a Research Fellow who is studying the immunological and virological characterization of HIV-1-infected patients who are taking antiretroviral therapy and various viral reactivation agents in several ongoing clinical trials. Pilar enjoys scuba diving, snowboarding, running and traveling in her free time.

 

Kevin Einkauf | keinkauf@mgh.harvard.edu

Kevin joined Dr. Yu’s and Dr. Lichterfeld’s labs as a Research Technician in June 2016 after receiving his B.A. in Neurobiology from Harvard College. In his undergraduate research, Kevin worked at McLean Hospital, studying the neural circuitry underlying depression and substance abuse. He also spent time as a research fellow at the Botswana-Harvard AIDS Institute Partnership in Gaborone, Botswana, studying HIV-1 drug resistance. Currently, Kevin is primarily focused on understanding the latent HIV-1 reservoir and how it responds to various clinical interventions. In his free time, Kevin enjoys hiking, traveling, and eating hot pot.

 

Shivaali Maddali  | smaddali@mgh.harvard.edu

Shivaali joined Dr. Yu’s and Dr. Lichterfeld’s labs in June 2017 as a Research Technician, Lab Manager, and Clinical Research Coordinator. She received her BS in Biomedical Engineering from Brown University, where she used 3D printing methods to develop biomimetic in vitro platforms to study cancer metastasis. Her current work utilizes flow cytometry to study peptide recognition in the context of the HIV-1 immune response. When not in the lab, Shivaali enjoys traveling, photography, watching football, playing soccer, and spending time with friends and family.

 

Ce (Charlie) Gao  | cgao4@mgh.harvard.edu

Ce (Charlie) joined Dr. Yu’s and Dr. Lichterfeld’s labs in July 2017 as a Bioinformatics Specialist. He received his PhD in Bioengineering from Northeastern University and worked as a Postdoctoral Fellow at Beth Israel Deaconess Medical Center/Harvard Medical School, where he worked on cancer immunotherapy projects. He is currently collaborating with researchers in the lab on various projects related to HIV and ZIKA, including analyses regarding genomics, transcriptomics, and proteomics. In addition, he is responsible for the computational infrastructure of the lab. Outside the lab, he enjoys running, swimming, reading/listening to books, and watching movies.

 

Chenyang Jiang  | cjiang5@mgh.harvard.edu

Chenyang joined Dr. Yu’s and Dr. Lichterfeld’s labs as a Research Technician II and Lab Manager in August 2017 after graduating from the University of Connecticut with MS in Pathobiology. She received her BS in Biological Sciences in 2016 from Sichuan University in China. Previously, Chenyang focused her research on house dust mite-induced allergic airway disease in murine models of sickle cell disease. She switched from Pathobiology to Virology and Immunology work, and is now investigating possible alterations of HIV-1 viruses in HIV elite controllers and viremic controllers by doing full genome sequencing. In her free time, she enjoys traveling, reading, watching movies, and exploring Boston cuisine with friends.

 

Xiaodong Lian  | xlian1@mgh.harvard.edu

Xiaodong joined Dr. Yu’s and Dr. Lichterfeld’s labs in September 2017 as a visiting PhD student. He is a graduate student from the Kunming Institute of Zoology, Chinese Academy of Sciences, where he studied MHC/HLA splicing variants and pig-tailed macaque animal models of HIV/AIDS. He currently works on understanding the viral reservoir in HIV controllers using viral genome sequencing. In his free time, Xiaodong enjoys watching movies, playing video games, hiking, and traveling with his friends.

 

Jane Blackmer  | jeblackmer@mgh.harvard.edu

Jane joined Dr. Yu’s and Dr. Lichterfeld’s labs in June 2018 as a Research Technician after graduating from Tufts University. At Tufts, she received her B.S. in Biology while studying trinucleotide repeat instability and DNA double-strand break repair in Drosophila. Currently, she is interested in doing molecular virology work to understand the latent HIV-1 reservoir. Outside of lab, Jane enjoys music, reading, and spending time with friends and family.

 

Joshua Chevalier  | jmchevalier@mgh.harvard.edu

Joshua joined Dr. Yu’s and Dr. Lichterfeld’s labs as a Research Technician in June 2018. He graduated from the University of Massachusetts Amherst with a B.S. in Biology, where he researched the replicative polymerases of the parasite Trypanosoma brucei. He has always been interested in studying infectious disease and will be analyzing the latent HIV-1 reservoir in HAART treated patients.  Outside of lab, Joshua enjoys exploring nature, traveling to new places, and spending time with friends.

Former Members

Samantha Chen | samantha.chen@mgh.harvard.edu

Samantha joined Dr. Yu’s lab in May 2017 as a Research Fellow. She received her PhD in Microbiology and Immunology from the AIDS Institute at the University of Hong Kong, where she studied HIV-specific immune responses after PD1-based DNA vaccination in murine and rhesus macaque models. She is now investigating adaptive and innate immunity of HIV elite controllers, viremic controllers and HIV-treated patients. When not in lab, Samantha enjoys seeing live music, rock climbing, exploring nature, and traveling around the world.

 

Enrique

Enrique Gayo | egayo@partners.org

Enrique obtained his PhD in Molecular Biology and Immunology in 2010 at the Universidad Autonoma de Madrid, under the supervision of Dr. Maria Luisa Toribio, where he studied the developmental origin of intrathymic dendritic cells and their contribution in the generation of natural T regulatory cells. After his PhD studies, he moved to Boston to join Dr. Yu’s group where he is currently studying the involvement of dendritic cell function in the spontaneous control of HIV-1 infection. In the past 5 years as a postdoctoral investigator, Enrique has produced 3 first authored publications and a bibliographical review. Additionally, he has been awarded two developmental awards from the Harvard University CFAR and the Massachusetts General Hospital ECOR programs. Enrique is a very social person who loves sports and every form of art, especially painting. He also enjoys hiking and everything related to nature and outdoor activities.

 

Aleksanyan
Naira Aleksanyan | naleksanyan@partners.org

Naira joined the Dr. Yu and Dr. Lichterfeld’s lab in 2016 as a research technician and clinical research coordinator. She received her BS in Biology from Suffolk University in Boston. In the past, Naira has investigated bacterial mating of Bacillus subtilis and Clostridium difficile attachment to intestinal cells. She is excited to switch from bacterial to viral work, and is currently learning to minimize killing PBMCs and infecting them with HIV. In her free time, Naira enjoys swimming, hiking, traveling, learning new idioms, and playing with goats.

 

Ouyang
Zhengyu Ouyang | zouyang@partners.org

Zhengyu Ouyang joined Yu’s group as bioinformatics specialist in June 2012. He prefers to be called “O’Young”. He received his Bachelor’s degree in telecommunication engineering and Master’s degree on pattern recognitions from Beijing University of Posts and Telecommunications (P.R. China). Ouyang earned his PhD in Computer Science (bioinformatics) from New Mexico State University in 2012. He focuses on computational and statistical analysis of molecular biological high-throughput genetic data to support biologists to test their hypotheses. Ouyang used to be a sprinter and still enjoys running, hiking and swimming, as well as other outdoor sports. Travelling and camping are definitely ranked on the top of his favorites.

 

Will.v1

William McNeil | wmcneil@partners.org

Will received his BS in Biology and Community Health from Tufts University, where he studied chitin deacetylase enzymes as potential drug targets against lymphatic filariasis.  He joined Dr. Yu’s lab in the spring of 2015 as a research technician studying the virology and immunology of the HIV-1 reservoir, as well as the role toll-like receptors play in regards to HIV infection and integration into host cell chromosomes. Will enjoys spending time outdoors running, hiking, and participating in adrenaline-filled activities such as windsurfing and skydiving. He also likes traveling and learning to cook dishes from around the world.

 

samantha

Samantha Tse | stse1@partners.org

Samantha is originally from Boston and received her BS in Biology at Boston College in the spring of 2014. She joined the Dr. Yu’s and Dr. Lichterfeld’s Labs shortly after in the summer of 2014 and is currently working as a Research Technician at the Ragon Institute with Dr. Dhohyung Kim studying systems biology in regards to elite controllers. When not in lab, she enjoys participating in adrenaline-inducing activities, such as rollercoasters, ziplining, and go-kart racing. She also enjoys hip hop dancing, karaoking, and hiking on long trails. Sammy is currently enrolled in a PhD/MD program at University of Massachusetts Medical School. She is interested in studying gut microbiome effects on the immune system.

 

Sean Harrington

Sean Harrington | sharrington7@partners.org

Sean received his BS in Biochemistry from Northeastern University in December 2013. He joined Dr. Yu’s and Dr. Lichterfeld’s labs as a research technician and a lab manager in the spring of 2014, working to further understand the HIV-1 reservoir. When not in the lab, he enjoys going on runs around Boston and baking. Sean currently conducts cancer research at Bluebird Bio in Cambridge.

 

 

Jacquie Cronin

Jacquie Cronin | jcronin7@partners.org

Jacquie received her BS in Biology from Saint Michael’s College in Vermont in 2013. The following summer she worked as a research technician at the University of Vermont, where she studied protein kinase A expression and interaction with other tyrosine kinases. Jacquie joined the Yu lab during the spring of 2014. She is currently a research technician studying the role of dendritic cells in HIV infection. When not in the lab, Jacquie loves spending time at the beach, anything fitness related, and teaching children how to ice skate. She is now conducting research on MERS-CoV in a government funded lab and enjoying the slopes and mountains in Montana.

 

Nina
Nina Orlova-Fink | norlova@partners.org

Nina joined Xu’s lab as a graduate research fellow in August 2013. She is investigating stem cell properties of CD4+ T cells for limiting HIV persistence. She studied Molecular Medicine at the University of Erlangen in Germany and did her PhD in Virology from a collaboration program between Harvard Medical School and University of Erlangen. When not in the lab she loves baking, spending time with friends, and dancing tango.

 

Dhohyung‎ Kim

Dhohyung Kim | dkim26@partners.org

Dhohyung Kim is a Research Fellow at the Ragon Institute. He received his PhD in Molecular, Cellular and Developmental Biology under the mentorship of Dr. Stefan Niewiesk, at the Ohio State University. In the Dr. Yu’s and Dr. Lichterfeld’s Labs, Dhohyung studies the host cyclin-dependent kinases and HIV-1 reverse transcription, as well as the T cell intrinsic responses in various patient cohorts to HIV-1 infections. When not at work he enjoys traveling and driving around the city.

 

Jordi

Jordi Negron | jnegron@partners.org

Jordi joined Dr. Xu Yu’s Lab in the summer of 2013 as a Research Technician and Lab Manager after graduating from Brown University with an ScB in Chemical Biology. He studies the role of CD8 T cell subsets in HIV infection through flow cytometry analysis. Outside of the lab, Jordi likes learning about other cultures and languages; this leads him to take trips around town looking for new areas to explore or to ask people at the Ragon what it is like living in different countries.

 

Taylor

Taylor Hickman

Taylor graduated from the University of New Hampshire with a BS in Biochemistry in 2012. She joined the Xu Yu lab in the summer of 2012 as a research technician studying the role of dendritic cells in HIV infection, and as a Yu lab manager. In her spare time, Taylor enjoys running and listening to country music. Taylor left the Xu lab in June 2014 to do Oncology research at Novartis.

 

Pat

Patrick Burke

Patrick is from outside of New Haven, CT and graduated from Boston College with a BS in Biology and a minor in Computer Science. After graduation, he spent two years working as a technician under the tutelage of Dr. Xu Yu at the Ragon Institute. He then moved on to study medicine at the Tufts University School of Medicine. After Pat’s third year, he was awarded a DDCF Clinical Mentorship grant to return to Dr. Yu’s lab for a year, where he currently studies the effects of a group of immunoregulatory receptors found in the adaptive immune system and their role in HIV infection. In addition to enjoying tennis and skiing, he is obsessed with outer space and has aspirations to visit it one day. Pat has returned to Tufts to complete his last year of school.

 

Amy

Amy Shaw

Amy received her BS in Microbiology and Immunology with a minor in Spanish from the University of Miami in 2012. She joined the Xu lab in early summer 2012, where she works as a research technician and as a lab manager in Dr. Yu’s and Dr. Lichterfeld’s labs. She currently works with Dr. Maria Buzon, conducting experiments to better understand the HIV-1 reservoir. When not at work, Amy enjoys going on nature walks with her dog, cooking new recipes, and going to Dave Matthews Band shows.

 

Selena
Selena Vigano

Selena is a postdoctoral fellow at the Ragon institute of MGH, MIT and Harvard. Her research is focused on the investigation of the role of distinct HIV-1-specific CD8 T cells subsets in controlling HIV-1 infection and their contribution to disease progression. She is also involved in a collaborative research project investigating the influence of HDAC inhibitor on the immune system of HIV-1 infected patients. Selena obtained her PhD in Immunology in 2013 from UNIL University and CHUV in Lausanne.