Mukerji Lab for Neuroinfectious Diseases

Overview

The Mukerji Lab explores how HIV and other infections affect the brain, with a focus on depression, cognitive changes, neuropathy, and the biological pathways that connect systemic health to neurological function. Despite effective viral suppression, many individuals continue to experience neurological complications. Our research seeks to understand why these problems persist, how early signs can be detected, and which biological factors shape long-term brain health in people with HIV. Through integrated biomarker, neuroimaging, and clinical studies, we aim to generate insights that directly inform the development of future diagnostic and therapeutic strategies in brain health.

Research Projects

Mood and Cognition in HIV

Depression is a critical health challenge for people with HIV, affecting mood, cognition, and overall quality of life, and many individuals do not fully respond to standard antidepressant treatments. Our research program investigates how brain, immune, and behavioral systems interact to shape depressive symptoms in this population, with the goal of identifying new therapeutic targets and improving functional outcomes. The SOOTHE trial (NCT05570812) examines whether neuroactive steroid modulation with pregnenolone can improve brain activity, reduce inflammation, and alleviate depressive symptoms. The COPE trial (ACTG A5402) directly compares pramipexole extended release and escitalopram to determine which treatment pathway offers greater benefit for depression and mild neurocognitive disorder in people with HIV. Together, these studies advance a mechanistic understanding of depression in HIV and evaluate treatment strategies tailored to this community.

For inquiries about SOOTHE, please call 857‑282‑9955 or email mghsoothe@partners.org.

For inquiries about COPE, please call 617‑726‑3819 or email findacure@partners.org.

Translational Neuro-HIV Research for Accessible Clinical Care

The Mukerji Lab is committed to closing the gap between scientific discovery and real-world brain health care for people with HIV by integrating biomarkers, clinical assessment tools, and evidence-based strategies that can be implemented directly in HIV clinical settings. We study blood-based biomarkers such as neurofilament light chain (NfL) and glial fibrillary acidic protein (GFAP) to identify early or subtle cognitive changes. Early findings show that higher levels of these markers are associated with poorer cognitive performance, and that NfL may help identify individuals whose cognition declines over time. Complementing these biological approaches, we evaluate innovations such as portable low-field MRI and machine-learning-based imaging to expand monitoring capabilities in outpatient settings. Together, these efforts aim to make brain-health care more equitable, actionable, and integrated for people aging with HIV.

HIV Persistence and Brain Reservoirs

The BEACON Legacy Program advances our understanding of how HIV persists in the brain by partnering with people with HIV who choose to make a lasting contribution to research through planned tissue donation. Even with effective antiretroviral therapy, HIV can remain hidden in brain cells, protected by biological barriers that make it inaccessible to routine clinical tests. Because these reservoirs cannot be safely studied during life, donated tissue provides the only opportunity to map where the virus resides and how it survives long-term treatment. Using state-of-the-art laboratory techniques, our multidisciplinary team analyzes donated brain tissue at the level of individual cells to identify intact and defective virus, determine how HIV integrates into DNA, and test whether dormant virus can be reactivated. This work brings us closer to understanding the mechanisms that allow HIV to persist in the brain and supports the development of future cure-directed therapies.

For inquiries about BEACON, please call 857-282-4657 or email mghbeacon@mgb.org.

Shibani S. Mukerji, MD, PhD
Associate Professor of Neurology, Harvard Medical School and Massachusetts General Hospital

Dr. Shibani S. Mukerji is an MD and PhD graduate of Case Western Reserve School of Medicine and completed a postdoctoral fellowship in Dr. Dana Gabuzda lab at the Dana Farber Cancer Center. Dr. Mukerji received specialized clinical training in the neurological management of infectious diseases from the Mass General Brigham/Harvard Medical School residency and fellowship programs and sees patients with HIV infection in the MGH Neurology Department and the Division of Infectious Diseases. Dr. Mukerji grew up in Phoenix and enjoys spending time biking and traveling with her husband and daughter.

Carson Quinn, MD
Advanced General and Autoimmune Neurology Fellow, PGY-5, Massachusetts General Hospital

Carson is a PGY-5 fellow with a clinical focus on infectious diseases of the nervous system. He graduated from UC San Francisco Medical School where he was awarded a global health research fellowship to perform clinical research on HIV-associated meningitis in Kampala, Uganda. There he specifically focused on diagnosis of and cognitive outcomes after TB Meningitis. Carson joined the Mukerji Lab in 2023 and is currently spearheading projects on diagnostic testing for neuroinvasive West Nile Virus infections. He is also a co-investigator on the SOOTHE trial. He also has a strong commitment to medical education and mentorship. After residency, Carson will be a fellow in the Mass General Advanced General Autoimmune and Infectious Neurology Fellowship. He will use this subspecialty expertise to further a career in clinical care, education, and clinical research in infectious and inflammatory neurologic diseases.

Elena Beideck, MD
Research Fellow

Hemi Park, MPH
Clinical Research Project Manager

Hemi manages operations and regulatory compliance for an ongoing Phase II clinical trial. She holds an MPH in Epidemiology from Temple University and joined the lab in January 2023. Her research interests include structural contributors to health inequities, with a focus on prevention gaps, disparities in access to care, and the influence of social determinants of health on outcomes.

Meghal Desai, MPH, BDS
Clinical Research Coordinator

Meghal Desai joined the Mukerji Lab as a Clinical Research Coordinator for the SOOTHE Trial in March 2024. She holds a Master’s in Public Health from the University of Miami. Previously, Meghal served as a Graduate Research Assistant at the University of Miami, where she contributed to projects on topics such as first health responders, cannabis users, and e-cigarette users. She also interned at the start-up company Surgo, where she played a key role in an extensive literature review for Surgo’s tool "Mosaic," which provides sociobehavioral data to pharmaceutical companies. Originally a dentist from India, Meghal aims to pursue a career in dentistry in the United States. In her free time, she enjoys reading, hiking, and traveling.

Malachi Keo, BA
Clinical Research Coordinator

Since Fall 2023, Malachi has been the coordinator for studies evaluating portable MRI technology (POCKET-MRI PWH study) and the analysis of HIV-1 proviral DNA within the CNS through autopsy tissue donation (BEACON study). His interests include HIV-associated neurocognitive disorder (HAND) and addressing structural barriers to care. He is involved in developing medical education for LGBTQ+ youth through qualitative research at Harvard Medical School, and advocacy to improve national mental health. Malachi graduated from UC Berkeley with BA degrees in Molecular & Cell Biology and Psychology. In his free time, he’s in search of spicy Cambodian food, true crime podcasts, and mastery of the Spanish language. He plans to attend medical school.

Daire Daly, BS
Research Technician

Daire joined the Mukerji lab as a Research Technician in February 2024. Before joining the lab, Daire worked in the CRM Flow Cytometry core at Massachusetts General Hospital, where she became familiar with the technique of Flow Cytometry. Daire graduated from Worcester Polytechnic Institute in 2021 with a degree in Bioinformatics, where she completed a project working to create a model for pathogenic yeast within the gut microbiome. In the Mukerji lab she is working to analyze the impact of pregnenolone on blood biomarkers in people with HIV. She is from Sharon, MA and in her free time she enjoys triathlons, hiking, skiing, and generally spending time outdoors.

Ali Han Yaramis, MD
Research Fellow

Ali Han Yaramis graduated from Bezmialem Medical Faculty in Istanbul, Turkey, in 2023. Following his graduation, he completed his mandatory state service in Turkey, serving for one year as a medical doctor in a community health center and hospital emergency department. Driven by his interest in Neuropsychiatry and neurology, he pursued research opportunities at the intersection of these fields. Ali Han is actively involved in projects at the intersection of neurology and neuroinfectious diseases. His work includes developing a machine learning model to predict cefepime neurotoxicity in clinical settings, aiming to improve early detection, risk stratification, and patient safety in those receiving this antibiotic. Ali Han is passionate about advancing brain health through clinical research. He enjoys discussing and conducting research, trying new recipes in the kitchen, maintaining a regular exercise routine, and practicing meditation.

Eneidy Pina, MD
Volunteer

Eneidy Pina is a graduate of Universidad Iberoamericana Medical School in her native Dominican Republic, where she concentrated in Tropical Medicine and Global Health. She is interested in how infectious diseases shape immune responses and neurological function. Eneidy aspires to integrate clinical medicine and research, with the long-term goal of reducing health disparities.

Douglas Wilcox, MD, PhD
Research Fellow

Doug works in the Mukerji Lab as a Resident Physician in the Harvard BWH-MGH Neurology Program. He completed both his MD and PhD from Northwestern University, where he worked with Dr. Richard Longnecker on the pathogenesis of Herpes Simplex Virus Encephalitis. Doug also works with Dr. Chenghua Gu at Harvard Medical School on the immune response to pathogens at the blood-brain barrier. In the Mukerji lab, his focus is on the pathogenesis of acute viral encephalitis, including Eastern Equine Encephalitis (EEE) and Herpes Simplex Encephalitis (HSE). Doug grew up in Durham, New Hampshire and enjoys hiking and traveling.

Publications

https://www.ncbi.nlm.nih.gov/myncbi/shibani.mukerji.1/bibliography/public/

Open Positions

We currently do not have any paid open positions. However, if you are interested in postdoctoral research opportunities or potential internship or volunteer roles, please reach out to brainID@partners.org with your CV, cover letter, and two writing samples.