Date of Award

Spring 5-15-2021

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Immunology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



The immune system is an integral part of a healthy functioning organism. Immune responses during the disease are complex and include the interplay of many cell subsets. Integrated genomics and bioinformatics usage can yield unique insights into the immune system’s function in health and disease at a single-cell resolution. Here we utilize complimentary single-cell profiling technologies, scRNA-seq and CyTOF, to explore immune responses across diseases and model organisms. Our approach included leveraging scRNA-seq on few samples to understand the immune response landscape and select key markers for a follow-up protein level validation using an appropriate number of replicates by FACS and CyTOF. Furthermore, we used single-cell TCR-sequencing data, obtained as a part of the scRNA-seq pipeline, to gain additional insight into the immune responses. First, we characterized tumor-infiltrating immune cells in the context of mouse tumors treated with aPD1, aCTLA4, combination treatment, or control antibodies. We used single-cell transcriptional (scRNA-seq) and protein (CyTOF) technologies to profile lymphoid and myeloid cell population changes between growing tumors and rejecting tumors following the successful treatment. We observed the macrophage compartment’s unexpected diversity, changing from anti-inflammatory to pro-inflammatory state, and explored the potential signals that drive the macrophage differentiation. We characterized the lymphocyte compartment, profiled the TCR repertoire of total CD8 T cells and CD8 T cells specific against known tumor antigen, and developed an in-house pipeline to analyze the TCR repertoire data across different conditions and experiments. Second, we applied this approach to study cerebrospinal (CSF) fluid in patients with demyelinating disorders, such as multiple sclerosis and anti-MOG disorder. We observed and reported a unique microglia-like population present in CSF in health and disease. Third, we profiled the lungs and blood of rhesus macaques with the active or latent form of tuberculosis using scRNA-seq and CyTOF. We were the first to describe the immune lung landscape during tuberculosis in non-human primates on the single-cell level. We found that CD27+ NK cells are one of the features of protection in TB latency. We characterized interferon-responsive macrophages, the influx of pDC, and T cells’ activation in macaques’ lungs with active tuberculosis. Fourth, as a response to the COVID-19 pandemic that emerged in 2020, we used CyTOF to profile blood in more than 50 COVID-19 patients and 23 non-COVID-19 patients with respiratory symptoms. We compared it to the blood’s immune subset changes in healthy aging using a dedicated cohort of more than 150 individuals from 25 to 80 years old. We found distinct T cell populations associated with age and COVID-19 disease, correlated clinical parameters with disease severity, and explored the patients’ plasma secretomes. In summary, we have developed multiple pipelines for scRNA/TCR and CyTOF data analysis and applied them to explore immune responses in mice, macaques, and humans across various diseases. Our data reveals a high-resolution transcriptional and protein profiling of immune system response in cancer, autoimmune and infectious diseases.


English (en)

Chair and Committee

Maxim Artyomov

Committee Members

Brian Edelson, Shabaana A. Khader, Naresha Saligrama, Robert Schreiber,