Nirjal Bhattarai, Ph.D.
Office of Tissues and Advanced Therapies
Division of Cellular and Gene Therapies
Gene Transfer and Immunogenicity Branch
Dr. Bhattarai earned his PhD in Molecular and Cellular Biology from the University of Iowa Carver College of Medicine. He completed his postdoctoral training in the Division of Infectious Diseases at the University of Iowa Hospitals and Clinics. Early in his career, Dr. Bhattarai discovered a novel mechanism used by a non-pathogenic human RNA virus (GB virus C, formerly known as hepatitis G virus) to evade host immune responses and establish viral persistence. Additional studies disclosed that similar mechanisms are commonly used by related RNA viruses to evade host immune responses; however, the molecular mechanisms differ among viruses. His studies also disclosed novel mechanisms by which hepatitis C virus (HCV) and Yellow Fever virus (YFV) evade host immune responses.
Currently, his lab studies how RNA viruses of the Flaviviridae family evade host immune responses and use this knowledge to develop novel immunomodulatory gene therapy vectors with lower immunogenicity profiles. His lab also studies inflammatory toxicities associated with engineered T cell therapy, such as CAR-T cells, in order to better understand mechanisms contributing to product toxicities and to develop novel strategies for increasing product safety. The long-term goal of his lab is to develop novel strategies to increase safety and efficacy of gene and cell therapy products.
Viral vector-based or cell-based gene therapies hold great potential for treating many human diseases. However, challenges such as host immune responses and inflammatory toxicities associated with these therapies can impede its development and widespread use. Pre-existing immunity against viruses used in gene therapies, de novo immune responses against viral vectors and transgene products, and inflammatory toxicities associated with CAR-T cell therapies, are some of the major challenges that must be addressed. The ability of these products to induce immune responses and inflammation (product immunogenicity) is a safety risk to patients and can also limit product efficacy. Thus, there is a need for novel strategies for reducing the immunogenicity of gene therapy products in order to improve their safety and efficacy.
Currently, we are studying the underlying mechanisms that trigger immune responses during gene therapy with viral vectors (e.g. lentiviral and AAV) and developing various strategies to reduce product immunogenicity. Our previous studies identified novel mechanisms of host immune modulation by RNA viruses. We are using these viral strategies to reduce the immunogenicity of gene therapy vectors. We are also studying mechanisms contributing to severe inflammation and toxicity during CAR-T cell therapies and developing strategies to reduce CAR-T cell product toxicities.
This work addresses a very important public health issue. Gene therapy with viral vectors or CAR-T cells have shown great potential to treat many human diseases, such as cancer, genetic diseases, chronic viral infections, and autoimmune diseases. However, host immune responses against these products can negatively affect product safety and efficacy. The innovation of our research relates to 1) using natural viral immunomodulatory strategies to reduce unwanted host immune responses against gene therapy vectors and 2) developing novel strategies to increase safety and efficacy of CAR-T cell therapy.
The scientific knowledge obtained from these studies might also help to evaluate the safety and efficacy of gene therapy product applications submitted to the FDA as well as help manufactures to improve the safety and efficacy of these products.
T cell receptor (TCR) signaling is required for T cell activation and development of T cell response against gene therapy vectors; it is also required for chimeric antigen receptor (CAR) T cell activation and function. Thus, understanding mechanisms regulating TCR signaling might help to develop strategies for reducing host immune responses during gene therapy or inflammation during CAR-T cell therapy.
One of the goals of our research program is to develop strategies to reduce host immune responses against viral vectors during gene therapy. Our previous studies on RNA viruses, such as hepatitis C virus (HCV) and Yellow Fever virus (YFV), identified novel mechanisms by which these viruses dampen host T cell response. We identified highly conserved immunomodulatory motifs in the viral protein and RNA that interfere with TCR signaling pathways. One mechanism is viral-RNA-mediated suppression of tyrosine phosphatase epsilon (PTPRE) expression, which impairs Lck activation. PTPRE is a novel regulator of TCR function and in cells expressing HCV and YFV RNA, PTPRE expression is reduced, impairing T cell function. Furthermore, PTPRE expression in liver tissue and peripheral blood mononuclear cells from HCV-infected or YFV-vaccinated humans is lower than that of controls. In preclinical studies, PTPRE expression in the liver and splenocytes of mice infected with YFV is reduced compared to mice infected with control (mumps) virus. In addition, inhibition of PTPRE by YFV in mice reduced the T cell response against heterologous antigen (ovalbumin) compared to uninfected or mumps-infected mice. Together, these studies suggest that inhibition of TCR signaling, either by viral-protein- mediated inhibition of Lck function or viral-RNA-mediated inhibition of PTPRE expression might reduce T cell response against heterologous antigens. Currently, we are developing novel strategies based on these viral immunomodulatory factors to reduce T cell response against gene therapy vectors and transgene products. Since T cell signaling plays an essential role in developing adaptive immune responses, inhibition of this signaling pathway might reduce both the T and B cell responses against gene therapy vectors.
We are also studying the underlying mechanisms for inflammatory toxicities during CAR-T cell therapy. Following activation of CAR-T cells, bystander immune cells such as monocytes and macrophages are also activated. Inflammatory factors (e.g. IL-6, IL-1β) released by activated myeloid cells contribute to severe inflammation and toxicity during CAR-T cell therapy. Treatment modalities that block such inflammatory factors, such as tocilizumab (anti-IL6R), anakinra (anti-IL1R) or steroids, are commonly used to manage severe inflammation. However, there are limitations with these therapies: steroids can impair CAR-T cell function and patients can develop tocilizumab-refractory cytokine release syndrome (CRS). Furthermore, these agents can have heterogeneous response in the human population. Furthermore, primary mechanisms leading to bystander immune cell activation and CRS/neurotoxicity development are not completely understood. Thus, there is a need to better understand underlying mechanisms contributing to inflammatory toxicities during CAR-T cell therapy. Our long-term goals are to understand mechanisms contributing to inflammatory toxicities during CAR-T cell therapy and develop novel strategies to improve safety and efficacy.
- Sci Rep 2018 Jul 19;8(1):10910.
Characterization of the effects of immunomodulatory drug fingolimod (FTY720) on human T cell receptor signaling pathways.
Baer A, Colon-Moran W, Bhattarai N
- PLoS One 2017 Oct 26;12(10):e0187123.
Src-family kinases negatively regulate NFAT signaling in resting human T cells.
Baer A, Colon-Moran W, Xiang J, Stapleton JT, Bhattarai N
- PLoS Pathog. 2017 Feb 24;13(2):e1006232.
Hepatitis C virus infection inhibits a Src-kinase regulatory phosphatase and reduces T cell activation in vivo.
Bhattarai N, McLinden JH, Xiang J, Mathahs MM, Schmidt WN, Kaufman TM, Stapleton JT.
- PLoS Pathog. 2015 Sep 30;11(9):e1005183.
Conserved Motifs within Hepatitis C virus Envelope RNA and Protein Independently inhibit T cell Activation.
Bhattarai N, McLinden JH, Xiang J, Kaufman TM, Stapleton JT.
- Virology. 2015 Nov;485:116-27.
Human Pegivirus (HPgV; formerly known as GBV-C) inhibits IL-12 dependent natural killer cell function.
Chivero ET, Bhattarai N, McLinden JH, Xiang J, Stapleton JT.