Under the Spell of Ian Tizard’s Veterinary Immunology!

I earned a doctoral degree in Microbiology and Immunology from the Medical College of Virginia of the Virginia Commonwealth University in Richmond, Virginia. Prior to this, I was educated in India earning both a B.Sc. degree in Chemistry, Zoology and Botany and an M.Sc. degree in Experimental Biology. The broad yet intense installation of biology during those formative years led to the foundational insight that biochemistry, cell biology and genetics form the “primary colors” from the blending of which emerges biology—an insight that I have utilized in pursuit of understanding various immunologic processes.  

Introduction to scientific method came via thesis research—which was unusual and uncommon when pursuing an M.Sc. degree in Indian universities in the 1980s. This research involved rudimentary histologic and histochemical investigations of the vomeronasal organ in a rodent. Nonetheless, this laboratory experience spurred an interest in neurobiology, which I pursued for a year—as a Junior Research Fellow of the Indian Council of Medical Research—studying neural correlates of pain perception. In a quest to understand the basis of pain caused by inflammation, I was introduced to Ian Tizard’s “Veterinary Immunology” (the 2nd Edition, I think) by a recently minted Ph.D. who had just returned from Copenhagen but whose name I have regrettably forgotten. This introduction led to readings on the Major Histocompatibility Complex and organ transplantation (J Klein, Science 203: 516—521, 1979; SG Nathenson et al. Annual Review of Biochemistry 50: 1025—1052, 1981), and, so also, the pursuit of a doctoral degree in immunology and post-doctoral training in molecular immunology under the tutelage of the now late Professor Stanley G. Nathenson—the lead author of the Annual Review paper above—then at Albert Einstein College of Medicine, in the Bronx, New York. The MHC is an incredibly beautiful genetic region that restricts the functions of T cells; both the MHC and T cells continue to preoccupy my thoughts even to this day. Other than these experiences, there was nothing out of the ordinary in these formative years that would have suggested that I would pursue a career in biological/biomedical research. In fact, if you—the reader of this passage—and I had met then, you would have quipped: "what a dull lad!" 

I began my independent scientific career in 1993 on tenure-track as an Assistant Professor of Microbiology and Immunology at The Milton S. Hershey College of Medicine of The Pennsylvania State University. For my scientific accomplishments and services to both the Department of Microbiology and Immunology and the University, I earned Associate Professorship with indefinite tenure in 1999. Shortly thereafter, I was recruited to Vanderbilt University as an Associate Professor and promoted with tenure to Professor of Microbiology and Immunology in 2005. Since the inception of a new Department in 2011, I now serve Vanderbilt University as its tenured Professor of Pathology, Microbiology and Immunology. In 2017, I was appointed as the Dorothy B. and Theodore R. Austin Chair in Pathology.  

Making Discoveries: Testing and Refining Beautiful Hypotheses with Ugly Data!

My research focuses on immunologic recognition, a biochemical process that controls T lymphocyte function in health and disease. Gaining fundamental insights into immunologic recognition requires an in-depth understanding of, (a) what T cells recognize during development and during an immune response against microbial pathogens and cancers; (b) how T cell antigens are processed and transported to cellular sites of assembly for presentation by MHC and MHC-like molecules; and (c) how antigen presentation leads to the induction of a protective immune response. Our laboratory addresses critical questions in these areas through four major projects: (a) large-scale T cell epitope discovery and mechanisms of action of new generation, subunit vaccine candidates; (b) mechanisms of peptide and lipid antigen processing and presentation; (c) adjuvant mechanism(s) and delivery platforms; and (d) the molecular basis of NKT cell development and function. We take a systematic, multi-disciplinary approach —i.e., immunologic, cell and molecular biologic, biochemical, proteomics and genomics approaches— to address questions in these areas.

Understanding the Cellular and Biochemical Bases for Ligand Presentation by MHC and CD1 Molecules to understand Adaptive and Innate-like T Lymphocyte Biology

This laboratory is best recognized for its contributions to the cell biology and biochemistry of MHC and MHC-like CD1d molecules. These molecules play important roles in protein and lipid antigen presentation and, thereby, control the biology of T cells and natural killer T (NKT) cells, respectively. We discovered (*collaborative works),

that MHC class I molecules bind and present peptides longer than the canonical length—i.e., longer than 9—11 amino acid residues:

Proc. Natl. Acad. Sci. USA 91: 4145—4159, 1994

J. Exp. Med. 203: 647—6659, 2006

the mouse H4 minor histocompatibility antigen and mechanisms of immune dominance that govern graft-versus-host disease:

J. Immunol. 170: 5429—5437, 2003

Immunity 17: 593—603, 2002

J. Immunol. 172: 6666—6674, 2004  

that components of the MHC class I antigen processing apparatus control MHC class II-restricted antigen processing and presentation:

J. Immunol. 186: 6683—6692, 2011

Eur. J. Immunol. 43: 1162—1172, 2013

that non-classical MHC-like molecules present peptide and lipid ligands: 

J. Exp. Med. 179: 579—588, 1994

Science 279: 1541—1544, 1998

Proc. Natl. Acad. Sci. USA 100: 1849—1854, 2003 

Proc. Natl. Acad. Sci. USA 101: 2022—2026, 2004  

that NKT cells are CD1d restricted:  

J. Exp. Med. 184: 1579—1584, 1996

Immunity 6: 469—477, 1997
that NKT cells recognize a self glycosphingolipid antigen:  

Proc. Natl. Acad. Sci. USA 100: 1849—1854, 2003 

J. Immunol. 173: 3693—3706, 2004
that the antigen receptor expressed by NKT cells recognizes its ligands in a manner distinct from that of conventional T cells:

J. Immunol. 171: 4539—4551, 2003 

EMBO J. 28: 3579—3590, 2009

that a unique gene regulatory network specifies NKT cell lineage commitment, ontogenetic progression and effector differentiation:

J. Exp. Med. 186: 331—336, 1997 

J. Exp. Med. 191: 771—780, 2000 

J. Immunol. 172: 2265—2273, 2004 

J. Immunol. 172: 4667—4671, 2004 

Proc. Natl. Acad. Sci. USA 102: 5114—5119, 2005 

Immunity 25: 487—497, 2006

J. Immunol. 187: 6335—6345, 2011.

Scientific Rep. 7: 15594, 2017 

Harnessing Immunity to Protect or Treat Cancer and Infectious Diseases  

In recent years, our research focus has turned toward harnessing what we have learnt in the above areas of basic immunology to augment immune reaction through vaccine and adjuvant design to prevent or treat microbial infections and cancer, deathly diseases that ail humankind. 

Neoantigens & Cancer Immunotherapy:

During infection, the presentation of self peptides is, in part, replaced by presentation of microbial peptides. However, little was known about the molecular characteristics of self peptides expressed during infection even though microbial infections alter host cell gene expression patterns and protein metabolism in a significant way. We discovered a profound shift in the self peptide repertoire with hundreds of self peptides uniquely presented after infection for which we have coined the term ‘self peptidome shift’. A large part (~40%) of the self peptidome shift was composed of peptides derived from type I interferon-induced genes, consistent with cellular response to viral infection. Interestingly, ~12% of self peptides presented after infection showed allelic variation when searched against ~300 human genomes. Further analyses revealed that ~10% of self peptides were derived from proteins that are known or are potential oncoproteins. Additional TSGene Database search identified over 85 HLA class I-restricted neoantigens that emerge from known cancer associated mutations (J. Clin. Invest. 123: 1976—1987; 2013; Proteomics—Clinical Applications, 9: 1035–1052; 2015). Hence, we are currently exploring ways to harness this new information on self peptidome shift in the context of oncolytic viral infection for CAR- (chimeric antigen receptor) T cell-based personalized cancer immunotherapy in a collaboration with Drs. JT Wilson of Chemical Engineering and Y-J Kim of Otolaryngology. 

Infection & Immunity; Vaccine Design & Delivery Platforms:

We recently reported a strategy for CD8+ T cell-targeted vaccine design to identify targets that confer protective immunity against poxvirus disease including smallpox (J. Clin. Invest. 123: 1976—1987; 2013). Using this model, we are currently focused on elucidating the mechanisms of induction, maintenance and action of tissue resident CD8+ T cells and how they impart pulmonary mucosal immunity (Cell Reports 16: 1800—1809; 2016). We are using this strategy to devise ways to identify, characterize and develop vaccine candidates against tuberculosis. 

We have recently initiated studies directed toward understanding the molecular mechanisms of pathogenesis of pulmonary tularaemia —an infectious disease caused by the bacterium Francisella tularensis. Exciting new evidence from this laboratory indicates that NKT cells —an immunoregulatory T cell subset that gets activated in several different infectious diseases— promote runaway inflammation that underlies tularaemia pathogenesis and, hence, play a detrimental role in this disease (PLoS Pathogens 11: e1004975). Our unpublished data indicates that a Francisella-derived glycolipid antigen activates NKT cells. By engineering a mutant bacterium deficient in the biosynthesis of the glycolipid antigen, we plan to generate a live attenuated vaccine against tularaemia. Even though a live vaccine strain against human tularaemia exists, for various reasons, it hasn't met FDA requirements for approval. It is hoped that our strategy to create a strain that will not stimulate NKT cells to keep runaway inflammation in check will fill the unmet need for a vaccine against tularaemia. 

Transcending Immunology to Understand How Cells Secrete Immune Mediators

Whilst the above projects focus on immunologic research that lend to discoveries in vaccine design as well as adjuvant mechanisms and delivery platforms, there are aspects of my research interests that transcend immunology: For example, our studies of antigen presentation mechanisms (J. Immunol. 186: 6683—6692, 2011; Eur. J. Immunol. 43: 1162—1172, 2013) have led to the discovery of a peptide/protein transporter that mediates antigen transfer from the cytoplasm to the endosome/lysosome. This transporter appears to pump cytoplasmic antigens into the endo/lysosomes. Therefore, one focus of this project is to develop a mechanistic understanding of how this transporter works and how it impacts CD4+ T cell responses to infectious diseases.

When this transporter is viewed from an evolutionary perspective, in all likelihood it may not have evolved solely for antigen transport purposes. We predict that this novel transporter may be involved in chaperone-mediated autophagy and/or unconventional secretion of soluble mediators directly from the cytoplasm to the outside of the cell. Hence, a second focus of this project is to test this hypothesis to attain mechanistic insights into chaperone-mediated autophagy and/or unconventional secretion. To accomplish the above goals, we have generated a germ-line gene knock-out mouse by targeting the transporter gene using CRISPR/Cas technology. As we expected, fundamental new insights in antigen processing and presentation are emerging that will directly impact our understanding of CD4+ T cell mediated immunity and, potentially, chaperone-mediate autophagy. 

We discovered that conventional secretion of cytokines by NKT cells is a regulated process, which entails packaging cytokines into vesicles, concentrating them and polarizing them to the immunologic synapse much alike axonal vesicles at the neuronal synapse. Studies with GM-CSF deficient mice revealed that regulated cytokine secretion is uniquely disrupted within NKT cells and that cytokine secretion by NKT cells is an instructed process that is learnt during thymic development (Immunity 25: 487—497, 2006). This project has lain dormant for a while but rekindled by our recent gene expression studies. The identification of several targets have awakened interest in seeking a mechanistic understanding of cytokine vesicle formation, its polarization to the T cell-antigen presenting cell synapse and eventual secretion. We anticipate that what we learn in this model for secretion will be distinct from that of neuronal synaptic vesicles because neuronal vesicles are pre-formed in contrast to cytokine vesicles, which are formed only upon T cell receptor triggering. Furthermore, whilst learning about the mechanisms underlying antigen processing and presentation as well as conventional cytokine secretion are of significant immunologic import, what we learn is bound to transcend immunology itself because regulated secretion is a fundamental biologic process with which cells communicate with each other locally and at a distance.

Honors & Awards

I pride most in the accomplishments of my students and fellows. Many have received Awards for research performed under my tutelage (for detailed description of student awards, see https://www.vumc.org/joyce-lab/awards-honors). They have gone on to occupy academic positions at Oxford, Harvard and Hokkaido University; as well as University of Wisconsin, Pennsylvania, Maryland, Texas, and Detroit.

Whilst the opportunity to write and re-write history from my scientific pursuits is honor itself, I am fortunate to have received recognition outside of this venue. Notably, my postdoctoral studies were supported by the coveted fellowship from the Cancer Research Institute, Inc., New York. Then, at the beginning of my independent career, I received the American Cancer Society’s Junior Faculty Research Award, which enabled studies on the molecular nature of minor histocompatibility antigens—the inciters of oft-times fatal graft-versus-host disease in bone marrow transplant recipients. In recognition of our work on CD1d and natural killer T cells, Japan Foundation for Aging and Health of the Ministry of Health in Japan, sponsored a Visiting Professorship at the National Centre for Neuroscience and Psychiatry at Kodairo in Japan. During the two-week stint, I delivered lectures related to our works at several institutions in Japan. At one such lecture, I was honoured with the Hokkaido University Seal by the Graduate School of Dental Medicine of the Hokkaido University at Hokkaido in Japan. Vanderbilt University recognized a collection of our works on the nature of T cell antigens with the Charles R. Park Faculty Research Award “For Basic Research Revealing Insights into Physiology and Pathophysiology”. In 2017, For distinguished contributions to the field of immunology, particularly for biochemical studies into the antigens recognized by cytotoxic T cells important for vaccine development I was elected Fellow of the American Association for the Advancement of Sciences.