Rochester Vaccine Fellowship
The Rochester Vaccine Fellowship is awarded annually to an outstanding postdoctoral fellow working in the area of vaccine-related research, who is mentored by a faculty member with a primary or secondary appointment in the Department of Microbiology and Immunology.
This fund was created by a donation from Dr. Michael Pichichero in honor of Dr. Porter Anderson
(Professor Emeritus of Pediatrics in Infectious Diseases), who co-invented the widely
administered vaccine for bacterial meningitis. Applications are requested and should consist
of (i) a brief (1 page or less) statement of research, (ii) the CV of the applicant fellow and
(iii) a short letter of support from the advisor. Approximately $5000 per year is available and can
be used to support research supplies and/or travel to present at national and international
scientific meetings or symposia. Salaries are not supported. Successful applications will
emphasize vaccine-related research. This is a one-year, non-renewable award.
I received a B.Sc., specializing in Immunology and
Infection, at the University of Alberta,
Edmonton, Alberta, Canada. During my undergraduate studies I had the opportunity to take
several courses instructed by Dr. Miodrag (Mike) Belosevic, whose research program focused on macrophage biology of bony fish. I found this topic very interesting, so I joined his lab as a
summer student and stayed on to do an undergraduate research
project. I very much enjoyed this research and the kind of
supervision and support that Mike provided, so I enrolled in a
graduate program in his lab.
My doctoral thesis was titled “The analysis of cytokine
regulation of macrophage antimicrobial responses of the
goldfish” and focused on gaining an understanding of the
mechanisms employed by these primordial vertebrates to
coordinate macrophage immune functions. While in Mike’s
lab, I attended several international conferences and
meetings in the field of comparative immunology and was presented the opportunity to meet many researchers, working in comparative model systems. One of these individuals was Dr. Jacques Robert, who’s students always presented very interesting work and seemed to be having the most fun during
these sessions and at the after-hours outings. After getting to know Jacques and his students, I decided that I very much wanted the join his lab as a postdoctoral fellow.
The primary objective of my postdoctoral research in the Robert lab is to gain insight into the mechanisms involved in macrophage development and differentiation of the amphibian Xenopus laevis. Macrophage-lineage cells are indispensable to vertebrate immunity, homeostasis and antigen presentation. While the pathways governing their development and heterogeneity remain poorly understood, macrophage progenitors are thought to originate from sites of hematopoiesis and rely on signaling through the colony-stimulating factor-1 receptor (CSF-1R) for differentiation and survival. Interestingly, an additional, structurally unrelated and potentially functionally disparate CSF-1R ligand, interleukin-34 (IL-34) has recently been identified. Our studies indicate that in contrast to other vertebrates, committed Xenopus laevis macrophage progenitors are not provided by the hematopoietic sub-capsular liver, but are instead supported by the bone marrow. Accordingly and in order to gain novel insight into the fundamental mechanisms of vertebrate monopoiesis and the sources of their heterogeneity, we identified and produced recombinant forms of the X. laevis CSF-1 and IL-34 for the purpose of functional studies. Notably, Xenopus represents a key stage in the evolution of vertebrate immunity and physiology; it exhibits extremely unique macrophage ontogeny, where monopoiesis is segregated from general hematopoiesis; and it offers external development and ease of experimentation. Thus, the Xenopus model system represents a powerful and inimitable platform for investigating the complex differentiation pathways and functions of macrophage lineage cells during development, wound healing and the immune response. We believe that greater insight into these biological processes will permit the design of more definitive vaccine strategies, tailored explicitly to the warranted immune responses.Return to the Postdoc Information Page
Arenaviruses cause zoonotic infections in humans that are commonly pathogenic and potentially fatal, and otherwise cause chronic, asymptomatic infections in rodents. Several members in the family can cause hemorrhagic fever (HF) in humans, including Lassa virus (LASV) and Lujo virus (LUJV) in Africa; and Machupo virus (MACV), Guanarito virus (GUAV), Junin virus (JUNV), Sabia virus (SABV) and Chapare virus (CHPV) in South America.
Cases of arenavirus HF are among the most devastating
emerging human diseases with fatality rates of 15-35%
and represent a serious public health problem in endemic
areas. Moreover, increased travel to and from these
regions has resulted in importation of HF cases into
non-endemic metropolitan areas. Public health concerns
posed by human-pathogenic arenaviruses are aggravated
by the lack of Food and Drug Administration (FDA)-licensed
vaccines and by current anti-arenaviral therapy being limited
to an off-label use of the nucleoside analog ribavirin that is
only partially effective and associated with significant
To generate recombinant arenaviruses, plasmid-based reverse genetics techniques have proven to be of great value. However, current reverse genetics approaches cannot be used to generate vaccine seeds because they are limited to murine cells. To overcome this problem, we have developed a human RNA polymerase I promoter-driven system allowing the generation of recombinant arenaviruses from human and FDA-approved (Vero) cells for vaccine development. Furthermore, we have combined RNA polymerase I and RNA polymerase II sequences within the same plasmid allowing the synthesis of negative-sense viral RNA and positive-sense mRNA, respectively, which halves the number of vectors required for arenavirus rescue. Reducing the number of plasmids is especially important for recovery of viruses in cell lines appropriated for human vaccine production that cannot be transfected at high efficiencies. We have shown the feasibility of this approach by recovering both Lymphocytic Choriomeningitis virus (LCMV) and JUNV (Candid#1 vaccine strain).
We aim to use the newly described reverse genetics techniques to generate recombinant arenaviruses that have potential as Live-Attenuated Arenavirus Vaccines (LAAV). Live-attenuated vaccines mimic the infectious life cycle and have been proven to provide better immunization and longer protection against several viral infections, compared to non-infectious counterparts. Using the techniques developed in our laboratory (unique for the development of vaccines against arenaviruses in FDA-approved cell lines) we will introduce mutations, similar to those found on the Candid#1 vaccine strain of JUNV, in the LCMV genome in order to reduce the viral ability to replicate in vitro. Furthermore, we can optimize these LAAVs by engineering previously described tri-segmented arenaviruses to contain additional genes of interest that can improve the quality of the immune response against the vaccine or additionally confer protection against other human infectious agents. This recently developed reverse genetics technique provides new avenues for the production of arenavirus vaccine candidates for the prevention of these important human pathogens infections as well as for uncovering critical aspects of arenavirus disease in humans.
Cancer vaccine or immunotherapy is based on the activation of the immune response with the goal of either preventing a malignant cell from establishing or specifically target and eradicate existing tumor cells. This can be achieved through a variety of different mechanisms including vaccination with known tumor-associated antigens, infusion of immune stimulating cytokines and/or distinct tumor specific effector cells. Although these approaches have achieved encouraging clinical results during the recent years there are still many questions and problems associated with cancer vaccination. For example, during tumorigenesis tumor progression is influenced by multiple, complex interactions between the malignant cell and the host immune system. In many cases tumor progression is strongly associated with immune evasion mechanisms that ultimately limit the success of tumor-associated antigen based vaccine strategies. For example, tumors often down-regulate classical MHC class Ia expression allowing the tumor cell to escape conventional T-cell mediated immune recognition. As a possible consequence many different types of tumors have been found to induce or upregulated expression of non-classical MHC class Ib genes, some of which are thought to serve as a mechanism to escape immune cell mediated elimination.
The comparative immuno-cancer model developed in the amphibian Xenopus laevis has been instrumental to explore novel approach for tumor vaccine. The high level of conservation of the Xenopus immune system with human, including anti-tumor immune effector cells, MHC class Ia and class Ib molecules, and the amenability of Xenopus to in vivo experimentation makes it a highly relevant non-mammalian model. We have focused our studies on the class Ib XNC10 molecule that we postulate to be critically involved in immune response against tumors that has downregulated class Ia antigens to escape immune recognition. Evidence from our lab suggests that XNC10 mediate the differentiation and activation of a subset of CD8+ innate α/βT cells that express an invariant TCR repertoire and that has anti-tumor activity.
To further characterize the function of these innate CD8+ T cells in anti-tumor response, we have generated XNC10 tetramers that specifically bind a population of innate like CD8dim+ cells in the spleen of adult frogs. We have also generated a soluble recombinant XNC10 molecule that can be produced by our tumor line, and that will allow us to identify putative tumor antigens. Our rational is that XNC10, since they are recognized by innate T cell, is likely to complex and present antigens that are of limited diversity and evolutionary conserved (e.g., pattern recognitions). We plan to further investigate the function of XNC10 in generating anti-tumor innate T cell effectors in vivo by transgenesis and tumor transplantation. Despite the fact that class Ib genes in humans and Xenopus are not homologs, their proposed function in tumor surveillance as well as the differentiation and activation of innate CD8+ T cells is likely to rely on conserved mechanisms. We aim to elucidate specific fundamental mechanisms underlying the observed role of class Ib molecules in tumor immunity with the ultimate goal of identifying suitable targets or antigens (likely to be structurally conserved) for novel tumor vaccine therapies.
Influenza is a globally important respiratory pathogen that causes nearly annual epidemics and occasional pandemics, including the 2009 H1N1 swine virus pandemic. Because influenza virus is continuously evolving, the emergence of new antigenic variants (drift strains) is constantly occurring. In addition, because all subtypes of influenza A are found in the aquatic bird reservoir from which new viruses emerge, influenza is not eradicable. Thus, the only pragmatic goal is prevention. Production of a sufficient amount of flu vaccines, as well as a vaccine which is effective for various age ranges is essential to limiting an outbreak. The problem that prevents large scale vaccine production is the fact that most of the human influenza A viruses, as well as the novel H1N1 strain do not grow well in embryonated eggs or tissue culture. Furthermore, additional live-attenuated vaccines to protect young children and the elderly, the populations most at risk, need to be developed. In order to generate these vaccines, a better understanding of virus assembly is necessary. The lack of knowledge concerning the molecular mechanism of virion formation and release hampers efforts to quickly and sufficiently produce vaccines or to develop safe live vaccines.
An essential step in virion formation is the transport of the viral nucleocapsid to the assembly sites. As part of my PhD studies, I investigated how the Sendai virus (SeV) nucleocapsid is transported through the cytoplasm to plasma membrane assembly sites. I found that Rab11a, a regulator of the recycling endosome pathway was involved in the trafficking of viral nucleocapsid. Consistent with my findings, a recent study reported that Rab11 is necessary for influenza A budding and virus production. It is still unknown how Rab11 plays a role in influenza assembly and how the nucleocapsid travels through the cytoplasm to the plasma membrane. My research will elucidate host cellular proteins that mediate intracellular nucleocapsid transport, and their interactions with viral proteins. We expect the data to provide important clues for designing recombinant viruses which grow efficiently in cells or live-attenuated viruses which replicate well but have attenuated progeny virion production.
University of Rochester School of Medicine and Dentistry, Rochester, NY
Department of Microbiology and Immunology
Postdoctoral Research Fellow, 2009-present
Mentor: Toru Takimoto, PhD
University of Rochester School of Medicine and Dentistry, Rochester, NY
Department of Microbiology and Immunology
Doctor of Philosophy, 2009
Mentor: Toru Takimoto, PhD
Texas State University, San Marcos, Texas
Department of Chemistry and Biochemistry
Master of Biochemistry, 2003
Mentor: Linda Watkins, Ph D
Texas State University, San Marcos, Texas
Bachelor of Science, 2001
Most immune responses to microbial infection are measured in the draining lymph node (mouse) or peripheral blood (human). A recent study from our laboratory demonstrated that early in Leishmania major infection in mice, the cytokine profile of CD4+ helper T cells in the infected tissue site did not reflect the cytokine profile of T cells in the draining lymph node. The concept that tissue resident pathogens may subvert the centrally generated cytokine repertoire by limiting the local recruitment or activation of specific effectors has important implications for the design and measurement of immune function in disease and vaccine settings. Where an immune response or vaccine, fails to control infection the host may nevertheless have generated a central pool of appropriate effectors with anti-microbial potential. We will thus test the hypothesis that Leishmania major exploits an intrinsic homing potential of IFN-γ-secreting (Th1) and IL-4 secreting (Th2) CD4+ T cells and modifies the infected tissue microenvironment so as to limit the ability of Th1 cells to migrate into that tissue. By flow cytometry, we will track the migration and accumulation of functionally-marked helper T cells into inflamed tissue (using fluorescent cytokine reporters), as well as evaluate complex surface marker expression on those cells that reach the tissue. By in vivo intravital multiphoton microscopy, we will compare the ability of Th1 and Th2 cells to extravasate into the inflamed tissue from the bloodstream, as well as their migratory characteristics within the tissue itself. With these tools in place, we will address biologically relevant settings on immune activation:
- Can the migratory potential of helper T cells be modulated by local changes induced by a pathogen?
- Can the migratory potential of helper T cells be modulated by altering inflammatory conditions at the time of immunization?
We highlight an emerging principle in pathogen-host interactions: that the lymph node-derived T cell cytokine repertoire can be edited by the pathogen at the infection site. Understanding pathogen-specific mechanisms of regulation at the tissue site becomes key to the design of appropriate therapeutics. Developing ways of harnessing a diverse LN repertoire to retune immune responses at the infection site, by manipulating the type of effectors generated and recruited to the site, has great therapeutic potential for many disease states.
University of Rochester - School of Medicine and Dentistry - Rochester ,NY
David H. Smith Center for Vaccine Biology and Immunology
Postdoctoral Training, 2008 - Present
Mentor: Deborah Fowell, D.Phil
Johns Hopkins University - Bloomberg School of Public Health - Baltimore, MD
Department of Molecular Microbiology and Immunology
Doctor of Philosophy, 2008
Mentor: Fidel Zavala, MD
Johns Hopkins University - Whiting School of Engineering - Baltimore, MD
Department of Biomedical Engineering
Bachelor of Science, 2002 Grade Point Average: 3.7
Graduated with University Honors and Department Honors
The research I am doing in the lab of Prof. Luis Martinez-Sobrido involves members and proteins of the family Arenaviridae. Arenaviruses are emerging viruses with a worldwide distribution. They are enveloped with a bi-segmented negative stranded RNA genome. Arenaviruses cause chronic and asymptomatic infections in rodents and can be transmitted to humans causing infections and in some cases leading to severe conditions such as hemorrhagic fever (HF) with fatality rate up to 35%. These HF arenaviruses poses a public health problem, as well a potential bioterrorism threat in the endemic regions. There is no specific anti-arenaviral therapeutic or vaccine available. Also, the study of the HF arenaviruses require BSL-4 containment. We are using reverse genetics techniques to rescue prototypic BSL-2 arenavirus Lymphocytic choriomeningitis virus (LCMV) in which the surface glycoprotein (GP) gene is replaced with a reporter gene/RG using LCMV GP expressing stable cell lines, which we developed in our laboratory. The replication of GP-deficient rLCMVs is limited to a single cycle in non-GP expressing cell lines. Parallel, we have developed cell lines expressing GP of the HF Lassa fever virus (LASV), and planning to extend our studies to other HF arenaviruses such as Junin virus (JUNV) and Machupo virus (MACV). These HF GP expressing cell lines will allow us to generate the corresponding GP-pseudotyped rLCMVΔGP/RG allowing its use and study under BSL-2. Once rescued, these viruses can be used in;
- The development of sensitive and specific high-through-put screening assays to evaluate anti-virals against different steps of the arenavirus life cycle.
- To detect and quantify neutralizing antibodies.
- As mentioned in our current proposal, for the development as safe and effective vaccine candidates againt HF arenaviruses.
Shanaka attended the University of Colombo, Faculty of Science, Sri Lanka from 1997 to 2001 on a “Mahapola higher education merit scholarship” and graduated with a Bachelor of Science (first class honors) in Biochemistry and Molecular Biology in December 2001. He carried out an undergraduate research project in isolation and characterization of banana streak virus for enzyme-linked immunosorbant assay and polymerase chain reaction identification, under the guidance of Professor W. Kumara Hirimburegama. He was at Unilever (Ceylon) Ltd., Colombo, Sri Lanka for industrial training as a part of his undergraduate training. After graduation he was appointed Assistant lecturer in Biochemistry, Molecular Biology and Pharmacy, in the Department of Chemistry, University of Colombo in 2001-2002. He was then appointed Research assistant in the same department in 2002-2003, to carryout research in “natural products chemistry”. Shanaka entered the Pathways of human disease (PWD) cluster on a graduate student fellowship, and began graduate studies in Pathology at the Department of Pathology and Laboratory Medicine at the University of Rochester School of Medicine and Dentistry, Rochester, NY, USA in the fall of 2003. He pursued research in the field of dengue virology under the guidance of Professor Robert C. Rose, Professor Jacob J. Schlesinger, and Professor Xia Jin. He investigated “the role of human Fcγ receptors in antibody-mediated dengue virus neutralization: implications for dengue disease pathogenesis”. Shanaka received his Master of Science degree in Pathology in the spring of 2006. He received the honor of being awarded for the outstanding research publication (2006-2007) of the year: Differential enhancement of dengue virus immune complex infectivity mediated by signaling-competent and signaling-incompetent human FcγRIA (CD64) or FcγRIIA (CD32). J. Virol. 2006 Oct; 80(20): 10128-38. He received the graduate student travel award (2007-2008) enabling him to present at the 57th American Society for Tropical Medicine and Hygiene annual meeting, New Orleans, LA, December 2008. He also received awards of achievement at the annual pathology research day poster sessions in 2007 and 2008. Shanaka received his Doctor of Philosophy degree in Pathology in the spring of 2009. Presently he is pursuing his post-doctoral fellowship under the mentorship of Professor Luis Martinez-Sobrido, at the Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, since April 2009. He is a member of American Society for Virology and a member of American Society for Tropical Medicine and Hygiene since 2006. He is also a life-time member of the Sri Lanka Association for the Advancement of Science.