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Functional
Pathogenomics of Mucosal Immunity (FPMI)
Overview
Mucosal immunity represents the broad range of host defenses
that prevent the attachment and invasion of infectious disease
agents at the body surfaces of the respiratory, digestive,
and reproductive tracts. The Functional Pathogenomics
of Mucosal Immunity (FPMI) program is utilizing the
power of genomics and bioinformatics to increase current
understanding of how mucosal immunity to infectious agents
operates, and how it may be enhanced to enable the rational
development of new and effective strategies for improving
human health, animal productivity and welfare, food safety
and the economic viability of the livestock industry in
the Prairies, Canada and elsewhere.
Unlike other efforts in this
field, the FPMI program is investigating mucosal immunity
using genomics approaches in a wide range of hosts, including
humans, chickens and cattle, and thus straddles the fields
of agriculture and health. This permits very broad conclusions
to be made about the mechanisms of immunity in these hosts,
as well as measures that will enhance immunity. The program
addresses important social and financial issues since infectious
diseases cost the livestock industry billions of dollars
annually, while human infectious diseases cause one third
of all deaths on the planet and are the major cause of loss
of productivity in our society.
The FPMI project team brings together the internationally
recognized livestock health research excellence of the Vaccine
and Infectious Diseases Organization, the R & D capacity
at Inimex Pharmaceuticals, and a network of world-class
genomics, bioinformatics, microbiology and immunology research
experts at the University of British Columbia, the University
of Saskatchewan, Simon Fraser University, and elsewhere
in Western Canada, who have been involved in major scientific
advances in understanding host:pathogen relationships.
Objectives
The overall objective for the FPMI program is to provide
new information about the processes of disease and innate
immunity to microbial pathogens. The results of this research
program will enable researchers to gain an increased understanding
of how the mucosal surfaces of bovine, chicken and human
hosts respond to the presence of infectious agents, and
to the adjuvants, immuno-modulators and vaccines designed
to combat these agents.
Specific Aim 1 – to characterize, using epithelial
and lymphoid cells, the host gene expression responses to
pathogens including the development of microarray platforms
Specific Aim 2 – to generate full genome chicken
microarray
Specific Aim 3 – to characterize host gene expression
responses in enteric and respiratory animal infections
Specific Aim 4 – to determine the influence of adjuvants,
immuno-modulatory agents including antimicrobial peptides,
and vaccines on host gene expression
Specific Aim 5 – to study the influence of pathogen
genetics on the host response
Progress
to date
Gene expression studies in host cells were conducted using
a bovine microarray developed at Pyxis, based on a library
of 7000 cDNAs, and human microarrays based initially on
21,000 oligo set from Qiagen and recently a 19,000 cDNAs
set. This data is being compiled in a database of human,
bovine and chicken genes regulated in isolated primary cells
and/or cell lines by exposure to various bacterial and viral
pathogens. To handle the high volume of data throughput,
a web-based, semi-automated, open source pipeline “ArrayPipe”
has been developed by our bioinformatics group at Simon
Fraser University for the initial pre-processing of microarray
data. Clustering analysis on potential co-regulated genes
is starting to indicate key genes and pathways to target
for future studies. Common sets of experiments being conducted
at both the Vaccine and Infectious Diseases Organization
and the University of British Columbia will help us examine
the interaction of bacterial pathogens and immune-modulating
compounds with human and bovine monocytes, for broad comparative
genomics analyses. Bovine and chicken model infections have
been established to validate host-pathogen responses in
vivo and are permitting functional genomics analyses in
infections of substantial economic importance.
Understanding the influence on host gene expression of
immunomodulatory agents, including antimicrobial peptides,
adjuvants and vaccines, will help us to develop novel compounds
for enhancing the innate and/or adaptive immune response,
and/or to reverse the harmful effects of an excessive inflammatory
response. Our data has demonstrated the ability of natural
and designed host defence peptides to protect against both
Gram negative and Gram positive bacterial infections in
mice. Studies of a broad range of such peptides and their
effect on gene expression of host cells has revealed a pattern
of gene expression that appears to reflect the ability of
these peptides to protect against infection in mouse infection
models.
We have also constructed a library of 10,000 random Pseudomonas
aeruginosa lux transposon mutants, and sequencing is completed
on 3200 PCR products. These results indicate that the library
contains knockout mutations in about 50% of non-essential
P. aeruginosa genes, two thirds of which are lux reporter
fusions. These mutants are being screened for phenotypic
characteristics to further our understanding of gene expression
and regulation in pathogenesis.
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