Biology of Infection: Microbial Strategies for Disease

One of the fundamental questions that motivates MoGen scientists working in the area of Molecular Microbiology & Infectious Disease is: how do microbial pathogens interact with host cells and cause disease? We address this question using cutting-edge approaches in a diversity of systems, including bacteria, viruses, and fungi. Professor John Brumell’s team pioneers a cell biological approach, with a focus on the foodborne pathogens Salmonella and Listeria. These bacteria have the remarkable ability to invade into, and replicate within our cells during an infection. An important question is how these bacteria can spread from one infected cell to another to perpetuate the disease. In a recent study published in Nature, Dr. Brumell's laboratory showed that Listeria can disguise itself as 'cellular garbage' to promote its uptake by neighbouring cells. These studies show how bacteria can exploit the natural process of digesting 'cellular garbage' (a process called efferocytosis), and identify new ways to treat infections. Professor Alex Ensminger has developed an interdisciplinary approach leveraging experimental evolution and genomics to understand the respiratory pathogen, Legionella pneumophila. In close collaboration with Public Health Ontario, the Ensminger team has taken advantage of a number of high-content screening tools and next generation sequencing to uncover phenotypic and genotypic variation between clinical samples collected throughout Ontario. The Ensminger team has begun to model these phenotypic differences through experimental evolution of pathogenesis under controlled laboratory conditions. In a separate set of experiments, they are using two independent robotic platforms within the departmental core to perform genetic interaction and chemogenomic studies to decipher the molecular mechanisms of disease. Beyond bacteria, MoGen professor Martha Brown utilizes a structure-function approach to understand the factors controlling the restricted tropism of enteric adenoviruses for the intestine, and professor Leah Cowen leverages functional genomics and proteomics to dissect the circuitry controlling virulence traits in fungal pathogens.

Gene Trafficking: Mobilizing Toxins and Drug Resistance

MoGen faculty have also made great strides towards addressing the fundamental question of: how are virulence genes regulated and transmitted? Professor William Navarre’s team has uncovered how many important bacterial pathogens including those that cause cholera, typhoid fever, and bubonic plague, utilize gene silencing to maintain the genes responsible for toxin production and antibiotic resistance. They discovered that Salmonella bacterial cells lacking the H-NS protein, responsible for bacterial gene silencing, grow poorly. Within a few days of laboratory passaging, however, these deficient Salmonella bacteria gain the ability to grow rapidly. Sequencing of the genomes of these bacteria reveals that they reproducibly shed the genes that encode a "Type-3 secretion system", a membrane pump that is required for the bacteria to secrete toxins into their mammalian hosts during infection. Further, without gene silencing these toxin pumps are overproduced, which compromises the integrity of the bacterial membrane. This demonstrates that H-NS is critical for bacteria to maintain genes involved in toxin production under conditions where the toxins are not needed, like when the bacteria exist outside the human body. Professor Barbara Funnell’s team explores mechanisms controlling segregation of bacterial plasmids, which can be vectors for the spread of genes conferring multi-drug resistance and virulence.

Mingling Microbes: Microbial Interactions in Health and Disease

The interactions among microbes that colonize the human body and their impact on human health are the central focus of a growing number of research initiatives in the department and worldwide. Research in professor Alan Davidson’s lab is focused on bacteriophages (phages), which are the most abundant organic entities on earth and play major roles in modulating bacterial populations both in the environment and in the human microbiome. The Davidson team is studying the mechanisms by which phages and related phage-like entities kill bacteria, and how bacteria resist predation by phages. They are also investigating the many ways in which phage genomes that are integrated within bacterial genomes (also known as prophages) alter bacterial physiology and virulence. In recent work published in Nature, they report on the discovery of a novel group of phage genes that inhibit the ubiquitous CRISPR-Cas system of bacteria, which is an adaptive immune system that resists phage infection. Professor Leah Cowen’s lab is focused on the fungal component of the microbiome of cystic fibrosis patient lungs and interactions with the bacterial microbiome. They utilize phenotypic screening and high-throughput metagenomic sequencing to characterize the diversity and dynamics of fungal communities in cystic fibrosis patient lungs during period of clinical stability and change, such as pulmonary exacerbations, establishment of chronic infection, and antimicrobial treatment. Professor John Parkinson’s team is developing powerful bioinformatics approaches for dealing with metagenomic datasets to understand microbial dynamics associated with disease and to analyze metatranscriptiome data of patterns of genomic expression across communities of species associated with human disease.

An Intimate Arms Race: Evasion and Activation of Host Immune Responses

Fundamental to any exploration of microbial pathogenesis, is an appreciation of the host response to infection. MoGen faculty are pioneering novel strategies to elucidate the diversity of strategies that microbial pathogens can exploit to evade effective immune protection. Professor Scott Gray-Owen’s research aims to understand how human-restricted bacterial pathogens colonize host tissues and evade effective immune protection. He uses the pathogenic Neisseria as a paradigm, since these bacteria stealthily avoid alerting the immune system as they infiltrate tissues yet cause disease because immune cells that detect the bacteria undergo an exaggerated and unfocused response that causes tissue damage. While the rapidly progressing sepsis and meningitis caused by Neisseria meningitidis and the sexually transmitted Neisseria gonorrhoeae seem unrelated, the lifestyle of these bacteria as they reside in the human respiratory tract and the urogenital mucosa, respectively, are very similar. Detailed molecular studies on these bacteria have provided new insights regarding the exquisite evolutionary adaptations that prevent them from infecting animals other than humans. These insights have allowed the Gray-Owen team to generate ‘humanized’ mice expressing human forms of the proteins that Neisseria require to establish an infection. N. meningitidis will infect these transgenic mice when administered intranasally, while N. gonorrhoeae will infect their genital tract, providing the first model that allows tissue colonization by these bacteria. Subsequent studies have provided a detailed description of molecular processes that occur when these bacteria bind to host tissues, new insight as to how Neisseria avoid being ‘remembered’ by the immune system, description of the molecular and immunological processes that drive the pathogenic response of immune cells during neisserial infection, and have allowed new vaccines and drugs that combat these processes to be developed and tested in vivo. Professor Jun Liu’s lab is focused on determining how pathogenic mycobacteria, such as M. tuberculosis, are able to evade the host immune system. They developed a zebrafish model of mycobacteria infection that enables analysis of specific immune responses to mycobacteria that have been genetically modified to lack or overexpress putative virulence factors. 

Microbes and Malignancy: Microbes Spur Development of Cancer

There is a growing appreciation that microbes induce a significant proportion of fatal cancers in humans. Professor Lori Frappier’s team is exploring the mechanisms by which a common virus called Epstein-Barr virus (EBV) induces the development of several types of cancer, including gastric cancer and post-transplant lymphomas. The Frappier lab has been studying the mechanism by which the key EBV protein, EBNA1, alters human cells to promote their continuous proliferation and survival. Proteomic approaches revealed that EBNA1 binds and manipulates two cellular proteins (CK2 and USP7) with strong ties to cancer and cell survival, including using them to induce the loss of promyelocytic leukemia (PML) tumour suppressor proteins. The cellular functions of CK2 and USP7 are only partly understood, and additional proteomic studies in the Frappier lab have revealed new potential cancer-related functions that may be manipulated by EBNA1 thereby contributing to EBV-induced cancers.   

The Next Frontier: New Therapeutic Strategies for Infectious Disease

Ultimately, basic biological discovery in the department of Molecular Genetics leads to the development of new therapeutic strategies of treat infectious disease. Professor Alan Cochrane’s team has made considerable advances in this area, focused on the discovery and analysis of small molecule modulators of RNA processing for their potential as therapeutics for viral infections. Efforts to date have resulted in the discovery of a structurally diverse set of compounds that potently suppress HIV-1 replication through distinct mechanisms. Subsequent tests have also demonstrated activity against another virus type. These findings have established that targeting RNA processing is possible and may prove useful in the control of multiple viral infections, including HIV. Research in Professor Sadhna Joshi's laboratory has been focused on the development of genetic strategies for HIV treatment and prevention. They are developing a gene therapy approach whereby patients’ own cells will be genetically modified to secrete antiviral proteins that inhibit HIV entry. Gene therapy is of interest as a one-time gene delivery procedure could provide a lifetime treatment and obviate the need for taking antiretroviral drugs for life. Four of the proteins tested in her laboratory were shown to confer 99% inhibition of HIV infection. These proteins are currently being tested in a humanized mouse model. The same antiviral proteins are secreted from strains of Lactobacillus that can colonize the vagina and gastrointestinal tract to develop microflora defence for preventing HIV transmission. As Lactobacillus is used to make yogurt, the engineered strains could be propagated and delivered orally. This would represent an affordable, accessible, nutritious, safe and easy-to-use preventive measure to block HIV transmission. Beyond viruses, professor Leah Cowen’s team has leveraged pharmacological screens and chemical genomics to identify new therapeutic strategies for life-threatening fungal infectious disease. Her work has led to collaborations with numerous pharmaceutical companies to translate basic science discoveries into therapeutic strategies to improve clinical outcome.