Lecture Summaries

WEEK # TOPICS LECTURE SUMMARIES
1 Introduction to the Course The first session will begin by introducing the instructors to the students and vice versa. We would like to learn why students have chosen to join the course and what they expect to learn and get from it. We also will review the course syllabus. The last part of the session will be used to introduce students to the scientific literature and its formats (primary research articles vs. reviews), the different flavors of journals and editing styles as well as the value of PubMed as an electronic library. This session aims to establish the group to help students feel comfortable engaging with one another and with the instructors.
2 Bacterial Effector Proteins that Hijack Host Cell Signaling: The Rho GTPase Story Bacteria have evolved a myriad of strategies to evade the human immune response over the course of our co-existence. A major strategy employed by many bacterial pathogens is to invade host cells to replicate and hide from the immune system. Host invasion is an active process and requires massive remodeling of the host actin cytoskeleton, a process that is largely controlled by Rho family GTPases. Not surprisingly, these proteins are targeted by many bacterial effectors and toxins to force the host to internalize the invaders. The article by Hardt et al., (1998) represents the first report of a bacterial effector protein that actively interferes with Rho GTPase signaling. The second paper describes a novel class of bacterial effector proteins that mimic Rho GTPase functions, thereby bypassing these signaling hubs to manipulate host cell signaling processes.
3 Bacterial Toxins and their Impact on the Host Immune System Many bacterial pathogens employ toxins—secreted proteins that harm the host—to facility host penetration. These toxins target different host cell processes among which are protein translation, MAP kinase signaling or cAMP-mediated signaling cascades to name a few. In this session, the two required readings are historic articles representing the first descriptions of two lethal bacterial toxins, Cholera toxin and Anthrax toxin. As you will learn, these two toxins manipulate related signaling cascades albeit sharing very limited functional and structural similarities. In addition to introducing bacterial toxins, this session also specifically aims at exposing students to primary literature from the pre-internet age to indicate how different some aspects of research were 30+ years ago.
4 Feeling Ill: Common Human Pathogens that Infect the Mucosal Epithelium This session will deal with bacterial pathogens that cause gastric infections. This type of infection is very common, and most humans are occasionally exposed to and infected by such bacteria. The symptoms associated with gut infections range from mild diarrhea to hemorrhage and multi-organ failure. Most bacterial gut infections are linked to Campylobacter spp., Salmonella spp. or Escherichia spp. Of particular interest is the enteropathogenic E. coli strain O157:H17, which causes a life-threatening hemorrhagic gastric infection. The first article describes this severe E. coli strain. Then we will analyze a different type of primary literature as presented by the second article, a medical case report describing a recent outbreak of E. coli O157:H7 in Canada.
5 Bacterial Pathogens and Innate Immunity: Caenorhabditis Elegans–Pseudomonas Aeruginosa Interactions as Model to Study Ancient Anti-bacterial Defense Mechamisms Mammals rely on both the innate and the adaptive immune systems to clear bacterial invaders. In contrast, less complex organisms such as the small nematode C. elegans fight pathogens with a limited arsenal of weapons available to their innate immune defense. C. elegans proved to be invaluable for research in innate immunity and allowed the testing of certain basic innate immunity concepts using this very powerful nematode model. The first article hallmarks a major break-through in our understanding of the innate immune defense and describes a signaling process essential for host protection. The second manuscript focuses on defensins, small peptide molecules that have proven anti-bacterial activities.
6 Two Strategies, Same Outcome: How Salmonella Typhimurium and Neisseria Gonorrhoeae Resist the Host's Attempts to Clear them from Mucosal Layers In addition to the innate and adaptive immune systems, infected mammalian hosts employ physical clearance strategies to eliminate pathogens. One mechanism protecting the mucosa is the rapid shedding of epithelial cells, also termed exfoliation. The first article introduces how Neisseria gonorrhoeae, the causative agent of gonorrhea, inhibits cell shedding to avoid clearance. By contrast, certain specialized bacteria evolved strategies to actually benefit from cell shedding, e.g. as a route of dispersion. The second article introduces such a cell shedding-like mechanism employed by S. typhimurium,—until recently the most common cause of food poisoning by Salmonella spp.—to release bacteria capable of being able to infect neighboring cells unusually rapidly.
7 Oral Presentations Each student should prepare a 15–20 minute presentation to introduce a self-chosen manuscript to the peers. The manuscript should be broadly related to the class's topic and must be submitted to the instructors for approval at least two weeks in advance. Instructors will check the manuscript for its suitability and ensure that no two students plan to present the same paper. Students are expected to lead a class discussion session focusing on their manuscript. The use of visual supports (PowerPoint presentation, flip chart, blackboard, etc.) is recommended. For the discussion, students should point out the key experiment(s) and control(s) and present their own conclusion whether the results support the claims made in the manuscript completely, partially or not at all.
8 Innate Immune Responses at Intestinal Mucosal Surfaces

The intestinal lumen is the home of several communites of commensal bacteria that digest otherwise indigestible polysaccharides, synthesize essential vitamins, stimulate the maturation of the immune system, and form an ecological niche that prevents the growth of pathogenic species. By contrast, the intestine provides commensals with a stable habitat rich in energy derived from ingested food. The mucosal epithelium provides a sophisticated interface separating the sterile milieu of our body from the external environment. By forming multiple layers of physical and immune protection, the epithelium blocks invasion by pathogenic and commensal bacteria. The mucin layer (mucus) that coats luminal epithelial cell surfaces physically prevents microbes from leaving the intestinal lumen. We will discuss a paper that shows how mucus can help block enteric S. typhimurium infection.

Below the intestinal epithelial layer is the lamina propria, a layer of connective tissue that together with the epithelium forms the intestinal mucosa. Different populations of innate (e.g. antigen-presenting cells such as dendritic cells (DCs) and macrophages) and adaptive (e.g. T and B lymphocytes) immune cells inhabit this well-vascularized and lymph-drained tissue. Proper immune responses require constant interaction between innate and adaptive immune cells: T lymphocytes can induce an immune response only if the antigen they recognize is displayed on the surface of an antigen-presenting cell. DCs are the cells most efficient at this function. They first ingest any antigens (e.g. a whole bacterium) that they come in contact with. Ingested antigens are then digested into short peptides, which are loaded onto the surface of the DC so that they can be presented to T lymphocytes. By extending long dendrites through the epithelium, lamina propria DCs can sample antigens present in the intestinal lumen without leaving their original location. This enables the immune system to monitor, and eventually respond to, antigens present in the intestinal lumen. In the second paper, we will discuss how this process is regulated.
9 Antibody-mediated Mechanisms against Invasion by Bacteria Because the gut epithelium has to maintain peace with the necessary commensals, the immune system at mucosal surfaces has to be tightly balanced to tolerate commensals while preventing their invasion into the tissue and being prepared to destroy pathogenic bacteria. A major defensive mechanism that excludes commensals from the mucosal surface relies on the secretion and function of a class of antibodies named immunoglobulin A (IgA) that is present in abundance at the mucosa surface. IgA, together with nonspecific protective factors such as mucus, can directly bind to bacteria present in the lumen and by doing so physically preclude microbial adhesion to epithelial cells and subsequent invasion by bacteria without causing a tissue-damaging inflammatory reaction. In this session we will discuss a paper showing that IgA antibodies protect against Salmonella invasion. Using the second paper, we will discus how a special type of lymphocytes called regulatory T cells control IgA selection that in turn shapes the microbial communities within the gut.
10 T-cell Responses at Intestinal Mucosal Surfaces In this session we will discuss the various types of cellular immune responses that help keep a intestinal mucosal surface healthy despite the constant antigen stimulation by commensals, all foreign bodies that could potentially stimulate a strong (and exacerbated) immune response. From one paper we will discuss how the microbiota educates the immune system, rendering it tolerant to commensals, focusing on the immune responses at the lamina propria. From the second paper we will discuss how lymphocytes present in the intraepithelial compartment are fine-tuned to induce an effector yet not harmful immune response.
11 Interplay between Gut Microbiome and Lymphocyte Fate and Function In this session we will discuss how the microbiota can shape the adaptive immune responses at the intestine surfaces. Some commensals, such as segmented filamentous bacteria (SFB) that colonize the small intestine, can skew the immune response towards a potentially pathogenic response while members of the Clostridium genus that inhabits the large intestine can promote the expansion of regulatory lymphocytes that regulate exacerbated immune response mediated by effector T cells. We will discuss a paper that led to the identification of the bacteria capable of selectively inducing antigen-specific effector T cells that produce a proinflammatory cytokine – IL-17. This paper provides some insight into how the commensal bacteria seem to skew the immune responses of the host. Using the second paper, we will analyze how cytokine signaling induced by the commensal SFB may lead to an effector immune response.
12 Dysbiosis and Autoimmune Conditions

We will discuss questions that might have come up while preparing the written assignment. We will then discuss the final topic – dysbiosis and its relationship to autoimmune diseases. Finally, we will gather feedback about the course to help us improve the quality of the course in the future.

Dysbiosis is a condition caused by an imbalance of the microbial population on or inside our bodies. Dysbiosis has been associated with a number of diseases, such as obesity, cancer, inflammatory bowel disease (IBD) and colitis. In this session we will discuss how alterations in our gut microbiota might affect (positively or negatively) disease conditions. We will examine two papers that found a correlation between members of indigenous microbiota and susceptibility to autoimmune diseases. In the first paper, the authors analyzed the microbiome of stool samples of patients afflicted or not by rheumatoid arthritis (RA) and correlated some bacterium species with the development of RA. In the second paper, the authors used an elegant approach to find different bacteria present in the human microbiota that could be related to the onset of IBD. In both papers, the authors validated their findings using mouse models of inflammatory diseases that will also be discussed in class.
13 Field Trip

Before the start of this final session, students should hand in their written assignments (both paper and electronic copies).

The microorganisms that inhabit our mucosal surfaces are collectively called the microbiota, and their genomes are called the microbiome. The beneficial effects of the microbiota to human health are numerous, varying from synthesis of essential vitamins to prevention of autoimmune diseases. Some individuals suffer from dysbiosis or microbial imbalance, a condition in which increased levels of harmful bacteria and reduced levels of beneficial bacteria predispose to colitis flare-ups and / or to infection by certain opportunistic bacteria, such as Clostridium difficile. Infection by these bacteria is a growing health problem in the United Stated, accounting to 29,000 deaths in 2011. Recurrent infections are a major challenge to overcome. Instead of treating this infection with strong antibiotics, some researches have proposed to treat recurrent C. difficile infections by adding the beneficial bacteria back to the microbiota of individuals afflicted by dysbiosis.

Eric Alm, MIT Director of the Center For Microbiome Informatics and Therapeutics, is heading a research lab at the Broad Institute focusing on the development of  therapeutics based on synthetic microbial communities and personalized medicine. We will visit his lab and receive a thoughtful introduction into his research including a demo of some techniques that are important for processing stool samples (liquid handling robot, anaerobic chamber, etc).