Global Burden of IBD

Inflammatory Bowel Disease (IBD) is a heterogeneous group of autoimmune disorders encompassing Crohn’s disease and Ulcerative Colitis. It is estimated to affect 0.3% of the population in industrialised nations, including over 5 million adults in the UK, and 1.6 million in USA.

The global prevalence of IBD is increasing rapidly as countries become more developed. In addition, instances of IBD in developing countries are thought to be accelerated by the presence of bacteria, such as segmented filamentous bacteria (SFB), in water sources influencing the gut microbiome and host immune response. Gram positive SFB have recently been implicated in promoting the development of lymphocytes and the growth of Th17 populations.

An additional effect of the signals required for Th17 differentiation is the inhibition of the production of Treg cells. Once fully differentiated, Th17 cells produce interleukin 17a (IL-17a) a proinflammatory cytokine. Elevated levels of IL-17a are associated with MS and the development of epilepsy and other autoimmune diseases.

Most diagnoses occur between the ages of 20 and 30; the disease presents a significant burden to patients, societies, and healthcare systems. Current treatment is focused on symptom management, frequently resulting in sub-optimal control despite the burden of long-term treatment. Common therapeutics, such as corticosteroids, require regular administration, have many side-effects, and are less accessible in the developing world. The aim of our project is to address these problems and meet the notable, yet currently unmet, need for curative treatments for autoimmune diseases. This will be achieved via regulation of Treg and T helper cell populations to ensure immune responses of the correct magnitude. The specific control mechanism is discussed below.

Pathogenesis

Immunodeficiency is a state where the immune system is unable to fight against infection due to a lack of, or suppression of cells of the innate or adaptive immune responses. Immunodeficiency can be either primary or secondary in nature. Primary immunodeficiency is the result of genetic mutations that lead to reduced immune responses. This is further categorised into B cell and T cell immunodeficiencies, severe combined immunodeficiency, complement defects and phagocyte disorders. Secondary cases are caused by environmental factors or diseases that induce weakening of the immune system.

A reduction in the population size of Th cells, as a method to counteract autoimmune diseases, increases the risk of development of immunodeficiency as a depleted population of Th cells will be unable to resist infection as successfully. Preventing the development of immunodeficiency is of particular importance in regions with poor sanitation where exposure to infection is more common.

To prevent the development of immunodeficiency in individuals that use our treatment, we have created a system that responds to two input values. Upon detection of the size of Th17 and Treg cell populations, the system responds to ensure optimum population sizes. If one cell population exceeds optimum levels, there is a response to restrict a further increase, preventing uncontrollable growth. This mechanism prevents both autoimmune disease and immunodeficiency by maintaining optimum population sizes for both cell types.

Human Microbiome

The microbiota refers to the population of symbiotic microorganisms, typically bacteria, that reside in the gut and are known to play a role in human health. It has been estimated that there are approximately ten times the number of microbial cells to human cells in adults. There are around 100 species of microorganism in the gut in young infants and this number steadily increases to around 1000 in adults. The populations that compose the community of the microbiota are stable within an individual; however, the composition of the microbiota is highly variable between individuals. The composition of the microbiome is determined as early as birth, for example, by the method of delivery. Babies that are born via the birth canal are exposed to vaginal bacteria and so have a different microbiome than those delivered via C-section, which are typically colonised by bacteria located on the skin. Age, gender, diet, exercise also play a role in determining the composition of the bacterial community within the gut.

Traditionally, the microbiota refers to the microorganisms, for example, bacteria, viruses and fungi that have colonised the human body. In contrast, the microbiome is the total sum of the genes that the species within the microbiota possess.

The microbiota differs between regions of the body. It should be noted that opportunistic pathogens are present in the microbiota alongside non-pathogenic species. High microbial diversity within the gut is known to be associated with good gut health and lower incidence of Inflammatory Bowel Disease.

Our Solution

We decided to develop a probiotic strain of E. coli as a novel, self-tuning therapeutic for IBD. Our core design consists of the following:

• Riboswitch-ribozyme-sRNA construct
• Membrane-anchored nucleoside hydrolase
• NO-dependent IL-10 secretion system
• Inducible kill switch
  This provides a framework that can be used in a huge range of new projects by future iGEM teams, including biosensors and therapeutics.
  Due to the size and impermeability of regulatory interleukin proteins to the bacterial cell membrane, we used adenosine and nitric oxide (NO) as metabolic markers of Treg and Th-17 function respectively. An imbalance in the levels correlates with the autoimmune response. We aim to restore these to healthy proportions by secreting Interleukin 10 (IL-10) - a signal protein which stimulates cell differentiation into T-reg cells. The localised action of IL-10 secreted from the engineered bacteria makes our therapeutic best suited to gastrointestinal-based autoimmune diseases. Thus, we decided to focus specifically on IBD.
  Our bacteria produce personalised and easily administered doses of IL-10. This avoids impracticalities of current, injection based techniques. The gut has greater ease of introduction to the body over other sites of T-cell populations and no biological barriers need to be crossed for the probiotic bacteria to reach their target. Our focus is on autoimmune diseases in developing countries triggered by ingested pathogenic bacteria. In these cases the disease starts in the gut making it the obvious place for us to target. We propose the cultures could be ingested in tablet form; this avoids the training needed for injections and minimises the risk of infection.
  As well as being a generalised marker of inflammation, NO is thought to be produced by Th cells as a signal to induce differentiation of precursors into Th cells, thereby influencing the relative populations of Th and Treg cells. Continuous production of NO makes it a suitable marker of the size of the population and severity of the autoimmune disease.
  A range of purines are used by Treg cells as immune signals. ATP is released from cells during stress or injury. To prevent it from causing excessive inflammation, ATP is rapidly metabolised into AMP then into Adenosine (Ado) by Treg cell surface enzymes. Ado is detected by GPCRs of Th cells, triggering increased cAMP in the cells. Inflammatory signals are inhibited and IL-10 production is enhanced in mature dendritic cells. Ado also induces semi-maturation of immature dendritic cells. Adenosine promotes Treg populations, adenosine generation and increases immunoregulatory activity. Production by Treg cells and its role in regulating T cell populations and IL-10 production make it a suitable marker of Treg function and degree of immunodeficiency.
  In our circuit, IL-10 is secreted in the presence of NO and absence of elevated adenosine levels. IL-10 expression is stimulated by the endogenous E. coli SoxR transcription factor, activated by free radicals and oxidative stress, while expression is inhibited in response to adenosine by means of an adenine riboswitch linked to sRNA synthesis which will selectively inhibit translation of IL-10 mRNA. We have implemented a membrane-anchored adenosine hydrolase to generate adenine which can then diffuse into the cytoplasm and control the negative feedback loop.
  We decided to use NO partly due to the work of the Stanford 2009 iGEM team, who used NO detection to activate synthesis of retinoic acid. We used the same SoxR/SoxS promoter system to detect NO but instead, are using it to stimulate IL-10 production.
  A single stimulus can result in false positives and excessive suppression, leading to immunodeficiency. Incorporation of a negative feedback loop signaling high Treg populations avoids oversuppression of the immune system. The defining aspect of our design is the integration of two signals in order to increase the specificity and accuracy of our system in equilibrating the populations of Treg and Th-17 cells.
  Another important consideration was to develop a system to enhance the safety of our probiotic. Therefore, we decided to design a kill switch which would be activated by an external supplement in order to account for the possibility of adverse reactions in patients. We linked the antimicrobial artilysin Art-175 with a DsbA periplasmic secretion tag, under the control of an inducible pTet promoter. Therefore, upon induction by a synthetic TetR inducer, expression of the artilysin composite would promote host cell lysis. Further biosafety considerations are explained on the ‘Safety’ page.