Background and Rationale
In 2019, an estimated 4.9 million people lived with inflammatory bowel disease (IBD) worldwide. (1) IBD represents a group of autoimmune diseases characterized by inflammation in the intestines. There are two existing subtypes of IBD: Crohn’s disease and ulcerative colitis each characterized by interspersed and continuous intestinal inflammation respectively. The incidence of IBD is on the rise, and Canada has among the highest prevalence globally. As of 2018, 270,000 Canadians were affected by IBD, with this number expected to rise to 403,000 by the year 2030. (2) Symptoms of IBD can include but are not limited to persistent diarrhea, fatigue, abdominal pain, and reduced appetite. (3) The development of this disease can be a result of both genetic and environmental factors, with alterations in gut microbiota being the leading hypothesis. The microorganisms of the human gut have a mutually symbiotic relationship with the host where changes in their composition can result in harmful imbalances such as the development of IBD.
There is no cure for ulcerative colitis or Crohn’s disease, apart from invasive surgical intervention. Current medical treatments available, such as aminosalicylates, corticosteroids, and biologics, are primarily focused on managing inflammation to achieve and maintain remission. However, these treatments often face limitations in terms of their success rates and can result in notable side effects.
Probiotics have been a promising approach in adjunctive therapy for patients with IBD. They have been studied for their immunomodulatory effects, ability to maintain gut barrier integrity, and to elicit cytoprotective and antipathogenic responses. (4–6) These mechanisms have therapeutic potential to ameliorate symptoms of IBD, given the crucial role of the gut microbiome and gut barrier permeability in disease progression.
Given this, we aim to focus on removing adherent-invasive E. coli (AIEC) bacteria, while also leveraging the benefits of probiotics in our implementation plan to create a better gut microbiome for IBD patients.
Project Description
In this project, we aimed to develop a genetic circuit that is able to detect inflammation, as well as eliminate harmful AIEC from the intestinal environment of IBD patients. This circuit is to detect the inflammation marker, nitric oxide (NO), as well as quorum sensing factors specific to virulent AIEC. Upon detection, colicin E1 and E9 are to be produced, effectively eliminating the AIEC.
Quorum sensing is the process used by bacteria to communicate and sense population density. (7,8) AIEC uses autoinducer-3 (AI-3), a quorum sensing molecule that regulates virulence and colonization. AI-3 serves as a marker in our genetic circuit to detect the presence of AIEC, and to trigger the subsequent expression of colicins E1 and E9.
The circuit is also able to detect NO, an important inflammatory marker in patients with IBD. Increased NO production is associated with tissue damage and inflammation in these patients, and therefore is used as a marker to trigger the activation of our genetic circuit. (9,10)
Colicin is a family of bacteriocins produced by E. coli that inhibit closely related strains. (11) Colicins E1 and E9 have been found effective in killing AIEC strain LF82 in both biofilm and planktonic states. (12) Colicin E1 forms a voltage-gated ion channel that depolarizes the bacterial inner membrane and has also been shown to have low cytotoxicity, while E9 is an enzymatic protein able to nick double stranded DNA, as well as single stranded DNA and RNA. (13–15)
Overall, the genetic circuit is able to detect AI-3 and NO, triggering the expression of colicins E1 and E9, allowing for the selective elimination of AIEC and inhibition of its virulence factors.
Human Practices
Throughout our project, we strove to center IBD patients and tailored our solution to not only address their medical conditions but also holistically improve their quality of life. Inspired by their life experiences, we wanted to honour IBD patients by consulting leading experts in the field to ensure a broad scope of knowledge and understanding while conducting community outreach campaigns to maximize our mission's potential influence.
Our team sought to raise awareness and educate various communities on IBD and the impact it has on individuals all throughout the world. Although IBD has a high prevalence in Canada, many people are unaware of IBD and the severity of this disease. Therefore, we worked to educate the younger generation on the significance of scientific research and outreach through our high school internship program. Through this internship, we hope to have inspired the interns to pursue a career in science by exposing them to the various components that make up the McMaster Synbio team and the prospects of diving deeper into gut microbial education and research.
Regarding education, our team collaborated with the University of Thessaly’s Synthetic Biology Team and acclaimed researchers Dr. Brian Coombes and Dr. Alexander Meziti to host a webinar to raise awareness about IBD and overall intestinal well-being. Dr. Brian Coombes spoke on his research centred around Crohn’s disease and his particular focus on the microbes that drive chronic inflammation during Crohn’s disease. Dr. Meziti spoke on her research focused on microbial ecology in aquatic environments and the gut microbiome under changing conditions. We believe the topics discussed in the webinar will inspire students to pursue research in the field of gastroenterology.
Furthermore, our team hosted an inspiring webinar on the topic of the microbiome with the renowned researcher Dr. John F. Rawls. Dr. Rawls is a professor and expert in the field of microbiology at the Duke University School of Medicine. Through collaborating with Dr. Rawls, our team was able to educate the public on the importance of the gut microbiome and what research on the gut microbiome could lead to.
Lastly, our team strove to spread awareness regarding IBD throughout the Hamilton community and beyond by publishing an article in the Hamilton Spectator regarding the lack of knowledge about IBD and their profound implications. Publications such as the one made on The Hamilton Spectator, with an average viewer count of over 7 million page viewers, allowed our team to extend community outreach initiatives further to educate the public about inflammatory Bowel Disease and several other topics surrounding this disease that we found to be of great value In addition, we involved local communities by hosting trivia nights and presentations within McMaster University, featuring on local podcasts, and speaking at other Ontario Universities such as York University. Through these initiatives, we were able to successfully raise awareness and educate a diverse variety of individuals on IBD and inspire future generations to become involved in gut microbiome research.
References
1. Wang R, Li Z, Liu S, Zhang D. Global, regional and national burden of inflammatory bowel disease in 204 countries and territories from 1990 to 2019: a systematic analysis based on the Global Burden of Disease Study 2019. BMJ Open [Internet]. 2023;13(3). Available from: https://bmjopen.bmj.com/content/13/3/e065186
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2. Kaplan GG, Bernstein CN, Coward S, Bitton A, Murthy SK, Nguyen GC, et al. The Impact of Inflammatory Bowel Disease in Canada 2018: Epidemiology. J Can Assoc Gastroenterol. 2019 Feb;2(Suppl 1):S6–16.
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3. Inflammatory bowel disease (IBD) - Symptoms and causes [Internet]. Mayo Clinic. [cited 2023 Jun 10]. Available from: https://www.mayoclinic.org/diseases-conditions/inflammatory-bowel-disease/symptoms-causes/syc-20353315
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4. Picardo S, Altuwaijri M, Devlin SM, Seow CH. Complementary and alternative medications in the management of inflammatory bowel disease. Ther Adv Gastroenterol. 2020 Jan 1;13:1756284820927550.
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5. Yan F, Polk DB. Probiotics and Probiotic-Derived Functional Factors—Mechanistic Insights Into Applications for Intestinal Homeostasis. Front Immunol [Internet]. 2020;11. Available from: https://www.frontiersin.org/articles/10.3389/fimmu.2020.01428
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7. Miller MB, Bassler BL. Quorum sensing in bacteria. Annu Rev Microbiol. 2001;55:165–99.
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8. Kim CS, Gatsios A, Cuesta S, Lam YC, Wei Z, Chen H, et al. Characterization of Autoinducer-3 Structure and Biosynthesis in E. coli. ACS Cent Sci. 2020 Feb 26;6(2):197–206.
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9. Sharma JN, Al-Omran A, Parvathy SS. Role of nitric oxide in inflammatory diseases. Inflammopharmacology. 2007 Dec;15(6):252–9.
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10. Avdagić N, Zaćiragić A, Babić N, Hukić M, Šeremet M, Lepara O, et al. Nitric oxide as a potential biomarker in inflammatory bowel disease. Bosn J Basic Med Sci. 2013 Feb;13(1):5–9.
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11. Brown CL, Smith K, McCaughey L, Walker D. Colicin-like bacteriocins as novel therapeutic agents for the treatment of chronic biofilm-mediated infection. Biochem Soc Trans. 2012 Dec 1;40(6):1549–52.
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12. Brown CL, Smith K, Wall DM, Walker D. Activity of Species-specific Antibiotics Against Crohn’s Disease-Associated Adherent-invasive Escherichia coli. Inflamm Bowel Dis. 2015 Oct;21(10):2372–82.
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13. Gouaux E. The long and short of colicin action: the molecular basis for the biological activity of channel-forming colicins. Struct Lond Engl 1993. 1997 Mar 15;5(3):313–7.
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14. Masi M, Vuong P, Humbard M, Malone K, Misra R. Initial steps of colicin E1 import across the outer membrane of Escherichia coli. J Bacteriol. 2007 Apr;189(7):2667–76.
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15. Pommer AJ, Cal S, Keeble AH, Walker D, Evans SJ, Kühlmann UC, et al. Mechanism and cleavage specificity of the H-N-H endonuclease colicin E9. J Mol Biol. 2001 Dec 7;314(4):735–49.