Solving a Medical Mystery: The Math Behind Crohn’s Disease

Akankshya Jena

Finding a cure for a disease is a seemingly insurmountable task. It is complicated enough that patients do not all have the same disease presentation or characteristics because of the diversity of their backgrounds. When considering environmental factors and genetics in the slew of possible causes, each patient now requires a unique treatment plan, from diagnosis to post-operative therapy (Figure 1). The scenario describes a wide range of complex diseases that, as one would expect, are too heterogenous to have an overarching cure. While biological research has made substantial contributions towards the cure of complex diseases, Dr. Terry Furey, a computational biologist in the UNC School of Medicine, approached the problem differently. In a world where technology has allowed scientists to collect more and more data, Dr. Furey recognized the growing importance of data in science and the need for computational analyses to translate it into applicable results. With this in mind, Dr. Furey decided to combine statistics and genetics to study the heterogeneity of Crohn’s disease. 1 Crohn’s disease (CD) falls under the umbrella of inflammatory bowel diseases (IBDs). IBDs are disorders resulting from abnormal immune system responses to intestinal bacteria, specifically in patients who are genetically predisposed to have the condition. 2 CD is a chronic condition known for causing inflammation in the ileum and colon of the gastrointestinal (GI) tract (Figure 1). When foreign bacteria enter the GI tract, the immune system creates ulcers to combat and engulf the bacteria. In

Dr. Terrence Furey

the case of CD, the immune system is unable to turn itself off, meaning the ulcers remain unless treated with medicine or surgery. Based on ulcer location, patients can experience a variety of symptoms, ranging from abdominal pain and diarrhea to loss of appetite and fatigue. 3 IBDs have remained a medical mystery for decades because of their heterogeneity; no single treatment can be assumed to treat all forms of the disease, and genetic testing reveals little about onset or subsequent treatment plans. However, finding similarities among subtypes of the disease provides insight on treatment plans that cater to a certain group of patients who experience similar symptoms or develop similar associated diseases.4 Thus, Dr. Furey and his colleagues have investigated the possibility of associating genetic factors with the diverseness of CD. He uses a process known as genetic association analysis, which is essentially a statistical test that matches genotypical, or genetic, features with the expressed phenotypical, Figure 1: Diagram of factors affecting origin and course of

Crohn’s Disease. Image courtesy of Dr. Terrence Furey.

or physical, features of the patients. 4 For instance, if the DNA of two patients contains the same nucleic acid sequence at a certain point—known as a loci— in their DNA strand and those patients exhibit similar symptoms of Crohn’s disease, then researchers could conclude that to be a match. 1 To find more matches, Dr. Furey and his team used a series of methods to achieve accurate classification of CD. Initially, the researchers tested for general gene expression using biopsies from patients with and without CD. Results showed that the expressed genes of the CD patients were divided into two categories, one of which correlated with those of the non-IBD patients. Next, the researchers looked for differentially expressed genes, or genes expressed at statistically significant levels, between these two groups. They found genes affecting tissue-specific patterns at higher levels; for example, the groups had either ileum-specific or colon-specific genes regardless of where the cells were sampled from. Genes like CEACAM7 were found more often in colon-like samples, while APOA1 was found more abundantly in ileum-like samples. 4 Based on these results, the researchers wanted to see how easily the cell could interact with its DNA, which would allow the cell to fundamentally change its cellular identity. A cell can respond differently to external factors based on what specific parts of its DNA sequence it uses to run itself. An ileum-like cell in a CD patient could easily respond to a certain treatment, while a colon-like cell may reject it. Dr. Furey and his team performed FAIRE-seq on all of the samples, which was a test to map the DNA regions where activity was occurring. It was found that colon-like and ileum-like samples both had increased activity in genes previously

Figure 2: Medical illustration of Crohn’s Disease. Image courtesy of Bruce Blaus [CC-BY-SA 4.0].

associated with CD, indicating their correlation. 4 To summarize, both assays support the hypothesis of two CD subtypes. The testing also confirms that the genomic effects of the cells arose internally, not due to external molecules or signals changing the cells. Aided with Dr. Furey’s recent work, researchers have been able to identify two subtypes of Crohn’s disease, specifically two distinct molecular signatures that correlate with distinct symptoms and subsequent treatment plans. Furthermore, these subtypes apply to individuals regardless of their age, status of treatment, or location of tissue sampling, which firmly supports the possibility of using genetic association analysis to distinguish affected individuals from those that are not. From here, options arise of detecting the disease earlier, confirming similar symptoms, and individualizing treatment. When applying the data clinically, testing patients for specific molecular signatures would allow for the creation of treatment subgroups, based on results showing that patients with colon-like CD were more likely to get a colectomy, while patients with ileum-like CD were more likely to develop ileum disease and would later need biological therapy. 4 Using classification to treat CD, and IBDs in general, could prove to be an effective method. To improve and support the results from this paper, the researchers want to closely analyze the clinical journey of both adult and pediatric patients, and to study the corresponding tissue for each age group. 4 Dr. Furey and his team aim to further such research to possibly find more specific subtypes of Crohn’s disease, and even apply this method to other complex diseases as well. It seems that, in a community heavily influenced by wet-lab research, math could be the key to providing answers that could shape the future of medicine.

References

1. Interview with Terrence Furey, Ph.D. 02/03/20 2. Center for Disease Control. Inflammatory Bowel Disease (IBD). https://www.cdc.gov/ibd/index.htm (accessed February 14th, 2020). 3. Baumgart, D.; Sandborn, W. The Lancet 2012, 380, 1590 – 1605. 4. Weiser, M.; Simon, J.M.; Kochar, B.; Tovar, A.; Israel, J.; Robinson, A.; Gipson, G.; Schaner, M.; Herfarth, H.; Sartor, R.; et al. Gut 2018, 67, 36 – 42.