Role of genetics in the diagnosis and prognosis of Crohn's disease

Predicting diagnostic biomarkers associated with immune infiltration in Crohn's disease based on machine learning and bioinformatics

OBJECTIVE

The objective of this study is to investigate potential biomarkers of Crohn's disease (CD) and the pathological importance of infiltration of associated immune cells in disease development using machine learning.

METHODS

Three publicly accessible CD gene expression profiles were obtained from the GEO database. Inflammatory tissue samples were selected and differentiated between colonic and ileal tissues. To determine the differentially expressed genes (DEGs) between CD and healthy controls, the larger sample size was merged as a training unit. The function of DEGs was comprehended through disease enrichment (DO) and gene set enrichment analysis (GSEA) on DEGs. Promising biomarkers were identified using the support vector machine-recursive feature elimination and lasso regression models. To further clarify the efficacy of potential biomarkers as diagnostic genes, the area under the ROC curve was observed in the validation group. Additionally, using the CIBERSORT approach, immune cell fractions from CD patients were examined and linked with potential biomarkers.

RESULTS

Thirty-four DEGs were identified in colon tissue, of which 26 were up-regulated and 8 were down-regulated. In ileal tissues, 50 up-regulated and 50 down-regulated DEGs were observed. Disease enrichment of colon and ileal DEGs primarily focused on immunity, inflammatory bowel disease, and related pathways. CXCL1, S100A8, REG3A, and DEFA6 in colon tissue and LCN2 and NAT8 in ileum tissue demonstrated excellent diagnostic value and could be employed as CD gene biomarkers using machine learning methods in conjunction with external dataset validation. In comparison to controls, antigen processing and presentation, chemokine signaling pathway, cytokine-cytokine receptor interactions, and natural killer cell-mediated cytotoxicity were activated in colonic tissues. Cytokine-cytokine receptor interactions, NOD-like receptor signaling pathways, and toll-like receptor signaling pathways were activated in ileal tissues. NAT8 was found to be associated with CD8 T cells, while CXCL1, S100A8, REG3A, LCN2, and DEFA6 were associated with neutrophils, indicating that immune cell infiltration in CD is closely connected.

CONCLUSION

CXCL1, S100A8, REG3A, and DEFA6 in colonic tissue and LCN2 and NAT8 in ileal tissue can be employed as CD biomarkers. Additionally, immune cell infiltration is crucial for CD development.

Multi-locus genetic risk score predicts risk for Crohn’s disease in Slovenian population

AIM: To develop a risk model for Crohn’s disease (CD) based on homogeneous population.

METHODS: In our study were included 160 CD patients and 209 healthy individuals from Slovenia. The association study was performed for 112 single nucleotide polymorphisms (SNPs). We generated genetic risk scores (GRS) based on the number of risk alleles using weighted additive model. Discriminatory accuracy was measured by area under ROC curve (AUC). For risk evaluation, we divided individuals according to positive and negative likelihood ratios (LR) of a test, with LR > 5 for high risk group and LR < 0.20 for low risk group.

RESULTS: The highest accuracy, AUC of 0.78 was achieved with GRS combining 33 SNPs with optimal sensitivity and specificity of 75.0% and 72.7%, respectively. Individuals with the highest risk (GRS > 5.54) showed significantly increased odds of developing CD (OR = 26.65, 95%CI: 11.25-63.15) compared to the individuals with the lowest risk (GRS < 4.57) which is a considerably greater risk captured than in one SNP with the highest effect size (OR = 3.24). When more than 33 SNPs were included in GRS, discriminatory ability was not improved significantly; AUC of all 74 SNPs was 0.76.

CONCLUSION: The authors proved the possibility of building accurate genetic risk score based on 33 risk variants on Slovenian CD patients which may serve as a screening tool in the targeted population.

Overcoming difficulty in diagnosis and differential diagnosis of Crohn's disease: the potential role of serological and genetic tests

Crohn's disease (CD) represents a heterogeneous group of chronic inflammatory disorders with various phenotypes. Establishing a definite diagnosis of CD should be based upon a combined assessment of clinical, endoscopic, radiological and pathological features. Although segmental disease distribution, transmural inflammation and non-caseating epithelioid granulomas have been considered as a 'hallmarks' for CD, clear diagnosis of CD in some patients has been challenging, due to overlapping endoscopic, radiographic and histologic features with other inflammatory bowel disease-like conditions. Laboratory markers (serological and genetic tests) may provide additional clues for the diagnosis and differential diagnosis of CD. This review focuses on the application of the currently available serological and genomic markers and in diagnosis and differential diagnosis of CD.

Bovine immunoglobulin protein isolates for the nutritional management of enteropathy

The gastrointestinal tract is responsible for a multitude of digestive and immune functions which depend upon the balanced interaction of the intestinal microbiota, diet, gut barrier function, and mucosal immune response. Disruptions in one or more of these factors can lead to intestinal disorders or enteropathies which are characterized by intestinal inflammation, increased gut permeability, and reduced capacity to absorb nutrients. Enteropathy is frequently associated with human immunodeficiency virus (HIV) infection, inflammatory bowel disease, autoimmune enteropathy, radiation enteritis, and irritable bowel syndrome (IBS), where pathologic changes in the intestinal tract lead to abdominal discomfort, bloating, abnormal bowel function (e.g., diarrhea, urgency, constipation and malabsorption). Unfortunately, effective therapies for the management of enteropathy and restoring intestinal health are still not available. An accumulating body of preclinical studies has demonstrated that oral administration of plasma- or serum-derived protein concentrates containing high levels of immunoglobulins can improve weight, normalize gut barrier function, and reduce the severity of enteropathy in animal models. Recent studies in humans, using serum-derived bovine immunoglobulin/protein isolate, demonstrate that such protein preparations are safe and improve symptoms, nutritional status, and various biomarkers associated with enteropathy. Benefits have been shown in patients with HIV infection or diarrhea-predominant IBS. This review summarizes preclinical and clinical studies with plasma/serum protein concentrates and describes the effects on host nutrition, intestinal function, and markers of intestinal inflammation. It supports the concept that immunoglobulin-containing protein preparations may offer a new strategy for restoring functional homeostasis in the intestinal tract of patients with enteropathy.

CARD15 Gene 3020insC Mutation with Inflammatory Bowel Diseases Patients in the Black Sea Region of Turkey

BACKGROUND: The role of the CARD15 gene 3020insC frameshift mutation in the pathogenesis of inflammatory bowel diseases (IBD) investigated without a definitive conclusion. The incidence of this mutation in Turkish patients with Crohn’s disease is not known.OBJECTIVE: We investigated whether the CARD15/NOD2 3020insC frameshift mutation is a risk factor for patients with inflammatory bowel disease in Black Sea Region population in Turkey.METHODS: We studied 3020insC mutation of CARD15/NOD2 gene by allele-specific multiplex PCR in 69 patients with IBD (18 Crohn’s disease [CD] and 51 ulcerative colitis [UC]) and 101 ethnically matched healthy controls.RESULTS: CARD15/NOD2 3020insC frameshift mutation was positive in 7/18 (38.8 %), 13/51 (25.5 %), and 4/101 (4 %) of CD, UC, and healthy control groups, respectively. None of the controls or patients with Crohn’s disease and ulcerative colitis was homozygous for this mutations.CONCLUSION: This study is to investigate a relation between CARD15/NOD2 3020insC frameshift mutation and in patients with IBD in the Turkish Population. C-insertion frameshift mutation is a major contributor to the susceptibility to both CD and UC, but it is not specific to patients with CD in Turkish population.

Role of the gut microbiota in inflammatory bowel disease pathogenesis: What have we learnt in the past 10 years?

Our understanding of the microbial involvement in inflammatory bowel disease (IBD) pathogenesis has increased exponentially over the past decade. The development of newer molecular tools for the global assessment of the gut microbiome and the identification of nucleotide-binding oligomerization domain-containing protein 2 in 2001 and other susceptibility genes for Crohn’s disease in particular has led to better understanding of the aetiopathogenesis of IBD. The microbial studies have elaborated the normal composition of the gut microbiome and its perturbations in the setting of IBD. This altered microbiome or “dysbiosis” is a key player in the protracted course of inflammation in IBD. Numerous genome-wide association studies have identified further genes involved in gastrointestinal innate immunity (including polymorphisms in genes involved in autophagy: ATG16L1 and IGRM), which have helped elucidate the relationship of the local innate immunity with the adjacent luminal bacteria. These developments have also spurred the search for specific pathogens which may have a role in the metamorphosis of the gut microbiome from a symbiotic entity to a putative pathogenic one. Here we review advances in our understanding of microbial involvement in IBD pathogenesis over the past 10 years and offer insight into how this will shape our therapeutic management of the disease in the coming years.

Oral manifestations of systemic autoimmune and inflammatory diseases: diagnosis and clinical management

CONTEXT

Systemic autoimmune and inflammatory diseases often manifest oral lesions in their earliest stages, and early diagnosis, which may be spurred by a dental examination, is key for improved outcomes. After systemic diagnosis, oral lesions benefit from specialized care by dentists in collaboration with the medical team. This review aims to educate dental clinicians about the most relevant systemic autoimmune and inflammatory conditions with accompanying oral lesions, their implications for health, and management strategies supported by the biomedical literature and clinical experience. Ulcerative conditions including Behcet and Crohn diseases are discussed, along with rheumatic conditions including Sjögren syndrome, lupus erythematosus, and rheumatoid arthritis.

EVIDENCE ACQUISITION

Evidence was accumulated through PubMed searches using pertinent keywords for each subsection. References were reviewed and original publications examined to verify the accuracy of the information. We focused on evidence included in current reviews and randomized trials. Recommendations were supported by multiple studies and consensus expert opinion.

EVIDENCE SYNTHESIS

Disease phenotypes described and clinical recommendations were synthesized from best-quality evidence available for each disease. Efforts were made to describe evidence selection within each disease section.

CONCLUSIONS

Dentists play an important role in the early detection and multidisciplinary medical management of complex autoimmune diseases. It is important to recognize prevalent medical and dental issues and special needs of patients with autoimmune conditions. The management of many inflammatory conditions is similar, and often begins with the use of topical steroids, analgesics, and antimicrobial treatments, in addition to careful attention to oral hygiene and appropriate fluoride usage. In this brief review, we aim to discuss the presentation/prevalence, diagnosis, and treatment of oral manifestations encountered in autoimmune, autoinflammatory and systemic chronic inflammatory diseases. Systemic autoimmune conditions are estimated to affect 5% to 8% of Americans.(1) Oral manifestations are encountered with high frequency, and are often the first clinical signs or symptoms of the general disease. Optimal management of complex autoimmune diseases requires a multidisciplinary medical team including dentists to care for lesions of the oral cavity. The dental practitioner may be asked to play a primary role in the diagnosis of such conditions and to participate with other health professionals working together to achieve effective clinical management. To aid in this process, we discuss in this article the current general knowledge of systemic autoimmune conditions that present with prevalent oral manifestations. The focus is on the diagnosis and management of the oral component of each disease. Importantly, whereas the etiology and pathogenesis and systemic clinical presentation may vary, presentation in the oral cavity is often similar and many conditions involve oral ulcerations. For this reason, we discuss the differential diagnosis and management of the most common oral ulcerations in a general section and subsequently address individual conditions that present with oral ulcerations. Similarly, treatment of various autoimmune/inflammatory oral conditions is often common and involves modulation or suppression of the immune response locally and/or systemically and will be therefore addressed in a common section as well as individually for each disease when unique treatment regimens are recommended. We present here our general treatment recommendations based on clinical experience and literature review; however, it is critical that good clinical judgment and specifics of an individual case should determine the appropriate dental/oral medicine intervention for a specific patient.