Phenotype classification in IBD: Is there an impact on therapy?

The Immune Landscape and Molecular Subtypes of Pediatric Crohn's Disease: Results from In Silico Analysis

Pediatric Crohn's disease (CD) presents a distinct phenotype from adult-onset disease. A dysregulated immune response is critical in CD pathogenesis; thus, it is clinically important to describe immune cell alterations and to identify a new molecular classification for pediatric CD. To this end, in this study, a RNA-seq derived dataset GSE101794-which contains the expression profiles of 254 treatment-naïve pediatric CD samples, including CIBERSORTx and weighted gene-co-expression network analysis (WGCNA)-were performed to estimate the ratio of immune cells and to identify modules and genes related to specific immune cell infiltration, respectively. Hub genes derived from WGCNA were further employed to create a molecular classification using unsupervised K-means clustering. In the pediatric CD samples, it was found that M2 macrophages, CD4⁺ memory resting T cells, CD8⁺ T cells, and resting mast cells were the most prominent immune cells in intestinal tissues. Then, 985 up-regulated genes and 860 down-regulated genes were identified in samples with high immune cell infiltration. Of these differential genes, 10 hub genes (APOA1, CYB5A, XPNPEP2, SLC1A7, SLC4A6, LIPE, G6PC, AGXT2, SLC13A1, and SOAT2) were associated with CD8⁺T cell infiltration. Clinically, the higher expression of these 10 hub genes was strongly associated with an earlier age of CD onset and colonic-type CD. Furthermore, based on these key genes, pediatric CD could be classified into three molecular subtypes, displaying a different immune landscape. Altogether, this in silico analysis provides a novel insight into the immune signature of pediatric CD, and a new classification of pediatric CD is presented, which may help us develop more personalized disease management and treatments for pediatric CD.

Protective Effects of Natural Antioxidants on Inflammatory Bowel Disease: Thymol and Its Pharmacological Properties

Inflammatory bowel disease (IBD) is a gastrointestinal disease that involves chronic mucosal or submucosal lesions that affect tissue integrity. Although IBD is not life-threatening, it sometimes causes severe complications, such as colon cancer. The exact etiology of IBD remains unclear, but several risk factors, such as pathogen infection, stress, diet, age, and genetics, have been involved in the occurrence and aggravation of IBD. Immune system malfunction with the over-production of inflammatory cytokines and associated oxidative stress are the hallmarks of IBD. Dietary intervention and medical treatment suppressing abnormal inflammation and oxidative stress are recommended as potential therapies. Thymol, a natural monoterpene phenol that is mostly found in thyme, exhibits multiple biological functions as a potential adjuvant for IBD. The purpose of this review is to summarize current findings on the protective effect of thymol on intestinal health in the context of specific animal models of IBD, describe the role of thymol in the modulation of inflammation, oxidative stress, and gut microbiota against gastrointestinal disease, and discuss the potential mechanism for its pharmacological activity.

Distinct clinical phenotypes for Crohn's disease derived from patient surveys

Background

Defining clinical phenotypes provides opportunities for new diagnostics and may provide insights into early intervention and disease prevention. There is increasing evidence that patient-derived health data may contain information that complements traditional methods of clinical phenotyping. The utility of these data for defining meaningful phenotypic groups is of great interest because social media and online resources make it possible to query large cohorts of patients with health conditions.

Methods

We evaluated the degree to which patient-reported categorical data is useful for discovering subclinical phenotypes and evaluated its utility for discovering new measures of disease severity, treatment response and genetic architecture. Specifically, we examined the responses of 1961 patients with inflammatory bowel disease to questionnaires in search of sub-phenotypes. We applied machine learning methods to identify novel subtypes of Crohn’s disease and studied their associations with drug responses.

Results

Using the patients’ self-reported information, we identified two subpopulations of Crohn’s disease; these subpopulations differ in disease severity, associations with smoking, and genetic transmission patterns. We also identified distinct features of drug response for the two Crohn’s disease subtypes. These subtypes show a trend towards differential genotype signatures.

Conclusion

Our findings suggest that patient-defined data can have unplanned utility for defining disease subtypes and may be useful for guiding treatment approaches.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12876-021-01740-6.

Montreal classification of patient operated for Crohn's disease and identification of surgical recurrence predictors

OBJECTIVE

to evaluate Crohn's disease recurrence and its possible predictors in patients undergoing surgical treatment.

METHODS

We conducted a retrospective study with Crohn's disease (CD) patients undergoing surgical treatment between January 1992 and January 2012, and regularly monitored at the Bowel Clinic of the Hospital das Clínicas of the UFMG.

RESULTS

we evaluated 125 patients, 50.4% female, with a mean age of 46.12 years, the majority (63.2%) diagnosed between 17 and 40 years of age. The ileum was involved in 58.4%, whereas stenotic behavior was observed in 44.8%, and penetrating, in 45.6%. We observed perianal disease in 26.4% of cases. The follow-up average was 152.40 months. Surgical relapse occurred in 29.6%, with a median time of 68 months from the first operation.

CONCLUSION

The ileocolic location, penetrating behavior and perianal involvement (L3B3p) were associated with increased risk of surgical recurrence.

Never underestimate inflammatory bowel disease: High prevalence rates and confirmation of high incidence rates in Australia

BACKGROUND AND AIMS

Regional variations in inflammatory bowel disease (IBD) rates have been observed. Limited epidemiological data are available from Australasia. IBD prevalence rates have never been assessed in an Australian population-based setting. In addition, there are few historical IBD incidence data to allow assessment of rate changes. The aims were to calculate Australia's first population-based IBD prevalence rates, to reassess local IBD incidence rates, and to establish a population-based inception cohort.

METHODS

An observational, prospective population-based epidemiological study was performed to assess IBD prevalence and incidence rates from July 2010 to June 2011 in a geographically defined Australian population (Barwon, Victoria).

RESULTS

There were 1011 prevalent IBD cases identified, representing a crude point prevalence rate of 344.6 per 100,000 on June 30, 2011. Crohn's disease was the most common prevalent subtype. Seventy-one incident cases of IBD were identified, with a crude incidence rate of 24.2 per 100,000. Crohn's disease was again more common. Local incidence rates have not changed between 2007 and the present study. All incident cases were successfully incorporated into an inception cohort.

CONCLUSION

The burden of IBD in our local region is high. Demographic similarities allow these results to be applied to the broader Australian community. We propose that the number of existing and new cases each year in Australia has been previously underestimated. These revised figures will be important when planning the provision of health resources for these patients in the future and when assessing need for research funding priorities.

Endoscopic biopsy samples of naïve "colitides" patients: role of basal plasmacytosis

BACKGROUND

Although it is usually not difficult to diagnose inflammatory bowel disease (IBD) on surgical resection specimens, difficulties sometimes arise in differentiating these entities from other forms of colitis on endoscopic biopsy specimens. Basal plasmacytosis is considered as an early feature of IBD colitis, but it is rare in non-IBD colitides.

AIMS

We assessed the value of basal plasmacytosis as an individual variable in untreated patients with colitis.

PATIENTS AND METHODS

Archival slides of patients with untreated colitis (66 IBD and 49 non-IBD) and 20 controls with complete (from the terminal ileum to the rectum) endoscopic biopsy sampling were evaluated blindly for the presence of basal plasmacytosis and a possible association with the presence of eosinophils in the same anatomical location.

RESULTS

Overall, basal plasmacytosis was present in at least one anatomical segment in 58% of cases, and it was always present in patients with IBD, whereas it was sparsely found (9%) in patients with other colitides and in controls. Basal plasmacytosis in three or more segments had more than 80% probability for a patient to be classified as IBD, with the segmental distribution being different between ulcerative colitis and Crohn's disease. Additionally, basal plasmacytosis was always accompanied by eosinophils intermingled with plasma cells in the same anatomical position.

CONCLUSION

As an individual feature, basal plasmacytosis (accompanied by eosinophils) is a strong feature suggesting IBD, particularly when present in three or more colonic segments. This fact may be useful in the evaluation of endoscopic biopsies from patients with "colitis".

Inflammatory bowel disease: one or two diseases?

This chapter addresses the longstanding question of whether inflammatory bowel disease (IBD) is really one or two diseases. The straightforward answer is that ulcerative colitis (UC) and Crohn's disease (CD) embody separate diseases more than a single syndrome. In reality, however, the question is more complex. This chapter makes the case that there are actually many more than just two diseases under the rubric of IBD.

Variation in care in pediatric Crohn disease

OBJECTIVES

Variation in medical care can be a barrier to improving clinical outcomes. We aim to describe the variation in care of Crohn disease as provided by a broad sample of pediatric gastroenterologists.

METHODS

Two hundred forty-six Crohn disease patients of 93 pediatric gastroenterologists from 48 practice sites starting treatment with either thiopurine or infliximab were studied. We assessed variation in diagnostic testing that had been performed to establish the diagnosis of Crohn disease and to assess the phenotype, extent, and severity of disease. We also assessed variation in initial thiopurine and infliximab dosage and in nutritional therapy.

RESULTS

Diagnostic studies in which care was uniform included complete blood count, performed in 100% of patients, erythrocyte sedimentation rate and colonoscopy in 96%, and upper endoscopy in 89%. However, imaging of the small bowel had not been performed in 19%, and a stool test for pathogens had not been performed in 29%. Thiopurine methyltransferase (TPMT) had been measured in 61% of patients before treatment with a thiopurine; in 85%, TPMT was normal. Nonetheless, even when TPMT was normal, 40% of patients received an initial dose of thiopurine that was lower than recommended. Testing for tuberculosis before initiating treatment with infliximab was not performed in 30%. In addition, 36% of severely underweight patients were not receiving a multivitamin supplement, supplemental formula, or tube feeding.

CONCLUSIONS

There is variation in diagnostic and therapeutic interventions in the management of pediatric Crohn disease, and gaps exist between recommended and actual care.