Endoscopy in the Diagnosis and Management of Complications of Inflammatory Bowel Disease

CANTARE: finding and visualizing network-based multi-omic predictive models

BACKGROUND

One goal of multi-omic studies is to identify interpretable predictive models for outcomes of interest, with analytes drawn from multiple omes. Such findings could support refined biological insight and hypothesis generation. However, standard analytical approaches are not designed to be "ome aware." Thus, some researchers analyze data from one ome at a time, and then combine predictions across omes. Others resort to correlation studies, cataloging pairwise relationships, but lacking an obvious approach for cohesive and interpretable summaries of these catalogs.

METHODS

We present a novel workflow for building predictive regression models from network neighborhoods in multi-omic networks. First, we generate pairwise regression models across all pairs of analytes from all omes, encoding the resulting "top table" of relationships in a network. Then, we build predictive logistic regression models using the analytes in network neighborhoods of interest. We call this method CANTARE (Consolidated Analysis of Network Topology And Regression Elements).

RESULTS

We applied CANTARE to previously published data from healthy controls and patients with inflammatory bowel disease (IBD) consisting of three omes: gut microbiome, metabolomics, and microbial-derived enzymes. We identified 8 unique predictive models with AUC > 0.90. The number of predictors in these models ranged from 3 to 13. We compare the results of CANTARE to random forests and elastic-net penalized regressions, analyzing AUC, predictions, and predictors. CANTARE AUC values were competitive with those generated by random forests and  penalized regressions. The top 3 CANTARE models had a greater dynamic range of predicted probabilities than did random forests and penalized regressions (p-value = 1.35 × 10-5). CANTARE models were significantly more likely to prioritize predictors from multiple omes than were the alternatives (p-value = 0.005). We also showed that predictive models from a network based on pairwise models with an interaction term for IBD have higher AUC than predictive models built from a correlation network (p-value = 0.016). R scripts and a CANTARE User's Guide are available at https://sourceforge.net/projects/cytomelodics/files/CANTARE/ .

CONCLUSION

CANTARE offers a flexible approach for building parsimonious, interpretable multi-omic models. These models yield quantitative and directional effect sizes for predictors and support the generation of hypotheses for follow-up investigation.

A literature-based approach for curating gene signatures in multifaceted diseases

BACKGROUND AND AIMS

The task of identifying a representative and yet manageable target gene list for assessing the pathogenesis of complicated and multifaceted diseases is challenging. Using Inflammatory Bowel Disease (IBD) as an example, we conceived a bioinformatic approach to identify novel genes associated with the various disease subtypes, in combination with known clinical control genes.

METHODS

From the available literature, we used Acumenta Literature Lab^TM (LitLab), network analyses, and LitLab Gene Retriever to assemble a gene pool that has a high likelihood of representing immunity-related subtype-specific signatures of IBD.

RESULTS

We generated six relevant gene lists and 21 intersections that contain genes with unique literature associations to Crohn's Disease (n = 60), Ulcerative Colitis (n = 17), and unclassified (n = 45) subtypes of IBD. From this gene pool, we then filtered and constructed, using network analysis, a final list of 142 genes that are the most representative of the disease and its subtypes.

CONCLUSIONS

In this paper, we present the bioinformatic construction of a gene panel that putatively contains subtype signatures of IBD, a multifactorial disease. These gene signatures will be tested as biomarkers to classify patients with IBD, which has been a clinically challenging task. Such approach to diagnose and monitor complicated disease pathogenesis is a stepping-stone towards personalized care.

Objective evaluation for treat to target in Crohn's disease

BACKGROUND

Crohn's disease (CD) is a chronic and destructive bowel disease; continued disease activity can lead to penetrating complications. With the recent advent of effective medications, the importance of using a treat-to-target approach to guide therapy is becoming important.

METHODS

In this review, we reviewed the previous evidence for evaluating CD lesions.

RESULTS

We describe ileocolonoscopy's role in assessing disease activity, as well as recent progress in modalities, such as balloon-assisted endoscopy, capsule endoscopy, magnetic resonance enterography, computed tomography enterography, and ultrasonography. Advances in modalities have changed CD assessment, with small-bowel involvement becoming more important.

CONCLUSIONS

Proper optimization is necessary in clinical practice.

Integrating omics for a better understanding of Inflammatory Bowel Disease: a step towards personalized medicine

Background

Inflammatory Bowel Disease (IBD) is a multifactorial chronic disease. Understanding only one aspect of IBD pathogenesis does not reflect the complex nature of IBD nor will it improve its clinical management. Therefore, it is vital to dissect the interactions between the different players in IBD pathogenesis in order to understand the biology of the disease and enhance its clinical outcomes.

Aims

To provide an overview of the available omics data used to assess the potential mechanisms through which various players are contributing to IBD pathogenesis and propose a precision medicine model to fill the current knowledge gap in IBD.

Results

Several studies have reported microbial dysbiosis, immune and metabolic dysregulation in IBD patients, however, this data is not sufficient to create signatures that can differentiate between the disease subtypes or between disease relapse and remission.

Conclusions

We summarized the current knowledge in the application of omics in IBD patients, and we showed that the current knowledge gap in IBD hinders the improvements of clinical decision for treatment as well as the prediction of disease relapse. We propose one way to fill this gap by implementing integrative analysis of various omics datasets generated from one patient at a single time point.

Even non-experts identify non-dysplastic lesions in inflammatory bowel disease via chromoendoscopy: results of a screening program in real-life

Background and study aims  Chromoendoscopy with targeted biopsy is the technique of choice for colorectal cancer screening in longstanding inflammatory bowel disease. We aimed to analyze results of a chromoendoscopy screening program and to assess the possibility of identifying low-risk dysplastic lesions by their endoscopic appearance in order to avoid histological analysis. Materials and methods  We retrospectively reviewed chromoendoscopies performed between February 2011 and June 2017 in seven Spanish hospitals in a standardized fashion. We analyzed the findings and the diagnostic yield of the Kudo pit pattern for predicting dysplasia. Results  A total of 709 chromoendoscopies (569 patients) were reviewed. Median duration of disease was 16.7 years (SD 8.1); 80.4 % had ulcerative colitis. A total of 2025 lesions (3.56 lesions per patient) were found; two hundred and thirty-two lesions were neoplastic (11.5 %) (223 were LGD (96.1 %), eight were HGD (3.4 %), and one was colorectal cancer (0.5 %). The correlation between dysplasia and Kudo pit patterns predictors of dysplasia (≥ III) was low, with an area under the curve of 0.649. Kudo I and II lesions were correctly identified with a high negative predictive value (92 %), even by non-experts. Endoscopic activity, Paris 0-Is classification, and right colon localization were risk factors for dysplasia detection, while rectum or sigmoid localization were protective against dysplasia. Conclusions  Chromoendoscopy in the real-life setting detected 11 % of dysplastic lesions with a low correlation with Kudo pit pattern. A high negative predictive value would prevent Kudo I and, probably, Kudo II biopsies in the left colon, reducing procedure time and avoiding complications.

Are random biopsies still useful for the detection of neoplasia in patients with IBD undergoing surveillance colonoscopy with chromoendoscopy?

BACKGROUND

Colonoscopy with pan-chromoendoscopy (CE) is superior to standard colonoscopy in detecting neoplasia in patients with IBD. Performing random biopsies in unsuspicious mucosa after CE remains controversial.

METHODS

Consecutive patients with IBD who underwent surveillance colonoscopy using CE were prospectively included. The standardised procedure used CE, performed targeted biopsies or endoscopic resection on suspicious lesions and then quadrant random biopsies every 10 cm. A panel of five expert pathologists reviewed histological slides with dysplasia. Logistic regression model was used to evidence the factors associated with neoplasia in any or in random biopsies.

RESULTS

1000 colonoscopes were performed in 1000 patients (495 UC, 505 Crohn's colitis). In 82 patients, neoplasia was detected from targeted biopsies or removed lesions, and among them dysplasia was detected also by random biopsies in 7 patients. Importantly, in 12 additional patients dysplasia was only detected by random biopsies. Overall, 140 neoplastic sites were found in 94 patients, 112 (80%) from targeted biopsies or removed lesions and 28 (20%) by random biopsies. The yield of neoplasia by random biopsies only was 0.2% per-biopsy (68/31 865), 1.2% per-colonoscopy (12/1000) but 12.8% per-patient with neoplasia (12/94). Dysplasia detected by random biopsies was associated with a personal history of neoplasia, a tubular appearing colon and the presence of primary sclerosing cholangitis (PSC).

CONCLUSIONS

Despite their low yield, random biopsies should be performed in association with CE in patients with IBD with a personal history of neoplasia, concomitant PSC or a tubular colon during colonoscopy.

TRIAL REGISTRATION NUMBER

IRB 001508, Paris 7 University.

Real-life chromoendoscopy for neoplasia detection and characterisation in long-standing IBD

OBJECTIVE

Outside clinical trials, the effectiveness of chromoendoscopy (CE) for long-standing IBD surveillance is controversial. We aimed to assess the effectiveness of CE for neoplasia detection and characterisation, in real-life.

DESIGN

From June 2012 to 2014, patients with IBD were prospectively included in a multicentre cohort study. Each colonic segment was evaluated with white light followed by 0.4% indigo carmine CE. Specific lesions' features were recorded. Optical diagnosis was assessed. Dysplasia detection rate between expert and non-expert endoscopists and learning curve were ascertained.

RESULTS

Ninety-four (15.7%) dysplastic (1 cancer, 5 high-grade dysplasia, 88 low-grade dysplasia) and 503 (84.3%) non-dysplastic lesions were detected in 350 patients (47% female; mean disease duration: 17 years). Colonoscopies were performed with standard definition (41.5%) or high definition (58.5%). Dysplasia miss rate with white light was 40/94 (57.4% incremental yield for CE). CE-incremental detection yield for dysplasia was comparable between standard definition and high definition (51.5% vs 52.3%, p=0.30). Dysplasia detection rate was comparable between expert and non-expert (18.5% vs 13.1%, p=0.20). No significant learning curve was observed (8.2% vs 14.2%, p=0.46). Sensitivity, specificity, and positive and negative predictive values for dysplasia optical diagnosis were 70%, 90%, 58% and 94%, respectively. Endoscopic characteristics predictive of dysplasia were: proximal location, loss of innominate lines, polypoid morphology and Kudo pit pattern III-V.

CONCLUSIONS

CE presents a high diagnostic yield for neoplasia detection, irrespectively of the technology and experience available in any centre. In vivo, CE optical diagnosis is highly accurate for ruling out dysplasia, especially in expert hands. Lesion characteristics can aid the endoscopist for in situ therapeutic decisions.

TRIAL REGISTRATION NUMBER

NCT02543762.

Endoscopic Fistulotomy Heals a Y-Shaped Entero-Entero-Cutaneous Fistula

Patients may develop fistulas due to Crohn’s disease or as a postoperative complication after restorative proctocolectomy with ileal pouch anal anastomosis. Unfortunately, the treatment of fistulas can be challenging. The current standard of care may include medical therapy and/or surgical intervention. However, endoscopic treatment for postoperative pouch complications has emerged as a valid alternative option. We describe a case of persistent drainage from a Y-shaped entero-entero-cutaneous fistula that resolved after endoscopic fistulotomy with needle knife.