Precision Medicine in Inflammatory Bowel Diseases

CT-based radiomics signature of visceral adipose tissue and bowel lesions for identifying patients with Crohn's disease resistant to infliximab

PURPOSE

To develop a CT-based radiomics model combining with VAT and bowel features to improve the predictive efficacy of IFX therapy on the basis of bowel model.

METHODS

This retrospective study included 231 CD patients (training cohort, n = 112; internal validation cohort, n = 48; external validation cohort, n = 71) from two tertiary centers. Machine-learning VAT model and bowel model were developed separately to identify CD patients with primary nonresponse to IFX. A comprehensive model incorporating VAT and bowel radiomics features was further established to verify whether CT features extracted from VAT would improve the predictive efficacy of bowel model. Area under the curve (AUC) and decision curve analysis were used to compare the prediction performance. Clinical utility was assessed by integrated differentiation improvement (IDI).

RESULTS

VAT model and bowel model exhibited comparable performance for identifying patients with primary nonresponse in both internal (AUC: VAT model vs bowel model, 0.737 (95% CI, 0.590-0.854) vs. 0.832 (95% CI, 0.750-0.896)) and external validation cohort [AUC: VAT model vs. bowel model, 0.714 (95% CI, 0.595-0.815) vs. 0.799 (95% CI, 0.687-0.885)), exhibiting a relatively good net benefit. The comprehensive model incorporating VAT into bowel model yielded a satisfactory predictive efficacy in both internal (AUC, 0.840 (95% CI, 0.706-0.930)) and external validation cohort (AUC, 0.833 (95% CI, 0.726-0.911)), significantly better than bowel alone (IDI = 4.2% and 3.7% in internal and external validation cohorts, both p < 0.05).

CONCLUSION

VAT has an effect on IFX treatment response. It improves the performance for identification of CD patients at high risk of primary nonresponse to IFX therapy with selected features from RM.

CRITICAL RELEVANCE STATEMENT

Our radiomics model (RM) for VAT-bowel analysis captured the pathophysiological changes occurring in VAT and whole bowel lesion, which could help to identify CD patients who would not response to infliximab at the beginning of therapy.

KEY POINTS

• Radiomics signatures with VAT and bowel alone or in combination predicting infliximab efficacy. • VAT features contribute to the prediction of IFX treatment efficacy. • Comprehensive model improved the performance compared with the bowel model alone.

Insilco prediction of the role of the FriZZled5 gene in colorectal cancer

INTRODUCTION

In this study, we aimed to elucidate the crosstalk between the Wnt/β-catenin signaling pathway and colorectal cancer (CRC) associated with inflammatory bowel disease (IBD) using a bioinformatics analysis of putative common biomarkers and a systems biology approach.

MATERIALS AND METHODS

The following criteria were used to search the GEO and ArrayExpress databases for terms related to CRC and IBD: 1. The dataset containing the transcriptomic data, and 2. Untreated samples by medications or drugs. A total of 42 datasets were selected for additional analysis. The GEO2R identified the differentially expressed genes. The genes involved in the Wnt signaling pathway were extracted from the KEGG database. Enrichment analysis and miRNA target prediction were conducted through the ToppGene online tool.

RESULTS

In CRC datasets, there were 1168 up- and 998 down-regulated probes, whereas, in IBD datasets, there were 256 up- and 200 down-regulated probes. There were 65 upregulated and 57 downregulated genes shared by CRC and IBD. According to KEGG, there were 166 genes in the Wnt pathway. FriZZled5 (FZD5) was a down-regulated gene in both CRC and IBD, as determined by the intersection of CRC- and IBD-related DEGs with the Wnt pathway. It was also demonstrated that miR-191, miR-885-5p, miR-378a-3p, and miR-396-3p affect the FriZZled5 gene expression.

CONCLUSION

It is possible that increased expression of miR-191 and miR-885-5p, or decreased expression of miR-378a -3p and miR396-3, in IBD and CRC results in decreased expression of the FZD5 gene. Based on the function of this gene, FZD5 may be a potential therapeutic target in IBD that progresses to CRC.

Intestinal stents: Structure, functionalization and advanced engineering innovation

Intestinal stents are a palliative treatment option that solves many shortcomings of traditional surgeries for cancer-induced intestinal obstructions. The present review provides an overview of the incidence, clinical manifestations and limitations in the treatment of intestinal cancers. The paper also discusses material property requirements, indications, complications and the future of stent-assisted therapy. The advantages and disadvantages of different materials and processing techniques for intestinal stents are reviewed along with new stent treatment combinations for colorectal cancer. Challenges that require further cooperative studies are also detailed. The future development of intestinal stents will depend on innovation in material designs as well as the utilization of multi-functional strategies and innovative engineering solutions.

Computational models in inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic and relapsing disease with multiple underlying influences and notable heterogeneity among its clinical and response-to-treatment phenotypes. There is no cure for IBD, and none of the currently available therapies have demonstrated clinical efficacies beyond 40%-60%. Data collected about its omics, pathogenesis, and treatment strategies have grown exponentially with time making IBD a prime candidate for artificial intelligence (AI) mediated discovery support. AI can be leveraged to further understand or identify IBD features to improve clinical outcomes. Various treatment candidates are currently under evaluation in clinical trials, offering further approaches and opportunities for increasing the efficacies of treatments. However, currently, therapeutic plans are largely determined using clinical features due to the lack of specific biomarkers, and it has become necessary to step into precision medicine to predict therapeutic responses to guarantee optimal treatment efficacy. This is accompanied by the application of AI and the development of multiscale hybrid models combining mechanistic approaches and machine learning. These models ultimately lead to the creation of digital twins of given patients delivering on the promise of precision dosing and tailored treatment. Interleukin-6 (IL-6) is a prominent cytokine in cell-to-cell communication in the inflammatory responses' regulation. Dysregulated IL-6-induced signaling leads to severe immunological or proliferative pathologies, such as IBD and colon cancer. This mini-review explores multiscale models with the aim of predicting the response to therapy in IBD. Modeling IL-6 biology and generating digital twins enhance the credibility of their prediction.

Strictures in Crohn's Disease: From Pathophysiology to Treatment

Despite recent advances aimed to treat transmural inflammation in Crohn's disease (CD) patients, the progression to a structuring behavior still represents an issue for clinicians. As inflammation becomes chronic and severe, the attempt to repair damaged tissue can result in an excessive production of extracellular matrix components and deposition of connective tissue, thus favoring the formation of strictures. No specific and accurate clinical predictors or diagnostic tools for intestinal fibrosis exist, and to date, no genetic or serological marker is in routine clinical use. Therefore, intestinal fibrosis is usually diagnosed when it becomes clinically evident and strictures have already occurred. Anti-fibrotic agents such as tranilast, peroxisome proliferator-activated receptor gamma agonists, rho kinase inhibitors, and especially mesenchymal stem cell therapy have provided interesting results, but most of the evidence has been derived from studies performed in vitro. Therefore, current therapy of fibrotic strictures relies mainly on endoscopic and surgical procedures. Although its long-term outcomes may be debated, endoscopic balloon dilation appears to be the safest and most effective approach to treat appropriately selected strictures. The use of endoscopic stricturotomy is currently limited by the expertise needed to perform it and by the few data available in the literature. Some good results have been achieved by the positioning of self-expandable metal stents (SEMS). However, there is no concordance regarding the type of stent to use and for how long it should be left in place. The development of new specific SEMS may lead to better outcomes and to an increased use of this alternative in CD-related strictures.

Intellectual Structure and Evolutionary Trends of Precision Medicine Research: Coword Analysis

BACKGROUND

Precision medicine (PM) is playing a more and more important role in clinical practice. In recent years, the scale of PM research has been growing rapidly. Many reviews have been published to facilitate a better understanding of the status of PM research. However, there is still a lack of research on the intellectual structure in terms of topics.

OBJECTIVE

This study aimed to identify the intellectual structure and evolutionary trends of PM research through the application of various social network analysis and visualization methods.

METHODS

The bibliographies of papers published between 2009 and 2018 were extracted from the Web of Science database. Based on the statistics of keywords in the papers, a coword network was generated and used to calculate network indicators of both the entire network and local networks. Communities were then detected to identify subdirections of PM research. Topological maps of networks, including networks between communities and within each community, were drawn to reveal the correlation structure. An evolutionary graph and a strategic graph were finally produced to reveal research venation and trends in discipline communities.

RESULTS

The results showed that PM research involves extensive themes and, overall, is not balanced. A minority of themes with a high frequency and network indicators, such as Biomarkers, Genomics, Cancer, Therapy, Genetics, Drug, Target Therapy, Pharmacogenomics, Pharmacogenetics, and Molecular, can be considered the core areas of PM research. However, there were five balanced theme directions with distinguished status and tendencies: Cancer, Biomarkers, Genomics, Drug, and Therapy. These were shown to be the main branches that were both focused and well developed. Therapy, though, was shown to be isolated and undeveloped.

CONCLUSIONS

The hotspots, structures, evolutions, and development trends of PM research in the past ten years were revealed using social network analysis and visualization. In general, PM research is unbalanced, but its subdirections are balanced. The clear evolutionary and developmental trend indicates that PM research has matured in recent years. The implications of this study involving PM research will provide reasonable and effective support for researchers, funders, policymakers, and clinicians.

Treatment Perspectives in Crohn's Disease

BACKGROUND

Crohn's disease (CD) is a chronic immune-mediated disorder of the gastrointestinal tract. The pathophysiological understanding of this disease is limited and no curative therapy is available so far. Therefore, most patients require long-lasting or even life-long immunosuppressive therapies for the suppression of symptoms to improve quality of life and reduction of long-term risks. However, in a relevant subgroup of patients, these therapeutic goals cannot be sufficiently attained.

SUMMARY

Clinically established therapies in active CD comprise corticosteroids and immunosuppressants such as azathioprine. After the introduction of anti-TNFα (Tumor necrosis factor alpha) antibodies, other biologicals (e.g., vedolizumab and ustekinumab) have also been approved. New drugs in the pipeline like filgotinib, upadacitinib, risankizumab or rifaximin could improve the therapy of CD in the near future. Thus, an individualized therapy management, based on optimal selection of therapeutic agents will become more important. Additionally, the local application of mesenchymal stem cells might be helpful in the management of fistulas. Key Messages: The targeted biological therapeutic agents (anti-TNFα antibodies, vedolizumab, ustekinumab) are well established for therapy in CD. There are several new substances in the pipeline with promising results in phase II trials (filgotinib, rifaximin, risankizumab, upadacitinib). The upcoming extension of the therapeutic arsenal will require methods for an optimized selection of substances, thus enabling a more individualized therapy.

Intestinal fibrosis

Extensive tissue fibrosis is the end-stage process of a number of chronic conditions affecting the gastrointestinal tract, including inflammatory bowel disease (Crohn's disease, ulcerative colitis), ulcerative jejunoileitis, and radiation enteritis. Fibrogenesis is a physiological, reparative process that may become harmful as a consequence of the persistence of a noxious agent, after an excessive duration of the healing process. In this case, after replacement of dead or injured cells, fibrogenesis continues to substitute normal parenchymal tissue with fibrous connective tissue, leading to uncontrolled scar formation and, ultimately, permanent organ damage, loss of function, and/or strictures. Several mechanisms have been implicated in sustaining the fibrogenic process. Despite their obvious etiological and clinical distinctions, most of the above-mentioned fibrotic disorders have in common a persistent inflammatory stimulus which sustains the production of growth factors, proteolytic enzymes, and pro-fibrogenic cytokines that activate both non-immune (i.e., myofibroblasts, fibroblasts) and immune (i.e., monocytes, macrophages, T-cells) cells, the interactions of which are crucial in the progressive tissue remodeling and destroy. Here we summarize the current status of knowledge regarding the mechanisms implicated in gut fibrosis with a clinical approach, also focusing on possible targets of antifibrogenic therapies.

A systems pharmacology model for inflammatory bowel disease

Motivation

The literature on complex diseases is abundant but not always quantitative. This is particularly so for Inflammatory Bowel Disease (IBD), where many molecular pathways are qualitatively well described but this information cannot be used in traditional quantitative mathematical models employed in drug development. We propose the elaboration and validation of a logic network for IBD able to capture the information available in the literature that will facilitate the identification/validation of therapeutic targets.

Results

In this article, we propose a logic model for Inflammatory Bowel Disease (IBD) which consists of 43 nodes and 298 qualitative interactions. The model presented is able to describe the pathogenic mechanisms of the disorder and qualitatively describes the characteristic chronic inflammation. A perturbation analysis performed on the IBD network indicates that the model is robust. Also, as described in clinical trials, a simulation of anti-TNFα, anti-IL2 and Granulocyte and Monocyte Apheresis showed a decrease in the Metalloproteinases node (MMPs), which means a decrease in tissue damage. In contrast, as clinical trials have demonstrated, a simulation of anti-IL17 and anti-IFNγ or IL10 overexpression therapy did not show any major change in MMPs expression, as corresponds to a failed therapy. The model proved to be a promising in silico tool for the evaluation of potential therapeutic targets, the identification of new IBD biomarkers, the integration of IBD polymorphisms to anticipate responders and non-responders and can be reduced and transformed in quantitative model/s.

Inflammatory Bowel Diseases and Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols: An Overview

Inflammatory bowel diseases (IBDs) are mainly represented by ulcerative colitis and Crohn's disease, and the increase in the incidence tends to follow the rapid industrialization and lifestyle of modern societies. FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) consist of molecules that are poorly absorbed in the small intestine and are fermented by bacteria in the colon leading to symptoms such as bloating, flatulence, diarrhea, and abdominal pain. Reduction of the ingestion of FODMAP could reduce the symptoms and improve the quality of life. This review aimed to summarize some important aspects of IBD and evaluate the effects of this diet on this inflammatory condition. Studies including the term FODMAP (and similar terms) and IBD were selected for this review (MEDLINE database was used PubMed/PMC). A low FODMAP diet may be an effective tool to the management of the common abdominal symptoms in patients with functional gastrointestinal symptoms once these molecules trigger these symptoms. This diet may also reduce the expression of pro-inflammatory markers such as C-reactive protein and fecal calprotectin and may interfere with the microbiome and its metabolites. The use of a low FODMAP diet can bring benefits to the IBD patients, but may also modify their nutritional status. Thus it should be utilized in appropriated conditions, and dietary supplements should be necessary to avoid deficiencies that could be caused by a low FODMAP diet over long periods. We suggest that further investigations are required to elucidate when and how to apply the FODMAP diet in IBD patients.

Inflammation: Treatment Progress and Limitations

There is an increasing understanding on the etiology of chronic immune-mediated inflammatory diseases such as inflammatory bowel disease (IBD), psoriasis, or rheumatoid arthritis. Large consortia contributed to the elucidation of the genetics, for instance, of IBD identifying a number of genes involved in innate mucosal defense and immune tolerance (most prominent, e.g., NOD2) and other related processes. For a number of such diseases, common genetic susceptibility loci were identified, suggesting overlapping immune response pathways, although there is no causality of single genetic traits.² In particular, the elucidation of main triggers of inflammation like tumor necrosis factor alpha (TNFα), integrins, specific cytokines like interleukin (IL)-6 or IL-23 launched the successful development of new pharmacological approaches, leading to a tremendous improvement of therapeutic outcomes.