Biomarkers of Inflammatory Bowel Disease: From Classical Laboratory Tools to Personalized Medicine

Modeling of Treatment Outcomes with Tofacitinib Maintenance Therapy in Patients with Ulcerative Colitis: A Post Hoc Analysis of Data from the OCTAVE Clinical Program

INTRODUCTION

Tofacitinib is an oral small molecule Janus kinase inhibitor for the treatment of ulcerative colitis (UC). This post hoc analysis assessed whether various statistical techniques could predict outcomes of tofacitinib maintenance therapy in patients with UC.

METHODS

Data from patients who participated in a 52-week, phase III maintenance study (OCTAVE Sustain) and an open-label long-term extension study (OCTAVE Open) were included in this analysis. Patients received tofacitinib 5 or 10 mg twice daily (BID) or placebo (OCTAVE Sustain only). Logistic regression analyses were performed to generate models using clinical and laboratory variables to predict loss of responder status at week 8 of OCTAVE Sustain, steroid-free remission (defined as a partial Mayo score of 0-1 in the absence of corticosteroid use) at week 52 of OCTAVE Sustain, and delayed response at week 8 of OCTAVE Open. Furthermore, differences in loss of response/discontinuation patterns between treatment groups in OCTAVE Sustain were established.

RESULTS

The generated prediction models demonstrated insufficient accuracy for determining loss of response at week 8, steroid-free remission at week 52 in OCTAVE Sustain, or delayed response in OCTAVE Open. Both tofacitinib doses demonstrated comparable response/remission patterns based on visualizations of disease activity over time. The rectal bleeding subscore was the primary determinant of disease worsening (indicated by an increased total Mayo score), and the endoscopy subscore was the primary determinant of disease improvement (indicated by a decreased total Mayo score).

CONCLUSION

Visualizations of disease activity subscores revealed distinct patterns among patients with UC that had disease worsening and disease improvement. The statistical models assessed in this analysis could not accurately predict loss of responder status, steroid-free remission, or delayed response to tofacitinib. Possible reasons include the small sample size or missing data related to yet unknown key variables that were not collected during these trials.

Serum proteome profiles in cats with chronic enteropathies

BACKGROUND

Serum protein biomarkers are used to diagnose, monitor treatment response, and to differentiate various forms of chronic enteropathies (CE) in humans. The utility of liquid biopsy proteomic approaches has not been examined in cats.

HYPOTHESIS/OBJECTIVES

To explore the serum proteome in cats to identify markers differentiating healthy cats from cats with CE.

ANIMALS

Ten cats with CE with signs of gastrointestinal disease of at least 3 weeks duration, and biopsy-confirmed diagnoses, with or without treatment and 19 healthy cats were included.

METHODS

Cross-sectional, multicenter, exploratory study with cases recruited from 3 veterinary hospitals between May 2019 and November 2020. Serum samples were analyzed and evaluated using mass spectrometry-based proteomic techniques.

RESULTS

Twenty-six proteins were significantly (P < .02, ≥5-fold change in abundance) differentially expressed between cats with CE and controls. Thrombospondin-1 (THBS1) was identified with >50-fold increase in abundance in cats with CE (P < 0.001) compared to healthy cats.

CONCLUSIONS AND CLINICAL IMPORTANCE

Damage to the gut lining released marker proteins of chronic inflammation that were detectable in serum samples of cats. This early-stage exploratory study strongly supports THBS1 as a candidate biomarker for chronic inflammatory enteropathy in cats.

The Current Status of Molecular Biomarkers for Inflammatory Bowel Disease

Diagnosis and prognosis of inflammatory bowel disease (IBD)-a chronic inflammation that affects the gastrointestinal tract of patients-are challenging, as most clinical symptoms are not specific to IBD, and are often seen in other inflammatory diseases, such as intestinal infections, drug-induced colitis, and monogenic diseases. To date, there is no gold-standard test for monitoring IBD. Endoscopy and imaging are essential diagnostic tools that provide information about the disease's state, location, and severity. However, the invasive nature and high cost of endoscopy make it unsuitable for frequent monitoring of disease activity in IBD patients, and even when it is possible to replace endoscopy with imaging, high cost remains a concern. Laboratory testing of blood or feces has the advantage of being non-invasive, rapid, cost-effective, and standardizable. Although the specificity and accuracy of laboratory testing alone need to be improved, it is increasingly used to monitor disease activity or to diagnose suspected IBD cases in combination with endoscopy and/or imaging. The literature survey indicates a dearth of summarization of biomarkers for IBD testing. This review introduces currently available non-invasive biomarkers of clinical importance in laboratory testing for IBD, and discusses the trends and challenges in the IBD biomarker studies.

Proteomic Analysis of Potential Targets for Non-Response to Infliximab in Patients With Ulcerative Colitis

Background: Infliximab (IFX) is a potent therapeutic agent used for the treatment of conventional refractory ulcerative colitis (UC). However, the high non-response rate of IFX brings difficulties to clinical applications. In the context of proteomics research, our study of differentially expressed proteins (DEPs) is essential for non-response to IFX in UC patients and provides powerful insights into underlying drug resistance mechanisms.

Methods: A total of 12 UC patients were divided into responders to IFX (UCinfG), non-responders to IFX (UCinfL), severe UC (UCsevere) without an IFX treatment history, and mild UC (UCmild) without an IFX treatment history. Subsequently, DEPs were identified from intestinal biopsy tissue between responders and non-responders to IFX by a label-free proteomic quantitative approach, and the general principle of functional protein screening was followed to deduce the potential drug targets and predictors for non-response to IFX in UC patients. Meanwhile, these targets excluded DEPs caused by the severity of inflammation for the first time. The differential expressions of candidate protein targets were validated at the gene sequence level using GEO2R analysis of the GEO database and qRT-PCR in some independent cohorts.

Results: A total of 257 DEPs were screened out by mass spectrometry between UCinfG and UCinfL groups, excluding 22 DEPs caused by the severity of inflammation, and compared and verified at the gene sequence level in the Gene Expression Omnibus (GEO) database. Finally, five DEPs, including ACTBL2 (Q562R1), MBL2 (P11226), BPI (P17213), EIF3D (O15371), and CR1 (P17927), were identified as novel drug targets and predictive biomarkers for non-response to IFX. The drug targets were confirmed in the GEO database of the microarray results from three independent cohorts of 70 human intestinal biopsies and validated in qPCR data from 17 colonic mucosal biopsies. Among them, CR1 might affect the activation of the lectin pathway via complement-coated bacteria to play an opsonizing role in inflammation-related pathways closely associated with non-responders to IFX.

Conclusion: This is the first report of proteomics analysis for the identification of novel drug targets based on intestinal biopsy tissue, which is significant for hypotheses for mechanistic investigation that are responsible for non-response to IFX and the development of clinical new pharmaceutical drugs.

Crohn's disease-related single nucleotide polymorphisms are associated with ileal pouch afferent limb stenosis

BACKGROUND

Ileal pouch-anal anastomosis (IPAA) is a common surgical treatment for ulcerative colitis. Afferent limb stenosis is an infrequent complication following IPAA, suggesting underlying Crohn's disease (CD). We hypothesized that CD-related single nucleotide polymorphisms (SNPs) are associated with afferent limb stenosis.

METHODS

Afferent limb stenosis and CD control group patients were recruited from a prospective institutional inflammatory bowel disease database and associated biobank. Patient demographics, Montreal classification, and medication use were recorded. Ten SNPs associated with stricturing Crohn's disease were examined in genomic DNA and compared among afferent limb stenosis, stricturing CD, and non-stricturing CD controls.

RESULTS

Twenty-seven afferent limb stenosis and 162 CD control group patients (108 stricturing, 54 non-stricturing) were identified. Patients were gender and race matched. Afferent limb stenosis and stricturing CD controls were younger at diagnosis (Montreal A1/A2 vs. A3) compared to non-stricturing CD controls (both p < 0.05). The majority of afferent limb stenosis patients were non-smokers compared to CD controls (74% vs. 36%, p < 0.01) and did not use biologic therapies (4% vs. 37%, p < 0.001). The FUT2 G allele was more frequent in afferent limb stenosis and stricturing CD controls compared to non-stricturing CD controls (both p < 0.05). The NOD2 T allele was more frequent in stricturing CD controls compared to afferent limb stenosis and non-stricturing CD controls (both p < 0.05).

CONCLUSION

Afferent limb stenosis patients are phenotypically similar to stricturing CD controls, but differ with lower smoking rates and lower NOD2 allele frequency. Such differences could contribute to the presentation delay with a stricturing phenotype. Selective SNP assessment may help categorize patients likely to develop afferent limb stenosis.

Proteomic insights on the metabolism in inflammatory bowel disease

Inflammatory bowel diseases (IBD) are chronic and relapsing inflammatory conditions of the gut that include Crohn's disease and ulcerative colitis. The pathogenesis of IBD is not completely unraveled, IBD are multi-factorial diseases with reported alterations in the gut microbiota, activation of different immune cell types, changes in the vascular endothelium, and alterations in the tight junctions’ structure of the colonic epithelial cells. Proteomics represents a useful tool to enhance our biological understanding and to discover biomarkers in blood and intestinal specimens. It is expected to provide reproducible and quantitative data that can support clinical assessments and help clinicians in the diagnosis and treatment of IBD. Sometimes a differential diagnosis of Crohn's disease and ulcerative colitis and the prediction of treatment response can be deducted by finding meaningful biomarkers. Although some non-invasive biomarkers have been described, none can be considered as the “gold standard” for IBD diagnosis, disease activity and therapy outcome. For these reason new studies have proposed an “IBD signature”, which consists in a panel of biomarkers used to assess IBD. The above described approach characterizes “omics” and in this review we will focus on proteomics.

Precision medicine in inflammatory bowel disease: concept, progress and challenges

Crohn's disease and ulcerative colitis are increasingly prevalent, relapsing and remitting inflammatory bowel diseases (IBDs) with variable disease courses and complications. Their aetiology remains unclear but current evidence shows an increasingly complex pathophysiology broadly centring on the genome, exposome, microbiome and immunome. Our increased understanding of disease pathogenesis is providing an ever-expanding arsenal of therapeutic options, but these can be expensive and patients can lose response or never respond to certain therapies. Therefore, there is now a growing need to personalise therapies on the basis of the underlying disease biology and a desire to shift our approach from "reactive" management driven by disease complications to "proactive" care with an aim to prevent disease sequelae. Precision medicine is the tailoring of medical treatment to the individual patient, encompassing a multitude of data-driven (and multi-omic) approaches to foster accurate clinical decision-making. In IBD, precision medicine would have significant benefits, enabling timely therapy that is both effective and appropriate for the individual. In this review, we summarise some of the key areas of progress towards precision medicine, including predicting disease susceptibility and its course, personalising therapies in IBD and monitoring response to therapy. We also highlight some of the challenges to be overcome in order to deliver this approach.

Candida utilis yeast as a functional protein source for Atlantic salmon (Salmo salar L.): Local intestinal tissue and plasma proteome responses

Microbial ingredients such as Candida utilis yeast are known to be functional protein sources with immunomodulating effects whereas soybean meal causes soybean meal-induced enteritis in the distal intestine of Atlantic salmon (Salmo salar L.). Inflammatory or immunomodulatory stimuli at the local level in the intestine may alter the plasma proteome profile of Atlantic salmon. These deviations can be helpful indicators for fish health and, therefore potential tools in the diagnosis of fish diseases. The present work aimed to identify local intestinal tissue responses and changes in plasma protein profiles of Atlantic salmon fed inactive dry Candida utilis yeast biomass, soybean meal, or combination of soybean meal based diet with various inclusion levels of Candida utilis. A fishmeal based diet was used as control diet. Inclusion of Candida utilis yeast to a fishmeal based diet did not alter the morphology, immune cell population or gene expression of the distal intestine. Lower levels of Candida utilis combined with soybean meal modulated immune cell populations in the distal intestine and reduced the severity of soybean meal-induced enteritis, while higher inclusion levels of Candida utilis were less effective. Changes in the plasma proteomic profile revealed differences between the diets but did not indicate any specific proteins that could be a marker for health or disease. The results suggest that Candida utilis does not alter intestinal morphology or induce major changes in plasma proteome, and thus could be a high-quality alternative protein source with potential functional properties in diets for Atlantic salmon.

Biomarker discovery in inflammatory bowel diseases using network-based feature selection

Reliable identification of Inflammatory biomarkers from metagenomics data is a promising direction for developing non-invasive, cost-effective, and rapid clinical tests for early diagnosis of IBD. We present an integrative approach to Network-Based Biomarker Discovery (NBBD) which integrates network analyses methods for prioritizing potential biomarkers and machine learning techniques for assessing the discriminative power of the prioritized biomarkers. Using a large dataset of new-onset pediatric IBD metagenomics biopsy samples, we compare the performance of Random Forest (RF) classifiers trained on features selected using a representative set of traditional feature selection methods against NBBD framework, configured using five different tools for inferring networks from metagenomics data, and nine different methods for prioritizing biomarkers as well as a hybrid approach combining best traditional and NBBD based feature selection. We also examine how the performance of the predictive models for IBD diagnosis varies as a function of the size of the data used for biomarker identification. Our results show that (i) NBBD is competitive with some of the state-of-the-art feature selection methods including Random Forest Feature Importance (RFFI) scores; and (ii) NBBD is especially effective in reliably identifying IBD biomarkers when the number of data samples available for biomarker discovery is small.

Common functional alterations identified in blood transcriptome of autoimmune cholestatic liver and inflammatory bowel diseases

Primary biliary cholangitis (PBC), primary sclerosing cholangitis (PSC), and inflammatory bowel diseases (IBDs), including Crohn’s disease (CD) and ulcerative colitis (UC), are heterogeneous chronic autoimmune diseases that may share underlying pathogenic mechanisms. Herein, we compared simultaneously analyzed blood transcriptomes from patients with PBC, PSC, and IBD. Microarray-based measurements were conducted using RNA isolated from whole blood samples from 90, 45, 95 and 93 patients with PBC, PSC, CD, and UC, respectively, and 47 healthy controls. Expression levels of selected transcripts were analyzed by quantitative reverse-transcribed PCR using an independent cohort of 292, 71 and 727 patients with PBC, PSC, and IBD, respectively. Of 4026, 2650 and 4967 probe sets differentially expressed (adjusted p-value < 0.05) in samples from patients with PBC, PSC, and IBD, respectively, compared with healthy controls, 1946 were common to all three comparisons. Functional analyses indicated that most terms enriched for genes differentially expressed in PBC, PSC, and IBD patients compared with healthy controls were related to mitochondrial function, the vesicle endomembrane system, and GTPase-mediated processes. This study indicates that microarray-based profiling of blood gene expression supports research into the molecular mechanisms underlying disease, rather than being useful for selection of diagnostic biomarkers for use in clinical practice.

Proteomics and Lipidomics in Inflammatory Bowel Disease Research: From Mechanistic Insights to Biomarker Identification

Inflammatory bowel disease (IBD) represents a group of progressive disorders characterized by recurrent chronic inflammation of the gut. Ulcerative colitis and Crohn's disease are the major manifestations of IBD. While our understanding of IBD has progressed in recent years, its etiology is far from being fully understood, resulting in suboptimal treatment options. Complementing other biological endpoints, bioanalytical "omics" methods that quantify many biomolecules simultaneously have great potential in the dissection of the complex pathogenesis of IBD. In this review, we focus on the rapidly evolving proteomics and lipidomics technologies and their broad applicability to IBD studies; these range from investigations of immune-regulatory mechanisms and biomarker discovery to studies dissecting host⁻microbiome interactions and the role of intestinal epithelial cells. Future studies can leverage recent advances, including improved analytical methodologies, additional relevant sample types, and integrative multi-omics analyses. Proteomics and lipidomics could effectively accelerate the development of novel targeted treatments and the discovery of complementary biomarkers, enabling continuous monitoring of the treatment response of individual patients; this may allow further refinement of treatment and, ultimately, facilitate a personalized medicine approach to IBD.

Clinical utility of currently available biomarkers in inflammatory enteropathies of dogs

Chronic inflammatory enteropathies (CIE) in dogs are a group of disorders that are characterized by chronic persistent or recurrent signs of gastrointestinal disease and histologic evidence of mucosal inflammation. These CIEs are classified as either food-responsive, antibiotic-responsive, or immunosuppressant-responsive enteropathy. Patients not clinically responding to immunomodulatory treatment are grouped as nonresponsive enteropathy and dogs with intestinal protein loss as protein-losing enteropathy. Disease-independent clinical scoring systems were established in dogs for assessment of clinical disease severity and patient monitoring during treatment. Histopathologic and routine clinicopathologic findings are usually not able to distinguish the subgroups of CIE. Treatment trials are often lengthy and further diagnostic tests are usually at least minimally invasive. Biomarkers that can aid in defining the presence of disease, site of origin, severity of the disease process, response to treatment, or a combination of these would be clinically useful in dogs with CIE. This article summarizes the following biomarkers that have been evaluated in dogs with CIE during the last decade, and critically evaluates their potential clinical utility in dogs with CIE: functional biomarkers (cobalamin, methylmalonic acid, folate, α1 -proteinase inhibitor, immunoglobulin A), biochemical biomarkers (C-reactive protein, perinuclear anti-neutrophilic cytoplasmic antibodies, 3-bromotyrosine, N-methylhistamine, calprotectin, S100A12, soluble receptor of advanced glycation end products, cytokines and chemokines, alkaline phosphatase), microbiomic biomarkers (microbiome changes, dysbiosis index), metabolomic biomarkers (serum metabolome), genetic biomarkers (genomic markers, gene expression changes), and cellular biomarkers (regulatory T cells). In addition, important performance criteria of diagnostic tests are briefly reviewed.

Inducible nitric oxide synthase as a potential blood-based biomarker in inflammatory bowel diseases

AIM

Here, we evaluated the role of (iNOS) as a blood-based biomarker of inflammatory bowel diseases (IBD).

BACKGROUND

Up-regulation of inducible nitric oxide synthase (iNOS) in the intestinal epithelial cells has been closely associated with the initiation and maintenance of intestinal inflammation in IBD.

METHODS

In a case-control design, 59 IBD patients and 30 healthy control subjects were participated in this study. A total of 10 ml blood sample was taken from each participant. Blood leukocytes were isolated and iNOS mRNA expression level was evaluated in the isolated leukocytes using relative quantitative Real-time PCR.

RESULTS

The patients' population included 40 ulcerative colitis (UC) and 19 Crohn's disease (CD) patients. The flare and remission phase of disease were seen in 43 and 16 patients, respectively. The mean iNOS mRNA expression was not significantly different between the IBD patients and healthy controls (p=0.056). The mean iNOS mRNA expression was significantly higher in the flare phase of the disease compared to the remission phase (p=0.039). No significant difference was observed between the mean iNOS mRNA expression in the blood leukocytes of UC and CD patients (p=0.82).

CONCLUSION

iNOS is differently expressed in the blood leukocytes of active vs. inactive IBD disease. Thus, it could be potentially used as a non-invasive blood-based biomarker of IBD.

Chemerin和粪便钙卫蛋白对炎症性肠病活动性的诊断价值

目的

探讨新型脂肪因子Chemerin与粪便钙卫蛋白(fecal calpotection, FCP)对炎症性肠病(inflammatorybowel disease, IBD)活动性的诊断价值, 以求更简单有效评价IBD患者疾病活动性的方法.

方法

研究共纳入2015-01/2016-05于同济大学附属东方医院住院, 住院前或住院期间行结肠镜检查的IBD患者121例, 其中克罗恩病(Crohn's disease, CD)患者72例, 溃疡性结肠炎(ulcerative colitis, UC)患者49例. 健康对照组68例. 对照组和IBD组在肠镜检查前1-2 d随机留取新鲜粪便标本2 g及新鲜血液标本6 mL. CD疾病活动性评价指标采用CD活动指数(Crohn's disease activity index, CDAI), UC病变范围采用蒙特利尔分类, 疾病活动性评价则采用改良的Mayo评分. 评价Chemerin与FCP对IBD活动性评分的相关性.

结果

IBD组Chemerin、FCP浓度均显著高于对照组, 组间比较差异均有统计学意义(P<0.05). 活动期CD和UC患者Chemerin、FCP浓度均分别显著高于缓解期CD和UC患者, 两者比较差异均有统计学意义(P<0.001). CD患者的Chemerin及FCP与CDAI具有一定的相关性(r_s分别为0.57和0.59, P<0.05). UC患者的Chemerin及FCP与改良的Mayo评分具有较好的相关性(r_s分别为0.65和0.72, P<0.001). CD和UC患者的Chemerin及FCP相关系数r_s分别为0.55和0.72(P<0.001).

结论

Chemerin是一种可靠评价IBD活动性的非侵入性生物标志物, 具有与FCP相似的IBD活动性评价准确性, 临床上可以通过联合检测Chemerin和FCP来实时评价IBD患者的疾病活动状态.

Serum miRNA signature diagnoses and discriminates murine colitis subtypes and predicts ulcerative colitis in humans

Inflammatory bowel disease (IBD) is difficult to diagnose due to nonspecific and variable symptoms, and lack of reliable diagnostic tests. Current methods are invasive, non-sensitive, non-predictive, and do not easily discriminate between its two main forms. Consequently, there remains a great need for reliable serum markers for IBD. Here, using a longitudinal study of various mouse models of colitis, we identified a serum miRNA signature that indicated the development of colitis and discriminated between inflammations of various origins (colitis from arthritis). Unlike the existing biomarkers, the newly identified signature also serves to distinguish individuals at risk, predict the type of inflammation, and evaluate the response to therapeutics. Moreover, the miRNA signature identified in mice predicted ulcerative colitis with 83.3% accuracy. In future, the signature identified herein could play a central role in monitoring inflammatory disorders and therapeutic responses in patients, thereby paving the way for personalized medicine.

Serum Calprotectin: A Novel Diagnostic and Prognostic Marker in Inflammatory Bowel Diseases

OBJECTIVES

There is an unmet need for novel blood-based biomarkers that offer timely and accurate diagnostic and prognostic testing in inflammatory bowel diseases (IBD). We aimed to investigate the diagnostic and prognostic utility of serum calprotectin (SC) in IBD.

METHODS

A total of 171 patients (n=96 IBD, n=75 non-IBD) were prospectively recruited. A multi-biomarker model was derived using multivariable logistic regression analysis. Cox proportional hazards model was derived to assess the contribution of each variable to disease outcomes.

RESULTS

SC correlated strongly with current biomarkers, including fecal calprotectin (FC) (n=50, ρ=0.50, P=1.6 × 10-4). SC was the strongest individual predictor of IBD diagnosis (odds ratio (OR): 9.37 (95% confidence interval (CI): 2.82-34.68), P=4.00 × 10-4) compared with other markers (C-reactive protein (CRP): OR 8.52 (95% CI: 2.75-28.63), P=2.80 × 10-4); albumin: OR 6.12 (95% CI: 1.82-22.16), P=0.004). In a subset of 50 patients with paired SC and FC, the area under receiver operating characteristic discriminating IBD from controls was better for FC than for SC (0.99, (95% CI 0.87-1.00) and 0.87 (95% CI:0.78-0.97), respectively; P=0.01). At follow-up (median 342 days; interquartile range: 88-563), SC predicted treatment escalation and/or surgery in IBD (hazard ratio (HR) 2.7, 95% CI: 1.1-4.9), in particular Crohn's disease (CD) (HR 4.2, 95% CI 1.2-15.3). A model incorporating SC and either CRP or albumin has a positive likelihood ratio of 24.14 for IBD. At 1 year, our prognostic model can predict treatment escalation in IBD in 65% of cases (95% CI: 43-79%) and 80% (95% CI: 31-94%) in CD if ≥2 blood marker criteria are met.

CONCLUSIONS

A diagnostic and prognostic model that combines SC and other blood-based biomarkers accurately predicts the inflammatory burden in IBD and has the potential to predict disease and its outcomes. Our data warrant further detailed exploration and validation in large multicenter cohorts.