A37 EXPLORING THE PROTEOMICS DIFFERENCES IN CROHN’S DISEASE PATIENTS

Abstract Background Canada has the highest prevalence rate of Crohn’s disease (CD) in North America. In Alberta, the yearly cost of anti-inflammatory drugs can be more than $25,000 per person; however, half of the patients do not respond to medication. CD is characterized by lesions in the small intestine due to inflammation, promoting diarrhea and abdominal pain. Prolonged chronic inflammation results in fibrotic strictures that are resistant to anti-inflammatory therapies and promote narrowing of the luminal space that ultimately require surgery. Currently, there is no biomarker to distinguish between the inflammatory or stricturing phenotype. Aims AIM 1: Profile serum samples from CD patients using a label-free shotgun-proteomics. AIM 2: Identify signatures and biomarkers that distinguish inflammatory and fibrotic strictures using a bioinformatics approach. Methods Serum samples from 15 CD patients with strictures and 15 CD patients without strictures (inflammatory phenotype), as diagnosed by ultrasound imaging, were analyzed by a standard shotgun-proteomics approach. Briefly, 200 µg of serum proteins were processed in a label-free protocol in combination with the filter-aided sample preparation (FASP) method. Liquid chromatography-tandem mass spectrometry was performed on an Orbitrap Fusion Lumos. Protein identification was accomplished by MaxQuant at a 1% false-discovery rate. Statistical significance was determined by the MSstats package, in the R software. To identify the biological significance of disturbed pathways, it was characterized by the protein-protein interactions and pathway enrichment analysis using String-DB and Metascape. Results It was identified a statistically significant protein panel between the two phenotypes. Proteins identified in the strictured group include JAK1 (Tyrosine-protein kinase), CD5 antigen-like protein (regulates inflammatory gene expression in Th17 cells), and neogenin (cell adhesion). Of the inflammatory patients, there was a significant elevation of PFK/FBPase 2 (synthesis and degradation of fructose 2,6-bisphosphate), vinculin (cell-matrix adhesion) and MMP-16/MT3-MMP (matrix metalloproteinase). Conclusions The identification of a distinct signature between both phenotypes provide important biological information about the disease progression and are a good sign that a biomarker discovery platform will be capable to differentiate between inflammatory and fibrostenotic strictures from serum samples of CD patients. Funding Agencies CAG, CIHRNSERC

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M1111 A Label-Free Proteomics Approach to Serum Biomarker Discovery for Crohn's Disease

Gastroenterology ◽

10.1016/s0016-5085(09)61614-0 ◽

2009 ◽

Vol 136 (5) ◽

pp. A-352

Author(s):

Paolo Nanni ◽

Giulia Roda ◽

Laura Mezzanotte ◽

Alessandra Caponi ◽

Fredrik Levander ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Biomarker Discovery ◽

Serum Biomarker ◽

Label Free ◽

Proteomics Approach

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Serum Metabolomics Identifies Altered Bioenergetics, Signaling Cascades in Parallel with Exposome Markers in Crohn’s Disease

Molecules ◽

10.3390/molecules24030449 ◽

2019 ◽

Vol 24 (3) ◽

pp. 449 ◽

Cited By ~ 12

Author(s):

Yunjia Lai ◽

Jingchuan Xue ◽

Chih-Wei Liu ◽

Bei Gao ◽

Liang Chi ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

High Resolution Mass Spectrometry ◽

Signaling Cascades ◽

Compound Identification ◽

Serum Samples ◽

Therapy Assessment ◽

Integral Role ◽

Important Pathway ◽

Biomarker Research

: Inflammatory bowel disease (IBD) has stimulated much interest due to its surging incidences and health impacts in the U.S. and worldwide. However, the exact cause of IBD remains incompletely understood, and biomarker is lacking towards early diagnostics and effective therapy assessment. To tackle these, the emerging high-resolution mass spectrometry (HRMS)-based metabolomics shows promise. Here, we conducted a pilot untargeted LC/MS metabolomic profiling in Crohn’s disease, for which serum samples of both active and inactive cases were collected, extracted, and profiled by a state-of-the-art compound identification workflow. Results show a distinct metabolic profile of Crohn’s from control, with most metabolites downregulated. The identified compounds are structurally diverse, pointing to important pathway perturbations ranging from energy metabolism (e.g., β-oxidation of fatty acids) to signaling cascades of lipids (e.g., DHA) and amino acid (e.g., L-tryptophan). Importantly, an integral role of gut microbiota in the pathogenesis of Crohn’s disease is highlighted. Xenobiotics and their biotransformants were widely detected, calling for massive exposomic profiling for future cohort studies as such. This study endorses the analytical capacity of untargeted metabolomics for biomarker development, cohort stratification, and mechanistic interpretation; the findings might be valuable for advancing biomarker research and etiologic inquiry in IBD.

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Targeted 1H NMR metabolomics and immunological phenotyping of human fresh blood and serum samples discriminate between healthy individuals and inflammatory bowel disease patients treated with anti-TNF

Journal of Molecular Medicine ◽

10.1007/s00109-021-02094-y ◽

2021 ◽

Author(s):

Sara Notararigo ◽

Manuel Martín-Pastor ◽

Juan E. Viñuela Roldán ◽

Adriano Quiroga ◽

J. Enrique Dominguez-Munoz ◽

...

Keyword(s):

Ulcerative Colitis ◽

Inflammatory Bowel Disease ◽

Crohn’S Disease ◽

Clinical Practice ◽

Crohn's Disease ◽

T Lymphocyte ◽

Fresh Blood ◽

Serum Samples ◽

Nmr Metabolomics ◽

Inflammatory Bowel

Abstract Inflammatory bowel disease is a multifactorial etiology, associated with environmental factors that can trigger both debut and relapses. A high level of tumor necrosis factor-α in the gut is the main consequence of immune system imbalance. The aim of treatment is to restore gut homeostasis. In this study, fresh blood and serum samples were used to identify biomarkers and to discriminate between Crohn’s disease and ulcerative colitis patients under remission treated with anti-TNF. Metabolomics based on Nuclear Magnetic Resonance spectroscopy (NMR) was used to detect unique biomarkers for each class of patients. Blood T lymphocyte repertories were characterized, as well as cytokine and transcription factor profiling, to complement the metabolomics data. Higher levels of homoserine-methionine and isobutyrate were identified as biomarkers of Crohn’s disease with ileocolic localization. For ulcerative colitis, lower levels of creatine-creatinine, proline, and tryptophan were found that reflect a deficit in the absorption of essential amino acids in the gut. T lymphocyte phenotyping and its functional profiling revealed that the overall inflammation was lower in Crohn’s disease patients than in those with ulcerative colitis. These results demonstrated that NMR metabolomics could be introduced as a high-throughput evaluation method in routine clinical practice to stratify both types of patients related to their pathology. Key messages NMR metabolomics is a non-invasive tool that could be implemented in the normal clinical practice for IBD to assess beneficial effect of the treatment. NMR metabolomics is a useful tool for precision medicine, in order to sew a specific treatment to a specific group of patients. Finding predictors of response to IFX would be desirable to select patients affected by IBD. Immunological status of inflammations correlates with NMR metabolomics biomarkers.

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Proteomics in Diagnosis of Prostate Cancer/ Протеомика Во Дијагноза На Простатниот Карцином

PRILOZI ◽

10.1515/prilozi-2015-0027 ◽

2015 ◽

Vol 36 (1) ◽

pp. 5-36 ◽

Cited By ~ 3

Author(s):

Katarina Davalieva ◽

Momir Polenakovic

Keyword(s):

Prostate Cancer ◽

Tumor Tissue ◽

Biomarker Discovery ◽

Molecular Level ◽

Specific Antigen ◽

Shotgun Proteomics ◽

Comparative Proteomics ◽

Label Free ◽

The Past ◽

Proteomics Research

Abstract Prostate cancer (PCa) is the second most frequently diagnosed malignancy in men worldwide. The introduction of prostate specific antigen (PSA) has greatly increased the number of men diagnosed with PCa but at the same time, as a result of the low specificity, led to overdiagnosis, resulting to unnecessary biopsies and high medical cost treatments. The primary goal in PCa research today is to find a biomarker or biomarker set for clear and effecttive diagnosis of PCa as well as for distinction between aggressive and indolent cancers. Different proteomic technologies such as 2-D PAGE, 2-D DIGE, MALDI MS profiling, shotgun proteomics with label-based (ICAT, iTRAQ) and label-free (SWATH) quantification, MudPIT, CE-MS have been applied to the study of PCa in the past 15 years. Various biological samples, including tumor tissue, serum, plasma, urine, seminal plasma, prostatic secretions and prostatic-derived exosomes were analyzed with the aim of identifying diagnostic and prognostic biomarkers and developing a deeper understanding of the disease at the molecular level. This review is focused on the overall analysis of expression proteomics studies in the PCa field investigating all types of human samples in the search for diagnostics biomarkers. Emphasis is given on proteomics platforms used in biomarker discovery and characterization, explored sources for PCa biomarkers, proposed candidate biomarkers by comparative proteomics studies and the possible future clinical application of those candidate biomarkers in PCa screening and diagnosis. In addition, we review the specificity of the putative markers and existing challenges in the proteomics research of PCa.

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Riboflavin Supplementation in Patients with Crohn’s Disease [the RISE-UP study]

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjz208 ◽

2019 ◽

Vol 14 (5) ◽

pp. 595-607 ◽

Cited By ~ 3

Author(s):

Julius Z H von Martels ◽

Arno R Bourgonje ◽

Marjolein A Y Klaassen ◽

Hassan A A Alkhalifah ◽

Mehdi Sadaghian Sadabad ◽

...

Keyword(s):

Oxidative Stress ◽

Crohn’S Disease ◽

Crohn's Disease ◽

Disease Activity ◽

Clinical Symptoms ◽

Fish Analysis ◽

Markers Of Inflammation ◽

Anti Inflammatory ◽

Faecal Microbiome ◽

Chronic Intestinal Inflammation

Abstract Background and Aims Crohn’s disease [CD] is characterised by chronic intestinal inflammation and dysbiosis in the gut. Riboflavin [vitamin B2] has anti-inflammatory, antioxidant and microbiome-modulatory properties. Here, we analysed the effect of riboflavin on oxidative stress, markers of inflammation, clinical symptoms, and faecal microbiome in patients with CD. Methods In this prospective clinical intervention study, patients received 100 mg riboflavin [DSM, Nutritional Products Ltd] daily for 3 weeks. Clinical disease activity [Harvey-Bradshaw Index: HBI], serum biomarkers of inflammation and redox status [plasma free thiols], and faecal microbiome taxonomical composition and functionality [fluorescent in situ hybridisation: FISH; and metagenomic shotgun sequencing: MGS], were analysed before and after riboflavin intervention. Results In total, 70 patients with CD with varying disease activity were included. Riboflavin supplementation significantly decreased serum levels of inflammatory markers. In patients with low faecal calprotectin [FC] levels, IL-2 decreased, and in patients with high FC levels, C-reactive protein [CRP] was reduced and free thiols significantly increased after supplementation. Moreover, HBI was significantly decreased by riboflavin supplementation. Riboflavin supplementation led to decreased Enterobacteriaceae in patients with low FC levels as determined by FISH; however, MGS analysis showed no effects on diversity, taxonomy, or metabolic pathways of the faecal microbiome. Conclusions Three weeks of riboflavin supplementation resulted in a reduction in systemic oxidative stress, mixed anti-inflammatory effects, and a reduction in clinical symptoms [HBI]. FISH analysis showed decreased Enterobacteriaceae in patients with CD with low FC levels, though this was not observed in MGS analysis. Our data demonstrate that riboflavin supplementation has a number of anti-inflammatory and anti-oxidant effects in CD.

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Crohn's disease therapy with Dietzia: the end of anti-inflammatory drugs

Future Microbiology ◽

10.2217/fmb.14.133 ◽

2015 ◽

Vol 10 (2) ◽

pp. 147-150 ◽

Cited By ~ 2

Author(s):

Robert E Click

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Disease Therapy ◽

Inflammatory Drugs ◽

Anti Inflammatory

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Immune system alterations in patients with inflammatory bowel disease during remission

Medicina ◽

10.3390/medicina44010005 ◽

2008 ◽

Vol 44 (1) ◽

pp. 27 ◽

Cited By ~ 14

Author(s):

Jurgita Šventoraitytė ◽

Aida Žvirblienė ◽

Gediminas Kiudelis ◽

Rimantas Žalinkevičius ◽

Aurelija Žvirblienė ◽

...

Keyword(s):

Ulcerative Colitis ◽

Inflammatory Bowel Disease ◽

Crohn’S Disease ◽

Crohn's Disease ◽

Bowel Disease ◽

Immune Homeostasis ◽

Th2 Cytokines ◽

Inflammatory Bowel ◽

Anti Inflammatory ◽

And Control

Objective. Perturbed immune homeostasis elicited by misbalanced production of proinflammatory and anti-inflammatory cytokines is characteristic of inflammatory bowel disease. The aim of this study was to evaluate cytokine profile in patients with different forms of inflammatory bowel disease – ulcerative colitis and Crohn’s disease – during clinical remission phase. Material and methods. Production of proinflammatory Th1 cytokines (tumor necrosis factoralpha (TNF-a), interferon-gamma (IFN-g)) and anti-inflammatory Th2 cytokines (interleukin- 10 (IL-10) and interleukin-13 (IL-13)) was analyzed in peripheral blood mononuclear cells of patients with inflammatory bowel disease (9 with ulcerative colitis and 9 with Crohn’s disease) and control subjects (n=11) by enzyme-linked immunosorbent assay (two-site ELISA). Results. The results of the study revealed that the level of TNF-a after stimulation with phytohemagglutinin in patients with Crohn’s disease was significantly higher in comparison to both patients with ulcerative colitis and controls (P<0.001 and P<0.01, respectively). The secretion of IFN-g both in patients with Crohn’s disease and ulcerative colitis was lower than that in controls (P=0.05 and P<0.01, respectively), but it normalized after stimulation with phytohemagglutinin. The levels of IL-10 and IL-13 were significantly (P<0.01) higher in patients with Crohn’s disease than in patients with ulcerative colitis and control group before and after stimulation with phytohemagglutinin. Conclusions. The results of our study provide evidence that in patients with inflammatory bowel disease, the imbalance between production of proinflammatory Th1 and anti-inflammatory Th2 cytokines persists even during remission of the disease, and disturbances of immune homeostasis are significantly more expressed in patients with Crohn’s disease than in patients with ulcerative colitis.

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The association between inflammatory potential of diet and disease activity: results from a cross-sectional study in patients with inflammatory bowel disease

BMC Gastroenterology ◽

10.1186/s12876-020-01435-4 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Carlijn R. Lamers ◽

Nicole M. de Roos ◽

Ben J. M. Witteman

Keyword(s):

Ulcerative Colitis ◽

Inflammatory Bowel Disease ◽

Crohn’S Disease ◽

Crohn's Disease ◽

Disease Activity ◽

Bowel Disease ◽

Activity Index ◽

Statistical Significance ◽

Inflammatory Bowel ◽

Anti Inflammatory

Abstract Background Diet may play a role in disease status in patients with inflammatory bowel disease. We tested whether the inflammatory potential of diet, based on a summation of pro- and anti-inflammatory nutrients, is associated with disease activity in patients with Crohn’s disease and ulcerative colitis. Methods Participants completed a disease activity questionnaire (short Crohn’s Disease Activity (sCDAI) or Patient Simple Clinical Colitis Activity Index (P-SCCAI)) and a Food Frequency Questionnaire (FFQ). FFQ data were used to calculate the Dietary Inflammatory Index (DII) which enables categorization of individuals’ diets according to their inflammatory potential on a continuum from pro- to anti-inflammatory. Associations with disease activity were investigated by multiple linear regression. Results The analysis included 329 participants; 168 with Crohn’s disease (median sCDAI score 93 [IQR 47–156]), and 161 with ulcerative colitis (median P-SCCAI score 1 [IQR 1–3]). Mean DII was 0.71 ± 1.33, suggesting a slightly pro-inflammatory diet. In Crohn’s disease, the DII was positively associated with disease activity, even after adjustment for confounders (p = 0.008). The mean DII was significantly different between participants in remission and with mild and moderately active disease (0.64, 0.97 and 1.52 respectively, p = 0.027). In ulcerative colitis, the association was not significant. Conclusions Disease activity was higher in IBD participants with a more pro-inflammatory diet with statistical significance in Crohn’s disease. Although the direction of causality is not clear, this association strengthens the role for diet in medical treatment, which should be tested in an intervention study.

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