DOP22 Integrative -omic analysis reveals microbiota mediated molecular mechanisms influencing host mucosal gene expression in Crohn’s Disease

Abstract Background Mechanistic evidence linking gut microbial changes and host mucosal barrier responses in patients with Crohn’s disease (CD) is lacking. In this study, we used a computational approach to integrate gut microbial and intestinal gene expression in CD patients. Methods Bacterial species, bacterial genes/transcripts with enhanced abundances/transcriptional activity in CD (t-statistic of > 2 and Q-value < 0.05), as well as mucosal (ileum/rectum) differentially expressed genes (DEGs) between CD (n =43) and non-IBD (n=22) subjects were retrieved from the Inflammatory Bowel Disease Meta -Omics Database (IBDMDB). The impact of bacterial proteins on host gene expression was inferred using MicrobioLink, a computational tool for inferring microbe-host interactions. Drug target information was retrieved from OpenTargets. Paired 16S read-outs from stool samples and gene expression data from ileal biopsies in CD patients (n=20) and non-IBD controls (n=15), cross-sectionally collected at our IBD referral center, were used for independent validation. Results Across the 8 identified bacterial species enriched in CD, 3.7% (n= 743) of the orthologous groups were identified as being able to bind to human proteins. Network diffusion analysis uncovered bacterial proteins which could cumulatively modulate the expression of 42% of the genes differentially expressed in the ileum of CD patients. Topological and pathway analysis of the inferred signaling network modulated by the microbiota revealed several key hub proteins and immune-related pathways associated with IL-4, IL-2 and IL-13 signaling, receptor tyrosine-kinases, NFkB, and toll-like receptors including TLR4. Seventy-eight percent of the DEGs in our discovery cohort were also differentially expressed in the validation cohort (R2 = 0.907). Bacterial proteins post-translationally modifying host receptors resulted in the up-regulation of several pro-inflammatory cytokines via critical hub proteins such as NFkB (Figure 1). We observed different levels of locational specificity (from 35 to 61%) for the top regulators such as SPI1, STAT1 and NFKB1in terms of genes regulated by them in ileum and rectum. 24 proteins including ITGA4 and JAK1 from the ileal and rectal signaling networks are existing targets of CD drugs such as vedolizumab and tofacitinib, filgotinib and upadacitinib respectively. Conclusion Our findings outline the potential mechanisms of microbiome-induced host responses and provide insights into designing microbiome-mediated therapies to prevent and/or treat CD.

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ZBTB6 is hyper-methylated and differentially expressed in the blood of patients with Crohn’s disease.

10.31219/osf.io/xne67 ◽

2020 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Gene Expression ◽

Crohn’S Disease ◽

Crohn's Disease ◽

The United States ◽

Differentially Expressed ◽

Economic Productivity ◽

Unbiased Manner ◽

Inflammatory Bowel ◽

Disease Analysis ◽

Broad Complex

Crohn’s disease, an inflammatory bowel disease of the gastrointestinal tract (1), causes significant morbidity and nearly 3.5 billion dollars in lost economic productivity in the United States (2) due to complications of the disease. We mined transcriptome and methylome datasets (3, 4) to understand, in an unbiased manner, the most significant changes in gene expression and DNA methylation in the hematopoietic system of patients with Crohn’s disease (CD). We identified the zinc finger and BTB (broad complex, tramtrack, bric-à-brac) domain-containing gene ZBTB6 (5, 6) as one of the most differentially expressed genes in the whole blood of patients with Crohn’s disease. Analysis of a separate data revealed that the ZBTB6 locus was one of the most differentially methylated sites globally in the blood of patients with Crohn’s disease when compared to the blood of healthy patients. ZBTB6 is differentially methylated and differentially expressed in the blood of patients with Crohn’s disease, and more significantly so than the vast majority of the human genome. These data point to inhibition of ZBTB6 gene expression by hyper-methylation of the ZBTB6 locus and suggest that titration of some function or transcriptional target of ZBTB6 may be an important event in the pathogenesis of Crohn’s disease.

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2′-5′-oligoadenylate synthetase 2 (OAS2) is differentially expressed in the blood of patients with Crohn’s disease.

10.31219/osf.io/mw2cy ◽

2020 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Gene Expression ◽

Crohn’S Disease ◽

Crohn's Disease ◽

Treatment Options ◽

Gastrointestinal Disorder ◽

The United States ◽

Differentially Expressed ◽

Inflammatory Disorder ◽

Oligoadenylate Synthetase ◽

Public Datasets

Crohn’s disease, a complex genetic inflammatory disorder of the gastrointestinal tract (1), has a prevalence of 214 per 100,000 in the United States (2), one of the highest in the world. Understanding of the interaction between genetic susceptibility loci (1) and triggers from the environment (3, 4) is growing but there are still no curative treatments for patients with Crohn’s disease (CD); some patients will fail even the most advanced treatment options (5). Though CD is considered a gastrointestinal disorder, hematologic disturbances are found in patients with Crohn’s disease and anemia is the most common extra-intestinal manifestation of Crohn’s disease (6). To understand the most significant gene expression changes in the hematologic system of patients with Crohn’s disease, we mined published and public datasets (7, 8) containing transcriptome data from the monocyte-derived macrophage (MDM) and multiplexed gene expression data from the regulatory T-cells (Treg) of patients with Crohn’s disease. We found that interferon-inducible nucleic acid sensor 2′-5′-oligoadenylate synthetase 2 (OAS2) (9) was among the most differentially expressed genes in both MDM and Treg from patients with Crohn’s disease. OAS2 expression was significantly lower in MDM and Treg from patients with Crohn’s disease compared to healthy controls. These data reveal compromised expression of an antiviral dsRNA sensor in the blood of patients with Crohn’s disease.

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IFITM1 is differentially expressed in the blood of patients with Crohn’s Disease.

10.31219/osf.io/khnm9 ◽

2020 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Gene Expression ◽

T Cells ◽

Crohn’S Disease ◽

Crohn's Disease ◽

Regulatory T Cells ◽

Whole Blood ◽

Differentially Expressed Gene ◽

Differentially Expressed ◽

Interferon Signaling ◽

Oligoadenylate Synthetase

The interferon pathway (1) is an innate immune signaling system that evolved to protect multicellular organisms from viral infections (2). The expression of multiple gene families is expressed following activation of interferon signaling (1); one of these is the antiviral interferon inducible transmembrane proteins, or IFITM gene family (3). Using publicly available datasets (4, 5), we identified the interferon induced transmembrane protein 1, IFITM1 (6-10), as a differentially expressed gene in the whole blood and CD4+ CD25+ regulatory T-cells of patients with Crohn’s Disease. IFITM1 was expressed at significantly higher levels in the whole blood and Treg of patients with Crohn's Disease than in non-affected control subjects. We previously reported that changes in gene expression of the double stranded ribonucleic acid sensor, 2’-5’-oligoadenylate synthetase, OAS2, were among the most significant quantitive differences in the gene expression of monocyte-derived macrophage and regulatory T-cells from patients with Crohn’s Disease when compared to those not affected. Together, these data suggest that a primary defect in the coordination of the host response to viral infection in the hematopoietic compartment, through nucleic acid sensing and subsequent interferon signaling may be fundamentally linked with the pathogenesis of Crohn’s Disease.

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Outcomes of Passable and Non-passable Strictures in Clinical Trials of Crohn’s Disease: A Post-hoc Analysis

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjab045 ◽

2021 ◽

Author(s):

Neeraj Narula ◽

Emily C L Wong ◽

Parambir S Dulai ◽

John K Marshall ◽

Jean-Frederic Colombel ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Activity Index ◽

Disease Activity Index ◽

Symptom Improvement ◽

Logistic Regression Models ◽

Post Hoc Analysis ◽

Endoscopic Remission ◽

Post Hoc ◽

The Impact

Abstract Background and Aims There is paucity of evidence on the reversibility of Crohn’s disease [CD]-related strictures treated with therapies. We aimed to describe the clinical and endoscopic outcomes of CD patients with non-passable strictures. Methods This was a post-hoc analysis of three large CD clinical trial programmes examining outcomes with infliximab, ustekinumab, and azathioprine, which included data on 576 patients including 105 with non-passable strictures and 45 with passable strictures, as measured using the Simple Endoscopic Score for Crohn’s Disease [SES-CD]. The impact of non-passable strictures on achieving clinical remission [CR] and endoscopic remission [ER] was assessed using multivariate logistic regression models. CR was defined as a Crohn’s Disease Activity Index [CDAI] <150, clinical response as a CDAI reduction of ≥100 points, and ER as SES-CD score <3. Results After 1 year of treatment, patients with non-passable strictures demonstrated the ability to achieve passable or no strictures in 62.5% of cases, with 52.4% and 37.5% attaining CR and ER, respectively. However, patients with non-passable strictures at baseline were less likely to demonstrate symptom improvement compared with those with passable or no strictures, with reduced odds of 1-year CR (adjusted odds ratio [aOR] 0.17, 95% CI 0.03–0.99, p = 0.048). No significant differences were observed between patients with non-passable strictures at baseline and those with passable or no strictures in rates of ER [aOR 0.82, 95% CI 0.23–2.85, p = 0.751] at 1 year. Conclusions Patients with non-passable strictures can achieve symptomatic and endoscopic remission when receiving therapies used to treat CD, although they are less likely to obtain CR compared with patients without non-passable strictures. These findings support the importance of balancing the presence of non-passable strictures in trial arms.

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Impact of aging on gene expression response to x-ray irradiation using mouse blood

Scientific Reports ◽

10.1038/s41598-021-89682-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Constantinos G. Broustas ◽

Axel J. Duval ◽

Sally A. Amundson

Keyword(s):

Gene Expression ◽

Differentially Expressed Genes ◽

Differentially Expressed ◽

X Rays ◽

Gene Expression Response ◽

X Ray ◽

The Impact ◽

Old Mice ◽

Radiation Biodosimetry ◽

Young Mice

AbstractAs a radiation biodosimetry tool, gene expression profiling is being developed using mouse and human peripheral blood models. The impact of dose, dose-rate, and radiation quality has been studied with the goal of predicting radiological tissue injury. In this study, we determined the impact of aging on the gene expression profile of blood from mice exposed to radiation. Young (2 mo) and old (21 mo) male mice were irradiated with 4 Gy x-rays, total RNA was isolated from whole blood 24 h later, and subjected to whole genome microarray analysis. Pathway analysis of differentially expressed genes revealed young mice responded to x-ray exposure by significantly upregulating pathways involved in apoptosis and phagocytosis, a process that eliminates apoptotic cells and preserves tissue homeostasis. In contrast, the functional annotation of senescence was overrepresented among differentially expressed genes from irradiated old mice without enrichment of phagocytosis pathways. Pathways associated with hematologic malignancies were enriched in irradiated old mice compared with irradiated young mice. The fibroblast growth factor signaling pathway was underrepresented in older mice under basal conditions. Similarly, brain-related functions were underrepresented in unirradiated old mice. Thus, age-dependent gene expression differences should be considered when developing gene signatures for use in radiation biodosimetry.

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Cell–cell coupling and DNA methylation abnormal phenotypes in the after-hours mice

Epigenetics & Chromatin ◽

10.1186/s13072-020-00373-5 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Federico Tinarelli ◽

Elena Ivanova ◽

Ilaria Colombi ◽

Erica Barini ◽

Edoardo Balzani ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Neuronal Networks ◽

Molecular Mechanisms ◽

Ex Vivo ◽

Neuronal Cultures ◽

Functional Impairments ◽

After Hours ◽

The Impact

Abstract Background DNA methylation has emerged as an important epigenetic regulator of brain processes, including circadian rhythms. However, how DNA methylation intervenes between environmental signals, such as light entrainment, and the transcriptional and translational molecular mechanisms of the cellular clock is currently unknown. Here, we studied the after-hours mice, which have a point mutation in the Fbxl3 gene and a lengthened circadian period. Methods In this study, we used a combination of in vivo, ex vivo and in vitro approaches. We measured retinal responses in Afh animals and we have run reduced representation bisulphite sequencing (RRBS), pyrosequencing and gene expression analysis in a variety of brain tissues ex vivo. In vitro, we used primary neuronal cultures combined to micro electrode array (MEA) technology and gene expression. Results We observed functional impairments in mutant neuronal networks, and a reduction in the retinal responses to light-dependent stimuli. We detected abnormalities in the expression of photoreceptive melanopsin (OPN4). Furthermore, we identified alterations in the DNA methylation pathways throughout the retinohypothalamic tract terminals and links between the transcription factor Rev-Erbα and Fbxl3. Conclusions The results of this study, primarily represent a contribution towards an understanding of electrophysiological and molecular phenotypic responses to external stimuli in the Afh model. Moreover, as DNA methylation has recently emerged as a new regulator of neuronal networks with important consequences for circadian behaviour, we discuss the impact of the Afh mutation on the epigenetic landscape of circadian biology.

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Endurance Training Regulates Expression of Some Angiogenesis-Related Genes in Cardiac Tissue of Experimentally Induced Diabetic Rats

Biomolecules ◽

10.3390/biom11040498 ◽

2021 ◽

Vol 11 (4) ◽

pp. 498

Author(s):

Mojdeh Khajehlandi ◽

Lotfali Bolboli ◽

Marefat Siahkuhian ◽

Mohammad Rami ◽

Mohammadreza Tabandeh ◽

...

Keyword(s):

Gene Expression ◽

Endurance Training ◽

Molecular Mechanisms ◽

Cardiac Tissue ◽

Critical Role ◽

Diabetic Rats ◽

Moderate Intensity ◽

Pcr Analysis ◽

Cardiac Tissues ◽

The Impact

Exercise can ameliorate cardiovascular dysfunctions in the diabetes condition, but its precise molecular mechanisms have not been entirely understood. The aim of the present study was to determine the impact of endurance training on expression of angiogenesis-related genes in cardiac tissue of diabetic rats. Thirty adults male Wistar rats were randomly divided into three groups (N = 10) including diabetic training (DT), sedentary diabetes (SD), and sedentary healthy (SH), in which diabetes was induced by a single dose of streptozotocin (50 mg/kg). Endurance training (ET) with moderate-intensity was performed on a motorized treadmill for six weeks. Training duration and treadmill speed were increased during five weeks, but they were kept constant at the final week, and slope was zero at all stages. Real-time polymerase chain reaction (RT-PCR) analysis was used to measure the expression of myocyte enhancer factor-2C (MEF2C), histone deacetylase-4 (HDAC4) and Calmodulin-dependent protein kinase II (CaMKII) in cardiac tissues of the rats. Our results demonstrated that six weeks of ET increased gene expression of MEF2C significantly (p < 0.05), and caused a significant reduction in HDAC4 and CaMKII gene expression in the DT rats compared to the SD rats (p < 0.05). We concluded that moderate-intensity ET could play a critical role in ameliorating cardiovascular dysfunction in a diabetes condition by regulating the expression of some angiogenesis-related genes in cardiac tissues.

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Anastomotic Ulcers After Ileocolic Resection for Crohn’s Disease Are Common and Predict Recurrence

Inflammatory Bowel Diseases ◽

10.1093/ibd/izz224 ◽

2019 ◽

Vol 26 (7) ◽

pp. 1050-1058 ◽

Cited By ~ 3

Author(s):

Robert P Hirten ◽

Ryan C Ungaro ◽

Daniel Castaneda ◽

Sarah Lopatin ◽

Bruce E Sands ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Multivariable Analysis ◽

Disease Recurrence ◽

Ileocolic Resection ◽

Anastomotic Ulcer ◽

Endoscopic Recurrence ◽

Academic Center ◽

Endoscopic Remission ◽

The Impact

Abstract Background Crohn’s disease recurrence after ileocolic resection is common and graded with the Rutgeerts score. There is controversy whether anastomotic ulcers represent disease recurrence and should be included in the grading system. The aim of this study was to determine the impact of anastomotic ulcers on Crohn’s disease recurrence in patients with prior ileocolic resections. Secondary aims included defining the prevalence of anastomotic ulcers, risk factors for development, and their natural history. Methods We conducted a retrospective cohort study of patients undergoing an ileocolic resection between 2008 and 2017 at a large academic center, with a postoperative colonoscopy assessing the neoterminal ileum and ileocolic anastomosis. The primary outcome was disease recurrence defined as endoscopic recurrence (>5 ulcers in the neoterminal ileum) or need for another ileocolic resection among patients with or without an anastomotic ulcer in endoscopic remission. Results One hundred eighty-two subjects with Crohn’s disease and an ileocolic resection were included. Anastomotic ulcers were present in 95 (52.2%) subjects. No factors were associated with anastomotic ulcer development. One hundred eleven patients were in endoscopic remission on the first postoperative colonoscopy. On multivariable analysis, anastomotic ulcers were associated with disease recurrence (adjusted hazard ratio [aHR] 3.64; 95% CI, 1.21–10.95; P = 0.02). Sixty-six subjects with anastomotic ulcers underwent a second colonoscopy, with 31 patients (79.5%) having persistent ulcers independent of medication escalation. Conclusion Anastomotic ulcers occur in over half of Crohn’s disease patients after ileocolic resection. No factors are associated with their development. They are associated with Crohn’s disease recurrence and are persistent.

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P237 Annual incidence and prevalence of ulcerative colitis and Crohn’s disease from 2010 to 2017 in four Nordic countries: Results from the TRINordic study

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjz203.366 ◽

2020 ◽

Vol 14 (Supplement_1) ◽

pp. S261-S262

Author(s):

M Lördal ◽

J Burisch ◽

E Langholz ◽

T Knudsen ◽

M Voutilainen ◽

...

Keyword(s):

Ulcerative Colitis ◽

Crohn’S Disease ◽

Crohn's Disease ◽

Observational Study ◽

Nordic Countries ◽

Annual Incidence ◽

University Hospital ◽

Retrospective Observational Study ◽

Western World ◽

The Impact

Abstract Background Incidence and prevalence of inflammatory bowel diseases (IBD) have been increasing for the past decades in the western world, however with an emerging trend of incidence stabilisation in recent years. There is an indication of higher IBD incidence and prevalence in northern Europe, especially in the Nordic region, compared with southern Europe. Methods This retrospective observational study collected data from the National Patient Registries and National Prescription Registries (Sweden [SWE], Norway [NOR], Denmark [DEN]) and one university hospital database (Turku, Finland [FIN]) during 2010–2017 to investigate the annual incidence and prevalence of ulcerative colitis (UC) and Crohn’s disease (CD). Patients with ≥2 ICD-10 diagnosis codes for UC (K51) or CD (K50) from 2010 or later and no K51 or K50 codes prior to 2010 were included; patients were classified according to their last code. The look-back period for SWE was until 2000, for NOR until 2008, for DEN until 1995, and for FIN until 2004. Incidence proportions highlight results through 2016, as 2017 patients had less than 1-year follow-up. Results In total, 69,876 patients were included (SWE n = 27,902, NOR n = 20,761, FIN n = 2,118, DEN n = 19,095), of which 44 367 patients were diagnosed with UC and 25,509 with CD. In 2016, the annual incidence of UC was 28 patients per 100,000 persons in NOR, 32 patients per 100,000 persons in DEN, 25 patients per 100,000 persons in SWE, and 44 patients per 100,000 in FIN. The corresponding results for the annual incidence of CD per 100,000 persons were 22 in NOR, 16 in DEN, 16 in SWE, and 21 in FIN. The prevalence per 100,000 persons of both UC and CD was the highest in DEN, followed by SWE and NOR, and lowest in FIN. Prevalence estimates increased in all four Nordic countries during 2010–2017: for UC, from 409 to 488 patients in SWE, from 256 to 428 in NOR, from 129 to 375 in FIN, and from 577 to 798 in DEN. For CD, it increased from 261 to 313 patients in SWE, from 164 to 258 in NOR, from 54 to 164 in FIN, and from 280 to 400 in DEN. Conclusion This retrospective observational study showed that during 2016, the annual incidence of UC ranged from 25–44 patients per 100,000 persons across the evaluated Nordic countries, whereas the annual incidence of CD was 16–22 patients per 100,000 persons. Prevalence of both UC and CD increased during 2010–2017 in all four countries. Estimates of UC and CD incidence and prevalence in this analysis are greater than reported in the published literature. Additional analyses are underway to further explore the impact of methodological decisions on the estimates of UC and CD annual incidence and prevalence.

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