bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-resolved metagenomics using environmental and clinical samples
Authors: Kayani Masood ur Rehman , Huang Wanqiu , Feng Ru , Chen Lei
Published: January 2021

Recent advances in high-throughput sequencing technologies and computational methods have added a new dimension to metagenomic data analysis i.e. genome-resolved metagenomics. In general terms, it refers to the recovery of draft or high-quality microbial genomes and their taxonomic classification and functional annotation. In recent years, several studies have utilized the genome-resolved metagenome analysis approach and identified previously unknown microbial species from human and environmental metagenomes. In this review, we describe genome-resolved metagenome analysis as a series of four necessary steps: (i) preprocessing of the sequencing reads, (ii) de novo metagenome assembly, (iii) genome binning and (iv) taxonomic and functional analysis of the recovered genomes. For each of these four steps, we discuss the most commonly used tools and the currently available pipelines to guide the scientific community in the recovery and subsequent analyses of genomes from any metagenome sample. Furthermore, we also discuss the tools required for validation of assembly quality as well as for improving quality of the recovered genomes. We also highlight the currently available pipelines that can be used to automate the whole analysis without having advanced bioinformatics knowledge. Finally, we will highlight the most widely adapted and actively maintained tools and pipelines that can be helpful to the scientific community in decision making before they commence the analysis.
Large-scale model selection in misspecified generalized linear models
Authors: Demirkaya Emre , Feng Yang , Basu Pallavi , Lv Jinchi
Published: January 2021

Model selection is crucial both to high-dimensional learning and to inference for contemporary big data applications in pinpointing the best set of covariates among a sequence of candidate interpretable models. Most existing work implicitly assumes that the models are correctly specified or have fixed dimensionality, yet both model misspecification and high dimensionality are prevalent in practice. In this paper, we exploit the framework of model selection principles under the misspecified generalized linear models presented in Lv & Liu (2014), and investigate the asymptotic expansion of the posterior model probability in the setting of high-dimensional misspecified models. With a natural choice of prior probabilities that encourages interpretability and incorporates the Kullback–Leibler divergence, we suggest using the high-dimensional generalized Bayesian information criterion with prior probability for large-scale model selection with misspecification. Our new information criterion characterizes the impacts of both model misspecification and high dimensionality on model selection. We further establish the consistency of covariance contrast matrix estimation and the model selection consistency of the new information criterion in ultrahigh dimensions under some mild regularity conditions. Our numerical studies demonstrate that the proposed method enjoys improved model selection consistency over its main competitors.
Mir21 modulates inflammation and sensorimotor deficits in cervical myelopathy: data from humans and animal models
Authors: Laliberte Alex M , Karadimas Spyridon K , Vidal Pia M , Satkunendrarajah Kajana , Fehlings Michael G
Published: January 2021

Degenerative cervical myelopathy is a common condition resulting from chronic compression of the spinal cord by degenerating structures of the spine. Degenerative cervical myelopathy present a wide range of outcomes, and the biological factors underlying this variability are poorly understood. Previous studies have found elevated MIR21-5p in the sub-acute and chronic neuroinflammatory environment after spinal cord injury. As chronic spinal cord neuroinflammation is a major feature of degenerative cervical myelopathy, we hypothesized that MIR21-5p may be particularly relevant to disease pathobiology, and could serve as a potential biomarker. A prospective cohort study of 69 human degenerative cervical myelopathy patients (36 male:33 female) between the ages of 30 and 78 years was performed to identify the relationship between MIR21-5p expression, symptom severity and treatment outcomes. Results from this study identified a positive correlation between elevated plasma MIR21-5p expression, initial symptom severity and poor treatment outcomes. Subsequent validation of these relationships using a mouse model of degenerative cervical myelopathy identified a similar elevation of MIR21-5p expression at 6 and 12 weeks after onset, corresponding to moderate to severe neurological deficits. To further determine how MIR21-5p affects cervical myelopathy pathobiology, this mouse model was applied to a Mir21 knockout mouse line. Deletion of the Mir21 gene preserved locomotor function on rotarod and forced swim tests, but also resulted in increased nociception based on tail flick, Von Frey filament and electrophysiological testing. Critically, Mir21 knockout mice also had reduced spinal cord inflammation, demonstrated by the reduction of Iba1+ microglia by ∼50% relative to wild-type controls. In vitro experiments using primary microglial cultures confirmed that MIR21-5p expression was greatly increased after exposure to lipopolysaccharide (pro-inflammatory), Il4 (anti-inflammatory) and hypoxia. Mir21 knockout did not appear to alter the ability of microglia to respond to these stimuli, as expression of key pro- and anti-inflammatory response genes was not significantly altered. However, target prediction algorithms identified the IL6/STAT3 pathway as a potential downstream target of MIR21-5p, and subsequent in vitro testing found that expression of components of the IL6 receptor complex, Il6ra and Il6st, were significantly higher in Mir21 knockout microglia. In aggregate, these data show that Mir21 plays a role in the progression of motor deficits and neuroinflammatory modulation in degenerative cervical myelopathy. Given this role in neuroinflammation, and its association with poor patient outcomes, MIR21-5p represents a potential therapeutic target and a new marker for prognostication.
Daily Consumption of a Specially Formulated Essential Amino Acid-Based Dietary Supplement Improves Physical Performance in Older Adults With Low Physical Functioning
Authors: Azhar Gohar , Wei Jeanne Y , Schutzler Scott E , Coker Karen , Gibson Regina V , Kirby Mitchell F , Ferrando Arny A , Wolfe Robert R
Published: January 2021

We have investigated the hypothesis that nutritional supplementation of the diet in low-physical-functioning older individuals with a specially formulated composition based on essential amino acids (EAAs) would improve physical function as compared to supplementation with the same amount of whey protein. A third group of comparable volunteers were given nutrition education but no supplementation of the diet. After 6 weeks of whey protein supplementation (n = 32), there was no effect on the distance walked in 6 minutes, but the distance walked improved significantly from the pre-value after 12 weeks of whey supplementation. EAA consumption (n = 28) significantly improved walking distance at both 6 and 12 weeks. The distance walked at 12 weeks (419.0 ± 25.0 m) was 35.4 m greater than the pre-value of 384.0 ± 23.0 m (p < .001). The increase in distance walked by the EAA group was also significantly greater than that in the whey group at both 6 and 12 weeks (p < .01). In contrast, a decrease in distance walked was observed in the control group (n = 32) (not statistically significant, NS). EAA supplementation also improved grip strength and leg strength, and decreased body weight and fat mass. Plasma low-density lipoprotein concentration was significantly reduced in the EAA group, as well as the concentration of macrophage migration inhibitory factor. There were no adverse responses in any groups, and compliance was greater than 95% in all individuals consuming supplements. We conclude that dietary supplementation with an EAA-based composition may be a beneficial therapy in older individuals with low physical functional capacity.

Clinical Trials Registration Number: This study was registered with ClinicalTrials.gov: NCT 03424265—“Nutritional interventions in heart failure.”
DIETARY FIBER GUAR GUM EXACERBATES COLONIC INFLAMMATION IN MULTIPLE EXPERIMENTAL MODELS OF INFLAMMATORY BOWEL DISEASE
Authors: Nair Divek V T , Paudel Devendra , Cantorna Margherita , Singh Vishal
Published: January 2021

The role of fermentable dietary fibers in patients with inflammatory bowel disease (IBD) is not understood. Herein, we elucidated the effect of dietary fiber guar gum, commonly added to a wide range of processed foods, on colonic inflammation. The use of three different IBD models allowed us to examine the effect of guar gum on various aspects of human IBD, such as immune hyperactivity [IL-10 receptor (IL-10R) neutralization], epithelial injury [dextran sulfate sodium (DSS)], and infection [Citrobacter rodentium (CR)]-mediated inflammation.

Wild-type (WT, C57BL/6) mice fed either control cellulose (insoluble fiber, aka non-fermentable fiber) or guar gum (soluble fiber, aka fermentable fiber, 7.5% w/w) were administered four weekly injections of IL-10R neutralizing antibody (α-IL-10R) to induce immune-hyperactivation mediated chronic colitis. Guar gum treated mice developed robust α-IL-10R mediated colitis. Guar gum fed mice had splenomegaly, colomegaly, elevated systemic proinflammatory markers [serum amyloid A (SAA), lipocalin 2 (Lcn2) and keratinocyte-derived chemokine (KC)] and elevated colonic Lcn2 and interleukin (IL)-1β, and histopathology scores compared to control, cellulose-fed, mice. Similar results were observed in Toll-like receptor 5 deficient mice, which are prone to develop microbiota-dependent colitis. Next, to examine the effect of guar gum on the epithelial injury model, mice were treated with DSS (1.4% w/v in drinking water) for seven days. The guar gum fed group developed severe colitis, including reduced body weight, diarrhea, rectal bleeding, shortening of colon length, and elevated levels of pro-inflammatory markers (Lcn2, KC, and SAA)compared to the control group. The last model to be tested was infection-induced colitis. Since inflammation is required to clear the infection, we hypothesized that guar gum fed mice might clear CR infection better than controls. To our surprise, guar gum fed WT mice shed higher numbers of CR in the feces than the cellulose group. The guar gum fed mice had lower body weights, colomegaly, an elevated level of colonic and serum Lcn2, and higher serum SAA than the control group. Collectively, guar gum failed to protect against CR-induced colonic pathology. Altogether, the work demonstrates that guar gum feeding may exacerbate colonic inflammation following immune-hyperactivation, chemical, and infectious injury. Cautioning IBD patients to monitor their consumption of guar gum fiber might be a way to reduce the severity of intestinal inflammation.
NANOPARTICLE-ENCAPSULATED BROMODOMAIN-CONTAINING PROTEIN 4 INHIBITORS FOR THERAPEUTICS OF INFLAMMATORY BOWEL DISEASE
Authors: Shah Mansi , Li Yi , Pingyuan Wang , Chen Haiying , Liu Zhiqing , Cong Yingzi , Pinchuk Irina , Rytting Erik , Zhou Jia , Tian Bing
Published: January 2021

Ulcerative Colitis (UC) and Crohn’s disease (CD), the two major types of inflammatory bowel disease (IBD), are chronic diseases with recurrent symptoms and significant morbidity. Long-term persistence of chronic inflammation in IBD is among the major factors contributing to neoplastic transformation and the development of colitis-associated colorectal cancer. There exists a lack of efficient medications for IBD, primarily due to either limited efficacy or side effects. Targeting bromodomain-containing protein 4 (BRD4) represents a novel therapeutic strategy for IBD. Recently, we have successfully identified proprietary, highly potent, and specific BRD4 inhibitors which significantly suppressed the initiation of mucosal inflammation and chronicity in proof-of-concept studies in several animal models of IBD.

One of the most pressing challenges in current IBD research is to develop technologies to enable mucosal targeted drug delivery systems that enhance efficacy and decrease side effects. Intriguingly, we found that local delivery of our first-generation BRD4 inhibitors encapsulated in nanoparticles can achieve significantly higher in vivo efficacy at much lower doses than that attained by systemic administration. Local delivery of nanoparticle-encapsulated BRD4 inhibitors by designing nanoparticles that bind to inflamed epithelium would offer superior pharmacotherapy for IBD with higher efficacy, specific delivery, long-lasting release, and a better therapeutic and safety window. We have successfully encapsulated our BRD4 inhibitors in biodegradable nanoparticles with excellent encapsulation efficiency and favorable particle size. Our new generation of BRD4 inhibitors ZL0513, ZL0742, and ZL0591 were encapsulated by a modified solvent displacement method using a polymeric matrix of PEGylated poly (lactic-co-glycolic acid) (PLGA). To evaluate their potential cytotoxic effects, we incubated human colonic epithelial cells (HCECs) and peripheral blood mononuclear cells (PBMCs) with PEGylated-PLGA-ZL0513, ZL0591, and ZL0742 overnight. No apparent increase in cell death was detected in HCECs or PBMCs even at 40 μM. Furthermore, oral administration of our nano-encapsulated BRD4 inhibitors at the dosage of 2 mg/kg effectively block colonic inflammation in both IBD animal models of dextran sulfate sodium (DSS)-induced colitis and oxazolone (OXA)-induced colitis.

Collectively, our compelling in vivo efficacy data support that our nano-encapsulated BRD4 inhibitors effectively block colonic inflammation in animal models of IBD. Local delivery of nanoparticle-encapsulated BRD4 inhibitors may offer superior pharmacotherapy for IBD patients.

Funding support: Crohn’s & Colitis Foundation Entrepreneurial Investing (EI) Initiative award and Litwin IBD Pioneers Program award from the Crohn’s & Colitis Foundation of America.
THE ROLE OF MYELOPEROXIDASE AND NEUTROPHIL EXTRACELLULAR TRAPS IN THE PATHOGENESIS OF INFLAMMATORY BOWEL DISEASE
Authors: Chami Belal , Ahmad Gulfam , Schroder Angie , Gabriel Patrick San , Witting Paul
Published: January 2021

Neutrophils are short-lived immune cells that represent the major cell type recruited to the inflamed bowel releasing their azurophilic granules containing enzymes myeloperoxidase (MPO). Fecal and serum MPO levels has previously been shown to correlate to disease severity in IBD patients. MPO, in the presence of H2O2 and free Cl- undergoes a halogenation cycle, yielding the two-electron oxidant, hypochlorous acid (HOCl) - a potent bactericidal agent. However, chronic intestinal exposure to MPO/HOCl due to perpetual inflammation may cause secondary host-tissue injury and cell death. Neutrophil Extracellular Trap (NET)osis is a specialised form of neutrophil death where MPO is entrapped in a DNA scaffold and continues to elicit HOCl activity and may further contribute to host-tissue injury.

We investigated the presence of NETs in surgically excised ileum samples from CD and healthy patients using advanced confocal microscopic techniques and found MPO, Neutrophil Elastase (NE) and Citrullinated Histone h3 (CitH3) - critical components of NET formation, individually positively correlate to the severity of histopathological intestinal injury. Furthermore, multiplex Opal™ IHC performed using LMS880 Airyscan-moduled microscopy with z-stacking revealed colocalization of NE, MPO, CitH3 and DAPI indicating the extensive presence of NETs in severely affected CD tissue. Using two pharmacological inhibitors of MPO in a dextran sodium sulphate (DSS) model of murine colitis, we demonstrated the pathological role of MPO in experimental colitis. MPO inhibitors, TEMPOL and AZD3241 delivered via daily i.p significantly rescued the course of colitis by abrogating clinical indices including body weight loss, disease activity index, inhibiting serum peroxidation, and preserving colon length, while significantly mitigating histoarchitectural damage associated with DSS-induced colitis. We also showed that MPO inhibition decreased neutrophil migration to the gut, suggesting MPO may play a role in perpetuating the inflammatory cell by further recruiting cells to the inflamed gut.

Collectively, we have shown for the first time that MPO is not only an important clinical marker of disease severity but may also play a critical role in perpetuating host-tissue damage and inflammation.
TOXICOLOGICAL FINDINGS OF A RECOMBINANT CHOLERA TOXIN B SUBUNIT VARIANT WITH THERAPEUTIC POTENTIAL IN ULCERATIVE COLITIS
Authors: Reeves Micaela , Tuse Daniel , Hamorsky Krystal , Royal Joshua , Matoba Nobuyuki
Published: January 2021

Background

The cholera toxin B subunit (CTB) is the nontoxic and homopentameric component of the holotoxin. Upon binding to GM1 ganglioside on the surface of epithelial cells, CTB mediates entry and retrograde transport through the endomembrane system and disengages the catalytic A subunit in the endoplasmic reticulum (ER). EPICERTIN (EPT) is a recombinant variant of CTB with a non-native C-terminal extension harboring an ER-retention motif, KDEL. We have found that increased ER-retention time resulting from this modification allowed EPT to induce an unfolded protein response and TGF-β signaling in colon epithelial cells, triggering wound healing activity in preclinical colitis models. The unique epithelial repair activity of EPT hints at its therapeutic potential in ulcerative colitis.

Objective

We aim to develop data supporting a first-in-human clinical trial with an EPT enema indicated for ulcerative colitis. Here, we evaluated the efficacy and toxicity of intrarectal (IR) administration of EPT in preclinical rodent models.

Results

IR administration of EPT at 0.1 and 1 µM to female C57/BL6 mice (0.6 and 6.1 μg/animal) with acute dextran sodium sulfate (DSS)-induced colitis resulted in decreased disease activity index scores and increased body weight recovery, supporting a target therapeutic dose of ≤1 µM for clinical administration. A dose-escalation study was performed following a single IR exposure at 1, 2 and 5 µM (61.4, 122.8 and 307 μg/animal) in male and female Sprague Dawley rats. No drug-related adverse effects were evident in clinical observations, including clinical pathology and gross necropsy, even at the highest dose tested. A pharmacokinetics study was performed in male and female mice dosed with a 1 or 10 µM (6.1 and 61.4 μg/animal) IV bolus of EPT. Plasma samples were collected periodically for up to 24 h postdose. EPT concentrations were highest at first collection and decreased steadily until unquantifiable by 4 h. The elimination phase half-life was 0.26 to 0.3 h. When healthy and DSS-induced colitic mice (n = 72) were dosed with 1 or 10 µM EPT IR, marginal amounts of EPT were found in only 4 plasma samples scattered across groups and time points, suggesting that systemic exposure after IR administration is negligible.

Conclusion

These data support further development of EPT as a potential therapeutic for ulcerative colitis.
COMPARATIVE EFFECTIVENESS AND SAFETY OF VEDOLIZUMAB AND ANTI-TUMOR NECROSIS FACTOR AGENTS IN OLDER ADULTS WITH INFLAMMATORY BOWEL DISEASES IN MEDICARE ADMINISTRATIVE CLAIMS DATABASE
Authors: Kochar Bharati , Pate Virginia , Kappelman Michael , Long Millie , Ananthakrishnan Ashwin , Chan Andrew , Sandler Robert
Published: January 2021

Background

The number of older adults with inflammatory bowel diseases (IBD) is increasing. Older adults with IBD are less likely to receive effective immunosuppression. We aimed to determine efficacy and safety of biologic therapies in older adults with IBD.

Methods

We conducted a retrospective cohort study using an active comparator, new user design in a 20% random sample from the 50 state Medicare claims database between May 2014 and December 2018. We included patients who initiated vedolizumab or an anti-tumor necrosis factor (TNF)-α agent (infliximab, adalimumab, golimumab or certolizumab) following 12-months of continuous enrollment in Medicare fee-for-service Parts A/B/D without either study drug. Patients were required to be ≥65 years old and have ≥2 international classification of disease (ICD) codes of Crohn’s disease (CD) or ulcerative colitis (UC). We excluded patients who received other biologic therapies and/or those who had ≥2 codes for other immunologic conditions. Pertinent co-variates included were age, sex, race Charlson Co-morbidity Index (CCI), predicted probability of frailty, healthcare utilization and baseline IBD medications. The outcomes of interest were hospitalizations, IBD-related surgery and new corticosteroid use ≥ 60 days after drug initiation. We described the study population, assessed health care utilization and use of other IBD medications. We estimated crude incidence rates and hazard ratios (HR) adjusted for the covariates using standardized mortality ratio (SMR) weights.

Results

We identified 488 vedolizumab users and 2,213 anti-TNF users. The median age was 72 years in the vedolizumab cohort and 71 years in the anti-TNF cohort; 12% of both cohorts were aged ≥80 years. Differences in the two cohorts existed with regards to sex, race, baseline healthcare utilization and IBD-related medications, but all the baseline differences were balanced by weighting measured by a standardized mean difference (SMD) <0.1 (Table 1). After weighting, vedolizumab users were less likely to be hospitalized in the 12 months after biologic initiation (HR: 0.81, 95% CI: 0.68 – 0.96). While there was no significant difference in IBD related hospitalizations, older adults with IBD were less likely to have an infection-related hospitalization (HR: 0.39, 95% CI: 0.23 – 0.65). There were no significant differences in IBD related surgery and steroid use after induction (Table 2).

Conclusions

In this large, retrospective cohort study of older IBD patients who were new users of vedolizumab and anti-TNF agents, we found that older patients initiated on vedolizumab were significantly less likely to have an infection-related hospitalization. However, there were no significant differences in IBD-related hospitalizations, IBD-related surgery or corticosteroid use after biologic induction.
REINVENTING INFLAMMATORY BOWEL DISEASE (IBD) CLINICAL TRIAL RECRUITMENT USING NOVEL DIGITAL MEDICINE TOOLS
Authors: Fasihuddin Farah , Wedel Nicole , Atreja Ashish , Madisetty Divya , Jain Charu Madhwani , Rogers Jason , Atreja Ashish , Kakkar Sarthak , Garge Shashank
Published: January 2021

Background

Issues with patient recruitment and enrolment are the primary barriers for missed clinical trial timelines; 8 out of 10 clinical trials are delayed or unable to be completed because of the lack of timely patient recruitment. Current patient recruitment efforts are inefficient as they are typically dependent on the manual screening of patients during face-to-face visits. With the rapid development of digital communication platforms within healthcare and the broad consumer adoption of smartphones, there are increasing opportunities to overcome some of these barriers. Digital platforms have great potential for research and clinical care of chronic conditions, such as inflammatory bowel disease (IBD), an often debilitating disease that currently affects over three million adults in the United States. In this paper, we utilized a digital medicine platform (Trialengage, Rx.Health, New York, NY) to improve patient recruitment for an ongoing mindfulness trial which had limited success in face-face enrolment (16 patients over 6 months).

Methods

Patients enrolled in the Mount Sinai Crohn’s and Colitis Registry (MSCCR) were remotely outreached about enrolling in a mindfulness study for IBD patients. A text-based clinical rules engine was used to inform registry patients about the trial and to allow patients to indicate interest in participating via text message. Eligible IBD patients were bulk “prescribed” a notification through RxHealth’s digital medicine platform, RxUniverse. Characteristics of the enrolled population, characteristics of patients who responded, and timeliness of responses were analyzed.

Results

Of the 1364 patients in the MSCCR with available phone numbers, 270 patients affirmatively replied they wanted to participate in the study. Patients who opted-in to receiving more information about the study were more likely to have inadequate control of their IBD (25.64% vs 18.97%; P<.05) and more likely to have a recent history of depression based on a validated patient health questionnaire (15.38% vs 8.4%; P<.05) than those who opted-out. There were no significant differences in terms of race, gender, and age between the two groups. In terms of timeliness of response among those enrolled, the majority of patients responded within 2 hours of notification.

Conclusion

Digital medicine software platforms can facilitate large-scale, lower-effort recruitment of eligible patients for clinical trials. Future research should be done to explore their expanded use for recruitment, patient education, and study data collection. Additional technologies such as patient-powered networks, social media, e-recruiting bots, and other remote engagement platforms can aid clinical trials by saving time and reducing costs of patient recruitment.
ROLE OF CHEMERIN IN THE PATIENTS WITH INFLAMMATORY BOWEL DISEASES
Authors: Sochal Marcin , Fichna Jakub , Bialasiewicz Piotr , Talar-Wojnarowska Renata , Gabryelska Agata , Malecka-Panas Ewa
Published: January 2021

Background and aims

Chemerin belongs to adipokines, which are proteins secreted by white adipose tissue. It has important role in angiogenesis, metabolism and correlates with severity of inflammation. The study aimed to investigate the correlation between the serum level of chemerin and the severity of inflammatory bowel disease (IBD), and examine the influence of anti-TNF treatment on the chemerin level.

Methods

One-hundred and nineteen participants were recruited for this study: 77 with IBD and 42 healthy control (HC). Venous blood was collected from all study participants. Twenty-six patients, who underwent 14-week anti-TNF therapy were re-examined (infliximab or adalimumab). The measurements were performed by ELISA method, according to the protocol supplied by the producer. The study was funded by Medical University of Lodz Grant (#564/1-000-00/564-20-024).

Results

Serum chemerin level were higher in ulcerative colitis (UC) patients (557.4 ng/ml ±219.9) compared to Crohn’s disease (CD; 446.0 ±252.6; p=0.048). IBD patients (492.3 ng/ml ±244.3) achieved higher chemerin level than HC control (404.5 ng/ml ±194.2; p=0.047). Patients with IBD exacerbation (559.1 ng/ml ±235.6) achieved higher chemerin levels compared to remission (381.7 ng/ml ±220.2; p=0.002). Chemerin correlated with the severity of the clinical condition of the CD (Harvey-Bradshaw index; r=0.478, p=0.001), but not with the severity of UC (Partial Mayo Score; r=0.03, p= 0.788). Serum level of chemerin decreased after 14 weeks of anti-TNF treatment (519.6 ng/ml IQR: 393.2–727.0 vs. 351.5 ng/ml IQR: 229.3–424.2; p=0.002). Patients treated with steroids obtained higher concentrations of chemern compared to patients who did not receive such treatment (p=0.049).

Conclusions

Chemerin correlates with the clinical severity of IBD and its level lowers after anti-TNF treatment, which suggests its participation in inflammation. However, many factors affect its concentration thus it does not seem to present high diagnostic value or present as a possible therapeutic target.
IMMATURE LOW-DENSITY NEUTROPHILS AS MEDIATORS OF PYODERMA GANGRENOSUM AND INFLAMMATORY BOWEL DISEASE PATHOGENESIS
Authors: Jatana Samreen , Rebert Nancy , Fernandez Anthony , Achkar Jean-Paul , McDonald Christine
Published: January 2021

Pyoderma gangrenosum (PG) is a debilitating skin condition characterized by deep, pus-filled, non-healing ulcers packed with neutrophils and is a common extraintestinal manifestation of inflammatory bowel disease (IBD). Strikingly, ~40% of people with an initial presentation of PG go on to be also diagnosed with IBD, suggesting that both diseases have common factors driving their pathogenesis. The molecular and cellular mechanisms of PG and IBD co-development are currently unknown, hampering the development of effective treatment strategies for individuals affected by both diseases. Prior studies of individuals with PG demonstrate an enrichment of circulating immature low-density neutrophils (LDGs) that are sensitized to undergo NETosis, a specialized form of cell death. NETosis induces inflammation and, when dysregulated, can promote chronic cycles of inflammation. We hypothesize that LDGs mediate NETosis-driven inflammation in both PG and IBD, but the LDGs from individuals that develop both diseases are functionally distinct. In this translational study, blood samples are collected from healthy subjects or individuals with only PG, only Crohn’s disease, only ulcerative colitis, or individuals with both PG and IBD for the analysis of neutrophil populations, neutrophil function, as well as circulating markers of inflammation and NETosis. Preliminary data from 45 subjects demonstrate an enrichment of circulatory LDGs (CD45+ CD15+ CD66b+ CD10+ CD16+ cells from the low density fraction) in individuals with inflammatory disease as compared to healthy subjects (19.2% +/- 2.81%, n=41 vs. 9.9% +/- 2.9%, n=4; p=0.04). This is correlated with increased NETosis in vitro, however differences in the responsiveness of LDGs to priming signals, such as IL-1β, TNFα, and IL-6, are emerging between disease sub-groups. There is considerable variation in the levels of LDGs within disease sub-groups and analyses are underway to determine whether this variation correlates with subject reported disease activity, inflammatory markers (serum C-reactive protein), or circulating markers of NETosis (serum citrullinated histone 3). These preliminary findings point to the presence of a unique population of cells potentially contributing to inflammatory cross-talk between the skin and gut. Further analysis of these potentially disease driving cells may result in more effective care of IBD patients with extraintestinal manifestations, such as PG, through more mechanistically targeted therapeutic approaches, as well as potential biomarker discovery that predicts which PG patients are more likely to develop IBD leading to earlier intervention and better disease outcomes.
IS ILEOANAL POUCH EXCISION A DESTINATION THERAPY FOR INFLAMMATORY BOWEL DISEASE? DATA FROM A QUATERNARY POUCH REFERRAL CENTER
Authors: Choi Sarah , Lightner Amy , Lipman Jeremy , Hull Tracy , Steele Scott , Holubar Stefan , Rieder Florian
Published: January 2021

Background

Although ileal pouch-anal anastomosis (IPAA) is the surgical procedure of choice of many patients with ulcerative colitis and other conditions, some patients may require pouch excision (PE). We aimed to describe our experience with pouch excisions and associated outcomes with an emphasis on late medical, endoscopic, and surgical interventions for IBD.

Methods

We performed a retrospective review of a prospective colorectal surgery database. All PEs performed at our quaternary pouch center from 2006 – 2019 were included; pelvic exenteration, PE with neo-IPAA or Kock-pouch were excluded. Early complications occurred <30 days, late complications >30 days. Medications taken prior to PE were included if taken within 12 weeks of pouch excision. Data are reported in frequency (proportion) or median (interquartile range).

Results

A total of 197 cases met inclusion criteria, and were performed by 23 surgeons, median 6 excision (IQR 2 - 14) cases over a 14-year period: of these, 105 had their index pouch created at our quaternary pouch referral center (overall PE rate 2.7%). Indications for PE are shown in Table 1. Median time to PE was 7 years and 94 (48%) patients had re-diversion prior to PE. Medications prior to PE: 34 (17%) steroids, 27 (14%) biologics, and 22 (11%) immune-modulators. The median duration of surgery was 4 hours (3.2–5). The median estimated blood loss was 263 ml (150–500) with 24 patients (12%) requiring at least one unit of packed red blood cells intra-operatively. Most pouch excisions were done through laparotomy; 2 cases (1%) were started robotically and 11 cases (10%) laparoscopically with a 26% conversion rate. Intersphincteric dissection was used in 172 cases (87%) while 26 cases (13%) required abdomino-perineal resection, of which 58% had a neoplastic indication. Intra-operative, early and late complications are shown in Table 2; 40 patients (20%) had perineal wound complications in less than 30 days, while 26 patients (13%) had long-term perineal wound complications, of which 15 patients required return to the operating room. After PE, 23 patients (12%) required continuation of IBD medications, 6 patients (3.1%) required surgery, and 4 patients (2%) required endoscopic intervention for their IBD.

Conclusions

In this large series of ileoanal pouch excisions, we found that perineal wound complications are common, but infrequently require operative intervention. For most IBD patients in this series, pouch excision did appear to be a destination therapy for IBD with a small minority requiring ongoing medical therapy for IBD.
URINARY BLADDER NECROSIS - AN EXTRAINTESTINAL MANIFESTATION OF INFLAMMATORY BOWEL DISEASE IN A PEDIATRIC PATIENT
Authors: Norris Nicholas , Schlomer Bruce , Gurram Bhaskar
Published: January 2021

Extraintestinal manifestations are common in inflammatory bowel disease (IBD), and genitourinary complications are known, including nephrolithiasis, fistulas, and ureteral obstruction. Bladder involvement is less common, and limited to cystitis including xanthogranulomatous cystitis. Bladder necrosis has not been previously described in association with IBD. Here, we describe an unusual case of IBD associated with total bladder necrosis at the time of initial diagnosis.

An 8-year-old female with a history of chronic microcytic anemia presented with 1 week of hematochezia, hematuria, and fever with associated abdominal pain. Her exam was significant for mild lower quadrant abdominal tenderness including the suprapubic area, but was otherwise unremarkable. Blood work showed microcytic anemia and mild thrombocytopenia, elevated inflammatory markers, and hypoalbuminemia. Infectious workup was unremarkable. Upon admission, she developed oliguria and hypertension and rapidly progressed to renal failure requiring dialysis catheter placement and renal replacement therapy. A kidney biopsy revealed acute tubular injury but showed no glomerular involvement and had no evidence of hemolytic uremic syndrome or vasculitis. Imaging obtained including CT of her abdomen showed a thickened transverse colon and a thickened bladder wall with dilation of the renal collecting system, worse on the left. Bladder biopsy showed full-thickness necrosis of unclear etiology and had negative staining for microorganisms. She had bilateral nephrostomy tubes placed for drainage of her kidneys and her renal function subsequently returned to normal. MR imaging also revealed necrosis and confirmed complete bladder involvement. Her renal failure was presumed to be a secondary to ureterovesical junction obstruction from the bladder necrosis. She underwent esophagogastroduodenoscopy (EGD) and colonoscopy due to persistent hematochezia. The EGD was unremarkable. Her colonoscopy was grossly abnormal with evidence of colitis from the cecum to the rectum. Biopsies revealed both active and chronic inflammation with sparing of the terminal ileum, and immunohistochemical staining for infection was negative. Capsule endoscopy was largely unremarkable. She was diagnosed with ulcerative colitis and started on steroids and sulfasalazine. Her abdominal pain and stool consistency improved and her bloody stools resolved. Steroids were tapered and she continued sulfasalazine as maintenance therapy.

This case presents a novel association of IBD and bladder necrosis. Vascular obstruction secondary to a hypercoagulable state might explain such an event, but this seems less likely given the diffuse nature of bladder involvement. A clinical index of suspicion for bladder involvement and/or necrosis is warranted in patients with IBD who present with obstructive urinary symptoms or hematuria.
IDENTIFICATION OF SELETIVE CLAUDIN CATION CHANNEL BLOCKERS
Authors: Ma Jingjing , Wu Emma , Li Ye , Seibel William , Shen Le , Khalili Fatemeh , Weber Christopher
Published: January 2021

Compromised epithelial barrier function is known to be associated with inflammatory bowel disease (IBD) and may contribute to disease development. One mechanism of barrier dysfunction is increased expression of paracellular tight junction ion and water channels formed by claudins. Claudin-2 and -15 are two such channels. We hypothesize that blocking these channels could be a viable therapeutic approach to treat diarrhea. In an effort to develop blockers of these channels, we turn to our previously developed and validated in silico models of claudin-15 (Samanta et al. 2018). We reasoned that compounds that can bind with the interior of claudin pores can limit paracellular water and ion flux. Thus, we used docking algorithms to search for putative small molecules that bind in the claudin-15 pore.

AutoDock Vina was initially used to assess rigid docking using small compound databases. The small molecules were analyzed based on binding affinity to the pore and visualized using VMD for their potential blockage of the channel. Clusters of binding modes were identified based on the prominent interacting residues of the protein with the small molecules. We initially screened 10,500 compounds from within the UIC Centre for Drug Discovery and a cross-section of 10,000 compounds from the NCI open compound repository. This initial screen allowed us to identify 2 first-in-class selective claudin-15 blockers with efficacy in MDCK monolayers induced to express claudin-15 and in wildtype duodenum.

Next, we screened the entire NCI open compound repository for additional molecules structurally related to our best initially identified molecule and this has allowed us to identify 13 additional molecules that increase TER of claudin-15 expressing MDCK monolayers by 90–160%. Additionally, these molecules possess similar structural components that will be collected in a fragment library and explored through molecular dynamics simulations.

We also developed a claudin-2 homology model on which we are performing docking studies and in vitro measurements, which we expect will result in similar candidate ligands for blocking claudin-2. Our study will provide important insight into the role of claudin-dependent cation permeability in fundamental physiology, which we believe will lead to the utility of claudin blockers as a novel and much needed approach to treat diseases such as IBD.
LOSS OF GLUTATHIONE PEROXIDASE 1 ATTENUATES COLITIS AND IS CRITICAL IN ACTIVATING EPITHELIAL REGENERATIVE RESPONSES
Authors: Hendren Jared , Kasnyik Koral , Williams Christopher , Short Sarah
Published: January 2021

Many selenium-containing “selenoproteins” function as antioxidants, and work by our lab and others has demonstrated that selenoproteins often protect against intestinal inflammatory diseases, including colitis. Glutathione peroxidase 1 (GPx1) is a ubiquitous, mitochondrial and cytosolic selenoprotein which catalyzes the reduction of hydrogen peroxide by glutathione. Previously, we determined that despite its antioxidant role, loss of GPx1 greatly reduced disease severity in the dextran sodium sulfate (DSS) colitis model. Furthermore, GPx1 loss increased baseline intestinal cell proliferation, enhanced enteroid plating efficiency, and induced expression of stem cell-associated genes, such as Lgr5.

Next, we aimed to determine the mechanism by which GPx1 modifies response to DSS. We observed that GPx1 is increased in colonic tissues from DSS-treated mice as compared to nontreated controls, suggesting that GPx1 may functionally contribute to intestinal injury responses. While GPx1 is expressed in both intestinal epithelial and immune cells, in situ hybridization to visualize Gpx1 identified epithelial cells as the most highly expressing cell type, with the greatest Gpx1 upregulation observed in wound-adjacent and regenerative crypts. Next, we investigated whether GPx1 loss affects stem cell function after injury. Here, we determined that both proliferation (p<0.01) and Lgr5 expression (p<0.05) were increased in the crypts of Gpx1-/- DSS-treated mice in comparison to WT controls. Similarly, organoids established from ulcerative colitis tissue displayed increased growth rates (p<0.01), expression of stem cell and Wnt target genes such as AXIN2 (p<0.0001) and LGR5 (p<0.01), and proliferation (p<0.05) following GPX1 knockdown. Together, these results indicate that GPx1 has an epithelial-cell autonomous role, and that its loss activates stem cell and proliferative responses which may both protect from intestinal injury and promote healing.

Interestingly, recent research has highlighted the role of cellular metabolism in maintaining intestinal stem cell function, and GPx1 has previously been implicated in these processes. RNA-sequencing from DSS-treated mice and gene set enrichment analysis identified a positive association with oxidative phosphorylation-associated genes in Gpx1-/- mice (NES: 1.78; FDR q-val: 0.01), suggesting altered metabolism which may favor stem cell function. Further analysis of cellular metabolism using GPX1 knockdown colorectal cancer cells observed higher basal respiration (p<0.0001) and ATP generation (p<0.0001). Together, these results suggest that unlike other intestinal selenoproteins studied to date, loss of GPx1 augments stem cell injury responses to protect against intestinal inflammation, likely via augmenting epithelial regenerative responses.
SPROUTY2 INHIBITS EXPRESSION OF THE HOST DEFENSE PEPTIDE RELMβ IN THE COLONIC EPITHELIUM
Authors: Schumacher Michael , Liu Cambrian , Hsieh Jonathan , Purnell Benjamin , Frey Mark
Published: January 2021

Background

Sprouty2 (Spry2) is an inflammation-responsive regulator of intracellular signaling that is suppressed in colitis. Loss of Spry2 levels leads to increased colonic tuft and goblet cell numbers; cell types protective against injury and infection. In particular, goblet cells produce host defense peptides (HDPs) which can enhance barrier effectiveness and limit pathogen colonization. While the activity of these cells is regulated and responsive to environmental cues, the precise mechanisms driving functional changes in goblet cells are largely unknown. Here, we tested the role of Spry2 in mediating colonic goblet cell function and HDP production.

Hypothesis

Spry2 regulates HDP production in colonic goblet cells and bacterial levels.

Methods

Distal colons from mice with an intestinal epithelial-specific Spry2 deletion (Spry2flox/flox;Villin-Cre, Spry2KOIE) and littermate controls were collected at 8 w of age, and analyzed by bulk and single-cell RNA sequencing. Fecal pellets from the distal colon were 16S sequenced to assess changes in microbial populations. Changes in HDP expression were assessed at the bulk tissue level and within individual cellular populations.

Results

Expression of the host defense peptide RELMβ, but not RELMα, RELMγ, or Resistin, was increased 15-fold (p<0.05) in Spry2KOIE mice in bulk RNA sequencing analysis. Single cell RNA sequencing showed RELMβ was highly enriched in Reg4+/Spink4+ putative crypt base goblet cells of both control and Spry2KOIE mice. Quantification of these cells by single-cell RNA sequencing revealed no significant difference in Reg4+/Spink4+ cell numbers in Spry2KOIE mice versus wild-type, suggesting increased RELMβ is due to goblet cell activation and not goblet cell population shifts. Taxonomic analysis of feces from 2 litters of mice showed a decreased abundance of Eggerthella spp. (reduced 61%, p<0.05) and Streptococcus spp. (reduced 50%, p<0.05), genera that have been identified in patients with inflammatory bowel disease.

Conclusion

Loss of epithelial Spry2 drives HDP production in the colon and alterations in the colonic microbiota. Impairment of this mechanism may impact colitis severity.
TRANSFER RNA QUEUOSINE MODIFICATION ENZYME MANIPULATES TIGHT JUNCTION PROTEINS IN INFLAMMATORY BOWEL DISEASE
Authors: Zhang Jilei , Zhang Yong-guo , Xia Yinglin , Sun Jun
Published: January 2021

Background

Transfer RNA (tRNA) queuosine (Q)-modification occur at the wobble anticodon position of four special cellular tRNAs. In eukaryotes, tRNA-Q modification relies on the intestinal microbial product queuine and eukaryotic tRNA-guanine transglycosylase complex contains of Q tRNA ribosyltransferase catalytic subunit 1 (QTRT1). Q-tRNA modification is critical for the fidelity and accuracy to translate RNA to protein. It is known that dysfunction of Q-tRNA associates with cancer proliferation and malignancy. However, mechanisms of how Q and Q-tRNA modifications influence intestinal epithelial biology and chronic inflammation are unknown.

Methods

We explored the expression of QTRT1 in patients with IBD by investigating human biopsy tissues and re-analyzing gene expression datasets (with both UC and CD patients). To further investigate the QTRT1 role in IBD, the dextran sodium sulfate (DSS) induced colitis mouse model and IL10-deficient mouse model were used to evaluate the molecular mechanism. We further investigated the impact of QTRT1 reduction on intestinal cells by generating QTRT1 knockdown HCT116 and Caco-2 BBE cells using a Double Nickase Plasmid.

Results

We found that the QTRT1 expression in IHC staining was significantly downregulated in the colon of both Ulcerative Colitis (UC) and Crohn’s Disease (CD) patients compared with normal controls. After extracting and analyzing the datasets, we found the gene expression of QTRT1 was significantly suppressed in colonic mucosa of UC and intestinal mucosa of CD, compared with controls. Moreover, the four tRNA-Q-related tRNA synthetase (asparaginyl-tRNA synthetase, aspartyl-tRNA synthetase, histidyl-tRNA synthetase and tyrosyl-tRNA synthetase) were also decreased in IBD patients. The decreased QTRT1-expression was further confirmed in both DSS-induced colitis mice and IL10-defecient mice. Meanwhile, the significantly downregulated beta-catenin and Claudin-5, and upregulated Caludin-2 were identified in these two colitis models. All these molecular alterations, which are important in cell adhesion and tight junction formation, were further verified in protein expression and mRNA level using QTRT1 reduction HCT116 and Caco-2 BBE cells in vitro.

Conclusion

Our results demonstrate that the QTRT1 plays a novel role in human IBD by altering intestinal cell adhesion and junctions. Microbiome-dependent Q supply can be altered during disease development or when a limited variety of food-types are ingested. Investigations on the gut microbiome-derived tRNA modification in IBD will uncover novel molecular mechanisms for potential prevention and therapy.