bluuebunny/crossref_metadata_2025_split huggingface dataset:
A NOVEL DRUG THERAPY INDUCES MITOCHONDRIAL BIOGENESIS AND ATTENUATES COLITIS
Authors: Bhogoju Sarayu , Kapur Neeraj , Chaiswing Luksana , Kim Jong Hyun , Awuah Samuel , Goretsky Tatiana , Barrett Terrence 
Published: January 2023

Abstract
Mitochondrial dysfunction is a characteristic feature of intestinal epithelium cells (IEC) in IBD patients, associated with oxidative stress and impaired ATP production. We posit that disrupted mitochondrial bioenergetics impairs ulcer healing in IBD. In the current study, we tested a novel gold-based compound (AuPhos) that improves mitochondrial function by increasing mitochondrial biogenesis and antioxidant enzymes in IEC and human colonic biopsies.
METHODS: Normal human colonic epithelial cells (NCM460) were used to evaluate the effect of AuPhos on mitochondrial proteins and anti-oxidant proteins by western blotting in the presence or absence of low-dose TNF (1ng/ml). To model mitochondrial deficiency, TFAM (mitochondrial transcriptional factor A) was silenced (shTFAM) in NCM460 cells. These cells were treated with low-dose TNF to mimic inflammatory conditions in the human intestine. The mitochondrial mass was assessed by flow cytometry using mito tracker green. The transcriptional activity of genes associated with mitochondrial biogenesis, mitochondrial complexes, and anti-oxidants was evaluated using RT-qPCR in AuPhos or vehicle-treated (overnight) cells with or without TNF. Human colonic biopsy samples were collected in Allprotect, treated ex-vivo with vehicle or AuPhos (3h, 4oC), and processed for RNA isolation followed by RT-qPCR.
RESULTS: Biochemical and mass spectrometry analyses revealed that AuPhos localizes to the mitochondria. We show here that AuPhos increases mitochondrial mass and mRNA for mitochondrial complexes [complex IV (Cox6A1) and complex V (ATP5A1)] in NCM460 cells in TNF or vehicle-treated cells. Similarly, AuPhos increased protein levels of upstream regulators of mitochondrial biogenesis such as TFAM, PGC-1α, and Nrf2 compared to nontreated cells. Further protein analysis of AuPhos-treated cells showed that AuPhos increases downstream antioxidant markers such as manganese superoxide dismutase (MnSOD), peroxidane 3 (Prd3), glutathione peroxidase 4 (GPX4), thioredoxin reductase2 (Trx2), and catalase expression when compared to the TNF or control samples. Interestingly, expression of genes associated with mitochondria-specific (MnSOD) and cytoplasmic superoxide dismutase (CuZnSOD) were also significantly increased in AuPhos-treated shTFAM NCM cells compared to vehicle or TNF-treated cells. AuPhos substantially upregulates the expression of mtCO1, mtCO2, Cox6A1, ATP5A1, NRF1, MnSOD, GPX, PRDX-2,-4, and -6, in ex vivo treated human colonic biopsies compared to vehicle or TNF-treated samples.

CONCLUSIONS: The current data suggest that the AuPhos compound improves mitochondrial function by promoting the expression of mitochondrial-associated proteins and antioxidant enzymes (Figure 1). We believe AuPhos can be used as a potential therapeutic in treating ulcerative colitis and Crohn’s disease by restoring mitochondrial biogenesis.
TRANSFER RNA MODIFICATION CONTRIBUTE TO PATHOGENESIS OF INTESTINAL INFLAMMATION BY ALTERING EPITHELIAL BARRIERS
Authors: Zhang Jilei , Zhang Yong-guo , Xia Yinglin , Sun Jun 
Published: January 2023

Abstract

BACKGROUNDS
Transfer RNA (tRNA) is the most extensively modified RNA in cells. Queuosine (Q)-modification is a fundamental process for fidelity and efficiency of translation from RNA to proteins. In eukaryotes, tRNA-Q-modification relies on the intestinal microbial product queuine. Growing evidence indicates that tRNA modifications play important roles in human diseases, e.g., type 2 diabetes. Q depletion led to endoplasmic reticulum stress in mouse liver. Q-tRNA modifications are dynamic and highly variable depending on the developmental stages and species type and tumorigenesis. However, the health consequences of disturbed availability of queuine and altered Q-tRNA modification remain to be investigated. The effects and mechanisms of Q-tRNA in intestinal bowel diseases (IBD) are unknown.

METHODS
We explored the Q-tRNA-related tRNA synthetases and expression of Q tRNA ribosyltransferase catalytic subunit 1 (QTRT1) in patients with IBD by investigating human biopsies and reanalyzing datasets. We used several colitis mouse models, organoids, and cultured cells for loss- and gain-of-function studies to investigate the mechanisms of Q-tRNA modifications in intestinal barrier functions, proliferation, and inflammation.

RESULTS
In ulcerative colitis and Crohn’s disease patients, QTRT1 expression was significantly downregulated. Altered QTRT1-related metabolites were found in human IBD. The four Q-tRNA-related tRNA synthetases, asparaginyl-aspartyl-, histidyl-, and tyrosyl-tRNA synthetase, were decreased in IBD patients. This reduction was further confirmed in DSS-induced colitis and IL10-deficient mice. Reduced QTRT1 was significantly correlated with intestinal junctions, including downregulated β-catenin and upregulated Claudin-2. These alterations were confirmed in vitro by deleting QTRT1 from cells. Queuine treatment significantly enhanced cell junctional functions and reduced inflammation in epithelial cells.

CONCLUSION
tRNA modifications play an unexplored novel role in the pathogenesis of intestinal inflammation by altering epithelial barriers. Insights into Q-tRNA modification in regulating barrier functions would facilitate the development of targeted interventions for IBD through queuine and tRNA modifications.
GUT MICROBIAL METABOLISM OF 5-ASA IS PROSPECTIVELY ASSOCIATED WITH TREATMENT FAILURE IN PATIENTS WITH IBD
Authors: Mehta Raaj , Mayers Jared , Zhang Yancong , Bhosle Amrisha , Nguyen Long , Ma Wenjie , Ananthakrishnan Ashwin , Franzosa Eric , Balskus Emily , Chan Andrew , Huttenhower Curtis 
Published: January 2023

Abstract

BACKGROUND
Variation in clinical response to 5-aminosalicylic acid (5-ASA) has been attributed in part to its inactivation by gut microbes. Recently, in the Inflammatory Bowel Disease (IBD) Multi’omics Database (IBDMDB), a multicenter year-long cohort of 100+ participants with IBD, we identified 12 gut microbial enzymes from two protein families that convert 5-ASA to N-acetyl 5-ASA, a compound that lacks anti-inflammatory effects. Within the IBDMDB, we then found that a subset of these enzymes was cross-sectionally linked with greater risk of treatment failure, defined by corticosteroid use. The aim of this study was to prospectively associate these drug-degrading gut microbial enzymes with treatment failure and to confirm in vitro conversion of 5-ASA by these enzymes.

METHODS
We examined the prospective association between gut microbial acetyltransferases with risk of 5-ASA treatment failure in the ongoing “Study of a Prospective Adult Research Cohort with IBD” (SPARC IBD). We included 208 participants who at study entry 1) gave a stool sample at baseline, 2) were on 5-ASA, and 3) were steroid-free. Fecal metagenomic data was processed by the same analysis pipeline (biobakery3) as in the IBDMDB. Exposure was defined identically as in the IBDMDB as metagenomic carriage of 3-4 drug-degrading acetyltransferases compared to 0-2 acetyltransferases. We calculated odds ratios (ORs) and 95% confidence intervals (CIs) of incident steroid use using multivariable generalized estimating equations, adjusting for age and sex. For biochemical characterization, the 12 enzymes identified in the IBDMDB were heterologously expressed by E. coli. A representative enzyme was selected from each protein family for purification, and then incubated with 5-ASA and acetyl CoA for 6 hr at 37C with 1 mM of each substrate and 50 μM enzyme. Using a custom LC–MS assay, we then detected N-acetyl 5-ASA production.

RESULTS
Over a median follow-up of 8 months, we identified 60 cases of corticosteroid use. Consistent with data from the IBDMDB, we found that metagenomic carriage of 3 or more microbial acetyltransferase genes in SPARC IBD (compared to 2 or fewer) was associated with treatment failure (OR 2.77, 95% CI 1.03-7.43). In a random effects meta-analysis of the two cohorts, we observed a three-fold increased risk of drug failure (OR 3.12, 95% CI 1.41-6.89) (Fig 1). In vitro biochemical experiments confirmed the ability of a thiolase and an acyl-CoA N-acetyltransferase to acetylate 5-ASA, generating product at levels consistent with &gt;25% conversion (Fig 2).

CONCLUSIONS
We characterized two gut microbial protein families that are directly involved in 5-ASA metabolism and, in turn, are prospectively associated with 5-ASA treatment failure. These findings advance the possibility of microbiome-based personalized medicine for patients with IBD.
MUCOSAL IMMUNE SIGNATURES OF PERIANAL FISTULIZING CROHN’S DISEASE BY MASS CYTOMETRY
Authors: Cao Siyan , Escudero Guadalupe Oliva , Deepak Parakkal , Cella Marina , Colonna Marco 
Published: January 2023

Abstract

BACKGROUNDS
Perianal fistulas occur in ~30-40% of patients associated with high morbidity and an impaired quality of life. The management of perianal fistulizing CD is a major clinical challenge, where its underlying etiology of is poorly understood.

METHODS
We recruited patients with a history of: 1) CD with perianal fistulas; 2) CD without perianal involvement; 3) idiopathic perianal fistulas. Biopsies were taken from the fistula tracts, external opening of the fistulas, and rectal mucosa during examination under anesthesia or colonoscopy. Isolated mucosal immune cells were analyzed using mass cytometry. Data was analyzed using viSNE for dimensionality reduction.

RESULTS
We have revealed previously unknown mucosal immune landscapes in perianal CD using mass cytometry. Key cell populations with significant difference in frequencies are summarize in Table 1 (data of external fistula opening not shown due to limited space): 1) CD45RO+ T cells including Tregs are elevated in CD fistulas compared to those from idiopathic fistulas, which is consistent with a prior histological study. The expression of co-inhibitory receptor TIGIT and co-stimulatory receptor CD226 are increased in Tregs in CD fistulas, although their function in IBD and especially perianal CD remains unclear. 2) Perianal CD is associated with increased Th17 cells in the fistula tracts and elevated IL-17-producing CD8 T cells (Tc17) in the rectum, which highlight the importance of IL-17 signaling in perianal CD. 3) CD fistulas show increased CD39 and decreased CD127 (IL-7Ra) in both CD4 and CD8 T cells. CD39 and CD127 are markers of T cell exhaustion, which may control the pathogenesis of perianal CD by regulating cytokine production. 4) Total B cells are elevated in CD fistulas compared to idiopathic fistulas. In contrast, regulatory B cells (Bregs), with immunomodulatory function in the gut, are dramatically diminished in CD fistulas compared to idiopathic fistulas. 5) Besides adaptive cells, CD3-CD19- innate immune cells including innate lymphoid cells (ILCs), macrophages, and NK cells are also skewed in perianal CD. Fistula tracts, external fistula opening (data not shown), and rectum of perianal CD all show dramatically elevated CD172+TREM1+ macrophages, which were previously found to promote chronic inflammation in luminal CD.

CONCLUSIONS
The immune responses in perianal CD demonstrate unique features that are not present in luminal CD (summarized in Figure 1). This indicates that perianal CD represents an immune identity distinct from luminal CD in the intestine. Importantly, altered T cell exhaustion markers (CD39 and CD127) and increased CD172+TREM1+ pathogenic macrophages are present in all three locations (fistula tracts, external opening, and rectum) of perianal CD, suggesting their roles in the pathogenesis of perianal CD and may become novel therapeutic targets.
PRO-INFLAMMATORY SIRPα-EXPRESSING MONOCYTES AND MACROPHAGES MEDIATE ANTI-TNF REFRACTORY CROHN'S DISEASE IN CHILDREN
Authors: Geem Duke , Maddipatla Sushma , Pelia Ranjit , Venkateswaran Suresh , Matthews Jason , Anbazhagan Murugadas , Kolachala Vasantha , Dodd Anne , Kugathasan Subra 
Published: January 2023

Abstract

BACKGROUND
Crohn’s disease (CD) is a chronic inflammatory disorder of the gastrointestinal tract with detrimental consequences on the pediatric population. Anti-tumor necrosis factor (aTNF) therapies are the only FDA-approved biologics for pediatric CD but one-third fail anti-TNF induction, and of those who initially respond, approximately 15% relapse every year. Consequently, there is a pressing need to elucidate the underlying immunogenetic mechanisms of anti-TNF refractory CD.

METHODS
A prospective cohort study was employed of treatment-naïve (TN-CD; n= 12), aTNF refractory (REF-CD; n=11), and endoscopic remission CD (REM-CD; n=16) along with non-IBD control (n=13) children. High dimensional flow cytometric analyses (HD FACS) of the blood, ileal and rectal biopsies were performed and analyzed by t-distributed stochastic neighbor embedding (t-SNE) clustering. Single-cell RNA sequencing (scRNA-seq) was conducted using the 10X Chromium platform with a 3’ reagent kit and sequenced on Illumina’s Novaseq600. The Seurat v4.1 workflow was used for the UMAP cell clustering algorithm. Effects of conditioned media (CM) from SIRPα cells on ileal organoids from non-IBD controls was assessed by enriching blood SIRPα+ cells from REF-CD via magnetic activated cell-sorting and stimulating with LPS (10 ng/mL) and flagellin (FLG; 10 ng/mL) for 96 hrs in culture. CM was collected and ileal organoids were treated for 72 hrs and re-stimulated with LPS+FLG followed by viability and intracellular cytokine staining. Descriptive statistics, one-way ANOVA with multiple comparisons testing, and univariate linear regression were utilized.

RESULTS
HD FACS revealed significant enrichment of SIRPα+CD11c+HLA-DR+CD64+ (SIRPα) cells in the ileum, rectum, and blood of REF-CD (P&lt; 0.05). These cells expressed pro-inflammatory cytokines, IL-1β, IL-6, and TNFα. Deeper characterization with scRNA-seq revealed SIRPα cells to be macrophages based on expression of: CD14, FCGR3A, CD68, CD163, FCGR1A, and MRC1. In addition to pro-inflammatory cytokines detected by HD FACS, SIRPα macrophages expressed TGFB1 and CXCL8. There were significant positive correlations of intestinal SIRPα macrophages with fecal calprotectin (P&lt;0.05) and CRP (P&lt;0.05). CM from SIRPα+ cells of REF-CD induced significant cell death and intracellular cytokine expression of TNFα and IL-1β from non-IBD ileal organoids.

CONCLUSION
SIRPα cells are a distinct pro-inflammatory macrophage population enriched in the blood and intestinal lamina propria of REF-CD that may mediate resistance to anti-TNF therapy via secretion of pro-inflammatory cytokines and disruption of the intestinal epithelial barrier. These findings provide mechanistic insight into pathogenesis of anti-TNF refractory CD in children and highlight these cells to be a potential therapeutic target.
GROWTH OUTCOMES OF IV ANTI-TNF BIOSIMILARS IN PEDIATRIC INFLAMMATORY BOWEL DISEASE
Authors: McClinchie Madeline , Lakhani Alyshah , Abdel-Rasoul Mahmoud , McNicol Megan , Shaikhkhalil Ala , Boyle Brendan , Maltz Ross 
Published: January 2023

Abstract

BACKGROUND
Biosimilars are biologic products similar in safety and efficacy to the originator product. Tumor necrosis factor-alpha inhibitors (anti-TNFs) are used in the treatment of inflammatory bowel diseases (IBD). There are limited studies evaluating the long-term outcomes of anti-TNF biosimilars in children with IBD. Growth is an important clinical outcome, especially in childhood-onset IBD. However, no study to date has compared growth outcomes in patients initiated on the IV anti-TNF originator as compared to a biosimilar.

METHODS
This was a single-center retrospective review of patients with IBD, younger than 16 years old, and initiated on the IV anti-TNF originator or a biosimilar between April 2016 and February 2021 at Nationwide Children’s Hospital. To be eligible for the study and evaluate the primary outcome, patients must remain on the IV anti-TNF therapy for at least 12-months. We used propensity score methodology to identify 37 pairs of matched patients based on baseline characteristics (age of anti-TNF initiation, disease (CD vs UC/IC), behavior, location, perianal type, race). Demographic data, laboratory values, disease activity scores, and growth values (z-scores were recorded for weight, height, and BMI) were collected at baseline (prior to anti-TNF initiation) and 6-months and 12-months post initiation. Linear mixed models with random intercepts accounting for within patient correlation of measurements were fit to test differences in measures over time and between study groups. Hypothesis testing was conducted at an alpha of 0.05 to be used for all statistical analyses.

RESULTS
There were 113 patients on the originator and 39 patients on a biosimilar who met our eligibility criteria. Nineteen percent of patients on the originator and 16% of patients on a biosimilar were excluded from analysis due to discontinuing the IV anti-TNF agent prior to 12 months. Weight, height, and BMI z-scores increased over time (from baseline to 12-months) for both groups (p&lt;0.05). There was not a significant difference in the rate of change for weight, height, or BMI z-scores between study groups. Clinical outcomes of lab values (albumin, c-reactive protein, and hemoglobin) were not statistically different in the rate of change from baseline to 12-months between patients initiated on the originator or biosimilar. There also was not a significant difference in the pediatric Crohn’s disease activity index, pediatric ulcerative colitis activity index, or the physician global assessment between patients initiated on the biosimilar or originator from baseline to 12-months.

CONCLUSIONS
There were similar improvements in growth and clinical outcomes in patients initiated on the IV anti-TNF originator compared to a biosimilar agent. This is the first study to evaluate whether anti-TNF biosimilars have similar growth outcomes in children with IBD.
PATIENT PERSPECTIVE OF BOWEL URGENCY AND BOWEL URGENCY-RELATED ACCIDENTS IN CROHN’S DISEASE
Authors: Jairath Vipul , Hunter Theresa , Moses Richard , Bleakman Alison Potts , Chatterton Kaitlin , Medrano Paolo , Walker Marisa , McLafferty Megan , Klooster Brittany , Delbecque Laure 
Published: January 2023

Abstract

OBJECTIVE
This study aimed to explore the Crohn’s disease (CD) patient experience of Bowel Urgency (BU) and BU-related accidents to identify what is most relevant and important to patients.

METHODS
Patients in the US were eligible to participate in this qualitative study if they were ≥18 years of age, had a diagnosis of moderate to severe CD for ≥6 months and had experienced BU in the last 6 months. Interviews were conducted to explore the signs, symptoms, and impacts related to BU and BU-related accidents. Specifically, patients were asked to describe BU and BU-related accident experiences of CD in their own words. Transcripts were coded and analyzed in ATLAS.ti 9 using a systematic thematic analysis.

RESULTS
A total of 15 patients participated; majority were female (53%), white (53%), receiving biologic and/or conventional therapy (87%), and mean age of 50 yrs. A majority of patients (80%) experienced BU at least once in the last week and 20% had experienced ≥1 BU-related accident in the last month. The time-sensitive need to use or be near the bathroom, uncertainty of BU, and fear of experiencing an accident were reported as the most bothersome aspects of the BU experience.
Patients reported 16 signs and symptoms that co-occur with BU, with abdominal pain (87%), fatigue (87%), and abdominal cramping (53%) being most frequently reported (Table 1). Patients reported 36 BU-related impact concepts across 16 domains (Table 1). Impact domains most frequently reported were adaptive behaviors (93%), household chores (87%), and social activities (87%). Impact concepts most frequently reported were dietary changes (87%) and inability to participate in social activities (87%). Inability to participate in family activities, interrupted work activities, and inability to participate in social activities were reported as the most bothersome impacts to patients.
All 15 patients reported ever experiencing BU-related accidents. Patients reported 12 signs and symptoms that co-occur with BU-related accidents, with abdominal pain (67%), fatigue (67%), and abdominal cramping (60%) being most frequently reported (Table 2). Patients reported 44 impacts of BU-related accidents across 16 domains (Table 2). Impact domains most frequently reported were adaptive behaviors (100%) and emotional functioning (87%). Impact concepts most frequently reported were dietary changes (80%) and embarrassment (60%).

CONCLUSION
This study revealed that the experience of BU and BU-related accidents is bothersome to patients with CD, impactful on their daily lives, and occurs despite the use of biologic and/or conventional therapy.
PATIENT PERSPECTIVES OF BOWEL URGENCY AND BOWEL URGENCY-RELATED ACCIDENTS IN ULCERATIVE COLITIS
Authors: Jairath Vipul , Hunter Theresa , Moses Richard , Bleakman Alison Potts , Chatterton Kaitlin , Medrano Paolo , Hoffman Ryan , Walker Marisa , McLafferty Megan , Klooster Brittany , Delbecque Laure 
Published: January 2023

Abstract

OBJECTIVE
This study aimed to explore the Ulcerative Colitis (UC) patient experience of Bowel Urgency (BU) and BU-related accidents to identify what is most relevant and important to patients.

METHODS
Patients in the US were eligible to participate in this qualitative study if they were ≥18 years of age, had a diagnosis of moderate to severe UC for ≥6 months and had experienced BU in the last 6 months. Interviews were conducted to explore the signs, symptoms, and impacts related to BU and BU-related accidents. Transcripts were coded and analyzed in ATLAS.ti 9 using a systematic thematic analysis.

RESULTS
15 patients with moderate to severe UC participated; majority were female (53%), white (80%), receiving biologic and/or conventional therapy (80%), and had a mean age of 51.6 years. A majority of patients (80%) indicated that they had experienced BU at least once in the last week and 33% indicated that they had experienced at least 1 BU-related accident in the last month.
Participants reported a total of 13 sign and symptom concepts that co-occur with BU, with abdominal pain (87%), fatigue (80%), abdominal cramping (67%), and diarrhea (33%) being the most frequently reported (Table 1). Abdominal pain (40%) and abdominal cramping (40%) were frequently reported as the most bothersome symptoms of BU to participants. A total of 32 BU-related impact concepts were reported by participants across 16 impact domains (Table 1). The impact domains most frequently reported by participants were adaptive behaviors (100%), emotional functioning (87%), and social activities (67%). The most frequently reported impact concepts were dietary changes (73%), inability to participate in social activities (67%), and difficulty running errands (60%). Inability to participate in social activities (27%) and bathroom mapping (20%) were frequently reported as the most bothersome impacts to participants.

A total of thirteen (87%) participants reported experiencing BU-related accidents. Of the 7 signs and symptoms reported by participants to co-occur with BU-related accidents, the most frequently reported were abdominal pain (77%), gas (77%), and abdominal cramping (69%) (Table 2). A total of 30 impact concepts of BU-related accidents were reported by participants across 13 impact domains (Table 2). The domains most frequently reported by participants were adaptive behaviors (100%), emotional functioning (69), and social activities (62%). The most frequently reported impact concepts were bathroom mapping (62%), inability to participate in social activities (62%), and embarrassment (54%).

CONCLUSION
This qualitative study revealed that BU, BU-related accidents, and BU co-occurring symptoms are bothersome, impactful on participants’ daily lives, and occur despite the use of biologic and/or conventional therapy.