bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiple mutations in RNA polymerase β-subunit gene (rpoB) in Streptomyces incarnatus NRRL8089 enhance production of antiviral antibiotic sinefungin: modeling rif cluster region by density functional theory
Authors: Ogawa Saori , Shimidzu Hitomi , Fukuda Koji , Tsunekawa Naoki , Hirano Toshiyuki , Sato Fumitoshi , Yura Kei , Hasunuma Tomohisa , Ochi Kozo , Yamamoto Michio , Sakamoto Wataru , Hashimoto Kentaro , Ogata Hiroyuki , Kanao Tadayoshi , Nemoto Michiko , Inagaki Kenji , Tamura Takashi
Published: January 2021

Streptomyces incarnatus NRRL8089 produces the antiviral, antifungal, antiprotozoal nucleoside antibiotic sinefungin. To enhance sinefungin production, multiple mutations were introduced to the rpoB gene encoding RNA polymerase (RNAP) β-subunit at the target residues, D447, S453, H457, and R460. Sparse regression analysis using elastic-net lasso-ridge penalties on previously reported H457X mutations identified a numeric parameter set, which suggested that H457R/Y/F may cause production enhancement. H457R/R460C mutation successfully enhanced the sinefungin production by 3-fold, while other groups of mutations, such as D447G/R460C or D447G/H457Y, made moderate or even negative effects. To identify why the rif cluster residues have diverse effects on sinefungin production, an RNAP/DNA/mRNA complex model was constructed by homology modeling and molecular dynamics simulation. The 4 residues were located near the mRNA strand. Density functional theory–based calculation suggested that D447, H457, and R460 are in direct contact with ribonucleotide, and partially positive charges are induced by negatively charged chain of mRNA.
Gastrodin attenuates lithium-pilocarpine-induced epilepsy by activating AMPK-mediated PPARα in a juvenile rat model
Authors: Yang Yanfei , Li Yabin , Han Jinli , Wang Yanfen
Published: January 2021

Gastrodin has shown the potential as an anticonvulsant. Epilepsy is a neurological disease with significant effects in children. In the current study, the therapeutic potential of gastrodin in handling pediatric epilepsy was explored by focusing on the AMPK/PPARα pathway. Three-week-old Sprague–Dawley rats were subjected to lithium-pilocarpine method to induce epileptic symptoms and then administrated with gastrodin. The effects of gastrodin on rats were first assessed using electroencephalogram (EEG) recording, Racine classification, Morris water maze test, and histological staining. The levels of BDNF and NGF, and the activity of AMPK/PPARα were measured. Based on the results of EEG, behavior analyses, and histological staining, epileptic symptoms were significantly alleviated by gastrodin. Moreover, the administration of gastrodin also suppressed the levels of BDNF and NGF, and activated the AMPK/PPARα pathway. In conclusion, our results demonstrated that gastrodin contributed to the alleviation of pediatric epilepsy by activating AMPK/PPARα signaling transduction.
Metabolic analysis of unripe papaya (Carica papaya L.) to promote its utilization as a functional food
Authors: Hiraga Yasuhide , Ara Takeshi , Sato Nao , Akimoto Nayumi , Sugiyama Kenjiro , Suzuki Hideyuki , Kera Kota
Published: January 2021

Papaya (Carica papaya L.) is widely cultivated in tropical and subtropical countries. While ripe fruit is a popular food item globally, the unripe fruit is only consumed in some Asian countries. To promote the utilization of unripe papaya based on the compositional changes of biological active metabolites, we performed liquid chromatography–Orbitrap–mass spectrometry-based analysis to reveal the comprehensive metabolite profile of the peel and pulp of unripe and ripe papaya fruits. The number of peaks annotated as phenolics and aminocarboxylic acids increased in the pulp and peel of ripe fruit, respectively. Putative carpaine derivatives, known alkaloids with cardiovascular effects, decreased, while carpamic acid derivatives increased in the peel of ripe fruit. Furthermore, the functionality of unripe fruit, the benzyl glucosinolate content, total polyphenol content, and proteolytic activity were detectable after heating and powder processing treatments, suggesting a potential utilization in powdered form as functional material.
Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6
Authors: Saha Indrajit , Ghosh Nimisha , Pradhan Ayan , Sharma Nikhil , Maity Debasree , Mitra Kaushik
Published: January 2021

Whole genome analysis of SARS-CoV-2 is important to identify its genetic diversity. Moreover, accurate detection of SARS-CoV-2 is required for its correct diagnosis. To address these, first we have analysed publicly available 10 664 complete or near-complete SARS-CoV-2 genomes of 73 countries globally to find mutation points in the coding regions as substitution, deletion, insertion and single nucleotide polymorphism (SNP) globally and country wise. In this regard, multiple sequence alignment is performed in the presence of reference sequence from NCBI. Once the alignment is done, a consensus sequence is build to analyse each genomic sequence to identify the unique mutation points as substitutions, deletions, insertions and SNPs globally, thereby resulting in 7209, 11700, 119 and 53 such mutation points respectively. Second, in such categories, unique mutations for individual countries are determined with respect to other 72 countries. In case of India, unique 385, 867, 1 and 11 substitutions, deletions, insertions and SNPs are present in 566 SARS-CoV-2 genomes while 458, 1343, 8 and 52 mutation points in such categories are common with other countries. In majority (above 10%) of virus population, the most frequent and common mutation points between global excluding India and India are L37F, P323L, F506L, S507G, D614G and Q57H in NSP6, RdRp, Exon, Spike and ORF3a respectively. While for India, the other most frequent mutation points are T1198K, A97V, T315N and P13L in NSP3, RdRp, Spike and ORF8 respectively. These mutations are further visualised in protein structures and phylogenetic analysis has been done to show the diversity in virus genomes. Third, a web application is provided for searching mutation points globally and country wise. Finally, we have identified the potential conserved region as target that belongs to the coding region of ORF1ab, specifically to the NSP6 gene. Subsequently, we have provided the primers and probes using that conserved region so that it can be used for detecting SARS-CoV-2. Contact:indrajit@nitttrkol.ac.inSupplementary information: Supplementary data are available at http://www.nitttrkol.ac.in/indrajit/projects/COVID-Mutation-10K
ICN: extracting interconnected communities in gene co-expression networks
Authors: Wu Qiong , Ma Tianzhou , Liu Qingzhi , Milton Donald K , Zhang Yuan , Chen Shuo
Published: January 2021

Motivation

The analysis of gene co-expression network (GCN) is critical in examining the gene-gene interactions and learning the underlying complex yet highly organized gene regulatory mechanisms. Numerous clustering methods have been developed to detect communities of co-expressed genes in the large network. The assumed independent community structure, however, can be oversimplified and may not adequately characterize the complex biological processes.

Results

We develop a new computational package to extract interconnected communities from gene co-expression network. We consider a pair of communities be interconnected if a subset of genes from one community is correlated with a subset of genes from another community. The interconnected community structure is more flexible and provides a better fit to the empirical co-expression matrix. To overcome the computational challenges, we develop efficient algorithms by leveraging advanced graph norm shrinkage approach. We validate and show the advantage of our method by extensive simulation studies. We then apply our interconnected community detection method to an RNA-seq data from The Cancer Genome Atlas (TCGA) Acute Myeloid Leukemia (AML) study and identify essential interacting biological pathways related to the immune evasion mechanism of tumor cells.

Availabilityand implementation

The software is available at Github: https://github.com/qwu1221/ICN and Figshare: https://figshare.com/articles/software/ICN-package/13229093.

Supplementary information

Supplementary data are available at Bioinformatics online.
Phylogenetic relationships inBrachyotumand allies (Melastomataceae, Melastomateae): a reassessment of the limits of the genera
Authors: Meyer Fabrício Schmitz , Reginato Marcelo , Smidt Eric Camargo , De Santiago Gómez Jesús Ricardo , Michelangeli Fabián A , Goldenberg Renato
Published: January 2021

In the past decade, several phylogenetic studies based on molecular data have been generated and changed our view on the evolutionary history and classification of Melastomataceae. Nonetheless, given the size of the family, some groups are still under-sampled and poorly understood, such as the clade formed by Brachyotum and allies in Melastomateae, including three genera, Andesanthus, Brachyotum and Chaetogastra. The principal objective of this work was to further test the relationships in this clade by increasing taxon and locus sampling and by including morphological character reconstructions. In this study, we included nuclear (nrITS, nrETS and waxy) and plastid sequences (accD-psaI, psbK-psbL, trnS-trnG) from 129 species and 29 genera of Melastomataceae, corresponding to c. 46.5% of the species belonging to the clade, and that were used to build phylogenetic hypotheses. We also estimated the evolution of 23 morphological characters through ancestral state reconstruction and the elevational ranges of the species. Our results recovered two major clades: (1) Brachyotum, with species traditionally recognized in Brachyotum, but also including a few species traditionally recognized in Tibouchina; and (2) Chaetogastra, with most species traditionally recognized in Tibouchina, mainly from Tibouchina sections Pseudopterolepis, Diotanthera, Simplicicaules and Purpurella. Andesanthus was placed as sister to Brachyotum and allies in previous phylogenetic analyses; however, in this study it has been recovered as sister to the clades formed by Heterocentron and allies, Monochaetum and allies, and Brachyotum and allies. Four morphological characters can be useful to distinguish genera and clades among Brachyotum and allies: habit; flower position; the angle formed by the petals in relation to the hypanthium; and stamen arrangement. We also find that species in the Brachyotum clade occur at higher elevations (1500–4700 m) than Chaetogastra spp. (sea level to c. 3200 m, but more common at lower elevations, c. 600 to 1800 m). Based on all this evidence we propose the maintenance of Brachyotum as a genus segregated from the recently reinstated Chaetogastra. This work is a contribution to the systematics of Melastomateae, with an improvement in the resolution of the trees in relation to previous phylogenetic analyses, indicating that subclades have a strong relationship with geographical distribution.
Cerebrospinal fluid liquid biopsy for detecting somatic mosaicism in brain
Authors: Ye Zimeng , Chatterton Zac , Pflueger Jahnvi , Damiano John A , McQuillan Lara , Simon Harvey A , Malone Stephen , Do Hongdo , Maixner Wirginia , Schneider Amy , Nolan Bernadette , Wood Martin , Lee Wei Shern , Gillies Greta , Pope Kate , Wilson Michael , Lockhart Paul J , Dobrovic Alexander , Scheffer Ingrid E , Bahlo Melanie , Leventer Richard J , Lister Ryan , Berkovic Samuel F , Hildebrand Michael S
Published: January 2021

Brain somatic mutations are an increasingly recognized cause of epilepsy, brain malformations and autism spectrum disorders and may be a hidden cause of other neurodevelopmental and neurodegenerative disorders. At present, brain mosaicism can be detected only in the rare situations of autopsy or brain biopsy. Liquid biopsy using cell-free DNA derived from cerebrospinal fluid has detected somatic mutations in malignant brain tumours. Here, we asked if cerebrospinal fluid liquid biopsy can be used to detect somatic mosaicism in non-malignant brain diseases. First, we reliably quantified cerebrospinal fluid cell-free DNA in 28 patients with focal epilepsy and 28 controls using droplet digital PCR. Then, in three patients we identified somatic mutations in cerebrospinal fluid: in one patient with subcortical band heterotopia the LIS1 p. Lys64* variant at 9.4% frequency; in a second patient with focal cortical dysplasia the TSC1 p. Phe581His*6 variant at 7.8% frequency; and in a third patient with ganglioglioma the BRAF p. Val600Glu variant at 3.2% frequency. To determine if cerebrospinal fluid cell-free DNA was brain-derived, whole-genome bisulphite sequencing was performed and brain-specific DNA methylation patterns were found to be significantly enriched (P = 0.03). Our proof of principle study shows that cerebrospinal fluid liquid biopsy is valuable in investigating mosaic neurological disorders where brain tissue is unavailable.
The Leiden Convention coronary coding system: translation from the surgical to the universal view
Authors: Koppel Claire J , Vliegen Hubert W , Bökenkamp Regina , ten Harkel A Derk Jan , Kiès Philippine , Egorova Anastasia D , Jukema J Wouter , Hazekamp Mark G , Schalij Martin J , Gittenberger-de Groot Adriana C , Jongbloed Monique R M
Published: January 2021

Aims

The Leiden Convention coronary coding system structures the large variety of coronary anatomical patterns; isolated and in congenital heart disease. It is widely used by surgeons but not by cardiologists as the system uses a surgeons’ cranial view. Since thoracic surgeons and cardiologists work closely together, a coronary coding system practical for both disciplines is mandatory. To this purpose, the ‘surgical’ coronary coding system was adapted to an ‘imaging’ system, extending its applicability to different cardiac imaging techniques.

Methods and results

The physician takes place in the non-facing sinus of the aortic valve, oriented with the back towards the pulmonary valve, looking outward from the sinus. From this position, the right-hand sinus is sinus 1, and the left-hand sinus is sinus 2. Next, a clockwise rotation is adopted starting at sinus 1 and the encountered coronary branches described. Annotation of the normal anatomical pattern is 1R-2LCx, corresponding to the ‘surgical’ coding system. The ‘imaging’ coding system was made applicable for Computed Tomography (CT), Magnetic Resonance Imaging (MRI), echocardiography, and coronary angiography, thus facilitating interdisciplinary use. To assess applicability in daily clinical practice, images from different imaging modalities were annotated by cardiologists and cardiology residents and results scored. The average score upon evaluation was 87.5%, with the highest scores for CT and MRI images (average 90%).

Conclusion

The imaging Leiden Convention is a coronary coding system that unifies the annotation of coronary anatomy for thoracic surgeons, cardiologists, and radiologists. Validation of the coding system shows it can be easily and reliably applied in clinical practice.
Double-Counting of Investment*
Authors: Barro Robert J
Published: January 2021

The national-income accounts double-count investment, which enters once when it occurs and again in present value as rental income on added capital. The double-counting implies that GDP and national income overstate sustainable consumption. An alternative measure, ‘permanent income,’ equals consumption in the steady state but deviates from consumption outside of the steady state because expensing of gross investment applies to the long-run flow, not the current value. The permanent-income perspective substantially affects measured factor-income shares. When computed in relation to permanent income, the U.S. labor-income share has been reasonably stable, in contrast to the declining share based on GDP.
Stereotactic ablative radiotherapy versus surgery in older patients with stage I lung cancer
Authors: Park Samina , Kim Hak Jae , Park In Kyu , Kim Young Tae , Kang Chang Hyun
Published: January 2021

OBJECTIVES

Surgical resection is the best option for the treatment of early-stage lung cancer. However, older patients are less likely to receive curative treatment. Therefore, we compared long-term survival rates between surgical resection and stereotactic ablative radiotherapy (SABR) for the treatment of early-stage lung cancer in older patients.

METHODS

From 2013 to 2016, 272 patients aged ≥75 years with clinical stage I lung cancer underwent surgical resection (n = 191) or SABR (n = 81). A propensity score-matched analysis was performed. Overall survival, cumulative incidence of cancer-related death and recurrence were compared between the 2 groups.

RESULTS

In the matched cohort, 48 well-balanced pairs were extracted. An overall survival benefit was associated with surgery (surgery vs SABR = 65.9% vs 40.3%; P = 0.034); however, there was no significant difference in the cumulative incidence of cancer-related death (P = 0.089) or recurrence (P = 0.111) between the 2 groups. Systemic dissemination was the dominant pattern of progression in both groups. The 3-year cumulative incidence of regional recurrence was significantly higher in the SABR group compared to the surgery group (surgery vs SABR = 0% vs 11.4%, P = 0.046).

CONCLUSIONS

Surgical resection with mediastinal lymph node dissection provides better long-term survival compared to SABR in older patients with stage I lung cancer. Surgery should be considered for older patients aged ≥75 years who are appropriate candidates for surgery. SABR remains an alternative treatment with comparable cancer-related death and recurrence for patients unsuitable for surgery.
Correlates of patterns of cannabis use, abuse and dependence: evidence from two national surveys in Ireland
Authors: Millar Seán R , Mongan Deirdre , O’Dwyer Claire , Long Jean , Smyth Bobby P , Perry Ivan J , Galvin Brian
Published: January 2021

Background

Knowledge of factors relating to patterns of cannabis use is important for informing drug policy. This study determined factors associated with recent and current cannabis use. In addition, we explored factors related to having a cannabis use disorder (CUD)—defined using the Diagnostic and Statistical Manual of Psychiatric Disorders—among current users.

Methods

We analyzed data from Ireland’s 2010–11 and 2014–15 National Drug Prevalence Surveys, which recruited 5134 and 7005 individuals respectively, aged 15 years or more, living in private households. Multinomial logistic regression was used to identify factors associated with recent (last year) and current (last month) cannabis use compared to experiential use. Binary logistic regression was used to determine factors related to CUD among current users.

Results

The weighted prevalence of experiential cannabis use was 18.3%, with 3.0% and 3.3% of participants indicating recent or current use, respectively; 41.3% of current users indicated having a CUD. Factors associated with both recent or current cannabis use included younger age, not being married or cohabiting, having no dependent children and current use of tobacco or alcohol. Male gender, younger age and lower educational levels were significantly related to CUD among current users.

Conclusions

Males, adolescents/young adults and individuals with lower educational levels are more likely to be current users of cannabis and are at a greater risk of having a CUD. Health professionals should be aware of these factors to improve detection and prevention of CUD.
THE CUMULATIVE INCIDENCE OF POUCHITIS AND POUCH-RELATED COMPLICATIONS IN PEDIATRIC PATIENTS WITH ULCERATIVE COLITIS
Authors: Cowherd Ellen , Egberg Matthew , Kappelman Michael , Zhang Xian , Long Millie , Lightner Amy , Sandler Robert , Herfarth Hans , Barnes Edward
Published: January 2021

Background & Aims

Despite highly effective therapies, many children develop medically refractory ulcerative colitis (UC) and undergo proctocolectomy with ileal pouch anal anastomosis (IPAA). There is little real world evidence regarding IPAA outcomes in pediatric UC patients. We sought to determine the risk of pouchitis, recurrent pouchitis, and change in diagnosis to Crohn’s disease (CD) within two years of IPAA surgery among pediatric patients with UC using a large, geographically diverse insurance claims database.

Methods

Within the IQVIA Legacy PharMetrics Adjudicated Claims Database, we identified pediatric patients (age <18 years) with UC who underwent proctocolectomy with IPAA between January 1, 2007 and June 30, 2015. We utilized International Classification of Diseases (ICD-9-CM or ICD-10-CM) codes to identify patients with UC and Current Procedural Terminology III codes to identify IPAA. The primary outcome was the development of pouchitis in the first 2 years following surgery, as identified by a previously validated case-finding definition. Secondary outcomes included the incidence of recurrent pouchitis, and the cumulative incidence of a new diagnosis of Crohn’s disease (CD) in the first two years post-IPAA. A change in diagnosis to CD was identified by an ICD-9-CM or ICD-10-CM code for CD on at least three separate occasions. Bivariate analyses were used for all comparisons, utilizing chi-square and t-test as appropriate.

Results

A total of 68 patients with an IPAA with at least two years of continuous health plan enrollment following surgery were identified. Among all patients undergoing surgery, the median age was 15 years (interquartile range 11.5–16), with 29 (43%) female patients. In the first 2 years following IPAA, the cumulative incidence of pouchitis was 54%. Characteristics and prior medical treatments in patients without pouchitis and with ≥ one episode of pouchitis were similar (Table 1). The cumulative incidence of recurrent pouchitis during this period was 22%. The cumulative incidence of a new diagnosis of CD in the two years after IPAA for UC was 9%.

Conclusions

In a geographically diverse cohort from the United States, 54% of pediatric patients undergoing proctocolectomy with IPAA for UC developed pouchitis within the first two years after surgery. Furthermore, 9% had a change in diagnosis to CD. These data indicate that for many pediatric UC patients, surgery is non-curative and patients continue to have a substantial burden of illness. Future efforts should attempt to identify novel, actionable, predictors of pouchitis in this population.
ADVANCING HIGH TECH DRUG DELIVERY SYSTEMS FOR THE TREATMENT OF CROHN’S DISEASE
Authors: Miller Douglas , Niichel Robert
Published: January 2021

Introduction

High tech drug delivery systems, which allow for precise location targeting and efficient delivery mechanisms, can reduce the risk of side effects and increase dosage effectiveness in the treatment of Crohn’s disease. We describe a revolutionary capsule technology which uses radiofrequency signaling to trigger an optimal release of the pharmaceutical contents to specified regions of the gastrointestinal tract.

System and method

Data were observed in two groups of female Yorkshire-Cross swine. Intra-cecal ports were surgically placed in Group 2 swine. After baseline analysis was complete, all study animals were administered the SmartTab capsule (Group 1 administration via balling device, Group 2 administration via intra-cecal port) containing caffeine, barium sulfate, citric acid, and sodium bicarbonate. SmartTab capsules were activated by a radiofrequency triggering event, immediately following administration in Group 2 swine and 30 minutes following administration in Group 1 swine. Blood samples were taken at 0.25, 0.50, 1, 2, 3, and 6 hours after dosing and capsule activation was confirmed using a C-Scan.

Results

Pharmacokinetic analysis revealed increased caffeine concentrations in the targeted areas. Absorption was significantly higher and more consistent in the cecum targeted administration of the SmartTab compared to the control. Although, caffeine concentrations in the stomach regions were fairly similar amongst both the experimental and control groups.

Conclusions

Via radiofrequency signaling, the SmartTab capsule can successfully administer active ingredients to the target site. With pre-installed onboard sensors, enabling the devices to send real-time data to physicians and personalize treatments using AI algorithms, this technique holds the potential to generate further advancement in high-tech drug delivery systems. Preparations are currently in order to reapply this technology in the form of an injection capsule.

All 6 PK Curves
MUC1-C IS A DRUGGABLE TARGET FOR TREATMENT OF COLITIS AND PROGRESSION OF COLITIS-ASSOCIATED COLORECTAL CANCER
Authors: Morimoto Yoshihiro , Li Wei , Zhang Ning , Takahashi Hidekazu , Jin Caining , Kufe Donald
Published: January 2021

The MUC1-C oncoprotein evolved in mammals to protect epithelial cells, such as those lining the gastrointestinal tract, from loss of homeostasis. In this way, MUC1-C activates pathways that contribute to inflammation, proliferation and remodeling associated with the wound healing response.

MUC1-C is upregulated in human tissues from inflamed ulcerative colitis (UC) mucosa as compared to that from normal and uninflamed UC mucosa. MUC1-C is also upregulated in a mouse MUC1+/-/IL-10-/- model of colitis, consistent with its involvement in the inflammatory response. MUC1-C forms a direct complex with NF-κB p65 and promotes the activation of NF-κB target genes, including MUC1 itself in an auto- inductive circuit. MUC1-C thereby drives proinflammatory NF-κB pathway genes in human inflamed UC tissues and in the genetically engineered mouse model (GEMM) of colitis. Mechanistically, MUC1-C induces the TGF-b-activated kinase 1 (TAK1), which is an essential effector of proinflammatory NF-κB signaling. Of further significance, MUC1-C drives the TAK1→NF-κB p65 pathway in human colon cancer cell lines, and MUC1 and TAK1 are upregulated in human colon cancers. These seminal findings supported the notion that MUC1-C contributes to colitis and progression to colon cancer.

To extend these studies, MUC1-C was targeted with an inhibitor that blocks its homodimerization and function. Remarkably, treatment of the MUC1+/-/IL-10-/- GEMM with the GO-203 inhibitor was associated with decreases in the severity of colitis and progression of colitis to dysplasia and carcinomas. Intestinal stem cells (ISCs) that express Lgr5 are of importance in the inflammatory response to colitis and in progression to colitis-associated colorectal cancer (CACC). Targeting MUC1-C with GO-203 in mouse models of colitis suppressed Lgr5 expression, as well as induction of MYC and other core pluripotency factors. By extension to human colon cancer cells, we found that MUC1- C drives MYC with activation of LGR5 and stemness. MUC1-C also induces cancer stem cell (CSC) markers (BMI1, ALDH1, FOXA1, LIN28B) and the OCT4, SOX2, and NANOG pluripotency factors. Consistent with driving the CSC state, targeting MUC1-C suppressed the capacity of CRC cells to promote wound healing, invasion, self-renewal, and tumorigenicity. Analysis of human tissues further demonstrated that MUC1 expression associates with activation of inflammatory pathways, development of colitis, and aggressiveness of CRCs.

These results collectively indicate that MUC1-C is of importance for integrating stemness and pluripotency in colitis and CRC. Of clinical relevance, the findings further indicate that MUC1-C represents a previously unrecognized target that is potentially druggable with orally administered GO-203 now being tested in the GEMMs for treating progression of colitis and CRC.
A BASELINE GENE EXPRESSION-BASED PROGNOSTIC FOR ANTI-TNFα THERAPY RESPONSE IN PATIENTS WITH INFLAMMATORY BOWEL DISEASE
Authors: Sakaram Suraj , He Yudong , Sweeney Timothy
Published: January 2021

Background

Although anti-TNFα therapies have revolutionized the management and care of IBD, their administration and usage remain suboptimal because 1) over 50% of patients do not have a lasting therapeutic response, 2) they increase risk of infections, liver problems, arthritis, and lymphoma, and 3) they are expensive. With approximately 1.6 million people suffering from IBD in the US and global prevalence of IBD on the rise, a predictive test for anti-TNFα response would greatly improve the efficacy and cost-to-benefit ratio of these biologics.

Methods

We hypothesized that a multicohort analysis of the publicly available IBD gene expression datasets would yield a robust set of mRNAs for distinguishing anti-TNFα responders vs non-responders in the IBD patient population prior to treatment. We identified 5 datasets (n = 160) where whole-genome transcriptomic data was derived from colonic mucosal biopsies of IBD patients who were then subjected to anti-TNFα therapy and subsequently adjudicated for response. We used the MetaIntegrator framework which leverages a leave-one-study-out cross-validation technique in conjunction with effect size and FDR adjusted p-value to identify significant differentially expressed (DE) genes associated with a patient’s predisposition to a response outcome. DE genes were subjected to a greedy forward search to derive a parsimonious gene signature for a response score (geometric mean of the expression level for all positive mRNAs minus the geometric mean of the expression level of all negative mRNAs, multiplied by the ratio of counts of positive to negative genes). Area under the receiver operating characteristic curve (AUC) was subsequently calculated in a leave-one-study-out manner to assess discriminatory performance.

Results

We first identified 170 genes that were present in at least 40% of cohorts and significantly differentially expressed between responders and non-responders with effect size > 0.8 and q value < 0.1. A score based on these genes predicts responder vs non-responder across the 5 discovery cohorts with AUC of 0.82. Optimizing the variables with a greedy forward search algorithm allowed us to downselect to 7 genes from the set, and a score based on this parsimonious set of 7 genes improved the discriminatory performance to an AUC of 0.87. Choosing a high sensitivity (90%) for a rule-in scenario, the score had moderate specificity (60%); alternatively choosing a high specificity (90%) for a rule-out scenario, the score still had a good sensitivity (80%).

Conclusions

These initial findings suggest that there is a strong signal for predicting anti-TNFα response in colonic biopsies. In particular, we showed using the leave-one-study-out approach that a predictive signature using mRNA can be generalizable (works in independent cohorts). These initial results warrant further investigation.
THE MUCOSAL MICRORNA PROFILE RELATES TO AGE AND SEVERITY OF DISEASE IN PATIENTS WITH ULCERATIVE COLITIS
Authors: Malham Mikkel , James Jaslin , Jakobsen Christian , Høgdall Estrid , Holmstroem Kim , Wewer Vibeke , Nielsen Boye S , Riis Lene
Published: January 2021

Despite significant evidence that the expression of several microRNA’s (miRNA) impacts on disease activity in patients with ulcerative colitis (UC), it remains unknown if the more severe disease phenotype seen in pediatric-onset UC can be explained by altered miRNA expression. In this study, we aimed to assess the relationship between miRNA expression, age, and disease severity in pediatric and adult patients with UC. Using RT-qPCR, we analyzed the expression of miR-21, miR-31, miR-126, miR-142, and miR-155 in paraffin-embedded rectum biopsies from 30 pediatric and 30 adult-onset UC patients, and found that lesions from adult patients had significantly higher expression levels of miR-21 compared to pediatric patients and that the expression levels of miR-31 (all patients) and miR-155 (pediatric patients only) correlated inversely with histological assessed disease severity. Using in situ hybridization followed by image analysis, the expression estimates of miR-21 and miR-126 were found to correlate with histological assessed disease severity. In conclusion, we found that the expression of miRNAs depends on the age of the patient and/or the severity of the disease, suggesting that miRNAs may contribute to the regulation of inflammation in UC and could be useful biomarkers in the surveillance of disease severity.
MODERATE TO SEVERE ENDOSCOPIC INFLAMMATION IS FREQUENT AFTER ACHIEVING CLINICAL REMISSION IN PEDIATRIC ULCERATIVE COLITIS
Authors: Sarbagili-Shabat Chen , Weiner Dror , Wardi Joram , Abramas Lee , Yaakov Michal , Levine Arie
Published: January 2021

Background

Pediatric ulcerative colitis (UC) is characterized by low sustained remission rates and frequent extension of disease even if clinical remission is obtained with therapy. Moderate to severe endoscopic activity is a risk factor for relapse while evidence regarding early mucosal healing or persistence of inflammation after remission in children is not available. Our aim was to evaluate if persistence of significant inflammation is common and could explain the high relapse rate in pediatric UC.

Methods

Pediatric UC patients with clinical remission, defined as pediatric UC activity index (PUCAI) scores < 10, were prospectively assessed for mucosal healing by endoscopy 3–5 months after remission was documented. Mayo score was assessed for each segment by a blinded adult gastroenterologist using central reading. Symptomatic patients prior to sigmoidoscopy were excluded Sustained remission was assessed retrospectively at 18 months follow-up.

Results

Forty-six children were enrolled, 28 children in continuous clinical remission at time of sigmoidoscopy were included in the final analysis. Mayo 0 was present in 12/28 (42.86%), Mayo 1 in 2/28 (7.1%) and Mayo 2–3 in 14/28 (50.0%) endoscopies. Among 23/28 patients with follow-up through 18 months, remission was sustained in 2/11 (18.18%) of patients with Mayo 2 and 3 versus 6/12 (50.0%) with Mayo score 0–1.

Conclusion

Over 50% of children assessed for mucosal healing 3–5 months after clinical remission is obtained have residual disease activity, primarily moderate to severe inflammation which was associated with lower sustained remission. Early sigmoidoscopy after clinical remission for assessment of mucosal disease should be considered in pediatric UC.
A RARE AND UNFORTUNATE CASE OF PARESTHESIAS SECONDARY TO INFLIXIMAB
Authors: Dasu Neethi , Blair Brian , Khalid Yaser
Published: January 2021

Introduction

The tumor necrosis factor-α (TNF-α) antagonists infliximab, adalimumab, and etanercept have been approved for treatment of inflammatory bowel disease (IBD). We describe a rare manifestation of a demyelinating neuropathy affecting the peripheral nervous system in a patient on Infliximab for the treatment of Crohn’s disease following progression of his disease.

Case Report

A 34-year-old male with a past medical history of Crohn’s disease presented for progressive and worsening diffuse numbness and paresthesias over two months in almost all of his extremities except the right side of his face, his sternum and center of his back. His symptoms were well controlled on mesalamine for 16 years until he had a progression of his disease which was seen on endoscopy and colonoscopy so he was switched to treatment with infliximab. He had finished induction with a third infusion two months prior to onset of parasthesias leading to control of symptoms. However, he started to experience non bloody diarrhea and diffuse, dull abdominal pain, weight loss of 15 pounds, gait dysfunction, lower extremity weakness, bilateral knee erythema and tenderness, and tight and stiff muscles, which were not typical for his Crohn’s disease flare-ups. On physical exam, his vitals were unremarkable and there was decreased sensation to light touch. He also had paresthesias as well as weakness most pronounced in his lower extremities. Laboratory tests and Imaging with CT, MRI, EMG, and Lumbar Puncture were all negative. The patient had 70% improvement of his symptoms following discontinuation of Infliximab, although his symptoms never completely resolved in his feet despite additional treatment with B12, thiamine, gabapentin, prednisone, and baclofen.

Conclusion

Due to the chronological progression and manifestation of the neurological symptoms with infliximab therapy for our patient, it is very likely that this drug triggered or caused his demyelinating neuropathy. There are only a few case reports in the literature and small review studies demonstrating Guillain-Barre Syndrome, demyelinating polyneuropathy, and neurologic disease due to infliximab. Various clinical patterns have been described. Chronic demyelinating neuropathy developed either after change of anti–TNF-α drug or spontaneously after treatment discontinuation without any drug reintroduction. There have been case reports describing treatment of demyelinating polyneuropathy related to TNF-alpha inhibitors with IVIG 1 or 2 g/kg with good results. Gabapentin has also been tried for treatment. Influence of anti–TNF-α treatment continuation on the long-term course of neuropathy is variable, suggesting that anti–TNF-α treatment withdrawal is not always necessary for neuropathy control. For future cases, our case highlights the importance of close inpatient and outpatient follow up for patients on infliximab.
COLON SPECIFIC ROLE FOR SELENOPROTEIN P IN COLITIS AND COLITIS-ASSOCIATED CARCINOMA
Authors: Short Sarah , Pilat Jennifer , Reddy Vishruth , Haberman Yael , Hendren Jared , Washington Mary , Hyams Jeffrey , Denson Lee , Rosen Michael , Williams Christopher
Published: January 2021

Selenium (Se) is an essential trace element incorporated into selenoproteins (SEPs), which provide a broad scope of antioxidant functions. Se status inversely correlates with inflammatory bowel disease (IBD) severity, and animal models have shown that Se deficiency worsens colitis and colitis-associated cancer (CAC). One of the most highly expressed and functionally critical SEPs is Selenoprotein P (SEPP1/SELENOP). SELENOP serves two known roles: 1) distributing Se throughout the organism, and 2) acting as a lipid peroxidase. SELENOP is also markedly reduced in IBD. Global SELENOP reduction augmented experimental CAC. SELENOP is primarily produced in the liver for tissue distribution through the plasma; however, liver-specific SELENOP deletion failed to modify CAC, thus implicating epithelial SELENOP as a primary disease modifier. As the roles of intestinal epithelial SELENOP in colitis and CAC remain unknown, we investigated these roles using the Vil-CreERT2 driver to inducibly delete intestinal epithelial SELENOP in AOM/DSS inflammatory carcinogenesis models.

First, Selenop deletion was confirmed in intestinal epithelial cells of tamoxifen-induced Vil-CreERT2; Selenopfl/fl mice (ΔIEC). Epithelial-specific SELENOP loss promoted tumor initiation, as evidenced by greater tumor multiplicity visible by colonoscopy in ΔIEC mice. Upon sacrifice, ΔIEC mice demonstrated increased colon tumor number and size. Additionally, ΔIEC colon tumors displayed greater apoptosis (cleaved caspase-3), DNA damage (pγH2AX), and dysplasia severity. Overall, these results are consistent with our model that epithelial SELENOP loss promotes tumor formation through increased intratumoral oxidative stress and resultant genomic instability. To further investigate SELENOP’s contributions in pure epithelial cultures, we determined that both CACO2 cells and human colonoids produce SELENOP in a sodium selenite-dependent fashion; furthermore, polarized CACO2 cells preferentially secrete SELENOP basolaterally, suggesting a local extracellular role for SELENOP in the immediate colonic epithelial microenvironment. Also, SELENOP knockdown in human intestinal organoids derived from ulcerative colitis (UC) patients increased oxidative stress, increased sensitivity to H2O2 treatment, and reduced organoid growth, implicating SELENOP in modulating the epithelial ROS-protective response. RNA-seq analysis from the PROTECT cohort revealed reduced SELENOP expression in pediatric UC biopsies that inversely correlated with disease activity and S100A8 (calprotectin) levels. Lastly, SELENOP RNA in situ hybridization of adult UC/Crohn’s Disease and CAC TMAs demonstrated decreased epithelial transcript in IBD and stage-dependent reductions in CAC. These data collectively indicate critical roles for SELENOP in epithelial and colonic microenvironment antioxidant defenses in IBD.
ELEVATED ADENOMATOUS POLYPOSIS COLI IN GOBLET CELLS IS ASSOCIATED WITH INFLAMMATION IN MOUSE AND HUMAN COLON
Authors: Gomez Christian , Neufeld Kristi
Published: January 2021

Adenomatous Polyposis Coli (APC) functions as an essential colon tumor suppressor. Roles for APC in other disease states such as Inflammatory Bowel Disease (IBD) remain less defined. In the process of characterizing Apc protein in gastrointestinal tissues from human patients with active IBD, we found a subset of goblet cells with elevated Apc staining intensity. While normal colon tissue was only sparsely populated with these “APChigh” goblet cells, tissue from patients with Ulcerative Colitis and Crohn’s Disease contained entire regions where almost every goblet cell was APChigh. In the descending colon, the APChigh goblet cells were prominent in patients with active Ulcerative Colitis but were mostly lacking in normal samples. In mice, APChigh cells were observed only in the small intestines and proximal/medial colons. Upon induction of colitis with Dextran Sodium Sulfate (DSS), the APChigh goblet cells remained in the proximal and medial colon, but also appeared in the distal colon. To better understand the link between APC expression, goblet cells, and inflammation, cultured human colon cells derived from normal tissue were depleted of APC and RNAseq analysis was performed. APC depletion resulted in reduced expression of mRNAs encoding IL1 signaling pathway components IL1b and IL1R, known regulators of Muc2 expression. Muc2 is the main constituent of goblet cell mucus, which is secreted to form a protective barrier for the epithelial cells lining the large intestine. We found that treating cancer cells lacking wild-type APC with IL1b resulted in increased IL1R and MUC2 expression. Induction of full-length APC in these cells led to a similar phenotype. Combining IL1β treatment with APC induction led to an increase of MUC2 expression greater than expected for additive affects, suggesting that APC sensitized these cells to IL1 signaling. These results illuminate a novel role for APC in goblet cells under conditions of inflammation. We postulate that the higher amount of APC in a subset of goblet cells might sensitize them to IL-1 signaling. During times of inflammation, such as active Ulcerative Colitis, goblet cells with higher APC levels would be more sensitive to IL-1-induced MUC2 expression than other goblet cells, perhaps protecting the intestinal lining from further barrier breaches.
INCREASED CATHEPSIN EXPRESSION CORRELATES WITH SARS-COV-2 INFECTION IN HUMAN IBD ENTEROIDS
Authors: Alvarado David , Castro Maria Gomez , Sonnek Naomi , Cui Xueyang , Ding Siyuan , Ciorba Matthew
Published: January 2021

Introduction

Coronavirus Disease 2019 (COVID-19) is an ongoing public health crisis that has sickened or precipitated death in millions. The etiologic agent of COVID-19, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), infects the intestinal epithelium, with viral RNA shed in the stool, and can induce GI symptoms similar to the human inflammatory bowel diseases (IBD). An international surveillance epidemiology study, SECURE-IBD, reported that the standardized mortality ratio trends higher in IBD patients (1.5–1.8) and that 5-aminosalicylic acid (5-ASA) therapy correlates with poor outcome. Together these data indicate patients with IBD may represent a particularly vulnerable population during this COVID-19 pandemic.

Methods

Published datasets GSE75214 and GSE16879 were downloaded and expression levels of select genes were querried using RStudio. Primary human ileal spheroids (enteroids), derived from healthy donors and patients with Crohn’s disease (CD), were grown on 2D transwells until confluent. Cells were then differentiated for 3d before infection with a modified vesicular stomatitis virus expressing the SARS-CoV-2 spike protein (VSV-SARS-CoV-2) and green fluorescent protein (GFP) for 1 h at a multiplicity of infection (MOI) of ~0.5. Healthy enteroids were treated with 10 ng/ml of human Tumor Necrosis Factor alpha (TNF-α) for 24h before infection via the basolateral reservoir or 5-ASA 5h before infection via the apical reservoir. 24h after infection, cells were processed for immunofluorescence or RNA expression of select genes by qRT-PCR.

Results

VSV-SARS-CoV-2 was able to infect both healthy and CD enteroids as determined by co-staining of GFP, indicative of virus infection, and the viral receptor ACE2. However, levels of GFP fluorescence did not correlate with ACE2 expression in CD enteroids. A subset of CD enteroids exhibited enhanced protease expression (TMPRSS2, TMPRSS4, CTSL), each of which correlated with higher viral RNA levels (P=0.04, P=0.002, P=0.006, respectively). In Vero E6 cells, 5-ASA inhibited the replication of a clinical isolate of SARS-CoV-2 in a concentration-dependent manner. Treating healthy enteroids with 5-ASA did not have any effect on viral proliferation, while TNF-α pretreatment reduced viral RNA. 5-ASA treatment caused a reduction of ACE2 and an increase in CTSL expression.

Conclusions

Host proteases, particularly the lysosomal protease CTSL, contribute to the infection of CD enteroids and may represent novel therapeutic targets in patients with IBD and COVID-19. 5-ASA modulates the expression of several epithelial genes relevant to SARS-CoV-2 infection, yet does not alter viral replication in healthy enteroids.