Patient demographics and disease specific characteristics.

Supplementary Figures and Methods in PDF format

Supplementary Figure 1. IL17RD potentiates EGF-induced EGFR signaling. A) Cellular proliferation of HT29 and HCT116 cells 96 hours after transfection with a plasmid encoding IL-17RD compared to an EV plasmid. B) Cellular proliferation of HT29 and HCT116 cells treated with EGF for 96 hrs following transfection with a plasmid encoding IL-17RD or EV plasmid. C) pEGFR, EGFR, pAKT, and pERK expression in HT29 cells 15 minutes after treatment with EGF ( ) or media without EGF (-) and transfected with Flag-tagged IL17RD, EV plasmid, or no transfection (vehicle) (representative images of two blots containing 3 samples per group). D) pAKT expression in HT29 cells 30 minutes after treatment with media with or without EGF and transfected with a Flag-tagged IL17RD plasmid or EV plasmid. E) EGFR expression in untreated cells 96 hours after transfection with IL17RD.

Supplementary Data from Targeted Inhibition of Inducible Nitric Oxide Synthase Inhibits Growth of Human Melanoma In vivo and Synergizes with Chemotherapy

Significantly Differentially Expressed miRNAs between UCN and Normal

Background and Aims:Endoscopic assessment is a co-primary end point in inflammatory bowel disease registration trials, yet it is subject to inter- and intraobserver variability. We present an original machine learning approach to Endoscopic Mayo Score (eMS) prediction in ulcerative colitis and report the model's performance in differentiating key levels of endoscopic disease activity on full-length procedure videos. Methods:Seven hundred ninety-three full-length videos with centrally-read eMS were obtained from 249 patients with ulcerative colitis, who participated in a phase II trial evaluating mirikizumab (NCT02589665). A video annotation approach was established to extract mucosal features and associated eMS classification labels from each video to be used as inputs for model training. The primary objective of the model was a categorical prediction of inactive vs active endoscopic disease evaluated against 2 independent test sets: a full set with a baseline single human expert read and a consensus subset in which 2 human reads agreed. Results:On the full test set of 147 videos, the model predicted inactive vs active endoscopic disease via the eMS with an area under the curve of 89%, accuracy of 84%, positive predictive value of 80%, and negative predictive value of 85%. In the consensus test set of 94 videos, the model predicted inactive vs active endoscopic disease with an area under the curve of 92%, accuracy of 89%, positive predictive value of 87%, and negative predictive value of 90%. Conclusion:We have demonstrated that this machine learning model supervised by mucosal features and eMS video annotations accurately differentiates key levels of endoscopic disease activity.

Abstract Background Previous studies have described machine learning (ML) models to predict how human readers would score disease activity in UC using the endoscopic Mayo Score (eMS). So far, none employed deep human annotation that considers all the endoscopic features making up the eMS. Here we report the results of an ML model that is trained on eMS features using centrally read endoscopies. Methods 793 full-length videos were obtained from 249 patients with UC who participated in NCT02589665, a phase 2 trial with mirikizumab in patients with UC and associated with centrally read (single reader) eMS (CReMS) as the primary dataset. After cleaning for usable frames, the data were split into training, validation and testing subsets. The ML workflow consisted of annotation, segmentation, and classification (e.g., erosions, ulcers, erythema, vascular pattern, and bleeding). Human image classification and segmentation with bounding boxes and was subjected to quality control adjudicated by one of three IBD specialists, generating more than 60,000 eMS-relevant annotation labels. The model was evaluated on a test set of 147 videos using the CReMS, and a consensus set of 94 test videos, where CReMS and annotator reported eMS (AReMS) were in agreement without adjudication. The primary objective of the model was a categorical prediction of endoscopically inactive disease (eMS 0 & 1) compared with active disease (eMS 2 & 3). The secondary objectives of the model were to predict endoscopic healing (eMS 0) and to predict severe disease (eMS 3). Results The model performances are in Table 1. On the full test set of 147 videos, the model predicted inactive disease compared with active disease with an accuracy of 84%, positive predictive value (PPV) of 80%, and negative predictive value (NPV) of 85%. In the subset of 94 videos with CreMS and AReMS consensus, the model predicted inactive disease compared with active disease with an accuracy of 89%, PPV 87%, and NPV of 90%. In this same subset, the model predicted endoscopic healing and severe disease with an accuracy of 95% and 85%, PPVs of 86% and 82% and NPVs of 95% and 87%, respectively. For the secondary objectives in the full set of 147 videos, the model predicted endoscopic healing and severe disease with an accuracy of 90% and 80%, PPVs of 44% and 86%, and NPVs of 95% and 86%, respectively. Conclusion We have developed a ML predictive model of the eMS in UC using centrally read videos and demonstrate excellent distinction between active and inactive disease, and clear discrimination between other levels of endoscopic activity. We propose that this unique ML approach to endoscopic assessment be considered as a substitute to human central reading in future clinical trials.

Supplemental Digital Content is available in the text. Objectives Primary nonresponse (PNR) to antitumor necrosis factor-α (TNFα) biologics is a serious concern in patients with inflammatory bowel disease (IBD). We aimed to identify the genetic variants associated with PNR. Patients and methods Patients were recruited from outpatient GI clinics and PNR was determined using both clinical and endoscopic findings. A case-control genome-wide association study was performed in 589 IBD patients and associations were replicated in an independent cohort of 293 patients. Effect of the associated variant on gene expression and TNFα secretion was assessed by cell-based assays. Pleiotropic effects were investigated by Phenome-wide association study (PheWAS). Results We identified rs34767465 as associated with PNR to anti-TNFα therapy (odds ratio: 2.07, 95% CI, 1.46–2.94, P = 2.43 × 10−7, [replication odds ratio: 1.8, 95% CI, 1.04–3.16, P = 0.03]). rs34767465 is a multiple-tissue expression quantitative trait loci for FAM114A2. Using RNA-sequencing and protein quantification from HapMap lymphoblastoid cell lines (LCLs), we found a significant decrease in FAM114A2 mRNA and protein expression in both heterozygous and homozygous genotypes when compared to wild type LCLs. TNFα secretion was significantly higher in THP-1 cells [differentiated into macrophages] with FAM114A2 knockdown versus controls. Immunoblotting experiments showed that depletion of FAM114A2 impaired autophagy-related pathway genes suggesting autophagy-mediated TNFα secretion as a potential mechanism. PheWAS showed rs34767465 was associated with comorbid conditions found in IBD patients (derangement of joints [P = 3.7 × 10−4], pigmentary iris degeneration [P = 5.9 × 10−4], diverticulum of esophagus [P = 7 × 10−4]). Conclusions We identified a variant rs34767465 associated with PNR to anti-TNFα biologics, which increases TNFα secretion through mechanism related to autophagy. rs34767465 may also explain the comorbidities associated with IBD.

Diarrhea remains a significant cause of morbidity and mortality among children in developing countries. Water, sanitation, and hygiene practices (WASH) have demonstrated improved diarrhea-related outcomes but may have limited implementation in certain communities. This study analyzes the adoption and effect of WASH-based practices on diarrhea in children under age five in the rural Busiya chiefdom in northwestern Tanzania. In a cross-sectional analysis spanning July-September 2019, 779 households representing 1338 under-five children were surveyed. Among households, 250 (32.1%) reported at least one child with diarrhea over a two-week interval. Diarrhea prevalence in under-five children was 25.6%. In per-household and per-child analyses, the strongest protective factors against childhood diarrhea included dedicated drinking water storage (OR 0.25, 95% CI 0.18–0.36; p < 0.001), improved waste management (OR 0.37, 95% CI 0.27–0.51; p < 0.001), and separation of drinking water (OR 0.38, 95% CI 0.24–0.59; p < 0.001). Improved water sources were associated with decreased risk of childhood diarrhea in per-household analysis (OR 0.72, 95% CI 0.52–0.99, p = 0.04), but not per-child analysis (OR 0.83, 95% CI 0.65–1.05, p = 0.13). Diarrhea was widely treated (87.5%), mostly with antibiotics (44.0%) and oral rehydration solution (27.3%). Targeting water transportation, storage, and sanitation is key to reducing diarrhea in rural populations with limited water access.

Background: As the field of brain and spine stereotactic radiosurgery (SRS) continues to grow, so will the need for a comprehensive evidence base. However, it is unclear to what degree trainees feel properly equipped to use SRS. We assess the perceptions and comfort level reported by neurosurgery and radiation oncology residents concerning the evidence-based practice of SRS. Methods: A continuing medical education (CME) course provided peer-reviewed updates regarding treatment with intracranial and spinal SRS. Presentations were given by neurosurgery and radiation oncology residents with mentorship by senior faculty. To gauge perceptions regarding SRS, attendees were surveyed. Responses before and after the course were analyzed using the Fisher’s exact test in R statistical software. Results: Participants reported the greatest knowledge improvements concerning data registries (P < 0.001) and clinical trials (P = 0.026). About 82% of all (n = 17) radiation oncology and neurosurgery residents either agreed or strongly agreed that a brain and spine SRS rotation would be beneficial in their training. However, only 47% agreed or strongly agreed that one was currently part of their training. In addition, knowledge gains in SRS indications (P = 0.084) and ability to seek collaboration with colleagues (P = 0.084) showed notable trends. Conclusion: There are clear knowledge gaps shared by potential future practitioners of SRS. Specifically, knowledge regarding SRS data registries, indications, and clinical trials offer potential areas for increased educational focus. Furthermore, the gap between enthusiasm for increased SRS training and the current availability of such training at medical institutions must be addressed.

Benign prostatic hyperplasia (BPH) is a leading cause of morbidity among men in the United States, with increasing prevalence over the past decades. Growing evidence suggests a potential link between nutrition, in particular the "Western-style diet," and BPH. Diets enriched in refined carbohydrates, red meat, fatty acids, cholesterol, and supplemental vitamins may increase the risk for BPH. However, a higher intake of complex carbohydrates, plant-based proteins, omega-3 fatty acids, and dietary vitamins may provide benefit for BPH patients. Here, we review the current literature in how nutritional elements and dietary patterns of the Western diet may affect the pathogenesis and incidence of BPH.

Abstract Cytosolic DNA is characteristic of chromosomally unstable metastatic cancer cells, resulting in constitutive activation of the cGAS–STING innate immune pathway. How tumors co-opt inflammatory signaling while evading immune surveillance remains unknown. Here, we show that the ectonucleotidase ENPP1 promotes metastasis by selectively degrading extracellular cGAMP, an immune-stimulatory metabolite whose breakdown products include the immune suppressor adenosine. ENPP1 loss suppresses metastasis, restores tumor immune infiltration, and potentiates response to immune checkpoint blockade in a manner dependent on tumor cGAS and host STING. Conversely, overexpression of wild-type ENPP1, but not an enzymatically weakened mutant, promotes migration and metastasis, in part through the generation of extracellular adenosine, and renders otherwise sensitive tumors completely resistant to immunotherapy. In human cancers, ENPP1 expression correlates with reduced immune cell infiltration, increased metastasis, and resistance to anti–PD-1/PD-L1 treatment. Thus, cGAMP hydrolysis by ENPP1 enables chromosomally unstable tumors to transmute cGAS activation into an immune-suppressive pathway. Significance: Chromosomal instability promotes metastasis by generating chronic tumor inflammation. ENPP1 facilitates metastasis and enables tumor cells to tolerate inflammation by hydrolyzing the immunotransmitter cGAMP, preventing its transfer from cancer cells to immune cells. This article is highlighted in the In This Issue feature, p. 995

Whether or not populations diverge with respect to the genetic contribution to risk of specific complex diseases is relevant to understanding the evolution of susceptibility and origins of health disparities. Here, we describe a large-scale whole-genome sequencing study of inflammatory bowel disease encompassing 1,774 affected individuals and 1,644 healthy control Americans with African ancestry (African Americans). Although no new loci for inflammatory bowel disease are discovered at genome-wide significance levels, we identify numerous instances of differential effect sizes in combination with divergent allele frequencies. For example, the major effect at PTGER4 fine maps to a single credible interval of 22 SNPs corresponding to one of four independent associations at the locus in European ancestry individuals but with an elevated odds ratio for Crohn disease in African Americans. A rare variant aggregate analysis implicates Ca2+-binding neuro-immunomodulator CALB2 in ulcerative colitis. Highly significant overall overlap of common variant risk for inflammatory bowel disease susceptibility between individuals with African and European ancestries was observed, with 41 of 241 previously known lead variants replicated and overall correlations in effect sizes of 0.68 for combined inflammatory bowel disease. Nevertheless, subtle differences influence the performance of polygenic risk scores, and we show that ancestry-appropriate weights significantly improve polygenic prediction in the highest percentiles of risk. The median amount of variance explained per locus remains the same in African and European cohorts, providing evidence for compensation of effect sizes as allele frequencies diverge, as expected under a highly polygenic model of disease.

The recognition of DNA as an immune-stimulatory molecule is an evolutionarily conserved mechanism to initiate rapid innate immune responses against microbial pathogens. The cGAS-STING pathway was discovered as an important DNA-sensing machinery in innate immunity and viral defense. Recent advances have now expanded the roles of cGAS-STING to cancer. Highly aggressive, unstable tumors have evolved to co-opt this program to drive tumorigenic behaviors. In this review, we discuss the link between the cGAS-STING DNA-sensing pathway and antitumor immunity as well as cancer progression, genomic instability, the tumor microenvironment, and pharmacologic strategies for cancer therapy. SIGNIFICANCE: The cGAS-STING pathway is an evolutionarily conserved defense mechanism against viral infections. Given its role in activating immune surveillance, it has been assumed that this pathway primarily functions as a tumor suppressor. Yet, mounting evidence now suggests that depending on the context, cGAS-STING signaling can also have tumor and metastasis-promoting functions, and its chronic activation can paradoxically induce an immune-suppressive tumor microenvironment.

The recognition of DNA as an immune-stimulatory molecule is an evolutionarily conserved mechanism to initiate rapid innate immune responses against microbial pathogens. The cGAS-STING pathway was discovered as an important DNA-sensing machinery in innate immunity and viral defense. Recent advances have now expanded the roles of cGAS-STING to cancer. Highly aggressive, unstable tumors have evolved to co-opt this program to drive tumorigenic behaviors. In this review, we discuss the link between the cGAS-STING DNA-sensing pathway and antitumor immunity as well as cancer progression, genomic instability, the tumor microenvironment, and pharmacologic strategies for cancer therapy. Significance: The cGAS-STING pathway is an evolutionarily conserved defense mechanism against viral infections. Given its role in activating immune surveillance, it has been assumed that this pathway primarily functions as a tumor suppressor. Yet, mounting evidence now suggests that depending on the context, cGAS-STING signaling can also have tumor and metastasis-promoting functions, and its chronic activation can paradoxically induce an immune-suppressive tumor microenvironment.

Introduction With an increasing number of available therapies for inflammatory bowel disease (IBD), little is known about patients’ attitudes regarding IBD-related direct-to-consumer advertising (IBD-DTCA) and its impact on treatment decisions in clinical practice. Methods We administered a 58-item, mailed questionnaire to patients with IBD receiving Gastroenterology subspecialty care at a large academic health system. The survey assessed patient awareness and perception of IBD-DTCA and its effect on IBD treatment discussions and decisions. We used bivariate analysis to evaluate patient-level factors associated with awareness and favorable perception of IBD-DTCA. Results We achieved a response rate of 15.2% ( n = 226 of 1486). Most patients (93.3%) reported awareness of IBD-DTCA, with adalimumab receiving the most exposure. A majority of respondents reported IBD-DTCA made them more aware of treatments they otherwise would not know about (53.6%), provided information in a balanced manner (63.5%), and taught them about new potential risks and side effects (64.5%). Patients without a college degree and those with a household income less than $75 k per year perceived IBD-DTCA more favorably. However, IBD-DTCA rarely changed IBD management, with only 7.6% of respondents having a discussion with their provider about the advertised drug and only two (0.9%) being initiated on the advertised drug. Conclusion IBD patients were aware of IBD-DTCA and perceived it favorably; however, IBD-DTCA rarely led to patient-provider discussions or changes in treatment regimen.

Epigenetics describes modifications that affect gene expression that are not encoded within the DNA sequence. DNA methylation is the longest appreciated epigenetic modification and has been accepted to play a critical role in maintaining euchromatin and silencing genes. Recently, a separate and distinct covalent modification has been recognized; hydroxymethylation, which has been associated with increased gene expression as opposed to gene silencing. However, traditional methods to study DNA methylation also recognized hydroxymethylation and did not distinguish between these two distinct DNA covalent modifications. Furthermore, TET enzymes have been identified to play a critical role in active hydroxymethylation of previously methylated cytosine residues and may further result in conversion to cytosine. TET1 plays a critical role in intestinal epithelial differentiation and development, and this is also correlated with increased hydroxymethylation in terminally differentiated epithelial cells. Colon cancer, which arises from the colonic epithelium, exhibits decreased hydroxymethylation and altered gene expression.