The mechanisms by which natural populations generate adaptive genetic variation are not well understood. Some studies propose that microsatellites can function as drivers of adaptive variation. Here, we tested a potentially adaptive role for transcribed microsatellites with natural populations of the common sunflower (Helianthus annuus L.) by assessing the enrichment of microsatellites in genes that show expression divergence across latitudes. Seeds collected from six populations at two distinct latitudes in Kansas and Oklahoma were planted and grown in a common garden. Morphological measurements from the common garden demonstrated that phenotypic variation among populations is largely explained by underlying genetic variation. An RNA-Seq experiment was conducted with 96 of the individuals grown in the common garden and differentially expressed (DE) transcripts between the two latitudes were identified. A total number of 825 DE transcripts were identified. DE transcripts and nondifferentially expressed (NDE) transcripts were then scanned for microsatellites. The abundance of different motif lengths and types in both groups were estimated. Our results indicate that DE transcripts are significantly enriched with mononucleotide repeats and significantly depauperate in trinucleotide repeats. Further, the standardized mononucleotide repeat motif A and dinucleotide repeat motif AG were significantly enriched within DE transcripts while motif types, C, AT, ACC and AAC in DE transcripts, are significantly differentiated in microsatellite tract length between the two latitudes. The tract length differentiation at specific microsatellite motif types across latitudes and their enrichment within DE transcripts indicate a potential functional role for transcribed microsatellites in gene expression divergence in sunflower.

Brown bowel syndrome is the name applied to a brown discoloration of the intestine. This is due to lipofuscin deposition in intestinal smooth muscle and occurs in association with malabsorption. Three cases occurring in a coeliac registry of 559 patients are described. One patient presented with acute massive bleeding per rectum, and two were diagnosed at autopsy. The syndrome may be accompanied by vitamin E deficiency and neurologic dysfunction. Two patients had evidence of peripheral neuropathy, and one had low vitamin E levels. Concomitant vitamin D deficiency was present. Fat-soluble vitamin malabsorption, especially if there is a poor response to a gluten-free diet or neuropathy, might alert the clinician to the possibility of brown-bowel syndrome and suggests careful search for lipofuscin in biopsy material, using special histologic techniques.

The intestinal epithelial barrier is comprised of a monolayer of specialized intestinal epithelial cells (IECs) that are critical in maintaining gut mucosal homeostasis. Dysfunction within various IEC fractions can increase intestinal permeability, resulting in a chronic and debilitating condition known as Crohn’s disease (CD). Defining the molecular changes in each IEC type in CD will contribute to an improved understanding of the pathogenic processes and the identification of potential therapeutic targets. Here we performed, for the first time at single-cell resolution, a direct comparison of the colonic epithelial cellular and molecular landscape between treatment-naïve adult CD and non-IBD control patients. Our analysis revealed that in CD patients there is a significant skew in the colonic epithelial cellular distribution away from canonical LGR5+ stem cells, located at the crypt-bottom, and toward one specific subtype of mature colonocytes, located at the crypt-top. Further analysis revealed unique changes to gene expression programs in every major cell type, including a previously undescribed suppression in CD of most enteroendocrine driver genes as well as L-cell markers including GCG. We also dissect a previously poorly understood SPIB+ cell cluster, revealing at least four sub-clusters that exhibit unique features. One of these SPIB+ sub-clusters expresses crypt-top colonocyte markers and is significantly up-regulated in CD, whereas another sub-cluster strongly expresses and stains positive for lysozyme (albeit no other canonical Paneth cell marker), which surprisingly is greatly reduced in expression in CD. Finally, through integration with data from genome-wide association studies, we show that genes implicated in CD risk exhibit heretofore unknown cell-type specific patterns of aberrant expression in CD, providing unprecedented insight into the potential biological functions of these genes.

The host receptor for SARS-CoV-2, angiotensin-converting enzyme 2 (ACE2), is highly expressed in small intestine. Our aim was to study colonic ACE2 expression in Crohn's disease (CD) and non-inflammatory bowel disease (non-IBD) controls. We hypothesized that the colonic expression levels of ACE2 impacts CD course. We examined the expression of colonic ACE2 in 67 adult CD and 14 NIBD control patients using RNA-seq and quantitative (q) RT-PCR. We validated ACE2 protein expression and localization in formalin-fixed, paraffin-embedded matched colon and ileal tissues using immunohistochemistry. The impact of increased ACE2 expression in CD for the risk of surgery was evaluated by a multivariate regression analysis and a Kaplan–Meier estimator. To provide critical support for the generality of our findings, we analyzed previously published RNA-seq data from two large independent cohorts of CD patients. Colonic ACE2 expression was significantly higher in a subset of adult CD patients which was defined as the ACE2-high CD subset. IHC in a sampling of ACE2-high CD patients confirmed high ACE2 protein expression in the colon and ileum compared to ACE2-low CD and NIBD patients. Notably, we found that ACE2-high CD patients are significantly more likely to undergo surgery within 5 years of CD diagnosis, and a Cox regression analysis found that high ACE2 levels is an independent risk factor for surgery (OR 2.17; 95% CI, 1.10–4.26; p = 0.025). Increased intestinal expression of ACE2 is associated with deteriorated clinical outcomes in CD patients. These data point to the need for molecular stratification that can impact CD disease-related outcomes.

SummaryThe spinal dorsal horn transforms incoming somatosensory information and transmits it supraspinally to generate modality-specific sensory percepts. The lack of an established framework for the molecular and cellular organization of the dorsal horn across species has greatly hampered delineating precisely how this region processes somatosensory information, including pain. Furthermore, the translation potential of the rodent work is unclear without data from higher order species. To fill these gaps, we performed single nucleus RNA-sequencing of Rhesus macaque dorsal horn and compared the results to a recently reported meta-analysis of mouse. Because dorsal horn laminae serve as a key organizing principle for function, we also determined the laminar location of each identified cell type. The work provides a comprehensive cross-species cellular and molecular database that will be critical for decoding the logic of dorsal horn somatosensory circuits and validating preclinical targets.

Background and AimsThe host receptor for SARS-CoV-2, angiotensin-converting enzyme 2 (ACE2), is highly expressed in small intestine. Our aim was to study colonic ACE2 expression in Crohn’s disease (CD) and non-inflammatory bowel disease (non-IBD) controls. We hypothesized that the colonic expression levels of ACE2 impacts CD course.MethodsWe examined the expression of colon ACE2 using RNA-seq and quantitative (q) RT-PCR from 69 adult CD and 14 NIBD control patients. In a subset of this cohort we validated ACE2 protein expression and localization in formalin-fixed, paraffin-embedded matched colon and ileal tissues using immunohistochemistry. The impact of increased ACE2 expression in CD for the risk of surgery was evaluated by a multivariate regression analysis and a Kaplan-Meier estimator. To provide critical support for the generality of our findings, we analyzed previously published RNA-seq data from two large independent cohorts of CD patients.ResultsColonic ACE2 expression was significantly higher in a subset of adult CD patients (ACE2-high CD). IHC in a sampling of ACE2-high CD patients confirmed high ACE2 protein expression in the colon and ileum compared to ACE2-low CD and NIBD patients. Notably, we found that ACE2-high CD patients are significantly more likely to undergo surgery within 5 years of diagnosis, with a Cox regression analysis finding that high ACE2 levels is an independent risk factor (OR 2.18; 95%CI, 1.05-4.55; p=0.037).ConclusionIncreased intestinal expression of ACE2 is associated with deteriorated clinical outcomes in CD patients. These data point to the need for molecular stratification that may impact CD disease-related outcomes.

No abstract

Bladder cancer is the fourth-most common cancer in men, one of the most expensive types of cancer to treat, and recurs frequently. While the genomic pathways associated with high-grade, muscle invasive (MI) tumors and low-grade, non-muscle invasive (NMI) tumors are well-established, recent studies have also found that MI and NMI tumors have unique methylation patterns, and that methylation may play a role in the development of early-stage bladder cancer. Interestingly, bladder cancer patients have frequent mutations in chromatin remodeling genes that alter known histone markers of DNA methylation. Since methylation marks are pharmacologically reversible, the identification of methylation biomarkers is a promising avenue for therapeutic treatment. Indeed, several candidate prognostic methylation biomarkers have been identified, but await prospective evaluation. The Bladder Cancer Biomarker Evaluation Tool (BC-BET) is a web-based resource for rapidly evaluating biomarkers in publicly available genomic datasets. Initially developed for gene expression biomarkers, BC-BET includes 1451 patients across 13 cohorts, and 40 bladder cancer cell lines, with gene expression profiles. In this work, we describe the addition of methylation data to BC-BET, so that candidate methylation biomarkers can be rapidly evaluated across multiple patient cohorts. BC-BET now contains methylation profiles from four patient cohorts (250 patients) and includes the available bladder cancer data from the Gene Expression Omnibus and The Cancer Genome Atlas. In "evaluation" mode, a user selects a gene of interest, and BC-BET evaluates whether the selected gene is differentially methylated between tumor vs. normal samples, NMI vs. MI tumors, and low- vs. high-grade tumors. Alternatively, the “biomarker discovery” mode allows a user to identify all differentially methylated genes at a desired false discovery rate (FDR). In both cases, graphical summaries of the results are displayed and statistical results can be downloaded to an Excel spreadsheet. The methylation module of BC-BET is implemented using shiny, a web application framework for R for developing interactive web pages. The addition of methylation data to BC-BET makes it a valuable resource for evaluating methylation biomarkers in bladder cancer. BC-BET is available from the following link: https://gdancik.github.io/bioinformatics/BCBET Citation Format: Meaghan M. Kennedy, Garrett M. Dancik. A database for evaluating methylation biomarkers in bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2610. doi:10.1158/1538-7445.AM2017-2610