Transcriptional dynamics of colorectal cancer risk associated variation at 11q23.1 correlate with tuft cell abundance and marker expression in silico

Colorectal cancer (CRC) is characterised by heritable risk that is not well understood. Heritable, genetic variation at 11q23.1 is associated with increased colorectal cancer (CRC) risk, demonstrating eQTL effects on 3 cis- and 23 trans-eQTL targets. We sought to determine the relationship between 11q23.1 cis- and trans-eQTL target expression and test for potential cell-specificity. scRNAseq from 32,361 healthy colonic epithelial cells was aggregated and subject to weighted gene co-expression network analysis (WGCNA). One module (blue) included 19 trans-eQTL targets and was correlated with POU2AF2 expression only. Following unsupervised clustering of single cells, the expression of 19 trans-eQTL targets was greatest and most variable in cluster number 11, which transcriptionally resembled tuft cells. 14 trans-eQTL targets were found to demarcate this cluster, 11 of which were corroborated in a second dataset. Intra-cluster WGCNA and module preservation analysis then identified twelve 11q23.1 trans-eQTL targets to comprise a network that was specific to cluster 11. Finally, linear modelling and differential abundance testing showed 11q23.1 trans-eQTL target expression was predictive of cluster 11 abundance. Our findings suggest 11q23.1 trans-eQTL targets comprise a POU2AF2-related network that is likely tuft cell-specific and reduced expression of these genes correlates with reduced tuft cell abundance in silico

Gene Co-Expression Network Analysis Identifies Vitamin D-Associated Gene Modules in Adult Normal Rectal Epithelium Following Supplementation

Colorectal cancer (CRC) is a common, multifactorial disease. While observational studies have identified an association between lower vitamin D and higher CRC risk, supplementation trials have been inconclusive and the mechanisms by which vitamin D may modulate CRC risk are not well understood. We sought to perform a weighted gene co-expression network analysis (WGCNA) to identify modules present after vitamin D supplementation (when plasma vitamin D level was sufficient) which were absent before supplementation, and then to identify influential genes in those modules. The transcriptome from normal rectal mucosa biopsies of 49 individuals free from CRC were assessed before and after 12 weeks of 3200IU/day vitamin D (Fultium-D3) supplementation using paired-end total RNAseq. While the effects on expression patterns following vitamin D supplementation were subtle, WGCNA identified highly correlated genes forming gene modules. Four of the 17 modules identified in the post-vitamin D network were not preserved in the pre-vitamin D network, shedding new light on the biochemical impact of supplementation. These modules were enriched for GO terms related to the immune system, hormone metabolism, cell growth and RNA metabolism. Across the four treatment-associated modules, 51 hub genes were identified, with enrichment of 40 different transcription factor motifs in promoter regions of those genes, including VDR:RXR. Six of the hub genes were nominally differentially expressed in studies of vitamin D effects on adult normal mucosa organoids: LCN2, HLA-C, AIF1L, PTPRU, PDE4B and IFI6. By taking a gene-correlation network approach, we have described vitamin D induced changes to gene modules in normal human rectal epithelium in vivo, the target tissue from which CRC develops

Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes

Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development

Shockwave lithotripsy is an efficacious treatment modality for obese patients with upper ureteral calculi: logistic regression and matched-pair analyses from a dedicated center comparing treatment outcomes by skin-to-stone distance

Objectives: To assess the association of skin-to-stone distance (SSD) and stone-free rates following extracorporeal shockwave lithotripsy (SWL) using two statistical methods: logistic regression and a matched-pair analysis approach. Patients and Methods: Patients with a solitary radio-opaque upper ureteral calculus diagnosed on noncontrast computed tomography were included. Patients were treated with a Sonolith I-Sys Lithotripter (focal depth 17 cm). Stone treatment success was defined as stone free (fragments ≤3 mm) at 3 months. Failure was defined as persistent fragments beyond 3 months or requirement for intervention with ureteroscopy. The outcome was assessed by a plain kidney, ureter, and bladder radiograph (KUB) at 2 weeks. Logistic regression was used to determine association of patient and stone factors with treatment failure. The patient cohort was divided into tertiles by SSD, and matched-pair analysis was undertaken between individuals from the top and bottom tertiles (SSD ≤12 cm and SSD ≥14 cm). Matching criteria consisted of age, sex, maximum stone diameter (±2 mm), and stone density (±250 HU). Results: From a database of 2849 patients who underwent SWL, 397 patients were identified who had treatment of a single upper ureteral stone. Age (odds ratio [OR]: 1.03, 95% confidence interval [CI]: 1.01-1.04, p = 0.007), SSD (OR: 1.16, 95% CI: 1.03-1.32, p = 0.02), stone side (OR: 1.65, 95% CI 1.01-2.73, p = 0.05), stone diameter (OR: 1.09, 95% CI: 1.00-1.19, p = 0.05), and multiple sessions (OR: 4.65, 95% CI: 2.61-8.29, p < 0.001) were significantly associated with treatment failure by logistic regression univariable analysis. Multiple sessions was the only factor significantly associated with treatment failure on multivariable analysis (OR: 4.03, 95% CI: 2.18-7.42, p < 0.001). From a cohort of 141 patients with SSD ≥14 cm and 174 patients with a SSD ≤12 cm, 66 matches were identified (132 patients). Forty-nine patients (74.2%) with SSD ≥14 cm were deemed stone free at follow-up vs 51 patients (77.3%) with SSD ≤12 cm (p = 0.85). Conclusion: This study demonstrates by two statistical methods that SWL can provide efficacious treatment of upper ureteral stones in obese patients and that the upper threshold of SSD for SWL with Sonolith I-SYS could be revised to allow these patients the benefits of SWL