Generation and multiomic profiling of a TP53/CDKN2A double-knockout gastroesophageal junction organoid model.

Inactivation of the tumor suppressor genes tumor protein p53 (TP53) and cyclin-dependent kinase inhibitor 2A (CDKN2A) occurs early during gastroesophageal junction (GEJ) tumorigenesis. However, because of a paucity of GEJ-specific disease models, cancer-promoting consequences of TP53 and CDKN2A inactivation at the GEJ have not been characterized. Here, we report the development of a wild-type primary human GEJ organoid model and a CRISPR-edited transformed GEJ organoid model. CRISPR-Cas9-mediated TP53 and CDKN2A knockout (TP53/CDKN2AKO) in GEJ organoids induced morphologic dysplasia and proneoplastic features in vitro and tumor formation in vivo. Lipidomic profiling identified several platelet-activating factors (PTAFs) among the most up-regulated lipids in CRISPR-edited organoids. PTAF/PTAF receptor (PTAFR) abrogation by siRNA knockdown or a pharmacologic inhibitor (WEB2086) reduced proliferation and other proneoplastic features of TP53/CDKN2AKO GEJ organoids in vitro and tumor formation in vivo. In addition, murine xenografts of Eso26, an established human esophageal adenocarcinoma cell line, were suppressed by WEB2086. Mechanistically, TP53/CDKN2A dual inactivation disrupted both the transcriptome and the DNA methylome, likely mediated by key transcription factors, particularly forkhead box M1 (FOXM1). FOXM1 activated PTAFR transcription by binding to the PTAFR promoter, further amplifying the PTAF-PTAFR pathway. Together, these studies established a robust model system for investigating early GEJ neoplastic events, identified crucial metabolic and epigenomic changes occurring during GEJ model tumorigenesis, and revealed a potential cancer therapeutic strategy. This work provides insights into proneoplastic mechanisms associated with TP53/CDKN2A inactivation in early GEJ neoplasia, which may facilitate early diagnosis and prevention of GEJ neoplasms.

Endoscopic submucosal dissection for colorectal dysplasia in inflammatory bowel disease: a US multicenter study.

Background and study aims In patients with inflammatory bowel disease (IBD), endoscopically visible lesions with distinct borders can be considered for endoscopic resection. The role of endoscopic submucosal dissection (ESD) for these lesions is not well defined because of a paucity of data. We aimed to evaluate the outcomes of colorectal ESD of dysplastic lesions in patients with IBD across centers in the United States. Patients and methods This was a retrospective analysis of consecutive patients with IBD who were referred for ESD of dysplastic colorectal lesions at nine centers. The primary endpoints were the rates of en bloc resection and complete (R0) resection. The secondary endpoints were the rates of adverse events and lesion recurrence. Results A total of 45 dysplastic lesions (median size 30mm, interquartile range [IQR] 23 to 42 mm) in 41 patients were included. Submucosal fibrosis was observed in 73 %. En bloc resection was achieved in 43 of 45 lesions (96 %) and R0 resection in 34 of 45 lesions (76 %). Intraprocedural perforation occurred in one patient (2.4 %) and was treated successfully with clip placement. Delayed bleeding occurred in four patients (9.8 %). No severe intraprocedural bleeding or delayed perforation occurred. During a median follow-up of 18 months (IQR 13 to 37 months), local recurrence occurred in one case (2.6 %). Metachronous lesions were identified in 11 patients (31 %). Conclusions ESD, when performed by experts, is safe and effective for large, dysplastic colorectal lesions in patients with IBD. Despite the high prevalence of submucosal fibrosis, en bloc resection was achieved in nearly all patients with IBD undergoing ESD. Careful endoscopic surveillance is necessary to monitor for local recurrence and metachronous lesions after ESD.

Improving Colonoscopy Lesion Classification Using Semi-Supervised Deep Learning.

While data-driven approaches excel at many image analysis tasks, the performance of these approaches is often limited by a shortage of annotated data available for training. Recent work in semi-supervised learning has shown that meaningful representations of images can be obtained from training with large quantities of unlabeled data, and that these representations can improve the performance of supervised tasks. Here, we demonstrate that an unsupervised jigsaw learning task, in combination with supervised training, results in up to a 9.8% improvement in correctly classifying lesions in colonoscopy images when compared to a fully-supervised baseline. We additionally benchmark improvements in domain adaptation and out-of-distribution detection, and demonstrate that semi-supervised learning outperforms supervised learning in both cases. In colonoscopy applications, these metrics are important given the skill required for endoscopic assessment of lesions, the wide variety of endoscopy systems in use, and the homogeneity that is typical of labeled datasets.

Sphingomonas histidinilytica sp. nov., isolated from a hexachlorocyclohexane dump site.

A Gram-negative, non-spore-forming, cream-coloured bacterial strain, UM2(T), was isolated from an open hexachlorocyclohexane (HCH) dump site at Ummari village in Lucknow, India. Data generated from a polyphasic approach including phenotypic, genotypic and chemotaxonomic analyses confirmed that strain UM2(T) belonged to the genus Sphingomonas. The highest similarity found to the 16S rRNA gene sequence of strain UM2(T) was 99.4 %, with Sphingomonas wittichii DSM 6014(T), whereas the DNA-DNA relatedness value between these strains was 31 %, indicating that they represent separate species. The DNA G+C content of UM2(T) was 66.9 mol%. The respiratory pigment ubiquinone Q-10 was present. The predominant fatty acids were summed feature 8 (C(18 : 1)omega6c and/or C(18 : 1)omega7c; 32.9 %), C(19 : 0) cyclo omega8c (15.5 %) and C(16 : 0) (12.1 %). The major polar lipids were phosphatidylcholine, phosphatidylglycerol and phosphatidyldimethylethanolamine. sym-Homospermidine was the major polyamine observed. On the basis of the data reported, it was concluded that UM2(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas histidinilytica sp. nov. is proposed. The type strain is UM2(T) (=MTCC 9473(T) =CCM 7545(T)).

Sphingobium chinhatense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite.

A yellow-pigmented, hexachlorocyclohexane (HCH)-degrading bacterium, strain IP26(T), was isolated from an HCH dumpsite and subjected to a polyphasic analysis in order to determine its taxonomic position. Strain IP26(T) showed maximum 16S rRNA gene sequence similarity with Sphingobium francense Sp+(T) (98.5 %), Sphingobium japonicum UT26(T) (98.4 %) and Sphingobium indicum B90A(T) (98.2 %). Phylogenetic analysis based on 16S rRNA gene sequences also showed that strain IP26(T) formed a cluster with these three HCH-degrading strains. Chemotaxonomic data (major polyamine, spermidine; major quinone, ubiquinone with ten isoprene units; major polar lipids, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, diphosphatidylglycerol, phosphotidylcholine; and presence of 2-hydroxy fatty acid) supported inclusion of strain IP26(T) in the genus Sphingobium. However, the results of DNA-DNA hybridization and morphological and biochemical tests clearly allowed phenotypic and genotypic differentiation of strain IP26(T) from recognized species of the genus Sphingobium. Strain IP26(T) thus represents a novel species of the genus Sphingobium for which the name Sphingobium chinhatense sp. nov. is proposed. The type strain is IP26(T) (=MTCC8598(T) =CCM 7432(T)).