Study on the Correlation Between Changes of Tongue Image and Gastrointestinal Function after Colorectal Cancer Surgery
Ontology highlight
ABSTRACT:
DISEASE(S): Colorectal Cancer
PROVIDER: 41426 | ecrin-mdr-crc |
REPOSITORIES: ECRIN MDR
Similar Datasets
Project description:Artificial intelligence has significantly advanced computational biology. Recent developments in omics technologies, such as single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST), provide detailed genomic data alongside tissue histology. However, current computational models often focus on either omics- or image-based analysis, lacking integration of both. To address this, we developed OmiCLIP, a visual-omics foundation model linking hematoxylin and eosin (H&E) images and transcriptomics using tissue patches from Visium data. For transcriptomics, we created 'sentences' by concatenating top-expressed gene symbols from tissue patches. We curated a dataset of 2.2 million paired tissue images and transcriptomic data across 32 organs to train OmiCLIP integrating histology and transcriptomics. Building on OmiCLIP, we created the Loki platform, which offers five key functions: tissue alignment, tissue annotation based on bulk RNA-seq or marker genes, cell type decomposition, image–transcriptomics retrieval, and ST gene expression prediction from H&E images. Compared with 22 state-of-the-art models on 5 simulations, 19 public, and 4 in-house experimental datasets, Loki demonstrated consistent accuracy and robustness in all tasks.
2025-04-01 | GSE293199 | GEO
Project description:Treatment of eosinophilic oesophagitis with an elemental diet is associated with changes in the microbial communities of the upper gastrointestinal tract
| PRJEB31840 | ENA
Project description:The gastrointestinal tract (GI) is a remarkably complex environment comprising a diverse array of cell types, microbes, and bioactive small molecules. To shed new light on how the gut is organized and senses its environment, we constructed a spatially resolved single-cell atlas of the mouse lower digestive tract using MERFISH with a specific focus on the thousands of receptors involved in small molecule sensation and microbial pattern recognition. We identified expected and novel cell types and charted their spatial organization across four GI regions. In addition, we discovered receptor expression gradients and heterogeneity cued by spatial location, and overall revealed divergent sensing capabilities across gut cell types, regions, and spatial contexts. In addition, we charted the remodeling of these features that occurs in the absence of the microbiome. Our atlas opens a new window into the molecular and cellular organization of gut sensation, which, given the pharmacological relevance of many receptors, may provide a clinically relevant resource.
2025-07-18 | GSE297799 | GEO
Project description:Fast and selective isolation of single cells with unique spatial and morphological traits remains a technical challenge. We address this by establishing high speed image-enabled cell sorting (ICS), which records multicolor fluorescence images, and sorts cells based on measurements from image data at speeds up to 15,000 events per second. We combine ICS with CRISPR-pooled screens to identify novel regulators of the NF-κB pathway, enabling the completion of genome-wide image- based screens in around nine hours of run-time.
2022-01-20 | GSE167944 | GEO
Project description:Recent advances in isolating cells based on visual phenotypes have transformed our ability to identify the mechanisms and consequences of complex traits. Micronucleus (MN) formation is a frequent outcome of genome instability, triggers extensive disease-associated changes in genome structure and signaling coincident with MN rupture, and is almost exclusively defined by visual analysis. Automated MN detection in microscopy images has proved extremely challenging, limiting unbiased discovery of the mechanisms and consequences of MN formation and rupture. In this study we describe two new MN segmentation modules: a rapid model for classifying micronucleated cells and their rupture status (VCS MN), and a robust model for accurate MN segmentation (MNFinder) from a broad range of fluorescence microscopy images. As a proof-of- concept, we define the transcriptome of non-transformed human cells with intact or ruptured MN after inducing chromosome missegregation by combining VCS MN with photoactivation-based cell isolation and RNASeq. Surprisingly, we find that neither MN formation nor rupture triggers a strong unique transcriptional response. Instead, transcriptional changes appear correlated with small increases in aneuploidy in these cell classes. Our MN segmentation modules overcome a significant challenge with reproducible MN quantification, and, joined with visual cell sorting, enable the application of powerful functional genomics assays, including pooled CRISPR screens and time-resolved analyses of cellular and genetic consequences, to a wide-range of questions in MN biology.
2025-04-15 | GSE291811 | GEO
Project description:Eosinophils are highly abundant throughout the gastrointestinal tract. However, their function in bacterially-induced gastrointestinal inflammatory disorders is poorly understood. In this study, we have examined the function and regulation of gastric eosinophils in the steady state and during infection with Helicobacter pylori. We find that eosinophils are recruited to sites of infection, make direct contact with live bacteria, and activate a signature transcriptional program.
2018-06-29 | GSE105143 | GEO
Project description:We detail an innovative non-invasive technique to predict gene and protein expression in pluripotent stem cells using advanced bright-field microscopy. The method employs machine learning algorithms to classify cells based on brightfield images, avoiding the need for traditional staining and manual annotation. Our approach uses DeepLearning technology to predict the gene expression (qPCR, RNA-seq) and protein expression (immunostaining, Flowcytometry) of cells from brightfield microscopy images. It provides a robust tool for non-destructive and continuous monitoring of the pluripotency status of stem cells, which will greatly advance regenerative medicine. It will be an approach that will contribute significantly to the manufacturing process of cellular products, especially where non-destructive and continuous monitoring is required.
2024-08-08 | GSE256303 | GEO
Project description:This study evaluates a range of endoscopic image enhancement techniques for assessing conditions involving the gastrointestinal tract.
This study aims to determine:
(i) the accuracy of different techniques to diagnose or grade severity of several gastrointestinal conditions
(ii) if image-enhancement techniques could potentially replace investigations currently used in daily practice (e.g. biopsy) with a view to reduce costs and shorten the interval to initiate treatment
| 2315944 | ecrin-mdr-crc
Project description:Endogenous intestinal microbiota have wide-ranging and largely uncharacterized effects on host physiology. Here, we used reverse-phase liquid chromatography-coupled tandem mass spectrometry to define the mouse intestinal proteome in the stomach, jejunum, ileum, cecum, and proximal colon under three colonization states: germ-free, monocolonized with Bacteroides thetaiotaomicron, and conventionally raised. Our analysis revealed distinct proteomic abundance profiles along the gastrointestinal tract. Unsupervised clustering showed that host protein abundance primarily depended on gastrointestinal location rather than colonization state and specific proteins and functions that defined these locations were identified by random forest classifications. K-means clustering of protein abundance across locations revealed substantial differences in host protein production between conventionally raised mice relative to germ-free and monocolonized mice. Finally, comparison to fecal proteomic datasets suggested that the identities of stool proteins are not biased to any region of the gastrointestinal tract, but are substantially impacted by the microbiota in the distal colon.
2015-11-25 | PXD002838 | Pride
Project description:EXOME ARRAY ANALYSIS OF ADVERSE REACTIONS TO FLUOROPYRIMIDINE-BASED THERAPY FOR GASTROINTESTINAL CANCER
| EGAD00010001499 | EGA