Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Inflammatory Bowel Disease II: Crohn's Disease01:30

Inflammatory Bowel Disease II: Crohn's Disease

248
Introduction
Inflammatory bowel disease, commonly known as IBD, refers to a collection of disorders that lead to persistent inflammation of the gastrointestinal tract. The two types of IBD are ulcerative colitis, which impacts the colon, and Crohn's disease, which can involve any part of the gastrointestinal segment.
Crohn's disease
Crohn's disease is a chronic, systemic inflammatory bowel disease (IBD) that predominantly affects the gastrointestinal tract. It is marked by...
248

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Guidelines for single-cell RNA sequencing analysis of eosinophils.

Journal of leukocyte biology·2026
Same author

RoCK and ROI: single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing.

Nature communications·2025
Same author

Systematic discovery of subcellular RNA patterns in the gut epithelium.

Genome biology·2025
Same author

Screening for Tumor Microtube-Targeting Drugs Identifies PKC Modulators as Multipotent Inhibitors of Glioblastoma Progression.

Cancer discovery·2025
Same author

Targeting long non-coding RNA <i>MALAT1</i> preserves endothelial cell integrity and protects against kidney fibrosis.

Molecular therapy. Nucleic acids·2025
Same author

Loss of proton-sensing GPR4 reduces tumor progression in mouse models of colon cancer.

Molecular oncology·2025

Related Experiment Video

Updated: Jul 5, 2025

In vivo Imaging Method to Distinguish Acute and Chronic Inflammation
07:10

In vivo Imaging Method to Distinguish Acute and Chronic Inflammation

Published on: August 16, 2013

20.2K

Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA).

Atefeh Lafzi1,2, Costanza Borrelli2, Simona Baghai Sain2

  • 1Roche Pharma Research and Early Development, Immunology Infectious Diseases and Ophthalmology Discovery and Translational Area, Grenzacherstrasse 124, 4070, Basel, Switzerland.

Molecular Systems Biology
|January 15, 2024
PubMed
Summary

We developed ISCHIA, a computational framework for spatial transcriptomics, to analyze cell co-occurrence and reconstruct cellular networks in tissues. This method reveals inflammation-induced networks in ulcerative colitis, offering new insights into tissue biology.

Keywords:
Cellular NetworksCo-occurrence AnalysisLigand–Receptor InteractionSpatial TranscriptomicsUlcerative Colitis

More Related Videos

Visualization, Quantification, and Mapping of Immune Cell Populations in the Tumor Microenvironment
11:00

Visualization, Quantification, and Mapping of Immune Cell Populations in the Tumor Microenvironment

Published on: March 25, 2020

17.1K
Identification of Disease-related Spatial Covariance Patterns using Neuroimaging Data
14:27

Identification of Disease-related Spatial Covariance Patterns using Neuroimaging Data

Published on: June 26, 2013

15.7K

Related Experiment Videos

Last Updated: Jul 5, 2025

In vivo Imaging Method to Distinguish Acute and Chronic Inflammation
07:10

In vivo Imaging Method to Distinguish Acute and Chronic Inflammation

Published on: August 16, 2013

20.2K
Visualization, Quantification, and Mapping of Immune Cell Populations in the Tumor Microenvironment
11:00

Visualization, Quantification, and Mapping of Immune Cell Populations in the Tumor Microenvironment

Published on: March 25, 2020

17.1K
Identification of Disease-related Spatial Covariance Patterns using Neuroimaging Data
14:27

Identification of Disease-related Spatial Covariance Patterns using Neuroimaging Data

Published on: June 26, 2013

15.7K

Area of Science:

  • Genomics
  • Computational Biology
  • Immunology

Background:

  • Sequencing-based spatial transcriptomics (ST) enables mapping RNA distribution in tissues.
  • The coarse resolution of ST is often seen as a limitation.
  • This study proposes leveraging spatial proximity for cellular network reconstruction.

Purpose of the Study:

  • To introduce ISCHIA (Identifying Spatial Co-occurrence in Healthy and InflAmed tissues), a novel computational framework.
  • To analyze spatial co-occurrence of cell types and transcripts within ST spots.
  • To identify inflammation-induced cellular networks and ligand-receptor interactions in ulcerative colitis.

Main Methods:

  • Development of the ISCHIA computational framework for co-occurrence analysis.
  • Application of ISCHIA to Visium ST data from human ulcerative colitis patients.
  • Validation of findings using matched single-cell hybridization-based data.

Main Results:

  • ISCHIA successfully reconstructs cellular networks by analyzing spatial co-occurrence.
  • Identification of inflammation-induced cellular networks involving M cells and fibroblasts.
  • Discovery of enriched ligand-receptor interactions and associated gene signatures in inflamed human colon.

Conclusions:

  • Spatial co-occurrence analysis is a powerful, complementary approach to differential gene expression in ST.
  • ISCHIA provides hypothesis-generating insights into tissue-specific cellular interactions.
  • The framework demonstrates broad applicability for analyzing spatial transcriptomics data.