LnCeCell 2.0: an updated resource for lncRNA-associated ceRNA networks and web tools based on single-cell and spatial...

Area of Science:

• Bioinformatics
• Genomics
• Molecular Biology

Background:

• Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation through competing endogenous RNA (ceRNA) networks.
• Understanding ceRNA interactions at single-cell and spatial resolutions is essential for deciphering complex biological processes and diseases.
• Existing resources often lack comprehensive data integration and advanced analytical tools for single-cell and spatial transcriptomics.

Purpose of the Study:

• To present LnCeCell 2.0, an updated and expanded resource for lncRNA-ceRNA networks derived from single-cell and spatial transcriptomics data.
• To provide a comprehensive collection of cell-specific and spatial spot-specific ceRNA interactions, lncRNA biomarkers, and associated clinical information.
• To develop and offer a suite of web tools for investigating ceRNA regulatory mechanisms at single-cell/spot resolution.

Main Methods:

• Integration of 257 single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics sequencing (stRNA-seq) datasets.
• Construction of cell-specific and spatial spot-specific ceRNA interactions and functional networks.
• Manual curation for detailed annotation of cell types, states, and subcellular/extracellular locations of ceRNAs.
• Development of 24 web tools, including CeCellTraject, for analyzing ceRNA networks and trajectories.

Main Results:

• LnCeCell 2.0 encompasses 836,581 ceRNA interactions across 1,002,988 cells and 367,971 spatial spots from 257 datasets.
• The database includes 15,489 experimentally supported lncRNA biomarkers and clinical data for 20,326 cancer patients.
• The developed tools enable detailed exploration of ceRNA distribution and dynamic changes in networks at single-cell/spot resolution.

Conclusions:

• LnCeCell 2.0 significantly enhances the study of lncRNA-ceRNA networks with unprecedented single-cell and spatial resolution.
• The resource and associated tools facilitate a deeper understanding of regulatory mechanisms in health and disease.
• This updated platform will accelerate research into the intricate roles of ceRNAs in complex biological systems.