Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal Cancer
Non-coding RNAs (ncRNAs) play crucial roles in colorectal cancer (CRC) development and progression. Recent developments in single-cell transcriptome profiling methods have revealed surprising levels of expression variability among seemingly homogeneous cells, suggesting the existence of many more ce...
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-03-01
|
| Series: | Non-Coding RNA |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2311-553X/11/2/24 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849714222065254400 |
|---|---|
| author | Mahnoor Naseer Gondal Hafiz Muhammad Umer Farooqi |
| author_facet | Mahnoor Naseer Gondal Hafiz Muhammad Umer Farooqi |
| author_sort | Mahnoor Naseer Gondal |
| collection | DOAJ |
| description | Non-coding RNAs (ncRNAs) play crucial roles in colorectal cancer (CRC) development and progression. Recent developments in single-cell transcriptome profiling methods have revealed surprising levels of expression variability among seemingly homogeneous cells, suggesting the existence of many more cell types than previously estimated. This review synthesizes recent advances in ncRNA research in CRC, emphasizing single-cell bioinformatics approaches for their analysis. We explore computational methods and tools used for ncRNA identification, characterization, and functional prediction in CRC, with a focus on single-cell RNA sequencing (scRNA-seq) data. The review highlights key bioinformatics strategies, including sequence-based and structure-based approaches, machine learning applications, and multi-omics data integration. We discuss how these computational techniques can be applied to analyze differential expression, perform functional enrichment, and construct regulatory networks involving ncRNAs in CRC. Additionally, we examine the role of bioinformatics in leveraging ncRNAs as diagnostic and prognostic biomarkers for CRC. We also discuss recent scRNA-seq studies revealing ncRNA heterogeneity in CRC. This review aims to provide a comprehensive overview of the current state of single-cell bioinformatics in ncRNA CRC research and outline future directions in this rapidly evolving field, emphasizing the integration of computational approaches with experimental validation to advance our understanding of ncRNA biology in CRC. |
| format | Article |
| id | doaj-art-4fb58746fd894208886a898e1f5eb29e |
| institution | DOAJ |
| issn | 2311-553X |
| language | English |
| publishDate | 2025-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Non-Coding RNA |
| spelling | doaj-art-4fb58746fd894208886a898e1f5eb29e2025-08-20T03:13:45ZengMDPI AGNon-Coding RNA2311-553X2025-03-011122410.3390/ncrna11020024Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal CancerMahnoor Naseer Gondal0Hafiz Muhammad Umer Farooqi1Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USALaboratory of Energy Metabolism, Division of Metabolic Disorders, Children’s Hospital of Orange County, Orange, CA 92868, USANon-coding RNAs (ncRNAs) play crucial roles in colorectal cancer (CRC) development and progression. Recent developments in single-cell transcriptome profiling methods have revealed surprising levels of expression variability among seemingly homogeneous cells, suggesting the existence of many more cell types than previously estimated. This review synthesizes recent advances in ncRNA research in CRC, emphasizing single-cell bioinformatics approaches for their analysis. We explore computational methods and tools used for ncRNA identification, characterization, and functional prediction in CRC, with a focus on single-cell RNA sequencing (scRNA-seq) data. The review highlights key bioinformatics strategies, including sequence-based and structure-based approaches, machine learning applications, and multi-omics data integration. We discuss how these computational techniques can be applied to analyze differential expression, perform functional enrichment, and construct regulatory networks involving ncRNAs in CRC. Additionally, we examine the role of bioinformatics in leveraging ncRNAs as diagnostic and prognostic biomarkers for CRC. We also discuss recent scRNA-seq studies revealing ncRNA heterogeneity in CRC. This review aims to provide a comprehensive overview of the current state of single-cell bioinformatics in ncRNA CRC research and outline future directions in this rapidly evolving field, emphasizing the integration of computational approaches with experimental validation to advance our understanding of ncRNA biology in CRC.https://www.mdpi.com/2311-553X/11/2/24single-cell sequencingcolorectal cancernon-coding RNAbioinformaticstherapeutics |
| spellingShingle | Mahnoor Naseer Gondal Hafiz Muhammad Umer Farooqi Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal Cancer Non-Coding RNA single-cell sequencing colorectal cancer non-coding RNA bioinformatics therapeutics |
| title | Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal Cancer |
| title_full | Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal Cancer |
| title_fullStr | Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal Cancer |
| title_full_unstemmed | Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal Cancer |
| title_short | Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal Cancer |
| title_sort | single cell transcriptomic approaches for decoding non coding rna mechanisms in colorectal cancer |
| topic | single-cell sequencing colorectal cancer non-coding RNA bioinformatics therapeutics |
| url | https://www.mdpi.com/2311-553X/11/2/24 |
| work_keys_str_mv | AT mahnoornaseergondal singlecelltranscriptomicapproachesfordecodingnoncodingrnamechanismsincolorectalcancer AT hafizmuhammadumerfarooqi singlecelltranscriptomicapproachesfordecodingnoncodingrnamechanismsincolorectalcancer |