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Related Concept Videos

RNA Splicing01:32

RNA Splicing

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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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Comparative RNA-Seq Analysis of Colon Spheroids and Patient-derived Tissues Identifies Non-Canonical Transcript

Tamara Babic1, Bojana Banovic Djeri1, Dunja Pavlovic1

  • 1Group for gene Regulation in Cancer, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.

Cancer Informatics
|November 28, 2025
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Summary

This study identified 32 transcript isoforms, including non-canonical transcripts, that show consistent expression changes in colon cancer cells and patient tissues, potentially regulating colon carcinogenesis.

Keywords:
colon cancerregulatory RNAsspheroidstranscript isoformstranscriptomics

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Area of Science:

  • Molecular Biology
  • Genomics
  • Cancer Research

Background:

  • Malignant transformation of gut mucosa involves complex genetic alterations.
  • Understanding transcript isoform dysregulation is crucial for identifying cancer biomarkers and therapeutic targets.

Purpose of the Study:

  • To identify transcript isoforms of protein-coding genes relevant to colon cancer development.
  • To compare transcriptomic profiles from cell lines with patient-derived tumor and non-tumor tissues.

Main Methods:

  • RNA sequencing of colon cancer cell lines (HCT116, DLD1, SW620) and healthy gut epithelial cells (HCEC-1CT).
  • Comparative analysis of RNA-seq data with existing datasets from 473 tumor and 417 non-tumor colon tissue samples.
  • In silico characterization of dysregulated transcripts for regulatory features.

Main Results:

  • 32 transcripts (4 up-regulated, 28 down-regulated) showed consistent expression patterns between cell lines and patient tissues.
  • All 32 transcripts possessed regulatory features (e.g., truncated protein isoforms, exosomal localization).
  • Key dysregulated transcripts include NTMT1-204 (up), BLOC1S6-218 (down), and DCTN1-205 (down).

Conclusions:

  • Identified 32 transcript isoforms, including 30 non-canonical ones, potentially regulating colon carcinogenesis.
  • These isoforms may play roles in gut epithelial cell biology and cancer development.
  • Further investigation of these regulatory RNAs is warranted for understanding colon cancer.