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<p>Non-coding RNAs (ncRNAs) are showing great potential as clinical indicators and are becoming essential regulators in gastrointestinal (GI) cancers. The computational discovery and subsequent confirmation of specific ncRNAs, such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), in the pathophysiology of GI cancer (GIC) is the primary focus of this study. We reviewed a rigorous, multi-step validation workflow that includes RNA sequencing and bioinformatic analysis for initial discovery, quantitative PCR for confirmation in tissue and liquid biopsies, and receiver operating characteristic (ROC) and survival analyses for evaluating clinical usefulness. We highlight, as a specific result, that a panel of lncRNAs (e.g., H19, NEAT1, OIP5-AS, MALAT1) and miRNAs (e.g., miR-21, miR-92a) have been consistently validated with excellent diagnostic accuracy and are strongly associated with poor overall survival. According to our findings, these computationally generated ncRNA signatures are practical tools for GIC prognosis and early diagnosis, opening the door for their incorporation into personalized oncology.</p> Graphical abstract <p>The process of finding gastrointestinal cancer biomarkers based on non-coding RNA (ncRNA) is shown in this graphical abstract. The first step is to utilize high-throughput RNA sequencing to identify various ncRNAs, including microRNA (miRNA), circular RNA (circRNA), and long non-coding RNA (lncRNA). After potential biomarkers have been identified through computational approaches and bioinformatics analysis, they are validated using focused techniques such as quantitative PCR (qPCR). Lastly, diagnostic and prognostic assessment is done to determine the clinical value of these validated biomarkers.</p> <p></p>

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Computational identification and validation of non-coding rna biomarkers in gastrointestinal cancer

  • 期刊论文

  • 发表日期：

    2025年11月19日

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  • Ghada Al-Assi,
  • Waleed K. Abdulsahib,
  • Wael Waleed Mustafa,
  • S. Renuka Jyothi,
  • Priya Priyadarshini Nayak,
  • J. Bethanney Janney,
  • Gurjant Singh,
  • Aashna Sinha,
  • Ravshan Sultanov

摘要

Non-coding RNAs (ncRNAs) are showing great potential as clinical indicators and are becoming essential regulators in gastrointestinal (GI) cancers. The computational discovery and subsequent confirmation of specific ncRNAs, such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), in the pathophysiology of GI cancer (GIC) is the primary focus of this study. We reviewed a rigorous, multi-step validation workflow that includes RNA sequencing and bioinformatic analysis for initial discovery, quantitative PCR for confirmation in tissue and liquid biopsies, and receiver operating characteristic (ROC) and survival analyses for evaluating clinical usefulness. We highlight, as a specific result, that a panel of lncRNAs (e.g., H19, NEAT1, OIP5-AS, MALAT1) and miRNAs (e.g., miR-21, miR-92a) have been consistently validated with excellent diagnostic accuracy and are strongly associated with poor overall survival. According to our findings, these computationally generated ncRNA signatures are practical tools for GIC prognosis and early diagnosis, opening the door for their incorporation into personalized oncology.

Graphical abstract

The process of finding gastrointestinal cancer biomarkers based on non-coding RNA (ncRNA) is shown in this graphical abstract. The first step is to utilize high-throughput RNA sequencing to identify various ncRNAs, including microRNA (miRNA), circular RNA (circRNA), and long non-coding RNA (lncRNA). After potential biomarkers have been identified through computational approaches and bioinformatics analysis, they are validated using focused techniques such as quantitative PCR (qPCR). Lastly, diagnostic and prognostic assessment is done to determine the clinical value of these validated biomarkers.