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A comprehensive analysis of coding and non-coding transcriptomic changes in cutaneous squamous cell carcinoma.

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This study identifies key protein-coding genes, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) involved in cutaneous squamous cell carcinoma (cSCC). These findings offer potential new therapeutic targets and biomarkers for cSCC.

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Area of Science:

  • Oncology
  • Molecular Biology
  • Genomics

Background:

  • Cutaneous Squamous Cell Carcinoma (cSCC) is a prevalent and aggressive skin cancer.
  • Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are emerging as critical regulators in cancer development.
  • Understanding the transcriptomic landscape of cSCC is crucial for identifying novel therapeutic strategies.

Purpose of the Study:

  • To identify differentially expressed messenger RNAs (mRNAs), lncRNAs, and circRNAs in cSCC.
  • To explore the regulatory roles of these non-coding RNAs in skin carcinogenesis.
  • To discover potential diagnostic biomarkers and therapeutic targets for cSCC.

Main Methods:

  • RNA sequencing (RNA-seq) was performed on cSCC and healthy skin samples.
  • NanoString nCounter assays were used for validation in an expanded cohort, including pre-cancerous lesions.
  • Bioinformatic analyses were conducted to identify differentially expressed transcripts and enriched pathways.

Main Results:

  • 5,352 protein-coding genes, 908 lncRNAs, and 55 circRNAs were found to be differentially expressed in cSCC.
  • Key transcription factors regulating skin development, such as MYC and TP63, showed altered expression.
  • A global downregulation of circRNAs was observed, with novel circRNAs like circ_IFFO2 and circ_POF1B identified.

Conclusions:

  • A comprehensive set of coding and non-coding transcripts associated with cSCC has been identified.
  • Dysregulated lncRNAs and circRNAs represent promising candidates for cSCC biomarkers and therapeutic interventions.
  • Further research into these transcripts could advance the understanding and treatment of cSCC.