Related Experiment Video
Updated: Mar 30, 2026
Detection of Targetable Alterations in Non-small Cell Lung Cancer using Next-generation Sequencing
Published on: October 10, 2025
Integrative Analyses of Lung Squamous Cell Carcinoma in Ten Chinese Patients with Transcriptome Sequencing
Lu-Lu Yang1, Xu-Chao Zhang2, Shao-Kun Chuai3
1Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China.
Abstract:
Few effective therapies have been developed for the treatment of lung squamous cell carcinoma (SQCC), in part due to a lack of understanding regarding the mechanisms underlying the initiation and development of this disease. Whole transcriptome sequencing not only provides insight into the expression of all transcribed genes, but offers an efficient approach for identifying genetic variations, including gene fusions, mutations and alternative splicing. In this study, we performed whole transcriptome sequencing of 10 patients with stage IIIA lung SQCC, and discovered a large number of single nucleotide variants (SNVs; mean of 12.2 SNVs/Mb), with C>T/G>A and A>G/T>C transitions being the most frequently observed. Additionally, a total of 132 gene fusions were identified based upon TopHat alignments, 70.5% (93/132) of which occurred as a result of intra-chromosomal rearrangements. Based on the number of supporting reads for each fusion, we further validated 20 of the 26 top gene fusions by RT-PCR and Sanger sequencing. Taken together, these data provide an in-depth view of transcriptional alterations in lung SQCC patients, and may be useful for identification of new therapeutic targets.
Insights
Whole transcriptome sequencing reveals numerous genetic variations in lung squamous cell carcinoma (SQCC). These findings offer insights into SQCC development and potential new therapeutic targets.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Lung squamous cell carcinoma (SQCC) lacks effective therapies due to poorly understood disease mechanisms.
- Whole transcriptome sequencing is a powerful tool for analyzing gene expression and identifying genetic variations.
Purpose of the Study:
- To investigate the transcriptional landscape of lung squamous cell carcinoma.
- To identify genetic variations and gene fusions in SQCC patients.
Main Methods:
- Whole transcriptome sequencing was performed on 10 patients with stage IIIA lung SQCC.
- Analysis included identification of single nucleotide variants (SNVs) and gene fusions.
- Top gene fusions were validated using RT-PCR and Sanger sequencing.
Main Results:
- A high frequency of SNVs was observed (mean of 12.2 SNVs/Mb), with C>T/G>A and A>G/T>C transitions being most common.
- 132 gene fusions were identified, with 70.5% arising from intra-chromosomal rearrangements.
- 20 out of 26 top gene fusions were successfully validated.
Conclusions:
- Transcriptional alterations in lung SQCC are extensive, including numerous SNVs and gene fusions.
- These findings provide a comprehensive view of the molecular basis of SQCC.
- The identified variations may serve as potential therapeutic targets for lung squamous cell carcinoma.
More Related Videos
07:59Author Spotlight: Advancements in Molecular Biomarker Testing for Non-Squamous Non-Small Cell Lung Cancer
Published on: September 8, 2023
11:20Simple and Rapid Method to Obtain High-quality Tumor DNA from Clinical-pathological Specimens Using Touch Imprint Cytology
Published on: March 21, 2018