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RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Author Spotlight: Advancements in Molecular Biomarker Testing for Non-Squamous Non-Small Cell Lung Cancer
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Transcriptome Analysis of the Effects of X-Ray Radiotherapy on Non-small-cell Lung Cancer Using Next-generation

Serhat Aras1,2, Tuğba Kul Köprülü3,4, Burçin Erkal Çam5

  • 1Department of Radiation Oncology, Haydarpasa Numune Training and Research Hospital, University of Health Sciences, Istanbul, Türkiye; serhat.aras@sbu.edu.tr.

In Vivo (Athens, Greece)
|August 28, 2025
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Summary

Flattening filter-free (FFF) beams significantly alter gene expression in non-small-cell lung cancer (NSCLC) more than flattening filter (FF) beams. Higher dose rates with FFF further amplified these genetic changes.

Keywords:
Lung cancerRNA sequencingflattering filterflattering filter freenext-generation sequencingradiotherapy

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Area of Science:

  • Oncology
  • Radiation Oncology
  • Molecular Biology

Background:

  • Non-small-cell lung cancer (NSCLC) treatment often involves radiotherapy.
  • The impact of different radiotherapy beam types on gene expression is crucial for understanding treatment efficacy and side effects.

Purpose of the Study:

  • To investigate the acute effects of flattening filter (FF) and flattening filter-free (FFF) beams on gene expression in NSCLC.
  • To compare the gene expression profiles induced by FF and FFF radiotherapy at varying dose rates.

Main Methods:

  • Gene expression analysis was performed on NSCLC models in athymic nude mice.
  • Mice received 20 Gy radiotherapy with FF (400 MU/min) or FFF (1,000 or 1,800 MU/min) beams.
  • Samples were collected 48 hours post-irradiation for genetic analysis.

Main Results:

  • Twelve common genes were identified across all radiotherapy groups, with expression changes correlating with dose rate.
  • Significant pathway alterations were observed in glutamatergic synapse, actin cytoskeleton, and steroid synthesis (FF-400, FFF-1000).
  • FFF-1800 showed pronounced changes in RNA transport, actin cytoskeleton, and phagosome pathways.

Conclusions:

  • Flattening filter-free (FFF) beams induce more extensive gene-expression changes in NSCLC compared to flattening filter (FF) beams.
  • The intensity of gene expression alterations is dose-rate dependent, particularly with FFF beams.