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Updated: Jun 28, 2025
Author Spotlight: Advancements in Molecular Biomarker Testing for Non-Squamous Non-Small Cell Lung Cancer
Published on: September 8, 2023
Molecular phenotyping of small cell lung cancer using targeted cfDNA profiling of transcriptional regulatory regions
Joseph B Hiatt1,2,3, Anna-Lisa Doebley4,5,6, Henry U Arnold1
1Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Abstract:
We report an approach for cancer phenotyping based on targeted sequencing of cell-free DNA (cfDNA) for small cell lung cancer (SCLC). In SCLC, differential activation of transcription factors (TFs), such as ASCL1, NEUROD1, POU2F3, and REST defines molecular subtypes. We designed a targeted capture panel that identifies chromatin organization signatures at 1535 TF binding sites and 13,240 gene transcription start sites and detects exonic mutations in 842 genes. Sequencing of cfDNA from SCLC patient-derived xenograft models captured TF activity and gene expression and revealed individual highly informative loci. Prediction models of ASCL1 and NEUROD1 activity using informative loci achieved areas under the receiver operating characteristic curve (AUCs) from 0.84 to 0.88 in patients with SCLC. As non-SCLC (NSCLC) often transforms to SCLC following targeted therapy, we applied our framework to distinguish NSCLC from SCLC and achieved an AUC of 0.99. Our approach shows promising utility for SCLC subtyping and transformation monitoring, with potential applicability to diverse tumor types.
Insights
This study presents a novel cell-free DNA sequencing method for small cell lung cancer (SCLC) phenotyping. The approach accurately identifies SCLC subtypes and monitors treatment-induced transformations.
Area of Science:
- Genomics
- Molecular Biology
- Oncology
Background:
- Small cell lung cancer (SCLC) is characterized by distinct molecular subtypes defined by transcription factor (TF) activation.
- Current phenotyping methods may not fully capture the dynamic molecular changes in SCLC, especially during treatment.
Purpose of the Study:
- To develop and validate a targeted sequencing approach for cancer phenotyping in SCLC using cell-free DNA (cfDNA).
- To assess the utility of cfDNA sequencing for identifying SCLC molecular subtypes and monitoring therapeutic transformations.
Main Methods:
- Design of a targeted capture panel analyzing chromatin organization at TF binding sites and gene transcription start sites, alongside exonic mutations.
- Sequencing of cfDNA from SCLC patient-derived xenograft models to capture TF activity and gene expression.
- Development of prediction models for TF activity (ASCL1, NEUROD1) and differentiation between SCLC and non-SCLC (NSCLC).
Main Results:
- The cfDNA sequencing approach successfully captured TF activity and gene expression, identifying informative genetic loci.
- Prediction models for ASCL1 and NEUROD1 activity achieved high performance (AUCs 0.84–0.88) in SCLC patients.
- The framework demonstrated excellent accuracy (AUC 0.99) in distinguishing SCLC from NSCLC, particularly in cases of therapeutic transformation.
Conclusions:
- Targeted cfDNA sequencing offers a promising non-invasive method for SCLC phenotyping and subtyping.
- This approach can effectively monitor SCLC transformation, especially in response to therapy.
- The methodology holds potential for application across various cancer types for phenotyping and monitoring.
