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Published on: September 8, 2023
True 3q chromosomal amplification in squamous cell lung carcinoma by FISH and aCGH molecular analysis: impact on
Matteo Brunelli1, Emilio Bria, Alessia Nottegar
1ISH Molecular Lab, Department of Pathology and Diagnostic, Azienda Ospedaliera Universitaria Integrata di Verona, University of Verona, Verona, Italy. matteo.brunelli@univr.it
Abstract:
Squamous lung carcinoma lacks specific "ad hoc" therapies. Amplification of chromosome 3q is the most common genomic aberration and this region harbours genes having role as novel targets for therapeutics. There is no standard definition on how to score and report 3q amplification. False versus true 3q chromosomal amplification in squamous cell lung carcinoma may have tremendous impact on trials involving drugs which target DNA zones mapping on 3q. Forty squamous lung carcinomas were analyzed by FISH to assess chromosome 3q amplification. aCGH was performed as gold-standard to avoid false positive amplifications. Three clustered patterns of fluorescent signals were observed. Eight cases out of 40 (20%) showed ≥8 3q signals. Twenty out of 40 (50%) showed from 3 to 7 signals. The remaining showed two fluorescent signals (30%). When corrected by whole chromosome 3 signals, only cases with ≥8 signals maintained a LSI 3q/CEP3 ratio >2. Only the cases showing 3q amplification by aCGH (+3q25.3-3q27.3) showed ≥8 fluorescent signals at FISH evidencing a 3q/3 ratio >2. The remaining cases showed flat genomic portrait at aCGH on chromosome 3. We concluded that: 1) absolute copy number of 3q chromosomal region may harbour false positive interpretation of 3q amplification in squamous cell carcinoma; 2) a case results truly "amplified for chromosome 3q" when showing ≥8 fluorescent 3q signals; 3) trials involving drugs targeting loci on chromosome 3q in squamous lung carcinoma therapy have to consider false versus true 3q chromosomal amplification.
Insights
Accurate assessment of chromosome 3q amplification is crucial for squamous lung carcinoma therapies. True amplification, indicated by ≥8 FISH signals, distinguishes from false positives, impacting targeted drug trial eligibility.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Squamous lung carcinoma lacks targeted therapies.
- Chromosome 3q amplification is a common genomic alteration, presenting potential therapeutic targets.
- Standardized scoring for 3q amplification is lacking, leading to potential misinterpretation.
Purpose of the Study:
- To establish a reliable method for scoring chromosome 3q amplification in squamous lung carcinoma.
- To differentiate true 3q amplification from false positives using FISH and aCGH.
- To inform the design and interpretation of clinical trials targeting chromosome 3q in lung cancer.
Main Methods:
- Analysis of 40 squamous lung carcinoma samples using Fluorescence In Situ Hybridization (FISH).
- Comparative Genomic Hybridization (aCGH) employed as the gold standard to validate FISH results.
- Evaluation of signal patterns and copy number ratios (LSI 3q/CEP3) to define amplification.
Main Results:
- FISH analysis revealed three signal patterns: ≥8 signals (20%), 3-7 signals (50%), and 2 signals (30%).
- Only cases with ≥8 FISH signals, correlating with a LSI 3q/CEP3 ratio >2, demonstrated true 3q amplification confirmed by aCGH.
- Cases with fewer than 8 FISH signals showed no significant genomic alteration on chromosome 3 via aCGH.
Conclusions:
- Absolute copy number scoring can lead to false positive 3q amplification in squamous cell carcinoma.
- A threshold of ≥8 fluorescent 3q signals by FISH is proposed to define true chromosome 3q amplification.
- Accurate differentiation between true and false 3q amplification is essential for clinical trials involving chromosome 3q-targeted therapies.
