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Targeting genomic alterations in squamous cell lung cancer.

ABSTRACT: Squamous cell lung cancer causes approximately 400,000 deaths worldwide per year. Identification of specific molecular alterations, such as activating mutations in the epidermal growth factor receptor kinase and echinoderm microtubule-associated protein-like 4/anaplastic lymphoma kinase fusions have led to significant therapeutic gains in patients with adenocarcinoma. However, meaningful therapeutic gains based on the molecular pathobiology of squamous cell lung cancer have not yet been realized. A comprehensive genomic characterization of 178 cases of squamous cell lung cancer has recently been reported. Squamous cell lung cancer appears to be characterized by a broader and more complex group of genomic alterations than adenocarcinoma. In this review, potentially targetable genes or pathways in squamous cell lung cancer are emphasized in relation to available therapeutic agents in development or active clinical trials. This organization of data will provide a framework for development for clinical investigation. Squamous cell lung cancer appears to be characterized by not only driver mutations in candidate genes but also gene copy number alterations resulting in tumor proliferation and survival. Better understanding of these genetic alterations and their use as therapeutic targets will require broad collaboration between industry, government, the cooperative groups, and academic institutions with the ultimate goal of rapid translation of scientific advancement to patient benefit.

SUBMITTER: Mantripragada K

PROVIDER: S-EPMC3733025 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Targeting genomic alterations in squamous cell lung cancer.

Mantripragada Kalyan K Khurshid Humera H

Frontiers in oncology 20130805

Squamous cell lung cancer causes approximately 400,000 deaths worldwide per year. Identification of specific molecular alterations, such as activating mutations in the epidermal growth factor receptor kinase and echinoderm microtubule-associated protein-like 4/anaplastic lymphoma kinase fusions have led to significant therapeutic gains in patients with adenocarcinoma. However, meaningful therapeutic gains based on the molecular pathobiology of squamous cell lung cancer have not yet been realized ...[more]

PMID: 23936763

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Project description:BackgroundTo determine genomic alterations in head and neck squamous cell carcinoma (HNSCC) using formalin-fixed, paraffin-embedded (FFPE) tumors obtained through routine clinical practice, selected cancer-related genes were evaluated and compared with alterations seen in frozen tumors obtained through research studies.Patients and methodsDNA samples obtained from 252 FFPE HNSCC were analyzed using next-generation sequencing-based (NGS) clinical assay to determine sequence and copy number variations in 236 cancer-related genes plus 47 introns from 19 genes frequently rearranged in cancer. Human papillomavirus (HPV) status was determined by presence of the HPV DNA sequence in all samples and corroborated with high-risk HPV in situ hybridization (ISH) and p16 immunohistochemical (IHC) staining in a subset of tumors. Sequencing data from 399 frozen tumors in The Cancer Genome Atlas and University of Chicago public datasets were analyzed for comparison.ResultsAmong 252 FFPE HNSCC, 84 (33%) were HPV positive and 168 (67%) were HPV negative by sequencing. A subset of 40 tumors with HPV ISH and p16 IHC results showed complete concordance with NGS-derived HPV status. The most common genes with genomic alterations were PIK3CA and PTEN in HPV-positive tumors and TP53 and CDKN2A/B in HPV-negative tumors. In the pathway analysis, the PI3K pathway in HPV-positive tumors and DNA repair-p53 and cell cycle pathways in HPV-negative tumors were frequently altered. The HPV-positive oropharynx and HPV-positive nasal cavity/paranasal sinus carcinoma shared similar mutational profiles.ConclusionThe genomic profile of FFPE HNSCC tumors obtained through routine clinical practice is comparable with frozen tumors studied in research setting, demonstrating the feasibility of comprehensive genomic profiling in a clinical setting. However, the clinical significance of these genomic alterations requires further investigation through application of these genomic profiles as integral biomarkers in clinical trials.

Project description:Background: The feasibility and value of pericardial effusion as a liquid biopsy sample for actionable alteration detection in patients with non-small cell lung cancer (NSCLC) has not been adequately investigated. Here, we aim to reveal genomic alterations between pericardial effusion and paired tumor tissue, plasma (plasma cfDNA), and pleural effusion supernatant (PE-cfDNA) based on second-generation sequencing technology. Material and methods: A total of 26 advanced NSCLC patients were retrospectively studied. The following samples were collected and sequenced using two targeted next-generation sequencing panels: pericardial effusion (n = 26), matched tumor tissue (n = 6), plasma (n = 16), and pleural effusion supernatant (n = 5). Results: A total of 10 actionable alterations were identified in pericardial effusion of the NSCLC patients, including MET amplification, EGFR L858R, EGFR T790M, EGFR exon 19 deletion, EGFR L861Q, KRAS G12C, EML4-ALK (exon 18: exon 20) fusion, EML4-ALK (exon 20: exon 20) fusion, EML4-ALK (exon 6: exon 20) fusion, and ERBB2 exon 20 insertion. All these actionable alterations harbored multiple drug-sensitive targets as well as several drug-resistant targets, such as EGFR T790M. Compared to plasma cfDNA of 16 patients, paired pericardial effusion had higher number of actionable alterations (p = 0.08) as well as higher percentage of the population with actionable alterations (p = 0.16). Moreover, 8 out of 10 actionable alterations with single nucleotide variations (SNVs) or insertions/deletions (indels) had a higher variant allele frequency (VAF) in pericardial effusion than plasma cfDNA. In addition, we identified two actionable alterations in paired pericardial effusion, which were absence in PE-cfDNA. Clearly, 2 out of 3 actionable alterations with SNVs/indels in pericardial effusion had a higher VAF than those in PE-cfDNA. Our finding suggested the importance of pericardial effusion in the optimal selection of patients for targeted therapy. Conclusion: Among liquid biopsy specimens from the advanced NSCLC patients, pericardial effusion may be a better candidate for genomic profiling than plasma cfDNA, while it could serve as a supplement to PE-cfDNA in detecting actionable alterations. Therefore, pericardial effusion might provide a new alternative for selection of patients for better treatment management.

Dataset Information

Targeting genomic alterations in squamous cell lung cancer.

Publications

Targeting genomic alterations in squamous cell lung cancer.

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