| Lung cancer is the most prevalent cancer and the leading cause of cancer-related death worldwide. Approximately 85% of the newly diagnosed lung cancers are non-small cell lung cancer (NSCLC). As one of the major histological subtypes, squamous cell lung cancers (SqCLC) are accounting for approximately 30% of NSCLC. The discoveries of epidermal growth factor receptor kinase inhibitors (EGFR-TKIs) and anaplastic lymphoma kinase (ALK) inhibitors dramatically improved the survival of NSCLC patients with EGFR sensitive mutation and ALK rearrangement. However, these targeted drugs are mainly developed for adenocarcinoma, and are largely ineffective for SqCLC. The identification of potential druggable molecular targets of therapeutic utility in SqCLC becomes a top research priority. This study detected the gene mutations and copy number variations, aiming to investigate the genetic alterations profile in Chinese patients with SqCLC, identify the potential druggable targets in SqCLC, facilitate the development of targetd therapies for SqCLC, elevate the integrative level of personalized treatment for SqCLC, and facilitate the development of precision medicine for SqCLC. The contents of this study are divided into two parts as followed:Chapter 1:Detection of gene mutations in squamous cell lung carcinomas by using targeted next generation sequencing. We analyzed approximately 2,800 COSMIC mutations from 50 oncogenes and tumor suppressor genes in 159 patients with SqCLC by using Ion Torrent targeted next-generation sequencing. The relationships between mutation profiles of SqCLC and clinicopathological characteristics, disease-free survival (DFS) and overall survival (OS) were analyzed. Genetic mutations were detected in 73.6% (117/159) of all patients with SqCLC. The most common mutated gene detected in this study were TP53 (89 cases,56.0%), followed by CDKN2A (14 cases,8.8%), PI3KCA (14 cases,8.8%), KRAS (7 cases,4.4%), EGFR (5 cases,3.1%), FBXW7 (2.5%, 4/159), PTEN (2.5%,4/159), FGFR3 (1.3%,2/159), AKT1 (1.3%,2/159) and KIT (0.6%, 1/159). In 117 patients with SqCLC harboring at least one mutation,89 (56.0%) patients harbored single mutation, and 28 (17.6%) patients showed two or more mutations, either in the same gene (double mutation) or in different genes (co-mutations). TP53 mutations were significantly more common in men and smokers, while the frequency of EGFR mutation was significantly higher in women and never smokers. No significant association was observed between mutation profiles and DFS and OS.Chapter 2:Detection of gene copy number variation in Chinese squamous cell lung carcinomas. We detected the gene status of FGFR1, EGFR, HER2, PDGFRA, CCND1, SOX2, CDKN2A, and PTEN in 250 SqCLC samples by using FISH. The PTEN protein expression status was also examined by IHC. The relationships between the status of the eight genes and clinicopathological characteristics, DFS and OS were analyzed. The frequencies of FGFR1 amplification, EGFR amplification, HER2 amplification, PDGFRA amplification, CCND1 amplification, SOX2 amplification, CDKN2A deletion, PTEN deletion and loss of PTEN expression were 13.7% (34/248),12.6% (31/246), 10.2% (25/246),7.7%(19/246),11.0% (27/246),32.1% (79/246),21.5% (53/246), 17.9% (44/246), and 43.5% (108/248), respectively. FGFR1 amplification, CCND1 amplification and SOX2 amplification were significantly associated with smoking. The incidence of FGFR1 amplification in patients without lymph node metastasis was significantly higher than that in patients with lymph node metastasis (19.4% vs.10.2%, P=0.043). The incidence of loss of PTEN protein expression in patients with pleural invasion was 51.2%, which was significantly higher than that in patients without pleural invasion (P=0.017). The loss of PTEN expression was significantly associated with PTEN gene deletion (P=0.025). PTEN gene deletion was significantly associated longer OS (P=0.044). There was no significant association of the status of FGFR1, EGFR, HER2, PDGFRA, CCND1, SOX2,and CDKN2A gene, and PTEN protein expression, with DFS and OS.In conclusion, we examined the gene mutations and copy number variations in Chinese SqCLC samples, and demonstrated the genetic alterations profile in Chinese SqCLC patients and their associations with clinicopathological features. These findings may provide reference data for basic and clinical research on the targeted therapy for SqCLC.Background:Identification of driver mutations has led to the dramatic improvement in personalized therapy for lung adenocarcinoma. However, few targeted therapeutics are approved for treatment of squamous cell lung carcinoma (SqCLC). The identification of druggable molecular targets in SqCLC has been becoming a top research priority. We therefore analyzed the gene mutations in a large cohort of Chinese SqCLCs to identify potential therapeutic targets.Methods:One hundred and fifty-nine SqCLC patients treated by surgery in Cancer Hospital of Chinese Academy of Medical Sciences from March 2011 to November 2011 were collected. All patients were diagnosed with histologically confirmed SqCLC. Approximately 2,800 COSMIC mutations from 50 oncogenes and tumor suppressor genes were interrogated by using Ion Torrent targeted next-generation sequencing. The relationships between gene mutations of SqCLC and clinicopathological characteristics, DFS and OS were analyzed.Results:Genetic mutations were detected in 73.6%(117/159) of all patients with SqCLC. The most common mutated gene detected in this study were TP53 (89 cases, 56.0%), followed by CDKN2A (14 cases,8.8%), PI3KCA (14 cases,8.8%), KRAS (7 cases,4.4%), EGFR (5 cases,3.1%), FBXW7 (2.5%,4/159), PTEN (2.5%,4/159), FGFR3 (1.3%,2/159), AKT1 (1.3%,2/159) and KIT (0.6%,1/159). In 117 patients with SqCLC harboring at least one mutation,89 (56.0%) patients harbored single mutation, and 28 (17.6%) patients showed two or more mutations, either in the same gene (double mutation) or in different genes (co-mutations). TP53 mutations were significantly more common in men and smokers, while the frequency of EGFR mutation was significantly higher in women and never smoker. No significant association was observed between mutation profiles and DFS and OS.Conclusions:Nearly three-fourth of patients (73.6%) with SqCLC were found to be harboring at least one gene mutation, and 17.6% were found to be having two and more gene mutations. Targeted next-generation sequencing can effectively, quickly, and precisely detect gene mutations in SqCLC, and the identified mutation profile could facilitate the development of targetd therapies and optimize the therapeutic strategies for patients with SqCLC.Background:The discoveries of epidermal growth factor receptor kinase inhibitors (EGFR-TKI) and anaplastic lymphoma kinase (ALK) inhibitors dramatically improved the survival of NSCLC patients with EGFR sensitive mutation and ALK rearrangement. But these targeted drugs are mainly developed for adenocarcinoma, and are largely ineffective for squamous cell lung carcinoma (SqCLC). The identification of novel molecular targets of therapeutic utility in SqCLC is important. Therefore, to identify potential molecular targets for SqCLC, we examined the copy number variation of eight genes, including FGFR1, EGFR, HER2, PDGFRA, CCND1, SOX2, CDKN2A, and PTEN.Methods:Two hundred and fifty SqCLC patients who underwent surgical resection of their tumors at Cancer Hospital of Chinese Academy of Medical Sciences Hospital between March 2011 and October 2013. All patients were diagnosed with histologically confirmed SqCLC. We detected the gene status of FGFR1, EGFR, HER2, PDGFRA, CCND1, SOX2, CDKN2A, and PTEN in 250 SqCLC by FISH. The PTEN protein expression status was also examined by IHC. The associations of the status of copy number variation of the eight genes and PTEN expression, with clinicopathological characteristics, DFS and OS were analyzed.Results:The frequencies of FGFR1 amplification, EGFR amplification, HER2 amplification, PDGFRA amplification, CCND1 amplification, SOX2 amplification, CDKN2A homozygous deletion, PTEN deletion and loss of PTEN expression were 13.7% (34/248),12.6% (31/246),10.2% (25/246),7.7% (19/246),11.0% (27/246), 32.1% (79/246),21.5% (53/246),17.9% (44/246) and 43.5% (108/248), respectively. FGFR1 amplification, CCND1 amplification and SOX2 amplification were significantly associated with smoking. The incidence of FGFR1 amplification in patients without lymph node metastal2.6sis was significantly higher than that in patients with lymph node metastasis (19.4% vs.10.2%, P=0.043). The incidence of loss of PTEN protein expression in patients with pleural invasion was 51.2%, which was significantly higher than that in patient without pleural invasion (P=0.017). The loss of PTEN expression was significantly associated with PTEN gene deletion (P=0.025). PTEN deletion was significantly associated with longer OS (P=0.044). There was no significant association between the status of FGFRl, EGFR, HER2, PDGFRA, CCND1, SOX2, and CDKN2A, and DFS and OS.Conclusions:More than three-fourth of patients (74.0%,182/246) with SqCLC were found to be harboring at least one gene copy number variation, suggesting that copy number variation was common genetic alteration in SqCLC. There were 37.0% (91/246) of all patients harboring two and more genes copy number variations, supporting that multiple oncogenes and tumor suppressor genes concurrently play important roles in the development of SqCLC. The results of this study can provide reference data for basic and clinical research on targeted therapies for SqCLC. |
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