Gene Mutations In Lung Cancer Research Articles

A Prospective Observational Study on Analyzing Lung Cancer Gene Mutation Variant Allele Frequency (VAF) and Its Correlation with Treatment Efficacy.

A few studies have reported on the variability of the variant allele frequency (VAF) of gene mutations and the relationship between VAF and the therapeutic effect of molecular-targeted drugs. This joint study was conducted from May 2020 to January 2022 between St. Marianna University School of Medicine and the DNA Chip Research Institute. Cytology samples were used to verify the usefulness of a lung cancer compact panel test, which is a high-sensitivity next-generation sequencing (NGS) gene panel test. We analyzed the distribution of VAF and the duration of the initial molecular-targeted drug administration in patients with advanced-stage epidermal growth factor receptor (EGFR) mutations. Of the 196 patients diagnosed with non-small cell carcinoma (NSCLC), gene mutations were detected in 114 (58.2%) cases and in 68.7% of patients with adenocarcinomas (an increased detection rate). A VAF of 30% or more for DNA mutations was confirmed in 35 patients (33.7%), 10% to <30% in 38 (36.5%), and <10% in 31 (29.8%), including 18 patients (17.3%) with <6%, which is considered the lower limit of the LOD for other companion diagnostic kits. EGFR mutations were detected in 59 patients (30%), of whom 35 were in an advanced stage and received molecular-targeted drugs as their initial treatment. Groups A and B comprised patients with a VAF of ≥10% and <10%, respectively, with 27 patients (median VAF 30.6%, range 11.4-77%) in group A and 8 (median VAF 5.4%, range 0.1-8.5%) in group B. The duration of the administration of molecular-targeted drugs was 17 months (range 3-42 months) in group A and 14 months (range 1-45 months) in group B, with no statistically significant difference between the two groups (p-value = 0.7). Twenty-seven percent of patients had a VAF < 10%. Even in patients with a low VAF for gene mutations, sufficient therapeutic effects were observed with molecular-targeted drugs, suggesting the importance of detecting mutations using a highly sensitive method at initial diagnosis. Further prospective validation studies of a larger number of cases are warranted.

CT Image Diagnostic Support System for Predicting EGFR Gene Mutations in Lung Cancer

CT Image Diagnostic Support System for Predicting EGFR Gene Mutations in Lung Cancer

Targeting immune cell types of tumor microenvironment to overcome resistance to PD-1/PD-L1 blockade in lung cancer.

Lung cancer is the common malignant tumor with the highest mortality rate. Lung cancer patients have achieved benefits from immunotherapy, including immune checkpoint inhibitors (ICIs) therapy. Unfortunately, cancer patients acquire adaptive immune resistance, leading to poor prognosis. Tumor microenvironment (TME) has been demonstrated to play a critical role in participating in acquired adaptive immune resistance. TME is associated with molecular heterogeneity of immunotherapy efficacy in lung cancer. In this article, we discuss how immune cell types of TME are correlated with immunotherapy in lung cancer. Moreover, we describe the efficacy of immunotherapy in driven gene mutations in lung cancer, including KRAS, TP53, EGFR, ALK, ROS1, KEAP1, ZFHX3, PTCH1, PAK7, UBE3A, TNF-α, NOTCH, LRP1B, FBXW7, and STK11. We also emphasize that modulation of immune cell types of TME could be a promising strategy for improving adaptive immune resistance in lung cancer.

The rational application of liquid biopsy based on next-generation sequencing in advanced non-small cell lung cancer.

Plasma and tissue biopsy have both used for targeting actionable driver gene mutations in lung cancer, whose concordance is imperfect. A reliable method to predict the concordance is urgently needed to ease clinical application. A total of 1012 plasma samples, including 519 with paired-tissue biopsy samples, derived from lung adenocarcinoma patients were retrospectively enrolled. We assessed the associations of several clinicopathological characteristics and serum tumor markers with the concordance between plasma and tissue biopsies. When carcinoembryonic antigen (CEA) levels were higher than thresholds of 15.01 ng/ml and 51.15 ng/ml, the positive predictive value of concordance reached 90% and 95%, respectively. When CEA levels were lower than thresholds of 5.19 ng/ml and 3.26 ng/mL, the negative predictive value of concordance reached 45% and 50%. The performance of CYFRA21-1 in predicting concordance was similar but inferior to CEA (AUC: 0.727 vs. 0.741, p=0.633). The performance of CEA combined with CYFRA21-1 in predicting the concordance was similar to that of the combination of independent factors derived from the LASSO regression model (AUC: 0.796 vs. 0.818, p=0.067). CEA (r=0.47, p < 0.01) and CYFRA21-1 levels (r=0.45, p < 0.05) were significantly correlated with the maximum variant allele frequency, respectively. CEA combined with CYFRA21-1 could effectively predict the concordance between plasma and tissue biopsies, which could be used for evaluating the priority of plasma and tissue biopsies for gene testing to timely guide clinical applications in advanced lung adenocarcinoma patients.

Correlation between MSI, TMB, and RAS gene mutation in solid tumors.

2624 Background: RAS gene family encodes a protein that is a member of the small GTPase super family and plays an important role in the regulation of cell proliferation and promoting oncogenic events. Studies have reported that RAS gene shows a high mutation frequency in lung cancer, colorectal cancer and pancreatic cancer. However, the relation between RAS-mutant and RAS-wild type tumors in tumor mutation burden (TMB) and microsatellite instability (MSI) remain unclear in pan-cancer. Methods: We retrospectively analyzed 15188 Chinese patients with pan-cancer from laboratory of Simcere Diagnosis (Nanjing, China) during 2019-2021. Somatic mutations in tumor samples were assessed by next-generation sequencing (NGS). We evaluated RAS (KRAS, NRAS and HRAS) mutation frequency, TMB and MSI in RAS-mutant and RAS wild-type tumors. Results: RAS mutations were detected in 2663 (17.5%) samples, including 88.7% of KRAS mutations, 9.1% of NRAS mutations and 3.5% of HRAS mutations. The top 6 frequently cancers were colorectal cancer (829, 31.1%), lung cancer (747, 28.1%), pancreatic cancer (358, 13.4%), biliary tract cancer (210, 7.9%), liver cancer (78, 2.9%), and gastric cancer (73, 2.7%). We found that the incidence of MSI-H in patients with RAS-mutant solid tumors was 3.3% and the frequency of MSI-H was significantly higher in RAS-mutant gastric cancer than that in RAS wild-type (RAS-MUT vs RAS-WT, 20.5% vs 3.5%, p &lt; 0.001). Contrary to our assumption, it was not observed in colorectal cancer (RAS-MUT vs RAS-WT, 5.8% vs 6.9%). In the analysis of TMB, RAS gene mutation was associated with higher TMB (P &lt; 0.01). 27.4% of RAS-mutant gastric cancer and 10.8% RAS wild-type gastric cancer were classified as TMB-H (TMB ≥10 muts/Mb) (P＜0.01), while 13.4% of RAS-mutant colorectal cancer was TMB-H, with no significant difference between RAS wild-type. However, we did not observe a close association between MSI, TMB and RAS gene mutations in lung cancer, pancreatic cancer, biliary tract cancer, and liver cancer. Conclusions: We analyzed RAS gene mutations in Chinese patients with solid tumor. Our data showed that RAS mutations were associated with TMB-H and MSI-H in solid tumors, especially gastric cancer. In colorectal cancer, RAS mutations were associated with higher TMB, but not TMB-H. It was showed that RAS mutations in specific cancer types, such as gastric cancer and colorectal cancer, may be related to the efficacy of immunotherapy.

Prediction of Target-Drug Therapy by Identifying Gene Mutations in Lung Cancer With Histopathological Stained Image and Deep Learning Techniques.

Lung cancer is a kind of cancer with high morbidity and mortality which is associated with various gene mutations. Individualized targeted-drug therapy has become the optimized treatment of lung cancer, especially benefit for patients who are not qualified for lung lobectomy. It is crucial to accurately identify mutant genes within tumor region from stained pathological slice. Therefore, we mainly focus on identifying mutant gene of lung cancer by analyzing the pathological images. In this study, we have proposed a method by identifying gene mutations in lung cancer with histopathological stained image and deep learning to predict target-drug therapy, referred to as DeepIMLH. The DeepIMLH algorithm first downloaded 180 hematoxylin-eosin staining (H&E) images of lung cancer from the Cancer Gene Atlas (TCGA). Then deep convolution Gaussian mixture model (DCGMM) was used to perform color normalization. Convolutional neural network (CNN) and residual network (Res-Net) were used to identifying mutated gene from H&E stained imaging and achieved good accuracy. It demonstrated that our method can be used to choose targeted-drug therapy which might be applied to clinical practice. More studies should be conducted though.

A Modified Method to Isolate Circulating Tumor Cells and Identify by a Panel of Gene Mutations in Lung Cancer.

The CellSearch system is the only FDA approved and successful used detection technology for circulating tumor cells(CTCs). However, the process for identification of CTCs by CellSearch appear to damage the cells, which may adversely affects subsequent molecular biology assays. We aimed to explore and establish a membrane-preserving method for immunofluorescence identification of CTCs that keeping the isolated cells intact. 98 patients with lung cancer were enrolled, and the efficacy of clinical detection of CTCs was examined. Based on the CellSearch principle, we optimized an anti-EpCAM antibody and improved cell membrane rupture. A 5 ml peripheral blood sample was used to enrich CTCs with EpCAM immunomagnetic beads. Fluorescence signals were amplified with secondary antibodies against anti-EpCAM antibody attached on immunomagnetic beads. After identifying CTCs, single CTCs were isolated by micromanipulation. To confirm CTCs, genomic DNA was extracted and amplified at the single cell level to sequence 72 target genes of lung cancer and analyze the mutation copy number variations (CNVs) and gene mutations. A goat anti-mouse polyclonal antibody conjugated with Dylight 488 was selected to stain tumor cells. We identified CTCs based on EpCAM+ and CD45+ cells to exclude white blood cells. In the 98 lung cancer patients, the detection rate of CTCs (≥1 CTC) per 5 ml blood was 87.76%, the number of detections was 1–36, and the median was 2. By sequencing 72 lung cancer-associated genes, we found a high level of CNVs and gene mutations characteristic of tumor cells. We established a new CTCs staining scheme that significantly improves the detection rate and allows further analysis of CTCs characteristics at the genetic level.

Is there a genomic fingerprint of Radon (Rn)-induced lung cancer (LC)? Comparison of genomic alterations in LC specimens from high and low Rn zones.

1572 Background: Rn-222 is a radioactive gas found in rocks and soil. It emits alpha particles that cause dsDNA breaks and increase potential for carcinogenesis. Rn is the 2nd leading cause of LC in the US after smoking. EPA estimates &gt;15,000 deaths/yr (9% of LC deaths) from Rn. We hypothesize that the impact of Rn exposure may be reflected in LC gene mutation (mut) profiles. Methods: Using commercial NGS assays, we retrospectively analyzed genomic DNA alterations in FFPE specimens from 159 LC patients (pts) from the Lifespan Cancer Institute in Rhode Island (2014- 2019), followed by validation in a larger cohort of 5,532 pts using Caris platform. Based on EPA Rn maps, we identified counties with high indoor Rn levels (&gt;4 pci/L; HR), and compared gene mut patterns with those from low Rn zones (&lt;4 pci/L; LR). Based on pt’s zip code of residence, we categorized them to HR and LR. In the validation cohort, p values adjusted for multiple comparison (q) of &lt; .05 were considered significant. Results: In the pilot cohort, 35 pts (22%) were in HR and 124 (78%) in LR zones. Adenocarcinoma histology was most frequent (73%) and smoking prevalence was high (75%) in both groups. Most prevalent alterations were TP53, KRAS and CDKN2A muts. In the HR, we noted more frequent recurrent muts in 2 DNA repair genes (DDR): ATM (11 vs 1%, p= .00086) and CHEK2 (6 vs 0%, p= .047) when compared to LR group. When classified into major pathways implicated in lung carcinogenesis, higher frequency of mutations were seen in DDR in HR zones vs. LR (29 vs 13%, p= .038). In the validation cohort, 1,433 (26%) pts were in HR and 4099 (74%) in LR zones. Among the DDR genes, ATM muts in HR group tended to be more frequent (4.7 vs 3.4% in LR, p= .03) as well as PALB2 (0.9 vs 0.4%, p= .02) while no difference seen in CHEK2. Other genes with significantly higher prevalence in HR were TP53, SMARCA4 and NFE2L2 (q&lt; .05); while KMT2D, KEAP1, CDKN2A, MET, NF2, DNMT3A, CCND1 and FAS show a trend (p&lt; .05). EGFR muts were significantly more frequent in LR zones (8.4 vs 14.6%, q= .001). Similar to the pilot cohort, DDR pathway alterations trend to be higher in HR zones (14 vs 12%, p= .05). Using a high TMB cut-off &gt;10, tumors from HR zones had significantly higher TMB when compared to LR zones (56 vs 48%, q= .0005). Conclusions: To our knowledge, this is the first attempt to elucidate the pathobiology of Rn induced LC using gene mut analyses. Our observations suggest that LC associated with higher Rn exposure may have disabled DNA repair pathways and higher TMB. Assuming uniform tobacco smoke exposure, higher Rn was not associated with EGFR mut.

Prevalence of the EGFR T790M and other resistance mutations in the Australian population and histopathological correlation in a small subset of cases

We sought to review the prevalence of EGFR T790M and other EGFR mutations associated with either proven or probable tyrosine kinase inhibitor (TKI) resistance in the Australasian lung cancer population and to perform histopathological correlation in a subset of cases. Retrospective statistical analysis was performed on a set of targeted lung cancer gene mutation tests (FIND IT gene panel) performed at Sonic Healthcare during 2018 and early 2019. A total of 1833 lung adenocarcinoma tumour samples underwent somatic mutation testing. EGFR mutations were found in 28% (n=514) of patients, in whom 9.3% (n=48) T790M mutations were present (always combined with other EGFR mutations) and 4.8% (n=25) exon 20 insertions were found. We also compared the prevalence of EGFR mutations identified in our population with that of the four largest publicly available lung cancer cohorts (total n=576 samples). Finally, a subset of 38 samples of primary/and or metastatic lung adenocarcinomas from 23 patients, including five with serial biopsies, underwent detailed morphological analysis. No reproducible morphological correlates were found to be associated with T790M, exon 20 resistance mutations or rarer co-occurring EGFR mutations. Although this may be subject to referral bias towards patients with resistant disease, the incidence of EGFR and T790M mutations is higher in this series from an Australasian population than in other similar publicly available lung adenocarcinoma cohorts. We conclude that histopathological features cannot be used to predict the acquisition of EGFR resistance.

A comparison of MASS-PCR and ARMS-PCR for the detection of lung cancer gene mutation

Background: Targeted therapy has been proven to be effective in lung cancer patients with specific driver gene mutations. At present, Sanger sequencing is still the gold standard in clinical practice to detect mutation, and amplification refractory mutation system PCR (ARMS-PCR) has become widely used due to its higher sensitivity and less limitation compared with Sanger sequencing. Mutation-selected amplification specific system PCR (MASS-PCR) is a novel gene detection technique with high specificity and sensitivity. This study aimed to compare the accuracy and sensitivity of ARMS-PCR and MASS-PCR and purposed to make an alternative choice in gene mutation detection in lung cancer. Method: A total of 293 formalin-fixed paraffin-embedded (FFPE) tissues were collected from 293 patients with lung cancer from 2017 to 2018. The sample mutation statuses were evaluated by ARMS-PCR and MASS-PCR. Sanger sequencing was also conducted to confirm the results further. The consistency of ARMS-PCR and MASS-PCR were analyzed, and receiver operating characteristic (ROC) curve was drawn to assess the sensitivity and specificity of MASS-PCR. Results: The consistency rate between the MASS-PCR and Sanger sequencing (kappa value =0.929) was higher than that between the MASS-PCR and ARMS-PCR (kappa value =0.821). There were 20 samples had inconsistent results among the three assays. For these samples, 11 positive samples were verified by the MASS-PCR and Sanger sequencing. Besides, 3 negative samples in Sanger sequencing were detected to be positive in MASS-PCR and ARMS-PCR. The ROC area under the curve (AUC) of assay panels was 0.930 referring to ARMS-PCR, and 0.967 as Sanger sequencing was referred to. Conclusions: Our study demonstrated a higher accuracy and sensitivity of MASS-PCR than ARMS-PCR. Therefore, MASS-PCR could be used in clinical practice to detect gene mutations in lung cancer patients.

A comparison of MASS-PCR and ARMS-PCR for the detection of lung cancer gene mutation.

BackgroundTargeted therapy has been proven to be effective in lung cancer patients with specific driver gene mutations. At present, Sanger sequencing is still the gold standard in clinical practice to detect mutation, and amplification refractory mutation system PCR (ARMS-PCR) has become widely used due to its higher sensitivity and less limitation compared with Sanger sequencing. Mutation-selected amplification specific system PCR (MASS-PCR) is a novel gene detection technique with high specificity and sensitivity. This study aimed to compare the accuracy and sensitivity of ARMS-PCR and MASS-PCR and purposed to make an alternative choice in gene mutation detection in lung cancer.MethodA total of 293 formalin-fixed paraffin-embedded (FFPE) tissues were collected from 293 patients with lung cancer from 2017 to 2018. The sample mutation statuses were evaluated by ARMS-PCR and MASS-PCR. Sanger sequencing was also conducted to confirm the results further. The consistency of ARMS-PCR and MASS-PCR were analyzed, and receiver operating characteristic (ROC) curve was drawn to assess the sensitivity and specificity of MASS-PCR.ResultsThe consistency rate between the MASS-PCR and Sanger sequencing (kappa value =0.929) was higher than that between the MASS-PCR and ARMS-PCR (kappa value =0.821). There were 20 samples had inconsistent results among the three assays. For these samples, 11 positive samples were verified by the MASS-PCR and Sanger sequencing. Besides, 3 negative samples in Sanger sequencing were detected to be positive in MASS-PCR and ARMS-PCR. The ROC area under the curve (AUC) of assay panels was 0.930 referring to ARMS-PCR, and 0.967 as Sanger sequencing was referred to.ConclusionsOur study demonstrated a higher accuracy and sensitivity of MASS-PCR than ARMS-PCR. Therefore, MASS-PCR could be used in clinical practice to detect gene mutations in lung cancer patients.

The diagnostic value of circulating tumor cells and ctDNA for gene mutations in lung cancer.

PurposeDetecting gene mutations by two competing biomarkers, circulating tumor cells (CTCs) and ctDNA has gradually paved a new diagnostic avenue for personalized medicine. We performed a comprehensive analysis to compare the diagnostic value of CTCs and ctDNA for gene mutations in lung cancer.MethodsPublications were electronically searched in PubMed, Embase, and Web of Science as of July 2018. Pooled sensitivity, specificity, and AUC, each with a 95% CI, were yielded. Subgroup analyses and sensitivity analyses were conducted. Quality assessment of included studies was also performed.ResultsFrom 4,283 candidate articles, we identified 47 articles with a total of 7,244 patients for qualitative review and meta-analysis. When detecting EGFR, the CTC and ctDNA groups had pooled sensitivity of 75.4% (95% CI 0.683–0.817) and 67.1% (95% CI 0.647–0.695), respectively. When testing KRAS, pooled sensitivity was 38.7% (95% CI 0.266–0.519) in the CTC group and 65.1% (95% CI 0.558–0.736) in the ctDNA group. The diagnostic performance of ctDNA in testing ALK and BRAF was also evaluated. Heterogeneity among the 47 articles was acceptable.ConclusionctDNA might be a more promising biomarker with equivalent performance to CTCs when detecting EGFR and its detailed subtypes, and superior diagnostic capacity when testing KRAS and ALK. In addition, the diagnostic performance of ctDNA and CTCs depends on the detection methods greatly, and this warrants further studies to explore more sensitive methods.

Next-generation sequencing of circulating tumor DNA for detection of gene mutations in lung cancer: implications for precision treatment.

BackgroundLung cancer remains a major global health problem, which causes millions of deaths annually. Because the prognosis is mainly determined by the stage of lung cancer, precise early diagnosis is of great significance to improve the survival and prognosis. Circulating tumor DNA (ctDNA) has been recognized as a sensitive and specific biomarker for the detection of early- and late-stage lung cancer, and next-generation sequencing (NGS) of ctDNA has been accepted as a noninvasive tool for early identification and monitoring of cancer mutations. This study aimed to assess the value of NGS-based ctDNA analysis in detecting gene mutations in lung cancer patients.MethodsA total of 101 subjects with pathological diagnosis of lung cancer were enrolled, and blood samples were collected. ctDNA samples were prepared and subjected to NGS assays.ResultsThere were 31 cases harboring 40 gene mutations, and EGFR was the most frequently mutated gene (27.72%). In addition, there were seven cases with double mutations and one case with triple mutations, with EGFR p.T790M mutation exhibiting the highest frequency.ConclusionOur findings demonstrate that NGS of ctDNA is effective in detecting gene mutations in lung cancer patients, and may be used as a liquid biopsy for lung cancer, which facilitates the development of precision treatment regimens for lung cancer.

Applicable Value of AMSS-PCR in Lung Cancer Gene Mutation Detection

背景与目的肺癌驱动基因检测具有重要意义，目前检测方法多样，临床适用性有差异。本研究旨在比较基于扩增阻碍突变系统-聚合酶链反应(Amplification Refractory Mutation System-polymerase chain reaction, ARMS-PCR)技术的试剂盒与一代测序及ARMS-qPCR检测肺癌突变基因的敏感性和特异性，探究突变位点特异扩增法(Amplification Mutation Specific System, AMSS)-PCR技术在肺癌突变基因检测中的应用价值。方法对前期已行ARMS-PCR检测的肿瘤标本进行一代测序及试剂盒检测，比较各种方法的检测结果，并对检测结果进行统计学分析。结果本研究共收集了309例肺癌标本。试剂盒与一代测序符合率97.41%，ARMS-PCR的符合率97.73%。试剂盒与一代测序、试剂盒与实时定量聚合酶链反应(quantitative real-time polymerase chain reaction, qPCR)、qPCR与一代测序一致性检验的Kappa值分别为0.946、0.953、0.913。试剂盒以一代测序为参照的受试者工作特征曲线(receiver operating characteristic curve, ROC)曲线下面积为0.976，以qPCR为参照的ROC曲线下面积为0.975。结论AMSS-qPCR技术能够有效检测肺癌突变基因，具有较好的临床应用价值。

Hotspot Mutations Detectable by Next-generation Sequencing in Exhaled Breath Condensates from Patients with Lung Cancer.

Genetic alterations occurring in lung cancer are the basis for defining molecular subtypes and essential for targeted therapies. Exhaled breath condensate (EBC) is a form of non-invasive sample that, amongst components, contains DNA from pulmonary tissue. Next-generation sequencing (NGS) was herein used to analyze mutations in EBC from patients with lung cancer. EBC was collected from 26 patients with cancer and 20 healthy controls. Amplicon-based sequencing using Ion Ampliseq Colon and Lung Cancer gene panel v2 was applied. The sequencing was successful in 17 patients and 20 controls. EBC from patients revealed 39 hotspot mutations occurring in: adenomatous polyposis coli (APC), v-raf murine sarcoma viral oncogene homolog B (BRAF), discoidin domain receptor tyrosine kinase 2 (DDR2), epidermal growth factor receptor (EGFR), erb-b2 receptor tyrosine kinase 4 (ERBB4), F-box and WD repeat domain containing 7 (FBXW7), fibroblast growth factor receptor 1 (FGFR1), FGFR3 (fibroblast growth factor receptor 3), Kirsten rat sarcoma viral oncogene homolog (KRAS), mitogen-activated protein kinase kinase 1 (MAP2K1), met proto-oncogene (MET), neuroblastoma RAS viral (v-ras) oncogene homolog (NRAS), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), phosphatase and tensin homolog (PTEN), ret proto-oncogene (RET), SMAD family member 4 (SMAD4), serine/threonine kinase 11 (STK11), and tumor protein p53 (TP53) genes. EBC from controls revealed 35 hotspot mutations. The average mutant allele fraction was higher in patients than controls. NGS can identify mutations in EBCs from patients with lung cancer. This could provide a promising non-invasive method for the assessment of gene mutations in lung cancer.

Distribution of KRAS, DDR2, and TP53 gene mutations in lung cancer: An analysis of Iranian patients.

PurposeLung cancer is the deadliest known cancer in the world, with the highest number of mutations in proto-oncogenes and tumor suppressor genes. Therefore, this study was conducted to determine the status of hotspot regions in DDR2 and KRAS genes for the first time, as well as in TP53 gene, in lung cancer patients within the Iranian population.Experimental designThe mutations in exon 2 of KRAS, exon 18 of DDR2, and exons 5–6 of TP53 genes were screened in lung cancer samples, including non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC) using PCR and sequencing techniques.ResultsAnalysis of the KRAS gene showed only a G12C variation in one large cell carcinoma (LCC) patient, whereas variants were not found in adenocarcinoma (ADC) and squamous cell carcinoma (SCC) cases. The Q808H variation in the DDR2 gene was detected in one SCC sample, while no variant was seen in the ADC and LCC subtypes. Variations in the TP53 gene were seen in all NSCLC subtypes, including six ADC (13.63%), seven SCC (15.9%) and two LCC (4.54%). Forty-eight variants were found in the TP53 gene. Of these, 15 variants were found in coding regions V147A, V157F, Q167Q, D186G, H193R, T211T, F212L and P222P, 33 variants in intronic regions rs1625895 (HGVS: c.672+62A>G), rs766856111 (HGVS: c.672+6G>A) and two new variants (c.560-12A>G and c.672+86T>C).ConclusionsIn conclusion, KRAS, DDR2, and TP53 variants were detected in 2%, 2.17% and 79.54% of all cases, respectively. The frequency of DDR2 mutation is nearly close to other studies, while KRAS and TP53 mutation frequencies are lower and higher than other populations, respectively. Three new putative pathogenic variants, for the first time, have been detected in Iranian patients with lung cancer, including Q808H in DDR2, F212L, and D186G in coding regions of TP53. In addition, we observed five novel benign variants, including Q167Q, P222P and T211T in coding sequence, and c.560-12A>G and c.672+86T>C, in intronic region of TP53. Mutations of KRAS and DDR2 were found in LCC and SCC subtypes, respectively, whereas mutations of TP53 were seen in SCC and ADC subtypes with higher frequencies and LCC subtype with lower frequency. Therefore, Iranian lung cancer patients can benefit from mutational analysis before starting the conventional treatment. A better understanding of the biology of these genes and their mutations will be critical for developing future targeted therapies.

Clinical potential of gene mutations in lung cancer.

Lung cancer is the most common cancer type worldwide and the leading cause of cancer related deaths in the United States. The majority of newly diagnosed patients present with late stage metastatic lung cancer that is inoperable and resistant to therapies. High-throughput genomic technologies have made the identification of genetic mutations that promote lung cancer progression possible. Identification of the mutations that drive lung cancer provided new targets for non-small cell lung cancer (NSCLC) treatment and led to the development of targeted therapies such as tyrosine kinase inhibitors that can be used to combat the molecular changes that promote cancer progression. Development of targeted therapies is not the only clinical benefit of gene analysis studies. Biomarkers identified from gene analysis can be used for early lung cancer detection, determine patient’s prognosis and response to therapy, and monitor disease progression. Biomarkers can be used to identify the NSCLC patient population that would most benefit from treatment (targeted therapies or chemotherapies), providing clinicians tools that can be used to develop a personalized treatment plan. This review explores the clinical potential of NSCLC genetic studies on diagnosing and treating NSCLC.

Abstract A47: Meta-analysis of MTHFR polymorphisms in lung cancer: Population health and mutations in the world

Abstract Purpose: The purpose of this meta-analysis is to identify the associations of methylene-tetra- hydrofolate reductase (MTHFR) gene mutations and smoking as risk factors for lung cancer (LC). LC is the leading cause of cancer-related death worldwide. To-date, population health in relations to the epigenetics pathways is not clearly understood. Inconsistent findings have been cumulated to-date on the case control studies of MTHFR gene mutations in LC around the world. Procedure: On-line databases were searched from PubMed (PM) and PM Central databases for meta-analyses by using a combination of key words including LC, MTHFR, and case control studies. Additional studies were located by cross reference method from located studies. For this analysis, 22 studies published within the last 17 years were identified, containing both control and LC cases of human samples. These papers were reviewed and evaluated using the criteria for the quality of studies by two raters. Relative risks (RR) were calculated for increased or decreased risks for LC. New Data Findings: Preliminary analyses included 11799 cases and 12322 controls associating MTHFR677 locus and LC in 22 studies; 6916 cases and 8526 controls for MTHFR1298 locus in 14 studies. MTHFR677 TT variant as homozygous mutation type was associated with increased LC risk for all race groups combined (pooled RR = 1.151, 95% CI = 1.045 - 1.267, p = 0.004); and also significant for subgroups of Asians (14 studies, RR = 1.080, 1.007 - 1.158, p = 0.031) and Caucasians (8 studies, RR = 1.334, 1.017-1.749, p = 0.037). Asians combined had greater mutation rates on MTHFR677 TT and TC (TT+TC=19.6+47.2=66.8% for cases and 17.8+47.3=65.1% for controls) than Caucasians (11.4+43.4=54.8% for cases and 9.2+41.9%=51.1% for controls). For association of smoking and LC risk, pooled results from 12639 cases and 11828 controls in 17 studies associating MTHFR gene and LC indicated that smoking increased LC risk (pooled RR=1.116, 1.072 - 1.162, P &amp;lt; 0.001). Conclusion: Meta-analyses of epigenetic risk factors associating gene mutations and health behaviors can provide useful insights to improve the quality of future cancer prevention and intervention studies. Further studies are needed to document population-based gene mutations in relation to epigenetics pathways for cancer prevention. Citation Format: Hsiao-Ling Chen, Shyang-Yun Pamela K. Shiao, Linda H. Chiang, Joyce Kusuma. Meta-analysis of MTHFR polymorphisms in lung cancer: Population health and mutations in the world. [abstract]. In: Proceedings of the Thirteenth Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2014 Sep 27-Oct 1; New Orleans, LA. Philadelphia (PA): AACR; Can Prev Res 2015;8(10 Suppl): Abstract nr A47.

Molecular mechanisms of lung cancer development at its different stages in nuclear industry workers

to assess mutational events in exons 5, 7, and 8 of the p53 gene and to reveal mutant p53 protein in verified cases of morphologically altered (proliferative and precancerous changes, lung cancer) and histologically unaltered, lung tissues in workers exposed to occupational radiation. The investigation used formalin-fixed paraffin-embedded unaltered and altered lung tissue blocks (FFPBs) obtained from the human radiobiological tissue repository. The shelf-life of FFPBs was 5-31 years. An immunohistochemical technique using mouse antibodies against p53 protein (<<DAKO>>, Denmark), stained with diaminobenzidine (DAB) chromogen, was employed to determine p53 protein. DNA was isolated from lung tissue FFPBs with QIAmp DNA FFPE Tissue Kit, (<<QIAGEN>>, USA). Polymerase chain reaction (PCR) was performed to amplify the p53 gene exons 5, 7, and 8 selected for examination, by applying the sequences of genes and primers, the specificity of which was checked using the online resource (http://www.ncbi.nlm.nih.gov/blast). PCR products were detected by temporal temperature gradient gel-electrophoresis and the Sanger sequencing method. The obtained DNA fragments were analyzed on a sequencer ABI Prism 3100 Genetic Analizer (<<Applied Biosystems>>, USA). Computer-aided DNA analysis was made using the BLAST program. A package of applied Statistica 6.0 programs was employed for statistical data processing. Results. Immunohistochemical analysis showed that mutant p53 protein was absent in the cells of unaltered lung tissue and the number of cells with mutant p53 protein increased in all the patients with proliferative and precancerous changes and lung cancer, suggesting p53 protein dysfunction. The total number of p53 gene mutations in exons 5, 7, and 8, if there were proliferative and precancerous lung tissue changes and lung cancer, were 25, 20, and 40%, respectively. All the found mutations were transversions (the substitution of purine for pyrimidine or, conversely), indicating the action of exogenous mutagens. The results of this investigation have confirmed other investigators' data showing that p53 gene mutations in lung cancer are observed in 40-70% of cases. The differences in the number of cases of altered lung tissue with mutations in the p53 gene (not more than 40%) and in those of p53 protein expression were found in 100%, suggesting the regulation of p53 gene function in the cell at multiple levels.

Highlights from Recent Cancer Literature

Highlights from Recent Cancer Literature