Caucasian Lung Adenocarcinoma Research Articles

Whole exome sequencing and MicroRNA profiling of lung adenocarcinoma identified risk prediction features for tumors at stage I and its substages

ObjectivesAbout 20% of stage I lung adenocarcinoma (LUAD) patients suffer a relapse after surgical resection. While finer substages have been defined and refined in the AJCC staging system, clinical investigations on the tumor molecular landscape are lacking. Materials and methodsWe performed whole exome sequencing, DNA copy number and microRNA profiling on paired tumor-normal samples from a cohort of 113 treatment-naïve stage I Taiwanese LUAD patients. We searched for molecular features associated with relapse-free survival (RFS) of stage I or its substages and validated the findings with an independent Caucasian LUAD cohort. ResultsWe found sixteen nonsynonymous mutations harbored at EGFR, KRAS, TP53, CTNNB1 and six other genes associated with poor RFS in a dose-dependent manner via variant allele fraction (VAF). An index, maxVAF, was constructed to quantify the overall mutation load from genes other than EGFR. High maxVAF scores discriminated a small group of high-risk LUAD at stage I (median RFS: 4.5 versus 69.5 months; HR = 10.5, 95% CI = 4.22–26.12, P < 0.001). At the substage level, higher risk was found for patients with high maxVAF or high miR-31; IA (median RFS: 32.1 versus 122.8 months, P = 0.005) and IB (median RFS: 7.1 versus 26.2, P = 0.049). MicroRNAs, miR-182, miR-183 and miR-196a were found correlated with EGFR mutation and poor RFS in stage IB patients. ConclusionDistinctive features of somatic gene mutation and microRNA expression of stage I LUAD are characterized to complement the survival prognosis by substaging. The findings open up more options for precision management of stage I LUAD patients.

Comprehensive analysis of PD-L1 expression, tumor-infiltrating lymphocytes, and tumor microenvironment in LUAD: differences between Asians and Caucasians

BackgroundsThe characteristics of programmed cell death protein-1 (PD-L1) expression, tumor-infiltrating lymphocytes (TILs), and tumor microenvironment (TME) in lung adenocarcinoma (LUAD) patients are closely related to immunotherapy, and there are differences between Asians and Caucasians.MethodsAcquire the transcriptome data of the Cancer Genome Atlas and Chinese LUAD patients. R software was used to analyze the differential expression of genes, prognosis, and gene function. Use CIBERSORT for TIL-related analysis and ESTIMATE for TME-related analysis.ResultsThe expression of PD-L1 in tumor tissues of Caucasian LUAD patients was lower than that in normal tissues, while there was no significant difference in Asians. There was no statistical difference between PD-L1 expression and prognosis. The composition of TILs between Caucasian and Asian LUAD patients was quite different. There was no correlation between TILs and prognosis in Caucasians. However, the higher content of resting mast cells indicated a better prognosis in Asians. The Caucasian patients with higher immune and estimate scores had a better prognosis (p = 0.021, p = 0.025). However, the Asian patients with a higher estimate score had a worse prognosis (p = 0.024). The high expression of COL5A2 (p = 0.046, p = 0.027) and NOX4 (p = 0.020, p = 0.019) were both associated with the poor prognosis in Caucasians and Asians.ConclusionThere are many differences in the characteristics of PD-L1 expression, TILs, and TME between Caucasian and Asian LUAD patients. This provides a certain hint for the selection of specific immunotherapy strategies separately for Caucasian and Asian LUAD patients.

A comparative genomics analysis of lung adenocarcinoma for Chinese population by using panel of recurrent mutations.

Previous studies have demonstrated that Chinese lung adenocarcinoma (LUAD) patients have unique genetic characteristics, however, the specific genomic features relating to the development and treatment of LUAD in the Chinese population are not fully understood. Here, we applied the ultra-deep targeted sequencing to 66 Chinese LUAD samples, accompanied by comparative analysis with 162 Caucasian LUAD in The Cancer Genome Atlas. We focused on the 68 recurrently mutated genes and results revealed that the panel-based tumor mutational burden (pTMB) is significantly higher in the Chinese LUAD (P=0.0017). Additionally, the percentage of smoking-associated C>A transversion is significantly lower in Chinese LUAD (15.5%vs. 39.7%, P=5.69×10−27), while C>T transition is more frequent in Chinese LUAD (35.8%vs. 25.7%, P=2.67×10−5), which indicated the ethnic difference in mutation types. Notably, novel driver genes (GNAS and JAK1) that are peculiar to Chinese LUAD were identified, and a more convergent distribution of mutations was observed in the Chinese cohort (P=0.012) compared with scattered mutations in Caucasian LUAD. Our results present a distinct genomic profile of Chinese LUAD compared to Caucasians LUAD and elucidate the ethnic difference in mutation distribution besides the type and rate.

Evaluation of the fully automated Idylla EGFR Mutation Assay in Chinese patients with lung adenocarcinoma.

e21716 Background: Epidermal growth factor receptor ( EGFR) mutation testing is nowadays an essential part of lung adenocarcinoma diagnosis. Its rapid detection is of utmost significance in order to ensure that patients receive timely and appropriate treatment. However, the current techniques for EGFR examination in China, ARMS-PCR and NGS, often take 3~7 days to deliver the final results. In contrast, the fully automated Idylla EGFR assay could detect 51 EGFR mutations directly from formalin-fixed, paraffin-embedded (FFPE) samples within 2.5 hours with &lt; 2 minutes of hands-on time. The test has proven both accurate and robust among Caucasian lung adenocarcinoma patients but has never been clinically validated in Chinese patients. Methods: FFPE samples were retrospectively collected from 94 lung adenocarcinoma patients followed by EGFR testing using the Idylla system. Seventy-eight samples were also previously assessed with ARMS-PCR, 9 with NGS and 7 with both. In case of discordance, repeat testing was performed on the same tissue block with a third method. The sensitivity and specificity of the Idylla EGFR assay were evaluated against ARMS-PCR or NGS. Mutations beyond the scope of detection by the Idylla EGFR assay were not included in the analyses. Results: Of the 94 tumors enrolled, 77 were stage I-II. The Idylla system was consistent with ARMS-PCR or NGS for the EGFR mutational profiles of 92 tumors: 80 positive and 12 negative. Among the 2 cases of discrepancy, one was wild-type using Idylla but were found to harbor G719X/S768I using ARMS-PCR (and confirmed by NGS), while the other one carried L858R according to Idylla, as confirmed by ARMS-PCR, but was discovered to have an additional mutation L861Q using NGS. The Idylla EGFR test had a sensitivity of 97.6%, a specificity of 100% and an overall concordance of 97.9%. Conclusions: The Idylla system provides a rapid, accurate and user-friendly solution to EGFR characterization, especially in time-sensitive scenarios where special expertise and staff training could be a challenge.

Expression level of ACE2 in lung adenocarcinoma.

e21022 Background: 2019-nCoV, a novel coronavirus (2019-nCoV), has infected tens of thousands of people in Wuhan, Hubei Province, China. This new coronavirus has led to hundreds of deaths, and especially threatened people with underlying diseases. ACE2 was reported as the 2019-nCoV putative receptor. The expression abundance of ACE2 may cause different disease progressions. Here, we evaluated the expression profile of ACE2 from 283 samples in lung adenocarcinoma . Methods: 283 samples from the public datasets (GEO: GSE31210 and GEO: GSE2109) were grouped by tissue, ethnicity and gender. The data was normalized by the RMA algorithm. Student 's t-test was used to compare the expression of ACE2 in different groups . Results: The expression level of ACE2 of primary lung tumor was significantly higher than normal lung tissue ( p &lt; 0.0001). ACE2 was significantly differential-expressed between Asian and Caucasian lung adenocarcinoma patients ( p &lt; 0.0001). However, no significant difference of the expression of ACE2 was observed by gender ( p = 0.33). Conclusions: ACE2 was highly expressed in primary lung adenocarcinoma , compared with normal lung tissues. The expression level of ACE2 was higher in Asian lung adenocarcinoma patients than Caucasian’s. These conclusions imply that Asian people with lung adenocarcinoma may be more vulnerable to 2019-nCoV.

Multiple genome pattern analysis and signature gene identification for the Caucasian lung adenocarcinoma patients with different tobacco exposure patterns.

BackgroundWhen considering therapies for lung adenocarcinoma (LUAD) patients, the carcinogenic mechanisms of smokers are believed to differ from those who have never smoked. The rising trend in the proportion of nonsmokers in LUAD urgently requires the understanding of such differences at a molecular level for the development of precision medicine.MethodsThree independent LUAD tumor sample sets—TCGA, SPORE and EDRN—were used. Genome patterns of expression (GE), copy number variation (CNV) and methylation (ME) were reviewed to discover the differences between them for both smokers and nonsmokers. Tobacco-related signature genes distinguishing these two groups of LUAD were identified using the GE, ME and CNV values of the whole genome. To do this, a novel iterative multi-step selection method based on the partial least squares (PLS) algorithm was proposed to overcome the high variable dimension and high noise inherent in the data. This method can thoroughly evaluate the importance of genes according to their statistical differences, biological functions and contributions to the tobacco exposure classification model. The kernel partial least squares (KPLS) method was used to further optimize the accuracies of the classification models.ResultsForty-three, forty-eight and seventy-five genes were identified as GE, ME and CNV signatures, respectively, to distinguish smokers from nonsmokers. Using only the gene expression values of these 43 GE signature genes, ME values of the 48 ME signature genes or copy numbers of the 75 CNV signature genes, the accuracies of TCGA training and SPORE/EDRN independent validation datasets all exceed 76%. More importantly, the focal amplicon in Telomerase Reverse Transcriptase in nonsmokers, the broad deletion in ChrY in male nonsmokers and the greater amplification of MDM2 in female nonsmokers may explain why nonsmokers of both genders tend to suffer LUAD. These pattern analysis results may have clear biological interpretation in the molecular mechanism of tumorigenesis. Meanwhile, the identified signature genes may serve as potential drug targets for the precision medicine of LUAD.

P2.03b-009 Brain Metastasis and Epidermal Growth Factor Receptor Mutations in Croatian Caucasians with Lung Adenocarcinoma: Topic: Brain Meta

The brain is a common site of metastasis in non-small cell lung cancer (NSCLC). The aim of this study was two-fold: 1) to determine the incidence of brain metastasis (BM) in Caucasian lung adenocarcinoma patients with epidermal growth factor receptor (EGFR) mutations and 2) to evaluate the frequencies and potential relationship of the different EGFR mutations with BM. A retrospective cohort study was conducted at a Croatian tertiary hospital (Clinic for Respiratory Diseases “Jordanovac”) using data collected from medical records. Caucasian patients with primary NSCLC who were tested for EGFR mutation status between January 2014 and October 2015 were included. Of 1040 NSCLC samples tested, 122 (11.7%) patients with lung adenocarcinoma harbored EGFR mutations; six EGFR positive (+) patients (four with BM) had repeat EGFR testing. The majority of EGFR mutants were females (n= 90, 77.6%), non-smokers (including never-smokers and former-smokers; n= 95, 92.2%), diagnosed with advanced disease (stage IIIB/IV) at first presentation (n= 75, 68.8%), and median age at initial diagnosis of primary lung cancer was 65 years (35 - 90). Twenty-three (19.8%) of 116 EGFR+ patients were diagnosed with BM; for six EGFR+ patients, data about BM was missing. Most were 64 years of age or younger (n= 15, 65.2%) at diagnosis of BM (median age: 62 years, 48 - 72). Synchronous BM disease at initial diagnosis of lung cancer was found in 43.5% of EGFR+ patients with BM (n= 10). There were more EGFR+ women with BM (n= 20, 87%) than men. Single exon 19 deletion and exon 21 L858R mutations were the most common subtypes in both EGFR+ patients without BM (n= 44, 47.3% and n= 27, 27.8%, respectively) and with BM (n= 13, 56.5% and n= 5, 21.7%, respectively). One BM patient (4.3%) had a double mutation (exon 19 and 21), while six non-BM patients (6.2%) had simultaneous pairings, most commonly between exon 19 and 20 (n=3, 3.1%). Although exon 18 mutations were seen in six patients without BM (6.2%), none were found in BM+EGFR+ patients. Exon 20 T790M mutation occurred in 17.4% of BM patients (n= 4) versus 15.3% of non-BM patients (n= 15). Rare EGFR double mutations (exon 18 and 20) were found in two non-BM patients (2.2%). Larger long-term prospective studies to explore and confirm these results in BM+EGFR+ patients are warranted. In the era of precision oncology, molecular testing of EGFR mutations may further clarify the pathogenesis of lung cancer-associated BM.

Abstract 4168: Mig-6 ablation cooperates with oncogenic Kras in promoting mouse lung tumorigenesis

Abstract Lung tumorigenesis is a stochastic multistep process, during which different gene mutations accumulate, and Kras is an oncogene with the most frequent mutation in the Caucasian lung adenocarcinoma. Although Mig-6 (mitogen-inducible gene 6) has been shown to be a tumor suppressor gene in lung, skin and uterus, the interplay between Mig-6 and Kras in lung tumorigenesis remains elusive. Here, we found Mig-6 expression was down-regulated in oncogenic KrasG12D-induced lung tumors and Mig-6d/dKrasG12D mice showed an earlier onset of pulmonary tumor development and a significantly reduced life span as compared to KrasG12D mice though no obvious lung phenotype was observed in Mig-6d/d mice. Meanwhile, ablation of Mig-6 can change the lung epithelial cell fate in KrasG12D mice. Furthermore, lung tumor tissues of Mig-6d/dKrasG12D mice showed decreased cellular apoptosis, elevated EGF/Akt signaling and increased severity of inflammation as compared to those of KrasG12D mice. Thus, ablation of Mig-6 cooperated with oncogenic Kras in promoting lung tumorigenesis and this novel murine model of lung cancer can be applied for future study. Citation Format: Jian Liu, Sung-Nam Cho, Nili Jin, Seyed Javad Moghaddam, Jennifer Gilbert, Ignacio Wistuba, Francesco J. DeMayo. Mig-6 ablation cooperates with oncogenic Kras in promoting mouse lung tumorigenesis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4168.

Prognostic value of the KRAS G12V mutation in 841 surgically resected Caucasian lung adenocarcinoma cases.

Background:Identifying patients who will experience lung cancer recurrence after surgery remains a challenge. We aimed to evaluate whether mutant forms of epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma viral oncogene homolog (KRAS) (mEGFR and mKRAS) are useful biomarkers in resected non-small cell lung cancer (NSCLC).Methods:We retrospectively reviewed data from 841 patients who underwent surgery and molecular testing for NSCLC between 2007 and 2012.Results:mEGFR was observed in 103 patients (12.2%), and mKRAS in 265 (31.5%). The median overall survival (OS) and time to recurrence (TTR) were significantly lower for mKRAS (OS: 43 months; TTR: 19 months) compared with mEGFR (OS: 67 months; TTR: 24 months) and wild-type patients (OS: 55 months; disease-free survival (DFS): 24 months). Patients with KRAS G12V exhibited worse OS and TTR compared with the entire cohort (OS: KRAS G12V: 26 months vs Cohort: 60 months; DFS: KRAS G12V: 15 months vs Cohort: 24 months). These results were confirmed using multivariate analyses (non-G12V status, hazard ratio (HR): 0.43 (confidence interval: 0.28–0.65), P<0.0001 for OS; HR: 0.67 (0.48–0.92), P=0.01 for TTR). Risk of recurrence was significantly lower for non-KRAS G12V (HR: 0.01, (0.001–0.08), P<0.0001).Conclusions:mKRAS and mEGFR may predict survival and recurrence in early stages of NSCLC. Patients with KRAS G12V exhibited worse OS and higher recurrence incidences.

K-Ras Mutations in Non-Small-Cell Lung Cancer: Prognostic and Predictive Value.

Non-small-cell lung cancer (NSCLC) is a heterogeneous disease due to the presence of different clinically relevant molecular subtypes. Until today, several biological events have been identified in lung adenocarcinoma, including epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase (ALK) translocations, offering new hopes to patients with metastatic disease. Unfortunately, in approximately 50% of adenocarcinoma and for those harbouring K-RAS mutations, the most frequent mutation in Caucasian lung adenocarcinoma, so far no specific drug demonstrated efficacy. The rat sarcoma (RAS) genes, including H-RAS, K-RAS, and N-RAS, encode a family of proteins regulating cell growth, differentiation, and apoptosis. K-RAS mutations are present in 20–30% of NSCLC and occur most commonly, but not exclusively, in adenocarcinoma histology and life-long smokers. Although in colorectal cancer patients K-RAS mutations represent a validated negative predictive biomarker for treatment with anti-EGFR monoclonal antibodies, their role in selecting specific treatment for NSCLC patients remains undefined. Aim of the present paper is to critically analyze the prognostic and predictive value of K-RAS mutations in NSCLC.