Genome-Wide Association Study Of Prognosis And Toxicity In Non-Small Cell Lung Cancer Patients Receiving Platinum-based Chemotherapy

Lung cancer, predominantly non-small-cell lung cancer (NSCLC), is the most common cancer around the world. In China, the morbidity and mortality of lung cancer have been increasing rapidly in last two decades, which is believed to be mainly due to continuous increases in tobacco consumption and environmental pollution. The current standard treatment for patients with early stage NSCLC is surgical resection, with or without adjuvant chemotherapy. However, most patients are diagnosed at advanced stage, where platinum-based chemotherapy is the mainstay of treatment.The traditional TNM staging system is not useful for predicting response to therapy, and molecular biomarkers can add value in this setting. It has been suggested that the discovery and application of molecular biomarkers to incorporate with traditional clinical prognostic factors could guide individualized treatment and improve the outcomes of cancer patients. Until now, many researches revealed that genetic variants, such as single nucleotide polymorphisms (SNPs) in certain genes involved in some biological pathways, play an important role in the prognosis and toxicity of NSCLC receiving platinum-based chemotherapy and thus inter-individual survival variability between patients. Genome-wide association studies (GWAS), emerging with the completion of Human Genome Project as well as promotion of HapMap and advances in genotyping technology, is one of the powerful tools for genetic susceptibility study of complex diseases. GWAS make no assumptions about the genomic location of the causal variants, are expected to complement the candidate gene approach.To date, only two papers had published on genome-wide association studies of lung cancer survival. However, no GWAS focus on NSCLC survival and toxicity receiving platinum-based chemotherapy in Chinese. In 2011, our group reported the first multistage GWAS of lung cancer susceptibility in the Chinese population. Most of NSCLC patients receiving platinum-based chemotherapy in this GWAS discovery phase contained data on overall survival and myelosuppression toxicity data. Based on the platform of our previous GWAS data, we conduct the first GWAS among NSCLC patients receiving platinum-based chemotherapy to identify some specific susceptibility loci for survival and myelosuppression in Chinese.We conducted a GWAS scan by genotyping 906,703 SNPs for association with survival in 535 advanced NSCLC and with myelosuppression toxicity in 333 NSCLC in Han Chinese. Fast-track replications were conducted in independent NSCLC subjects. The results of our study will be helpful for determining the genetic biomarkers for NSCLC survival and toxicity receiving platinum-based chemotherapy and provide theoretic guideline for personalized therapy.Part Ⅰ:Genome-Wide Association Study of Prognosis in Non-Small Cell Lung Cancer Patients Receiving Platinum-based ChemotherapyGWAS is one of the powerful tools for genetic susceptibility study of complex diseases. To date, only two groups conducted GWAS for lung cancer survival. Huang YT et al tested 100 early-stage NSCLC patients as a GWAS discovery set and 89 NSCLC patients as a validation set in Caucasian population. Five SNPs were validated with NSCLC survival in the replication cohort. Sato Y et al scanned 105 advanced NSCLC patients treated with carboplatin and found three SNPs were identified as new prognostic biomarker candidates for advanced NSCLC in Japanese, while no replication was conducted in this research. As no GWAS was done for NSCLC survival in Chinese, we will conducted GWAS of prognosis in NSCLC patients receiving platinum-based chemotherapyIn order to construct a relatively homogenous population with same treatment, our current study was restricted to stage Ⅲ or Ⅳ NSCLC patients treated with first-line platinum based chemotherapy without surgery. We conducted a genome-wide scan in 535 advanced-stage NSCLC patients from two independent cohorts (307 from Nanjing and 228 from Beijing). Specifically,307 patients recruited at the Affiliated Cancer Hospital and the First Affiliated Hospital of Nanjing Medical University (Nanjing Study), and 228 patients from the Cancer Hospital, Chinese Academy of Medical Sciences (Beijing Study), were included in the discovery set. The first replication included 340 NSCLC patients recruited from Nanjing Thoracic Hospital and Shanghai Chest Hospital (Southeastern China), and the second replication included 409 NSCLC patients from the Massachusetts General Hospital, Boston, USA (Harvard cohort). For fast-track replication, we selected 12 independent top SNPs that had (i) P<1×10-4 for all GWAS samples and (ii) a consistent association at P< 0.05 in both the Nanjing study and the Beijing study. Five SNPs that were found to be associated with overall survival at P values lower than 0.05 and had the same association direction as the GWAS scan were further genotyped in the second Caucasian validation set. All patients had histopathologically or cytologically confirmed NSCLC which was reviewed by at least two local pathologists.In the GWAS scan, we found 12 independent top SNPs associated with NSCLC survival (P<1×104). We tested these 12 SNPs in the first replication phase and found 5 SNPs remaining associated with lung cancer survival in the same direction. These 5 SNPs were rs7629386 at 3p22.1 region (nearby CTNNB1, P=3.63×10-5), rs969088 at 5p14.1 region (nearby CDH9, P=1.75×10-6), rs41997 at 7q31.31 region (near CFTR-WNT2-ST7, P=4.19×10"’), rs12000445 at 9p21.3 region (nearby HuB, P= 7.12×10-6) and rs3850370 at 14q24.3 region (nearby SNW1-ALKBH1-NRXN3, P= 2.92×10-5). The minor allele of three SNPs (rs7629386 at 3p22.1, rs969088 at 5p14.1 and rs3850370 at 14q24.3) were associated with worse NSCLC survival while 2 (rs41997 at 7q31.31 and rs12000445 at 9p21.3) were associated with better NSCLC survival. In addition, rs7629386 at 3p22.1 (CTNNB1) and rs3850370 at 14q24.3 (SNW1-ALKBH1-NRXNS) were further replicated in the Caucasian population.In this three-stage genome-wide association studies, we identified five SNPs as markers for survival of advanced-stage NSCLC patients treated with first-line platinum-based chemotherapy in Chinese Han populations. Two of these SNPs, rs7629386 and rs3850370, could also be markers for survival among Caucasian patients. These results advanced our understanding of the mechanism of lung cancer prognosis and highlighted potential pathways that integrate genetic variants in personal therapyPart Ⅱ:Genome-Wide Association Study of Myelosuppression Toxicity in Non-Small Cell Lung Cancer Patients Receiving Platinum-based ChemotherapyChemotherapy with platinum agents is the standard treatment for NSCLC. These platinum-based regimens bring modest benefits but also life-threatening toxicity, especially myelosuppression. Beyond the impact on quality of life, severe myelosuppression toxicity may necessitate dose reduction, delay, or even cessation of treatment. Studies have suggested effectiveness and toxicities of the platinum-based chemotherapy vary greatly between individuals. Thus, the identification of predictive markers for optimal individualized therapy with minimal toxicity and better efficacy remains a continuing challenge in NSCLC treatment. Many studies have been conducted to explore polymorphisms in candidate genes and platinum-induced myelosuppression in NSCLC. No GWAS was conducted in myelosuppression to platinum-based chemotherapy in NSCLC patients.We conducted a genome wide scan of 906,703 single-nucleotide polymorphisms (SNPs) in 333 NSCLC patients.24 independent top SNPs (P<1×10-4) were genotyped for the 378 patients in the validation phase by iPLEX Sequenom MassARRAY platform. All the subjects were recruited from the Cancer Hospital of Jiangsu Province, the First Affiliated Hospital of Nanjing Medical University, and Nanjing Thoracic Hospital (replication phase only), Nanjing, China. All the patients had histopathologically or cytologically confirmed incident NSCLC, without previous chemo-or radio-therapy but given the first-line platinum-based chemotherapy. Acquired platinum-induced myelosuppression toxicities were evaluated according to Common Terminology Criteria Adverse Events Version (CTCAE 3.0). Myelosuppression was classified into grade 1 to 4 as the nadir value for leukocytes, neutrophils, hemoglobin and platelets at sampling occasions 21 (±3) days post each chemotherapy cycle. The highest myelosuppression toxicity grade during the initial 3 cycles of therapy was collected for analysis.Twenty-four independent SNPs, associated with platinum-induced myelosuppression in NSCLC in the discovery phase (P<10-4), were tested in the replication phase. Among the 24 SNPs, rs12883763 at 14q21.3 (nearby MDGA2-POLE2-Arf6) was still significantly associated with platinum-induced myelosuppression (Dominant model:OR=1.84,95%CI=1.22-2.76, P=0.003; Additive model:OR=1.37,95%CI=1.03-1.82, P=0.03). In the combined analyses, the minor T allele of rs 12883763 also significantly increase the risk of myelosuppression (Dominant model:OR=2.29,95%CI=1.71-3.07, P=3.02×10-8; Additive model:OR=1.62,95%CI=1.31-2.00, P=6.18×10-6). No heterogeneity was found in any stratified analysis.Our results indicated that genetic variation rsl2883763 at 14q21.3 was identified that may be independent factor with platinum-induced myelosuppression in NSCLC. Further studies with larger sample size or different ethnic background are needed to validate and extend our findings.