1 Supplementary Material 3 Tumour Biol. 4 5 6 VCP Gene Variation Predicts Outcome of Advanced Non-Small-Cell Lung Cancer Platinum-Based Chemotherapy 7 8 9 10 Running head: VCP variation predicts NSCLC chemotherapy outcome J. Peng 1, PhD; L. X. Yang, MD; X. Y. Zhao 1, PhD; Z. Q. Gao 3, MD; J. Yang 4, MD; 11 W. T. Wu 1, PhD; H. J. Wang 1, PhD; J. C. Wang 1, PhD; J. Qian 1, MS; H. Y. Chen 1, PhD; 1 L. Jin 1, PhD; C. X. Bai 5, MD; B. H. Han, MD; W. M. Wang 6, PhD & D. R. Lu 1, PhD 13 14 1 State Key Laboratory of Genetic Engineering and MOE Key Laboratory of 15 Contemporary Anthropology, Institute of Genetics, School of Life Sciences, Fudan 16 University, Shanghai, China; Department of Cardiothoracic Surgery,Changhai 17 Hospital of Shanghai, Second Military Medical University, Shanghai, China; 18 3 Department of Respiratory Disease, Shanghai Chest Hospital, Shanghai Jiaotong 19 University, Shanghai, China; 4 Department of Toxicology, School of Public Health, 0 Hangzhou Normal University, Hangzhou, China; 5 Department of Pulmonary 1 Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; 6 Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine Technique, 3 College of Life Sciences, China Jiliang University, Hangzhou, China 4 1
5 * Correspondence to: 6 Prof. D. R. Lu, School of Life Sciences, Fudan University, Shanghai, 00433, China. 7 8 9 30 31 Tel: +86-01-6564799; Fax: +86-01-6564799; E-mail: drlu@fudan.edu.cn; and Prof. W. M. Wang, College of Life Sciences, China Jiliang University, Hangzhou, 310018, China. Tel: +86-0571-8691444; Fax: +86-0571-8691444; E-mail: wwm1970@hotmail.com Both authors contributed equally to this work.
3 33 34 35 36 37 38 39 40 41 4 43 44 45 46 47 48 49 50 51 5 53 Patients and methods Patient recruitment and study design Patients with histologically confirmed stage IIIA-IV NSCLC who fulfilled all of the following criteria were eligible for this study: at least 18 years of age; the presence of a measurable lesion; Eastern Cooperative Oncology Group performance status (ECOG PS) between 0 and ; absolute neutrophil count (ANC) 1.5 10 9 cells/l; platelets count 100 10 9 cells/l; serum creatinine 1.5 upper limit of normal; aspartate aminotransferase (AST) and alanine aminotransferase (ALT) 1.5 upper limit of normal; creatinine clearance 60 ml/min; availability of informed consent; and adherence to the treatment schedule. Patients were excluded if they had prior surgery, radiotherapy, or concurrent chemoradiotherapy for this cancer; prior malignancy in the past 5 years (except for treated non-melanoma skin cancer, carcinoma in situ of the uterine cervix, or any other cured malignant tumor); active congestive heart failure, cardiac arrhythmia, or recent myocardial infarction; severe psychological factors; or uncontrolled clinical infections. We systematically collected patients clinical data, including age, gender, ECOG PS, family history of cancer, tumor-node-metastasis (TNM), pathological and histological typing, and smoking status. Survival data were collected from the Social Security Death Index, follow-up calls, and inpatient and outpatient clinical medical records. There was no significant difference observed in the distribution of demographic and clinical features between hospitals. Medical history, performance status, routine clinical biochemistry tests, chest 3
54 55 56 57 58 59 60 61 6 63 64 65 radiographs, and computed tomography scans of the chest were evaluated before any treatment course was started. The 663 eligible patients were treated with first-line platinum-based chemotherapy: cisplatin 75 mg/m, or carboplatin area under concentration-time curve (AUC) 5, both administered on day 1 every 3 weeks, in combination with navelbine, 5 mg/m, day 1 and day 8 every 3 weeks, or with gemcitabine, 150 mg/m, day 1 and day 8 every 3 weeks, or with paclitaxel, 175 mg/m, day 1 every 3 weeks, or with docetaxel, 75 mg/m, day 1 every 3 weeks. These chemotherapeutic drugs were administered intravenously for 6 cycles. The evaluation and quantification of toxicities during chemotherapy were determined according to the National Cancer Institute Common Toxicity Criteria version 3.0, while the assessment and classification of treatment response were in accordance with the Response Evaluation Criteria in Solid Tumors (RECIST) guidelines. 66 67 68 69 70 71 Genotyping To verify the genotyping results, quality control standards were set as follows: SNP genotyping call rate > 0.95, MAF 0.05, and GenCall score > 0.. The genotyping result had a concordance of 100% between replicates. GenomeStudioV010.1 and GeneMap software were used to analyze the data and generate reports. 4
7 Supplemental Table 1 Association between VCP variants and treatment efficacy Polymorphisms Genotype Event/overall * OR (95% CI) P Response rate rs1053318 C/C 106/541 1.000 (Reference) A/C 13/109 1.857 (0.99 3.479).053 A/A 1/7.06 (0.3 17.71).53 rs51449 G/G 40/19 1.000 (Reference) A/G 50/37 1.491 (0.93.384).096 A/A 30/138 0.99 (0.573 1.715).976 rs074549 A/A 53/79 1.000 (Reference) A/G 46/98 1.58 (0.809 1.955).308 G/G 19/73 0.659 (0.355 1.).185 Clinical benefit rs1053318 C/C 43/541 1.000 (Reference) A/C 8/109 1.353(0.85.19).31 A/A 3/7 6.6(1.33 9.648).01 rs51449 G/G 156/19 1.000 (Reference) A/G 50/37 1.96(0.84.038).61 A/A 111/138 1.001(0.567 1.766).999 rs074549 A/A 17/79 1.000 (Reference) A/G 34/98 0.936(0.64 1.40).747 G/G 60/73 0.686(0.348 1.353).77 Polymorphisms Genotype MST, month HR (95% CI) P PFS rs1053318 C/C 6.57 1.000 (Reference) A/C 6.0 1.076 (0.844 1.37).556 A/A.00.113 (0.864 5.168).101 rs51449 G/G 6.67 1.000 (Reference) A/G 6.57 1.093 (0.877 1.36).47 A/A 6.0 0.944 (0.718 1.40).678 rs074549 A/A 6.37 1.000 (Reference) A/G 6.57 0.961 (0.787 1.174).698 G/G 5.90 0.849 (0.616 1.17).31 OS rs1053318 C/C 18.43 1.000 (Reference) A/C 17.40 1.0 (0.798 1.309).864 A/A / 0.440 (0.104 1.384).160 rs51449 G/G 17.83 1.000 (Reference) A/G 17.60 1.005 (0.811 1.45).966 A/A 1.00 0.889 (0.681 1.160).385 rs074549 A/A 18.57 1.000 (Reference) A/G 17.37 1.154 (0.949 1.404).151 G/G.83 0.89 (0.597 1.151).63 5
73 Abbreviation: CI, confidence interval; MST, median survival time; HR, hazard ratio; PFS, 74 progression-free survival; OS, overall survival. 75 * Numbers indicate: CR+PR (response rate); CR+PR+SD (clinical benefit) 76 Data were calculated by unconditional logistic regression and adjusted for age, gender, and type 77 of treatment regimen. 78 Data were estimated from Multivariate Cox proportional hazards models and adjusted for age, 79 gender, and type of treatment regimen. 6