#METABOLOMICS WORKBENCH zj1234_20220217_030421 DATATRACK_ID:3090 STUDY_ID:ST002120 ANALYSIS_ID:AN003471 PROJECT_ID:PR001345 VERSION 1 CREATED_ON March 31, 2022, 7:10 am #PROJECT PR:PROJECT_TITLE Non-Small Cell Lung Cancer Detection and Subtyping by UPLC-HRMS Based Tissue PR:PROJECT_TITLE Metabolomics PR:PROJECT_TYPE non-targeted metabolomics analysis PR:PROJECT_SUMMARY Non-small cell lung cancer (NSCLC) is the prevalent histological subtype of lung PR:PROJECT_SUMMARY cancer. In this study, we performed ultraperformance liquid chromatography - PR:PROJECT_SUMMARY high resolution mass spectrometry (UPLC-HRMS) based metabolic profiling of 227 PR:PROJECT_SUMMARY tissue samples from 79 lung cancer patients with adenocarcinoma (AC) or squamous PR:PROJECT_SUMMARY cell carcinoma (SCC). oPLS-DA analysis showed detections of AC, SCC and NSCLC PR:PROJECT_SUMMARY were possible with good accuracies (91.3%, 100% and 88.3%), sensitivities PR:PROJECT_SUMMARY (85.7%, 100% and 83.9%), and specificities (94.3%, 100% and 90.7%), PR:PROJECT_SUMMARY respectively. Valine, sphingosine, Glu γ-methyl ester and LPC 16:0 contributed PR:PROJECT_SUMMARY to AC detection and significantly altered in tumor. Valine, sphingosine, LPC PR:PROJECT_SUMMARY 18:1 and leucine derivative contributed to SCC detection. Classification of AC PR:PROJECT_SUMMARY and SCC was also possible (accuracy of 96.8%, sensitivity of 98.2% and PR:PROJECT_SUMMARY specificity of 85.7%) with a panel of 5 metabolites, of which valine and PR:PROJECT_SUMMARY creatine were significantly changed. The classification models were confirmed PR:PROJECT_SUMMARY with external validation sets, showing promise for NSCLC detection and PR:PROJECT_SUMMARY subtyping. PR:INSTITUTE OUC PR:DEPARTMENT Department of Medicine and Pharmacy PR:LABORATORY Analytical chemistry PR:LAST_NAME Zang PR:FIRST_NAME Xiaoling PR:ADDRESS No. 5 Yushan Road, Qingdao, Shandong, China PR:EMAIL zangxiaoling@ouc.edu.cn PR:PHONE 15863037065 PR:FUNDING_SOURCE OUC PR:PROJECT_COMMENTS OUC PR:PUBLICATIONS OUC PR:CONTRIBUTORS OUC #STUDY ST:STUDY_TITLE Feasibility of detecting AC and SCC using UPLC-HRMS based tissue metabolomics ST:STUDY_SUMMARY UPLC-HRMS analysis was performed on AC and SCC patients. OPLSDA classfication ST:STUDY_SUMMARY was performed on tumor vs. ANT&DNT samples. Panels of discriminant features were ST:STUDY_SUMMARY identified.The biomarkers identified in discovery set samples for each binary ST:STUDY_SUMMARY classification were confirmed by using a set of validation samples, which were ST:STUDY_SUMMARY run separately. Additionally, paired analysis shows the abundance of ST:STUDY_SUMMARY discriminant metabolic features has significant altered in tumor tissues ST:STUDY_SUMMARY compared to corresponding DNT and ANT samples, indicating metabolic ST:STUDY_SUMMARY reprogramming during tumorigenesis in AC and SCC. ST:INSTITUTE Ocean University of China ST:LAST_NAME Zang ST:FIRST_NAME Xiaoling ST:ADDRESS No.5 Yushan Road, Qingdao, Shandong, China ST:EMAIL xlingzang@163.com ST:PHONE +86 0532 82032064 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:GENDER Male and female #FACTORS #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - 138ade_norm Tissue type:adenorm RAW_FILE_NAME=138 SUBJECT_SAMPLE_FACTORS - 143ade_norm Tissue type:adenorm RAW_FILE_NAME=143 SUBJECT_SAMPLE_FACTORS - 146ade_norm Tissue type:adenorm RAW_FILE_NAME=146 SUBJECT_SAMPLE_FACTORS - 152ade_norm Tissue type:adenorm RAW_FILE_NAME=152 SUBJECT_SAMPLE_FACTORS - 155ade_norm Tissue type:adenorm RAW_FILE_NAME=155 SUBJECT_SAMPLE_FACTORS - 158ade_norm Tissue type:adenorm RAW_FILE_NAME=158 SUBJECT_SAMPLE_FACTORS - 161ade_norm Tissue type:adenorm RAW_FILE_NAME=161 SUBJECT_SAMPLE_FACTORS - 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5squ_side Tissue type:squside RAW_FILE_NAME=5 SUBJECT_SAMPLE_FACTORS - 151squ_tumor Tissue type:squtumor RAW_FILE_NAME=151 SUBJECT_SAMPLE_FACTORS - 169squ_tumor Tissue type:squtumor RAW_FILE_NAME=169 SUBJECT_SAMPLE_FACTORS - 187squ_tumor Tissue type:squtumor RAW_FILE_NAME=187 SUBJECT_SAMPLE_FACTORS - 214squ_tumor Tissue type:squtumor RAW_FILE_NAME=214 SUBJECT_SAMPLE_FACTORS - 255squ_tumor Tissue type:squtumor RAW_FILE_NAME=255 SUBJECT_SAMPLE_FACTORS - 258squ_tumor Tissue type:squtumor RAW_FILE_NAME=258 SUBJECT_SAMPLE_FACTORS - 323squ_tumor Tissue type:squtumor RAW_FILE_NAME=323 SUBJECT_SAMPLE_FACTORS - 368squ_tumor Tissue type:squtumor RAW_FILE_NAME=368 SUBJECT_SAMPLE_FACTORS - 12squ_tumor Tissue type:squtumor RAW_FILE_NAME=12 SUBJECT_SAMPLE_FACTORS - 18squ_tumor Tissue type:squtumor RAW_FILE_NAME=18 SUBJECT_SAMPLE_FACTORS - 6squ_tumor Tissue type:squtumor RAW_FILE_NAME=6 SUBJECT_SAMPLE_FACTORS - 3squ_tumor Tissue type:squtumor RAW_FILE_NAME=3 SUBJECT_SAMPLE_FACTORS - 9squ_tumor Tissue type:squtumor RAW_FILE_NAME=9 SUBJECT_SAMPLE_FACTORS - 15squ_tumor Tissue type:squtumor RAW_FILE_NAME=15 #COLLECTION CO:COLLECTION_SUMMARY The patient tissue specimens from 79 NSCLC patients including the two most CO:COLLECTION_SUMMARY prevalent histological subtypes adenocarcinoma (ade) and squamous cell (squ) CO:COLLECTION_SUMMARY tumor (65 ade patients with age range 36-84; 14 squ patients with age range CO:COLLECTION_SUMMARY 49-78) were obtained from Beijing Hospital. Primary tumor tissues, paired CO:COLLECTION_SUMMARY adjacent non-cancerous tissues (ANT) (within 2 cm apart from tumor edge) and CO:COLLECTION_SUMMARY distant normal tissues (DNT) ( > 2 cm apart from tumor edge) were surgically CO:COLLECTION_SUMMARY resected and frozen at −80 °C until metabolite extraction. The study was CO:COLLECTION_SUMMARY approved by the Research Ethics Committee of Beijing Hospital CO:COLLECTION_SUMMARY (2019BJYYEC-206-02) and also approved by the Ocean University of China CO:COLLECTION_SUMMARY (OUC-HM-2022-002). CO:SAMPLE_TYPE Lung CO:COLLECTION_METHOD Surgical resect CO:COLLECTION_LOCATION Beijing Hospital CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY No. Only cancer and noncancerous tissues. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Frozen tissue samples were thawed on ice. Each tissue sample was cut into small SP:SAMPLEPREP_SUMMARY pieces and accurately weighed. One mL of precooled 80% methanol was added to 100 SP:SAMPLEPREP_SUMMARY mg of tissue and the sample mixture was homogenized (60 Hz, 90 seconds). In a SP:SAMPLEPREP_SUMMARY tissue homogenizer with precooled module, followed by vortex-mixing for 1 min SP:SAMPLEPREP_SUMMARY and incubation at -80 °C for 4 h to allow for sufficient metabolite extraction. SP:SAMPLEPREP_SUMMARY Subsequently, the samples were centrifuged at 14,000 × g for 10 min at 4 °C, SP:SAMPLEPREP_SUMMARY and the supernatant was collected and dried under vacuum. Sample blanks were SP:SAMPLEPREP_SUMMARY prepared using water following the same experimental procedure. Before analysis, SP:SAMPLEPREP_SUMMARY dried metabolites were reconstituted with 100 μL LC-MS grade water, SP:SAMPLEPREP_SUMMARY vortex-mixed, and centrifuged at 14,000 × g for 10 min to remove insoluble SP:SAMPLEPREP_SUMMARY particles prior to UPLC-HRMS analysis. Quality control (QC) samples were SP:SAMPLEPREP_SUMMARY prepared by pooling a small volume from samples with enough volume. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Agilent 1290 Infinity CH:COLUMN_NAME Waters Acquity BEH C18 (50 x 2.1mm, 1.7 um) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo LTQ XL MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS capillary temperature 300 °C, capillary voltage 20 V, tube lens 20 V, spray MS:MS_COMMENTS voltage 4.0 kV for positive ion mode, auxiliary gas, sheath gas and sweep gas MS:MS_COMMENTS flow rate 10, 40, and 0 arbitrary units MS:MS_RESULTS_FILE ST002120_AN003471_Results.txt UNITS:Peak Area Has m/z:Yes Has RT:Yes RT units:Minutes #END