#METABOLOMICS WORKBENCH zj1234_20231116_050235 DATATRACK_ID:4463 STUDY_ID:ST002996 ANALYSIS_ID:AN004921 PROJECT_ID:PR001866 VERSION 1 CREATED_ON December 4, 2023, 4:22 am #PROJECT PR:PROJECT_TITLE Tissue Lipidomic Profiling for Detection of Non-Small Cell Lung Cancer PR:PROJECT_TYPE non-targeted lipidomics analysis PR:PROJECT_SUMMARY NSCLC is the most prevalent type of lung cancer with high mortality rates. In PR:PROJECT_SUMMARY this study, we performed nontargeted lipidomic profiling study of 230 tissue PR:PROJECT_SUMMARY samples from 79 NSCLC patients with adenocarcinoma (AC) or squamous cell PR:PROJECT_SUMMARY carcinoma (SCC) using UPLC-HRMS. oPLS-DA classification models enabled PR:PROJECT_SUMMARY discrimination of tumor from adjacent noncancerous tissue (ANT) and distant PR:PROJECT_SUMMARY noncancerous tissue (DNT) samples in NSCLC and AC with good accuracies (94.1 and PR:PROJECT_SUMMARY 92.0%), sensitivities (93.8 and 91.1%), and specificities (94.2 and 92.5%) using PR:PROJECT_SUMMARY 7 and 8 discriminant compounds, respectively. The discriminant feature panels PR:PROJECT_SUMMARY were verified by external validation sets, revealing characteristic lipid PR:PROJECT_SUMMARY signatures associated with NSCLC and showing prospects for entering the next PR:PROJECT_SUMMARY evaluation stage of biomarker discovery for NSCLC detection and subtyping. PR:INSTITUTE OUC PR:DEPARTMENT Department of Medicine and Pharmacy PR:LABORATORY Analytical chemistry PR:LAST_NAME Zhang PR:FIRST_NAME Jie PR:ADDRESS No. 5 Yushan Road, Qingdao, Shandong, China PR:EMAIL zhangjieqau@163.com PR:PHONE 17806277823 PR:FUNDING_SOURCE OUC PR:PROJECT_COMMENTS OUC PR:PUBLICATIONS OUC PR:CONTRIBUTORS OUC #STUDY ST:STUDY_TITLE Tissue Lipidomic Profiling for Detection of Non-Small Cell Lung Cancer ST:STUDY_SUMMARY UPLC-HRMS analysis was performed on AC and SCC patients. OPLSDA classfication ST:STUDY_SUMMARY was performed on tumor vs. ANT and DNT samples. Panels of discriminant features ST:STUDY_SUMMARY were identified. The biomarkers identified in discovery set samples for each ST:STUDY_SUMMARY binary classification were confirmed by using a set of validation samples, which ST:STUDY_SUMMARY were run separately. Additionally, paired analysis showed the abundance of ST:STUDY_SUMMARY discriminant compounds has significant altered in tumor tissues compared to ST:STUDY_SUMMARY corresponding DNT and ANT samples, reflecting the lipid characteristics related ST:STUDY_SUMMARY to tumor in situ and cancer cell signaling. ST:INSTITUTE OUC ST:DEPARTMENT Department of Medicine and Pharmacy ST:LABORATORY Analytical chemistry ST:LAST_NAME Zhang ST:FIRST_NAME Jie ST:ADDRESS No. 5 Yushan Road, Qingdao, Shandong, China ST:EMAIL zhangjieqau@163.com ST:PHONE 17806277823 #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 SA204001 138ade_norm Tissue type:adenorm RAW_FILE_NAME=138 SUBJECT_SAMPLE_FACTORS SA204002 143ade_norm Tissue type:adenorm RAW_FILE_NAME=143 SUBJECT_SAMPLE_FACTORS SA204003 146ade_norm Tissue type:adenorm RAW_FILE_NAME=146 SUBJECT_SAMPLE_FACTORS SA204004 152ade_norm Tissue type:adenorm RAW_FILE_NAME=152 SUBJECT_SAMPLE_FACTORS SA204005 155ade_norm Tissue type:adenorm RAW_FILE_NAME=155 SUBJECT_SAMPLE_FACTORS SA204006 158ade_norm Tissue type:adenorm RAW_FILE_NAME=158 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322squ_side Tissue type:squside RAW_FILE_NAME=322 SUBJECT_SAMPLE_FACTORS SA204211 11squ_side Tissue type:squside RAW_FILE_NAME=L11-2 SUBJECT_SAMPLE_FACTORS SA204212 8squ_side Tissue type:squside RAW_FILE_NAME=L8-2 SUBJECT_SAMPLE_FACTORS SA204213 14squ_side Tissue type:squside RAW_FILE_NAME=L14-2 SUBJECT_SAMPLE_FACTORS SA204214 17squ_side Tissue type:squside RAW_FILE_NAME=L17-2 SUBJECT_SAMPLE_FACTORS SA204215 2squ_side Tissue type:squside RAW_FILE_NAME=L2-2 SUBJECT_SAMPLE_FACTORS SA204216 5squ_side Tissue type:squside RAW_FILE_NAME=L5-2 SUBJECT_SAMPLE_FACTORS SA204217 151squ_tumor Tissue type:squtumor RAW_FILE_NAME=151 SUBJECT_SAMPLE_FACTORS SA204218 169squ_tumor Tissue type:squtumor RAW_FILE_NAME=169 SUBJECT_SAMPLE_FACTORS SA204219 187squ_tumor Tissue type:squtumor RAW_FILE_NAME=187 SUBJECT_SAMPLE_FACTORS SA204220 214squ_tumor Tissue type:squtumor RAW_FILE_NAME=214 SUBJECT_SAMPLE_FACTORS SA204221 255squ_tumor Tissue type:squtumor RAW_FILE_NAME=255 SUBJECT_SAMPLE_FACTORS SA204222 258squ_tumor Tissue type:squtumor RAW_FILE_NAME=258 SUBJECT_SAMPLE_FACTORS SA204223 323squ_tumor Tissue type:squtumor RAW_FILE_NAME=323 SUBJECT_SAMPLE_FACTORS SA204224 368squ_tumor Tissue type:squtumor RAW_FILE_NAME=368 SUBJECT_SAMPLE_FACTORS SA204225 12squ_tumor Tissue type:squtumor RAW_FILE_NAME=L12-2 SUBJECT_SAMPLE_FACTORS SA204226 18squ_tumor Tissue type:squtumor RAW_FILE_NAME=L18-2 SUBJECT_SAMPLE_FACTORS SA204227 6squ_tumor Tissue type:squtumor RAW_FILE_NAME=L6-2 SUBJECT_SAMPLE_FACTORS SA204228 3squ_tumor Tissue type:squtumor RAW_FILE_NAME=L3-2 SUBJECT_SAMPLE_FACTORS SA204229 9squ_tumor Tissue type:squtumor RAW_FILE_NAME=L9-2 SUBJECT_SAMPLE_FACTORS SA204230 15squ_tumor Tissue type:squtumor RAW_FILE_NAME=L15-2 #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.To 100 mg tissue sample, 1 mL precooled 80% SP:SAMPLEPREP_SUMMARY methanol was added and the sample was homogenized (60 Hz, 90 s) in a tissue SP:SAMPLEPREP_SUMMARY homogenizer (Jingxin, JX-24, Shanghai, China). After vortexing for 1 min, the SP:SAMPLEPREP_SUMMARY mixture was incubated at -80 °C for 4 hours, followed by centrifuging at 14,000 SP:SAMPLEPREP_SUMMARY × g for 10 min at 4 °C. The supernatant was transferred to a new tube. To the SP:SAMPLEPREP_SUMMARY rest of the sample, 400 μL dichloromethane/ methanol (3:1, v/v) was added for SP:SAMPLEPREP_SUMMARY lipid extraction. The sample mixture was then vortexed twice, each time for 30 SP:SAMPLEPREP_SUMMARY s, followed by incubation at -80 °C for 30 min. After homogenization (60 Hz, 90 SP:SAMPLEPREP_SUMMARY s) and centrifugation of the sample at 14,000 × g for 10 min at 4 °C, the SP:SAMPLEPREP_SUMMARY supernatant was collected and dried under a speed vacuum concentrator. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Agilent 1290 Infinity CH:COLUMN_NAME Waters ACQUITY UPLC BEH C18 (50 x 2.1mm,1.7um) CH:SOLVENT_A acetonitrile/water CH:SOLVENT_B 2-propanol/acetonitrile CH:FLOW_GRADIENT 0-2 min, 60%-57% A, 2-2.1 min 57%-50% A, 2.1-12 min 50%-46% A, 12-12.1 min CH:FLOW_GRADIENT 46%-30% A, 12.1-18 min 30%-1% A CH:FLOW_RATE 0.3 mL min-1 CH:COLUMN_TEMPERATURE 50 #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 35 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. Progenesis QI version 2.4 was used for MS:MS_COMMENTS raw data processing. FORTRAN based home-built secondary data processing was MS:MS_COMMENTS applied for artefact removal, blank correction, QC -based signal correction and MS:MS_COMMENTS normalization, etc. MS:MS_RESULTS_FILE ST002996_AN004921_Results.txt UNITS:Peak area Has m/z:Yes Has RT:Yes RT units:Minutes #END