{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002532","ANALYSIS_ID":"AN004166","VERSION":"1","CREATED_ON":"March 28, 2023, 6:46 pm"},

"PROJECT":{"PROJECT_TITLE":"Nontargeted metabolomics studies","PROJECT_TYPE":"LC‒MS","PROJECT_SUMMARY":"Nontargeted metabolomics analysis was carried out using the kidney tissues of mice killed at Day 3 after cisplatin treatment.","INSTITUTE":"Children's Hospital of Nanjing Medical University","LAST_NAME":"xiaolu","FIRST_NAME":"zhang","ADDRESS":"72 Guangzhou Road","EMAIL":"zxiaolu0802@163.com","PHONE":"18351976523"},

"STUDY":{"STUDY_TITLE":"Nontargeted metabolomics analysis on kidney tissue treated with cisplatin","STUDY_TYPE":"Nontargeted metabolomics analysis","STUDY_SUMMARY":"Cisplatin-induced acute kidney injury (AKI) is a severe clinical complication with no satisfactory therapies in the clinic. Tumor necrosis factor receptor (TNFR)-associated factor 1 (TRAF1) plays an important role in both inflammation and metabolism. However, the role of TRAF1 in cisplatin-induced AKI needs to be evaluated. In this study, TRAF1 expression was decreased in cisplatin-treated mice and mouse proximal tubular cells (mPTCs), suggesting a potential role of TRAF1 in cisplatin-associated kidney injury. Thus, TRAF1 plasmids were introduced into male C57BL/6J mice by a tail vein high-pressure injection method to overexpress TRAF1. Then, cisplatin was administrated by a single intraperitoneal (i.p.) injection (20 mg/kg). Mice were sacrificed 72 h after cisplatin administration. Serum and kidney tissues were collected for further analysis. In vitro, mPTCs were transfected with TRAF1 plasmids before treatment with cisplatin (5 µg/mL) for 24 h. Western blotting, Masson’s trichrome and hematoxylin-eosin (HE) staining and tandem mass spectrometry (LC‒MS/MS) analysis were employed to evaluate kidney injury. Following cisplatin treatment, we observed a marked downregulation of TRAF1 in mouse kidneys and mPTCs treated with cisplatin. In mice, TRAF1 overexpression attenuated cisplatin-induced AKI, as evidenced by decreased levels of serum creatinine (Scr) and blood urea nitrogen (BUN). Moreover, TRAF1 delivery obviously ameliorated cisplatin-induced renal tubular injury, as shown by the improved histological damage and blocked upregulation of NGAL and KIM-1. Moreover, the NF-κB activation and inflammatory cytokine production enhanced by cisplatin were significantly blunted by TRAF1. In line with the attenuated inflammatory response, the increased number of apoptotic cells (TUNEL staining) and enhanced expression of BAX and cleaved Caspase-3 were markedly decreased by TRAF1 overexpression. In vitro, TRAF1 also attenuated renal tubular cell inflammation and apoptosis induced by cisplatin. In addition, disordered cellular metabolism, which was reported as an important pathogenic factor of AKI, was examined by metabolomics analysis. Interestingly, a significant correction of the metabolic disturbance, including perturbations in energy generation and lipid and amino acid metabolism, was observed in the kidneys of cisplatin-treated mice. In conclusion, TRAF1 overexpression significantly attenuated cisplatin-induced nephrotoxicity, possibly by correcting the impaired metabolism, inhibiting inflammation, and blocking apoptosis in renal tubular cells.","INSTITUTE":"Children's Hospital of Nanjing Medical University","LAST_NAME":"xiaolu","FIRST_NAME":"zhang","ADDRESS":"72 Guangzhou Road","EMAIL":"zxiaolu0802@163.com","PHONE":"18351976523"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"T-A1",
"Factors":{"Genotype":"control","Strain":"WT"},
"Additional sample data":{"Age":"C57BL/6","Sex":"8 weeks   male","RAW_FILE_NAME":"T-A1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"T-A2",
"Factors":{"Genotype":"control","Strain":"WT"},
"Additional sample data":{"Age":"C57BL/6","Sex":"8 weeks   male","RAW_FILE_NAME":"T-A2.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"T-A3",
"Factors":{"Genotype":"control","Strain":"WT"},
"Additional sample data":{"Age":"C57BL/6","Sex":"8 weeks   male","RAW_FILE_NAME":"T-A3.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"T-A4",
"Factors":{"Genotype":"control","Strain":"WT"},
"Additional sample data":{"Age":"C57BL/6","Sex":"8 weeks   male","RAW_FILE_NAME":"T-A4.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"T-A5",
"Factors":{"Genotype":"control","Strain":"WT"},
"Additional sample data":{"Age":"C57BL/6","Sex":"8 weeks   male","RAW_FILE_NAME":"T-A5.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"T-A6",
"Factors":{"Genotype":"vehicle+cisplatin","Strain":"WT"},
"Additional sample data":{"Age":"C57BL/6","Sex":"8 weeks   male","RAW_FILE_NAME":"T-A6.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"T-A7",
"Factors":{"Genotype":"vehicle+cisplatin","Strain":"WT"},
"Additional sample data":{"Age":"C57BL/6","Sex":"8 weeks   male","RAW_FILE_NAME":"T-A7.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"T-A8",
"Factors":{"Genotype":"vehicle+cisplatin","Strain":"WT"},
"Additional sample data":{"Age":"C57BL/6","Sex":"8 weeks   male","RAW_FILE_NAME":"T-A8.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"T-A9",
"Factors":{"Genotype":"vehicle+cisplatin","Strain":"WT"},
"Additional sample data":{"Age":"C57BL/6","Sex":"8 weeks   male","RAW_FILE_NAME":"T-A9.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"T-A10",
"Factors":{"Genotype":"vehicle+cisplatin","Strain":"WT"},
"Additional sample data":{"Age":"C57BL/6","Sex":"8 weeks   male","RAW_FILE_NAME":"T-A10.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"T-A11",
"Factors":{"Genotype":"cisplatin+TRAF1","Strain":"WT"},
"Additional sample data":{"Age":"C57BL/6","Sex":"8 weeks   male","RAW_FILE_NAME":"T-A11.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"T-A12",
"Factors":{"Genotype":"cisplatin+TRAF1","Strain":"WT"},
"Additional sample data":{"Age":"C57BL/6","Sex":"8 weeks   male","RAW_FILE_NAME":"T-A12.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"T-A13",
"Factors":{"Genotype":"cisplatin+TRAF1","Strain":"WT"},
"Additional sample data":{"Age":"C57BL/6","Sex":"8 weeks   male","RAW_FILE_NAME":"T-A13.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"T-A14",
"Factors":{"Genotype":"cisplatin+TRAF1","Strain":"WT"},
"Additional sample data":{"Age":"C57BL/6","Sex":"8 weeks   male","RAW_FILE_NAME":"T-A14.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"T-A15",
"Factors":{"Genotype":"cisplatin+TRAF1","Strain":"WT"},
"Additional sample data":{"Age":"C57BL/6","Sex":"8 weeks   male","RAW_FILE_NAME":"T-A15.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"8 weeks old C57BL/6 male mice were randomly divided into three groups: control group (control; n=8), cisplatin-induced AKI group (cisplatin; n=8), and cisplatin plus TRAF1 plasmid injection group (cisplatin + TRAF1; n=8). Both cisplatin and cisplatin + TRAF1 groups were given 20 mg/kg cisplatin intraperitoneal (i.p.) injection, while the control group received the same amount of saline i.p. injection. The mice in cisplatin + TRAF1 group were pretreated with TRAF1 performed by a hydrodynamic-based gene delivery approach 36 h before cisplatin administration. Mice in the three groups were sacrificed after cisplatin treatment for 72 h. The kidney tissues were cut horizontally and collected.","COLLECTION_PROTOCOL_FILENAME":"protocol.pdf","SAMPLE_TYPE":"Kidney"},

"TREATMENT":{"TREATMENT_SUMMARY":"8 weeks old C57BL/6 male mice were randomly divided into three groups: control group (control; n=8), cisplatin-induced AKI group (cisplatin; n=8), and cisplatin plus TRAF1 plasmid injection group (cisplatin + TRAF1; n=8). Both cisplatin and cisplatin + TRAF1 groups were given 20 mg/kg cisplatin intraperitoneal (i.p.) injection, while the control group received the same amount of saline i.p. injection. The mice in cisplatin + TRAF1 group were pretreated with TRAF1 performed by a hydrodynamic-based gene delivery approach 36 h before cisplatin administration. Mice in the three groups were sacrificed after cisplatin treatment for 72 h. The kidney tissues were cut horizontally and collected.","TREATMENT_PROTOCOL_FILENAME":"protocol.pdf"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"1. Take all samples into a 2 mL EP tube, add 2 steel balls, put them into the tissue grinder, grind at 50 Hz for 60 s, and then homogenize the samples; 2. Accurately weigh 100 mg (±1%) of the homogenized sample into a 2 mL EP tube, add accurately 0.6mL of methanol (including internal standard), and vortex for 30 s 3. Add 2 steel balls, put them into the tissue grinder, and grind for 60 s at 50 Hz; 4. Centrifuge at 4 ℃ for 10 min at 12000 rpm, and the supernatant was filtered through 0.22 µm membrane to obtain the prepared samples for LC-MS; 5. Take 20 µL from each sample to the quality control (QC) samples; (These QC samples were used to monitor deviations of the analytical results from these pool mixtures and compare them to the errors caused by the analytical instrument itself) 6. Use the rest of the samples for LC-MS detection.","SAMPLEPREP_PROTOCOL_FILENAME":"protocol.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Ultimate 3000","COLUMN_NAME":"Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)","SOLVENT_A":"0.1% formic acid in water and 0.1% formic acid in acetonitrile","SOLVENT_B":"5 mM ammonium formate in water and acetonitrile","FLOW_GRADIENT":"0~1 min, 2% B.D  1~9 min, 2%~50% B.D  9~12 min, 50%~98% B.D  12~13.5 min, 98% B.D  13.5~14 min, 98%~2% B.D  14~20 min, 2% D-positive model (14~17 min, 2% B-negative model)","FLOW_RATE":"0.25 mL/min","COLUMN_TEMPERATURE":"40","METHODS_FILENAME":"protocol.pdf"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","ANALYSIS_PROTOCOL_FILE":"protocol.pdf"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Focus","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"-","MS_RESULTS_FILE":"ST002532_AN004166_Results.txt UNITS:peak area Has m/z:Yes Has RT:Yes RT units:Minutes"}

}