{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001434","ANALYSIS_ID":"AN002397","VERSION":"1","CREATED_ON":"July 28, 2020, 11:10 am"},

"PROJECT":{"PROJECT_TITLE":"ALDH4A1 is a novel atherosclerosis auto-antigen and a target of protective 6 antibodies","PROJECT_TYPE":"LC-MS Untargeted Lipidomics","PROJECT_SUMMARY":"Cardiovascular disease (CVD) is the leading cause of mortality in the world, with most CVD deaths resulting from myocardial infarction and stroke. The main cause underlying thrombosis and cardiovascular events is atherosclerosis, an inflammatory disease that can remain asymptomatic for long periods of time. There is an urgent need for new therapeutic and diagnostic options in this area. Atherosclerotic plaques have long been known to contain autoantibodies 1, 2, and there is a well-accepted connection between atherosclerosis and autoimmunity 3. However, the immunogenic trigger and the impact of the autoantibody response during atherosclerosis are not well understood 3, 4, 5. Here we performed a high-throughput single-cell analysis of the atherosclerosis-associated antibody repertoire. Antibody gene sequencing of more than 1700 B cells from atherogenic LDLR-/- mice and control animals identified 56 antibodies expressed by in-vivo-expanded clones of B lymphocytes in the context of atherosclerosis. A third of the expanded antibodies showed reactivity against the atherosclerotic plaque, indicating that various antigens in the lesion can trigger antibody responses. A deep proteomics analysis revealed aldehyde dehydrogenase 4 family member A1 (ALDH4A1), a mitochondrial dehydrogenase involved in proline metabolism, as target antigen of one of these autoantibodies, A12. We show that ALDH4A1 distribution is altered during atherosclerosis and circulating levels of ALDH4A1 are increased in mice and humans with atherosclerosis, supporting the potential use of ALDH4A1 as disease biomarker. A12 antibody infusion into LDLR-/- mice delayed plaque formation and reduced circulating levels of free cholesterol and LDL suggesting that anti-ALDH4A1 antibodies can play a protective role in atherosclerosis progression and might have therapeutic potential. Our study reveals a new auto-antigenic trigger target of the atherosclerosis-associated antibody response and opens new avenues for diagnostic and therapeutic interventions in CVD.","INSTITUTE":"Centro Nacional de Investigaciones Cardiovasculares Carlos III","LAST_NAME":"Ferrarini","FIRST_NAME":"Alessia","ADDRESS":"Calle de Melchor Fernández Almagro, 3, 28029 Madrid","EMAIL":"aferrarini@cnic.es","PHONE":"+34 914 53 12 00"},

"STUDY":{"STUDY_TITLE":"Untargeted lipidomics of liver to assess the potential protective role in atherosclerosis progression of A12 antibodies infusion into LDLR-/-mice","STUDY_TYPE":"LC-MS Untargeted Lipidomics","STUDY_SUMMARY":"In order to assess the therapeutic potential of A12 antibodies in atherosclerosis, untargeted lipidomics of liver samples was performed. LDLR-/-mice were treated with a fully murine version of the A12 antibody (mA12-IgG2b), with the isotype control antibody mB1.8-IgG2b (n=16) or with PBS as controls.","INSTITUTE":"Centro Nacional de Investigaciones Cardiovasculares Carlos III","LAST_NAME":"Ferrarini","FIRST_NAME":"Alessia","ADDRESS":"Calle de Melchor Fernández Almagro, 3, 28029 Madrid","EMAIL":"aferrarini@cnic.es","PHONE":"+34 914 53 12 00","NUM_GROUPS":"3","TOTAL_SUBJECTS":"18"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"A12_01",
"Factors":{"Antibody Group":"A12"},
"Additional sample data":{"RAW_FILE_NAME":"P_A12_01;N_A12_01"}
},
{
"Subject ID":"-",
"Sample ID":"A12_02",
"Factors":{"Antibody Group":"A12"},
"Additional sample data":{"RAW_FILE_NAME":"P_A12_02;N_A12_02"}
},
{
"Subject ID":"-",
"Sample ID":"A12_03",
"Factors":{"Antibody Group":"A12"},
"Additional sample data":{"RAW_FILE_NAME":"P_A12_03;N_A12_03"}
},
{
"Subject ID":"-",
"Sample ID":"A12_04",
"Factors":{"Antibody Group":"A12"},
"Additional sample data":{"RAW_FILE_NAME":"P_A12_04;N_A12_04"}
},
{
"Subject ID":"-",
"Sample ID":"A12_05",
"Factors":{"Antibody Group":"A12"},
"Additional sample data":{"RAW_FILE_NAME":"P_A12_05;N_A12_05"}
},
{
"Subject ID":"-",
"Sample ID":"A12_06",
"Factors":{"Antibody Group":"A12"},
"Additional sample data":{"RAW_FILE_NAME":"P_A12_06;N_A12_06"}
},
{
"Subject ID":"-",
"Sample ID":"B18_01",
"Factors":{"Antibody Group":"B1.8"},
"Additional sample data":{"RAW_FILE_NAME":"P_B18_01;N_B18_01"}
},
{
"Subject ID":"-",
"Sample ID":"B18_02",
"Factors":{"Antibody Group":"B1.8"},
"Additional sample data":{"RAW_FILE_NAME":"P_B18_02;N_B18_02"}
},
{
"Subject ID":"-",
"Sample ID":"B18_03",
"Factors":{"Antibody Group":"B1.8"},
"Additional sample data":{"RAW_FILE_NAME":"P_B18_03;N_B18_03"}
},
{
"Subject ID":"-",
"Sample ID":"B18_04",
"Factors":{"Antibody Group":"B1.8"},
"Additional sample data":{"RAW_FILE_NAME":"P_B18_04;N_B18_04"}
},
{
"Subject ID":"-",
"Sample ID":"B18_05",
"Factors":{"Antibody Group":"B1.8"},
"Additional sample data":{"RAW_FILE_NAME":"P_B18_05;N_B18_05"}
},
{
"Subject ID":"-",
"Sample ID":"B18_06",
"Factors":{"Antibody Group":"B1.8"},
"Additional sample data":{"RAW_FILE_NAME":"P_B18_06;N_B18_06"}
},
{
"Subject ID":"-",
"Sample ID":"CTRL_01",
"Factors":{"Antibody Group":"PBS"},
"Additional sample data":{"RAW_FILE_NAME":"P_CTRL_01;N_CTRL_01"}
},
{
"Subject ID":"-",
"Sample ID":"CTRL_02",
"Factors":{"Antibody Group":"PBS"},
"Additional sample data":{"RAW_FILE_NAME":"P_CTRL_02;N_CTRL_02"}
},
{
"Subject ID":"-",
"Sample ID":"CTRL_03",
"Factors":{"Antibody Group":"PBS"},
"Additional sample data":{"RAW_FILE_NAME":"P_CTRL_03;N_CTRL_03"}
},
{
"Subject ID":"-",
"Sample ID":"CTRL_04",
"Factors":{"Antibody Group":"PBS"},
"Additional sample data":{"RAW_FILE_NAME":"P_CTRL_04;N_CTRL_04"}
},
{
"Subject ID":"-",
"Sample ID":"CTRL_05",
"Factors":{"Antibody Group":"PBS"},
"Additional sample data":{"RAW_FILE_NAME":"P_CTRL_05;N_CTRL_05"}
},
{
"Subject ID":"-",
"Sample ID":"CTRL_06",
"Factors":{"Antibody Group":"PBS"},
"Additional sample data":{"RAW_FILE_NAME":"P_CTRL_06;N_CTRL_06"}
},
{
"Subject ID":"-",
"Sample ID":"QC_01",
"Factors":{"Antibody Group":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"P_QC_01;N_QC_01"}
},
{
"Subject ID":"-",
"Sample ID":"QC_02",
"Factors":{"Antibody Group":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"P_QC_02;N_QC_02"}
},
{
"Subject ID":"-",
"Sample ID":"QC_03",
"Factors":{"Antibody Group":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"P_QC_03;N_QC_03"}
},
{
"Subject ID":"-",
"Sample ID":"QC_04",
"Factors":{"Antibody Group":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"P_QC_04;N_QC_04"}
},
{
"Subject ID":"-",
"Sample ID":"QC_05",
"Factors":{"Antibody Group":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"P_QC_05;N_QC_05"}
},
{
"Subject ID":"-",
"Sample ID":"QC_06",
"Factors":{"Antibody Group":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"P_QC_06;N_QC_06"}
},
{
"Subject ID":"-",
"Sample ID":"QC_07",
"Factors":{"Antibody Group":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"P_QC_07;N_QC_07"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Liver were collected after mice sacrifice, frozen in liquid N2 and store at -80°C until the day of analysis.","SAMPLE_TYPE":"Liver"},

"TREATMENT":{"TREATMENT_SUMMARY":"LDLR-/-mice under high fat diet were injected with mA12-IgG2b and PBS or a B1-8 IgG2b isotype as control antibody"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Frozen liver tissues were lysed in 0.5X PBS (sample:solvent 1:10 ratio) containing 1 mg/mL butylhydroxytoluene (BHT) solution in methanol (proportion 200 µL per g of tissue), with FastPrep-24 5G instrument (MP Biomedicals, USA). 25 µL aliquots of homogenate were collected and stored at -80°C until lipidomic extraction. Tissue homogenates were thawed and extracted with methyl-tert-butylether (MTBE) as described in [Matyash, V., et al., Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics. Journal of lipid research, 2008. 49(5): p. 1137-46]. 900 µL of organic phase were dried-out in speedvac and resuspended in 50 µL of ACN:H2O (20:80, v:v) just before injection."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"Agilent mRP-Recovery C18 column (100 × 0.5 mm, 5 µm)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"MS was operating in full scan mode from 70 to 1700 m/z at 60000 resolution. Data processing was carried-out using Compound Discoverer (ThermoFisher; USA) with the Metaboprofiler node.","MS_RESULTS_FILE":"ST001434_AN002397_Results.txt UNITS:peak area Has m/z:Yes Has RT:No RT units:No RT data"}

}