{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002805","ANALYSIS_ID":"AN004561","VERSION":"1","CREATED_ON":"August 2, 2023, 12:34 pm"},

"PROJECT":{"PROJECT_TITLE":"IL-1β-mediated adaptive re-programming of endogenous human cardiac fibroblasts to cells with immune features during fibrotic remodeling","PROJECT_SUMMARY":"The source and roles of fibroblasts and CD4 helper T-cells during maladaptive remodeling and myocardial fibrosis in pulmonary arterial hypertension (PAH) have been long debated. We demonstrate, using single-cell mass cytometry, a sub-population of endogenous human cardiac fibroblasts expressing increased levels of CD4, a helper T-cell marker, in addition to myofibroblast markers distributed in human fibrotic RV tissue, interstitial/perivascular lesions of SUGEN/Hypoxia (SuHx) rats and fibroblasts labelled with pdgfrα CreERt2/+ in R26R-tdTomato mice. Recombinant IL-1β increases IL-1R, CCR2 receptor expression, modifies the secretome, and differentiates cardiac fibroblasts to form CD68 positive cell clusters. IL-1β also activates stemness markers such as NANOG and SOX2 and genes involved in de-differentiation, lymphoid cell function and metabolic reprogramming. IL-1β induction of lineage traced primary mouse cardiac fibroblasts causes these cells to lose their fibroblast identity and acquire an immune phenotype. Our results identify IL-1β induced immune-competency in human cardiac fibroblasts and suggest that fibroblast secretome modulation may constitute a therapeutic approach to PAH and other diseases typified by inflammation and fibrotic remodeling.","INSTITUTE":"Brown University","DEPARTMENT":"MPPB","LABORATORY":"Siamwala Lab","LAST_NAME":"Siamwala","FIRST_NAME":"Jamila","ADDRESS":"830 Chalkstone Avenue, Building 35","EMAIL":"jamila_siamwala@brown.edu","PHONE":"6192136223"},

"STUDY":{"STUDY_TITLE":"IL-1β-mediated adaptive re-programming of endogenous human cardiac fibroblasts to cells with immune features during fibrotic remodeling","STUDY_SUMMARY":"The source and roles of fibroblasts and CD4 helper T-cells during maladaptive remodeling and myocardial fibrosis in pulmonary arterial hypertension (PAH) have been long debated. We demonstrate, using single-cell mass cytometry, a sub-population of endogenous human cardiac fibroblasts expressing increased levels of CD4, a helper T-cell marker, in addition to myofibroblast markers distributed in human fibrotic RV tissue, interstitial/perivascular lesions of SUGEN/Hypoxia (SuHx) rats and fibroblasts labelled with pdgfrα CreERt2/+ in R26R-tdTomato mice. Recombinant IL-1β increases IL-1R, CCR2 receptor expression, modifies the secretome, and differentiates cardiac fibroblasts to form CD68 positive cell clusters. IL-1β also activates stemness markers such as NANOG and SOX2 and genes involved in de-differentiation, lymphoid cell function and metabolic reprogramming. IL-1β induction of lineage traced primary mouse cardiac fibroblasts causes these cells to lose their fibroblast identity and acquire an immune phenotype. Our results identify IL-1β induced immune-competency in human cardiac fibroblasts and suggest that fibroblast secretome modulation may constitute a therapeutic approach to PAH and other diseases typified by inflammation and fibrotic remodeling.","INSTITUTE":"Brown University","DEPARTMENT":"Molecular Pharmacology, Physiology and Biotechnology","LABORATORY":"Siamwala Lab","LAST_NAME":"Siamwala","FIRST_NAME":"Jamila","ADDRESS":"830 Chalkstone Avenue, Building 35","EMAIL":"jamila_siamwala@brown.edu","PHONE":"6192136223"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","AGE_OR_AGE_RANGE":"63 - 73","GENDER":"Male and female"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"62122_c",
"Factors":{"Sex":"M","Treatment":"Control"},
"Additional sample data":{"Sample type":"Human cardiac fibroblast cells","RAW_FILE_NAME":"120319QJS1.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"1281202_c",
"Factors":{"Sex":"M","Treatment":"Control"},
"Additional sample data":{"Sample type":"Human cardiac fibroblast cells","RAW_FILE_NAME":"120319QJS2.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"534282_c",
"Factors":{"Sex":"F","Treatment":"Control"},
"Additional sample data":{"Sample type":"Human cardiac fibroblast cells","RAW_FILE_NAME":"120319QJS3.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"62122_t",
"Factors":{"Sex":"M","Treatment":"IL-1B"},
"Additional sample data":{"Sample type":"Human cardiac fibroblast cells","RAW_FILE_NAME":"120319QJS4.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"1281202_t",
"Factors":{"Sex":"M","Treatment":"IL-1B"},
"Additional sample data":{"Sample type":"Human cardiac fibroblast cells","RAW_FILE_NAME":"120319QJS5.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"534282_t",
"Factors":{"Sex":"F","Treatment":"IL-1B"},
"Additional sample data":{"Sample type":"Human cardiac fibroblast cells","RAW_FILE_NAME":"120319QJS6.wiff"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Metabolomics of conditioned media was performed at the Beth Israel Deaconess Medical Center Mass Spectrometry Core according to published protocols (M. Yuan, S. B. Breitkopf, X. Yang, J. M. Asara, A positive/negative ion-switching, targeted mass spectrometry-based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue. Nat Protoc 7, 872-881 (2012)). hVCF (2 x 106) were seeded and grown to confluence and treated with IL-1β (10 ng/ml) for 24h. Conditioned media (1ml) from the vehicle or IL-1β treated hVCF cells were used for the metabolomics analysis.","SAMPLE_TYPE":"Cultured fibroblasts"},

"TREATMENT":{"TREATMENT_SUMMARY":"hVCF (2 x 106) were seeded and grown to confluence and treated with IL-1β (10 ng/ml) for 24h. Conditioned media (1ml) from the vehicle or IL-1β treated hVCF cells were used for the metabolomics analysis."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"500 μL of chilled -80°C 80% methanol was added to 15ml tubes containing 1ml of conditioned media and evaporated using Speedvac to pellet the metabolites. SRM with polarity switching with a QTRAP 5500 mass spectrometer (AB/SCIEX) was used to assay 300 polar molecules, based on the previously published protocol."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Shimadzu Prominence UFLC HPLC","COLUMN_NAME":"Waters XBridge Amide (100 x 4.6mm,3.5um)","SOLVENT_A":"20 mM ammonium hydroxide/20 mM ammonium acetate (pH=9.0) in 95:5 water:acetonitrile","SOLVENT_B":"HPLC grade acetonitrile","FLOW_GRADIENT":"Gradients were run with a Prominence UFLC HPLC (Shimadzu) starting from 85% buffer B (HPLC grade acetonitrile) to 42% B from 0-5 minutes; 42% B to 0% B from 5-16 minutes; 0% B was held from 16-24 minutes; 0% B to 85% B from 24-25 minutes; 85% B was held for 7 minutes to re-equilibrate the column.","FLOW_RATE":"400uL/min","COLUMN_TEMPERATURE":"475","METHODS_FILENAME":"nprot_2012_024_v2.pdf"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","ANALYSIS_PROTOCOL_FILE":"nprot_2012_024_v2.pdf"},

"MS":{"INSTRUMENT_NAME":"ABI Sciex 6500 QTrap","INSTRUMENT_TYPE":"QTRAP","MS_TYPE":"Other","ION_MODE":"UNSPECIFIED","MS_COMMENTS":"Ion Mode Positive/Negative Switching: Metabolomics of conditioned media was performed at the Beth Israel Deaconess Medical Center Mass Spectrometry Core according to published protocols (M. Yuan, S. B. Breitkopf, X. Yang, J. M. Asara, A positive/negative ion-switching, targeted mass spectrometry-based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue. Nat Protoc 7, 872-881 (2012)). hVCF (2 x 106) were seeded and grown to confluence and treated with IL-1β (10 ng/ml) for 24h. Conditioned media (1ml) from the vehicle or IL-1β treated hVCF cells were used for the metabolomics analysis. 500 μL of chilled -80°C 80% methanol was added to 15ml tubes containing 1ml of conditioned media and evaporated using Speedvac to pellet the metabolites. Samples were re-suspended using 20 mL HPLC grade water for mass spectrometry. 5-7 μL were injected and analyzed using a hybrid 6500 QTRAP triple quadrupole mass spectrometer (AB/SCIEX) coupled to a Prominence UFLC HPLC system (Shimadzu) via selected reaction monitoring (SRM) of a total of 283 endogenous water soluble metabolites for steady-state analyses of samples. Some metabolites were targeted in both positive and negative ion mode for a total of 304 SRM transitions using positive/negative ion polarity switching. ESI voltage was +4950V in positive ion mode and –4500V in negative ion mode. The dwell time was 3 ms per SRM transition and the total cycle time was 1.39 seconds. Approximately 10-14 data points were acquired per detected metabolite. Samples were delivered to the mass spectrometer via hydrophilic interaction chromatography (HILIC) using a 4.6 mm i.d x 10 cm Amide XBridge column (Waters) at 400 μL/min. Gradients were run with a Prominence UFLC HPLC (Shimadzu) starting from 85% buffer B (HPLC grade acetonitrile) to 42% B from 0-5 minutes; 42% B to 0% B from 5-16 minutes; 0% B was held from 16-24 minutes; 0% B to 85% B from 24-25 minutes; 85% B was held for 7 minutes to re-equilibrate the column. Buffer A was comprised of 20 mM ammonium hydroxide/20 mM ammonium acetate (pH=9.0) in 95:5 water:acetonitrile. Peak areas from the total ion current for each metabolite SRM transition were integrated using MultiQuant v3.0 software (AB/SCIEX)"},

"MS_METABOLITE_DATA":{
"Units":"Q3 Peak Area (area under curve)",

"Data":[{"Metabolite":"1-Methyl-Histidine","62122_c":"62421.04863","1281202_c":"56011.57737","534282_c":"92018.25178","62122_t":"104642.0462","1281202_t":"37576.33151","534282_t":"38900.13063"},{"Metabolite":"1-Methyladenosine","62122_c":"6735.478569","1281202_c":"3304.400403","534282_c":"8249.980851","62122_t":"9842.184295","1281202_t":"7387.284692","534282_t":"5025.969712"},{"Metabolite":"1,3-diphopshateglycerate","62122_c":"12798.52329","1281202_c":"8132.178918","534282_c":"11698.36388","62122_t":"4456.909412","1281202_t":"4957.432549","534282_t":"7904.69915"},{"Metabolite":"2-Aminooctanoic acid","62122_c":"4803.817247","1281202_c":"8855.850251","534282_c":"13096.38278","62122_t":"12225.44434","1281202_t":"7825.744618","534282_t":"8597.503669"},{"Metabolite":"2-dehydro-D-gluconate","62122_c":"25541.63674","1281202_c":"21404.67235","534282_c":"18119.59466","62122_t":"17337.25752","1281202_t":"14830.07313","534282_t":"26435.97041"},{"Metabolite":"2-deoxyglucose-6-phosphate","62122_c":"95635.78431","1281202_c":"91987.89581","534282_c":"65142.01119","62122_t":"78534.23648","1281202_t":"67128.78065","534282_t":"39249.43657"},{"Metabolite":"2-Hydroxy-2-methylbutanedioic acid","62122_c":"182388.9684","1281202_c":"208942.4793","534282_c":"167598.4861","62122_t":"247821.5211","1281202_t":"98909.99432","534282_t":"129494.9978"},{"Metabolite":"2-hydroxygluterate","62122_c":"546168.6423","1281202_c":"440719.0491","534282_c":"523984.3575","62122_t":"427070.7483","1281202_t":"427068.9629","534282_t":"499403.5025"},{"Metabolite":"2-Isopropylmalic acid","62122_c":"67570.60213","1281202_c":"77186.31725","534282_c":"72808.32332","62122_t":"95264.82075","1281202_t":"61779.02982","534282_t":"524067.0633"},{"Metabolite":"2-keto-isovalerate","62122_c":"460564.3872","1281202_c":"355279.1512","534282_c":"284451.011","62122_t":"287121.4855","1281202_t":"330449.1084","534282_t":"323522.127"},{"Metabolite":"2-ketohaxanoic acid","62122_c":"21009.38488","1281202_c":"9204.90578","534282_c":"12420.13678","62122_t":"8325.297575","1281202_t":"15602.50556","534282_t":"N/A"},{"Metabolite":"2-oxo-4-methylthiobutanoate","62122_c":"14556.38804","1281202_c":"5704.960931","534282_c":"16780.52251","62122_t":"21906.84581","1281202_t":"21596.29839","534282_t":"32814.20619"},{"Metabolite":"2-oxobutanoate","62122_c":"152997.5874","1281202_c":"136358.8649","534282_c":"93485.7779","62122_t":"79773.99059","1281202_t":"127597.9024","534282_t":"192107.267"},{"Metabolite":"2,3-dihydroxybenzoic acid","62122_c":"104250.7913","1281202_c":"86045.13895","534282_c":"84184.06248","62122_t":"71482.09557","1281202_t":"62568.67541","534282_t":"20371.0193"},{"Metabolite":"2,3-Diphosphoglyceric acid","62122_c":"3663.147139","1281202_c":"4953.316617","534282_c":"N/A","62122_t":"N/A","1281202_t":"N/A","534282_t":"4102.961071"},{"Metabolite":"3-hydroxybuterate","62122_c":"22153.72249","1281202_c":"9098.419999","534282_c":"9111.579414","62122_t":"21704.20192","1281202_t":"20036.35201","534282_t":"22988.70586"},{"Metabolite":"3-methylphenylacetic acid","62122_c":"8862.527879","1281202_c":"21354.53875","534282_c":"7738.425205","62122_t":"21993.51417","1281202_t":"21573.59759","534282_t":"4010.285601"},{"Metabolite":"3-phospho-serine","62122_c":"2481.564756","1281202_c":"1655.424581","534282_c":"N/A","62122_t":"1655.258127","1281202_t":"N/A","534282_t":"1655.424578"},{"Metabolite":"3-phosphoglycerate","62122_c":"14570.94733","1281202_c":"12666.62164","534282_c":"8492.067921","62122_t":"8711.44152","1281202_t":"17147.94896","534282_t":"13121.44378"},{"Metabolite":"3-S-methylthiopropionate","62122_c":"2477.632204","1281202_c":"N/A","534282_c":"N/A","62122_t":"N/A","1281202_t":"N/A","534282_t":"7428.43208"},{"Metabolite":"4-aminobutyrate","62122_c":"N/A","1281202_c":"N/A","534282_c":"N/A","62122_t":"7368.117952","1281202_t":"N/A","534282_t":"N/A"},{"Metabolite":"4-phosphopantothenate","62122_c":"2513.401934","1281202_c":"5023.981375","534282_c":"N/A","62122_t":"4189.487597","1281202_t":"N/A","534282_t":"1676.297587"},{"Metabolite":"4-Pyridoxic acid","62122_c":"42399.21784","1281202_c":"10329.84277","534282_c":"19819.74368","62122_t":"24255.44533","1281202_t":"18666.63876","534282_t":"33660.6524"},{"Metabolite":"5-methoxytryptophan","62122_c":"N/A","1281202_c":"3302.694673","534282_c":"2479.383357","62122_t":"5780.697336","1281202_t":"N/A","534282_t":"11560.21705"},{"Metabolite":"5-methyl-THF","62122_c":"N/A","1281202_c":"N/A","534282_c":"N/A","62122_t":"N/A","1281202_t":"N/A","534282_t":"N/A"},{"Metabolite":"5-phosphoribosyl-1-pyrophosphate","62122_c":"N/A","1281202_c":"N/A","534282_c":"N/A","62122_t":"N/A","1281202_t":"4955.325782","534282_t":"N/A"},{"Metabolite":"6-phospho-D-gluconate","62122_c":"N/A","1281202_c":"7435.318166","534282_c":"5771.126844","62122_t":"N/A","1281202_t":"1652.642084","534282_t":"6608.118943"},{"Metabolite":"7-methylguanosine","62122_c":"14875.83057","1281202_c":"16517.00732","534282_c":"9909.223236","62122_t":"20644.56786","1281202_t":"4951.398371","534282_t":"15675.65091"},{"Metabolite":"7,8-dihydrofolate","62122_c":"N/A","1281202_c":"N/A","534282_c":"N/A","62122_t":"N/A","1281202_t":"N/A","534282_t":"N/A"},{"Metabolite":"a-ketoglutarate","62122_c":"5589169.66","1281202_c":"5475922.053","534282_c":"6309820.523","62122_t":"5510113.043","1281202_t":"5473937.152","534282_t":"3725444.947"},{"Metabolite":"acadesine","62122_c":"N/A","1281202_c":"N/A","534282_c":"5780.133117","62122_t":"N/A","1281202_t":"N/A","534282_t":"N/A"},{"Metabolite":"acetoacetate","62122_c":"97556.02426","1281202_c":"106598.9211","534282_c":"70268.07056","62122_t":"81954.77303","1281202_t":"144383.009","534282_t":"108584.1052"},{"Metabolite":"acetoacetyl-CoA-posi","62122_c":"N/A","1281202_c":"N/A","534282_c":"N/A","62122_t":"N/A","1281202_t":"N/A","534282_t":"N/A"},{"Metabolite":"acetyl-CoA-posi","62122_c":"N/A","1281202_c":"N/A","534282_c":"N/A","62122_t":"N/A","1281202_t":"N/A","534282_t":"N/A"},{"Metabolite":"Acetylcarnitine DL","62122_c":"49602.11903","1281202_c":"45812.68699","534282_c":"32621.97701","62122_t":"33012.42776","1281202_t":"9079.087953","534282_t":"36223.42405"},{"Metabolite":"Acetyllysine","62122_c":"9810.285328","1281202_c":"13259.55595","534282_c":"5788.404409","62122_t":"29736.20189","1281202_t":"6634.754626","534282_t":"12452.07389"},{"Metabolite":"acetylphosphate","62122_c":"N/A","1281202_c":"12089.55508","534282_c":"70930.81776","62122_t":"49631.32651","1281202_t":"N/A","534282_t":"N/A"},{"Metabolite":"aconitate","62122_c":"123846.6044","1281202_c":"125871.9413","534282_c":"86957.38455","62122_t":"152248.6898","1281202_t":"112889.8855","534282_t":"87824.99397"},{"Metabolite":"adenine","62122_c":"415012.486","1281202_c":"413768.0193","534282_c":"385602.6813","62122_t":"368883.6467","1281202_t":"498190.1712","534282_t":"346924.7575"},{"Metabolite":"adenosine","62122_c":"13847.64091","1281202_c":"9002.538396","534282_c":"4208.093068","62122_t":"3978.001357","1281202_t":"2477.658771","534282_t":"3314.999414"},{"Metabolite":"adenosine 5-phosphosulfate","62122_c":"N/A","1281202_c":"N/A","534282_c":"N/A","62122_t":"N/A","1281202_t":"N/A","534282_t":"N/A"},{"Metabolite":"Adenylosuccinate","62122_c":"164348.1074","1281202_c":"94148.04132","534282_c":"86714.0138","62122_t":"75152.29672","1281202_t":"113141.3356","534282_t":"124708.0176"},{"Metabolite":"ADP-D-glucose","62122_c":"N/A","1281202_c":"N/A","534282_c":"N/A","62122_t":"4119.500535","1281202_t":"N/A","534282_t":"N/A"},{"Metabolite":"ADP-nega","62122_c":"9082.925489","1281202_c":"N/A","534282_c":"N/A","62122_t":"N/A","1281202_t":"N/A","534282_t":"N/A"},{"Metabolite":"alanine","62122_c":"5376216.365","1281202_c":"4792675.036","534282_c":"5516011.453","62122_t":"6026657.105","1281202_t":"5343504.352","534282_t":"3018220.983"},{"Metabolite":"allantoate","62122_c":"7383.34914","1281202_c":"N/A","534282_c":"N/A","62122_t":"3267.047272","1281202_t":"4033.695735","534282_t":"N/A"},{"Metabolite":"allantoin","62122_c":"15094.24261","1281202_c":"8599.371663","534282_c":"24858.69767","62122_t":"34176.99424","1281202_t":"31231.27543","534282_t":"14533.04525"},{"Metabolite":"Aminoadipic acid","62122_c":"604824.4813","1281202_c":"548636.3275","534282_c":"434156.2712","62122_t":"448858.2786","1281202_t":"582850.4828","534282_t":"204322.0422"},{"Metabolite":"aminoimidazole carboxamide ribonucleotide","62122_c":"N/A","1281202_c":"N/A","534282_c":"N/A","62122_t":"N/A","1281202_t":"N/A","534282_t":"N/A"},{"Metabolite":"AMP","62122_c":"4955.196625","1281202_c":"N/A","534282_c":"N/A","62122_t":"N/A","1281202_t":"N/A","534282_t":"N/A"},{"Metabolite":"anthranilate","62122_c":"12180.37855","1281202_c":"27099.10425","534282_c":"8625.976361","62122_t":"21644.80523","1281202_t":"18907.27462","534282_t":"16853.3334"},{"Metabolite":"arginine","62122_c":"48281152.31","1281202_c":"55992349.65","534282_c":"54212599.4","62122_t":"55145204.02","1281202_t":"61742251.44","534282_t":"44744033.67"},{"Metabolite":"arginosuccinic acid","62122_c":"34534.89906","1281202_c":"46599.14234","534282_c":"52731.02478","62122_t":"31999.147","1281202_t":"39442.43017","534282_t":"40389.72602"},{"Metabolite":"Ascorbic acid","62122_c":"1807930.889","1281202_c":"2621292.307","534282_c":"1700216.776","62122_t":"1282679.622","1281202_t":"2733923.441","534282_t":"1126553.906"},{"Metabolite":"asparagine","62122_c":"6708305.553","1281202_c":"7475690.076","534282_c":"7555886.699","62122_t":"7061255.258","1281202_t":"6368976.461","534282_t":"4830244.977"},{"Metabolite":"aspartate","62122_c":"3632102.289","1281202_c":"2514522.28","534282_c":"2346025.523","62122_t":"2735726.858","1281202_t":"2800160.341","534282_t":"3429226.955"},{"Metabolite":"ATP-nega","62122_c":"3308.242861","1281202_c":"N/A","534282_c":"N/A","62122_t":"N/A","1281202_t":"N/A","534282_t":"N/A"},{"Metabolite":"Atrolactic acid","62122_c":"27104.69156","1281202_c":"32998.44097","534282_c":"53645.95693","62122_t":"66144.68461","1281202_t":"57378.93184","534282_t":"69590.18706"},{"Metabolite":"betaine","62122_c":"1112611.704","1281202_c":"1264289.339","534282_c":"833463.2414","62122_t":"786853.1903","1281202_t":"994827.3528","534282_t":"1289283.084"},{"Metabolite":"betaine aldehyde","62122_c":"56523.98693","1281202_c":"60199.47008","534282_c":"28445.7671","62122_t":"50821.46861","1281202_t":"35778.86486","534282_t":"48221.69027"},{"Metabolite":"biotin","62122_c":"45557.44164","1281202_c":"39478.97929","534282_c":"53895.60291","62122_t":"51944.89476","1281202_t":"62553.12474","534282_t":"153402.0241"},{"Metabolite":"Carbamoyl 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}

}