#METABOLOMICS WORKBENCH STUDY_ID:ST000275 ANALYSIS_ID:AN000438 PROJECT_ID:PR000219 VERSION 1 CREATED_ON 2016-09-17 #PROJECT PR:PROJECT_TITLE Metabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fiboblasts and Human PR:PROJECT_TITLE & Normal Lung Fiboblasts #2 PR:PROJECT_TYPE Glycolysis/TCA/Nucleotide analysis (tissue/cells) PR:PROJECT_SUMMARY Hedgehog signaling plays important roles in cell development and PR:PROJECT_SUMMARY In this study, the ability of Sonic Hedgehog (SHH) to induce myofibroblast PR:PROJECT_SUMMARY was analyzed in isolated human lung fibroblasts, and its in vivo significance PR:PROJECT_SUMMARY evaluated in rodent bleomycin-induced pulmonary fibrosis. The results showed PR:PROJECT_SUMMARY SHH could induce myofibroblast differentiation in human lung fibroblasts in a PR:PROJECT_SUMMARY and Gli1-dependent manner. Gel shift analysis, chromatin immunoprecipitation PR:PROJECT_SUMMARY and site-directed mutagenesis revealed that a Gli1 binding consensus in the PR:PROJECT_SUMMARY gene promoter was important for mediating SHH-induced myofibroblast PR:PROJECT_SUMMARY Analysis of Hedgehog reemergence in vivo revealed that of all three Hedgehog PR:PROJECT_SUMMARY only SHH was significantly induced in bleomycin-injured lung along with Gli1. PR:PROJECT_SUMMARY induction of SHH was only noted in epithelial cells, and its expression was PR:PROJECT_SUMMARY in lung fibroblasts or macrophages. Transforming growth factor (TGF)-? induced PR:PROJECT_SUMMARY significantly in cultured alveolar epithelial cells, whereas SHH induced TGF-? PR:PROJECT_SUMMARY lung fibroblasts. Pulmonary fibrosis and ?-smooth muscle actin (?-SMA) PR:PROJECT_SUMMARY were significantly reduced in mice that were Smo deficient only in type I PR:PROJECT_SUMMARY cells. Thus, the reemergence of SHH in epithelial cells could result in PR:PROJECT_SUMMARY of myofibroblast differentiation in a Smo-dependent manner and subsequent Gli1 PR:PROJECT_SUMMARY of the ?-SMA promoter. PR:INSTITUTE University of Michigan PR:DEPARTMENT Deaprtment of Pathology PR:LABORATORY Sem H. Phan PR:LAST_NAME Hu PR:FIRST_NAME Biao PR:ADDRESS Ann Arbor, MI PR:EMAIL biaohu@med.umich.edu PR:PHONE 734-7635731 #STUDY ST:STUDY_TITLE Metabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fiboblasts and Human ST:STUDY_TITLE & Normal Lung Fiboblasts (Part 2) ST:STUDY_TYPE Glycolysis/TCA/Nucleotide analysis. Ceramide analysis for parp1 wild type lung ST:STUDY_TYPE after saline or bleomycin treatment. ST:STUDY_SUMMARY This study is a part of series performed for the same researcher through ST:STUDY_SUMMARY grant program, so the publication is relevant reference for other studies ST:STUDY_SUMMARY ST000183)This specific experiment is a small pilot study to establish method ST:STUDY_SUMMARY it includes four biological replicas of identical cell cultures after the ST:STUDY_SUMMARY treatment and a single tissue sample. ST:INSTITUTE University of Michigan ST:DEPARTMENT Deaprtment of Pathology ST:LABORATORY Sem H. Phan ST:LAST_NAME Hu ST:FIRST_NAME Biao ST:ADDRESS Ann Arbor, MI ST:EMAIL biaohu@med.umich.edu ST:PHONE 734-7635731 ST:NUM_GROUPS 1 ST:TOTAL_SUBJECTS 5 ST:STUDY_COMMENTS http://www.atsjournals.org/doi/full/10.1165/rcmb.2014-0108OC#.Vmb9VVWrRhE #SUBJECT SU:SUBJECT_TYPE Animal SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 SU:SPECIES_GROUP Mammal #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - S00014994 Sample type:Cell culture | Genetic background:B6 wt | bleomycin:yes SUBJECT_SAMPLE_FACTORS - S00014995 Sample type:Cell culture | Genetic background:B6 wt | bleomycin:yes SUBJECT_SAMPLE_FACTORS - S00014996 Sample type:Cell culture | Genetic background:B6 wt | bleomycin:yes SUBJECT_SAMPLE_FACTORS - S00014997 Sample type:Cell culture | Genetic background:B6 wt | bleomycin:yes SUBJECT_SAMPLE_FACTORS - S00014998 Sample type:Tissue | Genetic background:B6 wt | bleomycin:yes #COLLECTION CO:COLLECTION_SUMMARY - CO:SAMPLE_TYPE Cells #TREATMENT TR:TREATMENT_SUMMARY - #SAMPLEPREP SP:SAMPLEPREP_SUMMARY - SP:SAMPLEPREP_PROTOCOL_FILENAME Gly-TCA-nucleotides_analysis_protocol-2015-03-09.docx #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Agilent 1260 CH:COLUMN_NAME Phenomenex Luna NH2 (150 x 1mm, 3um) CH:METHODS_ID AQM020 CH:METHODS_FILENAME QTOF-002-HILIC-35min-1mm.m #ANALYSIS AN:ANALYSIS_TYPE MS AN:LABORATORY_NAME MRC2 (University of Michigan) AN:ACQUISITION_PARAMETERS_FILE Column1_solv1_jetstream+_grad9.m AN:PROCESSING_PARAMETERS_FILE EX00310-MassHunterQuant-GlyTCA-DataAnalysis-LCMS-Method.m #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Agilent 6530 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE NEGATIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS µM (500µl of extraction solvent) MS_METABOLITE_DATA_START Samples S00014994 S00014995 S00014996 S00014997 S00014998 Factors Sample type:Cell culture | Genetic background:B6 wt | bleomycin:yes Sample type:Cell culture | Genetic background:B6 wt | bleomycin:yes Sample type:Cell culture | Genetic background:B6 wt | bleomycin:yes Sample type:Cell culture | Genetic background:B6 wt | bleomycin:yes Sample type:Tissue | Genetic background:B6 wt | bleomycin:yes 2 or 3-phosphoglycerate_2PG/3PG 1.1577 1.1884 0.9990 0.7757 1.1878 6-Phosphogluconate 0.2863 0.2394 0.2879 0.1559 0.5618 Acetyl-CoA 0.1172 0.0648 0.0967 0.1000 0.0553 ADP 3.4110 3.5422 2.4469 2.0365 8.5675 AMP 5.5347 5.7634 3.5449 3.3430 303.2638 ATP 41.3260 36.0813 33.8644 30.5504 3.1217 Citrate or Isocitrate 32.8578 43.3185 35.1965 47.1062 24.9626 Erythrose 4-phosphate 2.8414 2.7062 2.4028 2.4877 16.5782 flavin adenine dinucleotide 0.0535 0.0524 0.0490 0.0475 0.4202 Fructose 1_6-bisphosphate 8.5102 7.9560 6.4152 5.8557 5.5311 Glucose 6-phosphate or fructose-6-phosphate 2.3811 1.7382 1.6978 1.4426 9.6583 Malate 11.3931 12.8468 10.8206 12.2637 20.9530 Nicotinamide Adenine Dinucleotide oxidized 1.8427 1.4685 1.5589 1.2770 0.0905 nicotinamide adenine dinucleotide phosphate oxidized 0.2135 0.1981 0.1568 0.1050 0.7036 nicotinamide adenine dinucleotide phosphate reduced 1.5520 1.2917 1.5221 1.7584 0.0968 Nicotinamide Adenine Dinucleotide reduced 0.2007 0.1058 0.2323 0.2723 0.3241 Phosphoenolpyruvate 0.6961 0.6103 0.7216 0.6450 0.2821 Ribose-5-phosphate or xylulose 5-phosphate 0.6749 0.6488 0.5681 0.5436 19.1959 sedoheptulose Sedoheptulose 7-phosphate 1.0500 0.9529 0.8679 0.8941 6.9018 Sucrose 1.2615 1.5337 1.1406 1.5901 2.6906 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name moverz_quant ri ri_type pubchem_id inchi_key kegg_id other_id other_id_type 2 or 3-phosphoglycerate_2PG/3PG 724 C00597 2PG/3PG UM_Target_ID 6-Phosphogluconate 91493 C00345 6PG UM_Target_ID Acetyl-CoA 444493 C00024 aCoA UM_Target_ID ADP 6022 C00008 ADP UM_Target_ID AMP 6083 C00020 AMP UM_Target_ID ATP 5957 C00002 ATP UM_Target_ID Citrate or Isocitrate 311 C00158 CIT/ICIT UM_Target_ID Erythrose 4-phosphate 122357 C00279 E4P UM_Target_ID flavin adenine dinucleotide 643975 C00016 FAD UM_Target_ID Fructose 1,6-bisphosphate 172313 C00354 FBP UM_Target_ID Glucose 6-phosphate or fructose-6-phosphate 5958 C00092 G6P/F6P UM_Target_ID Malate 222656 C00149 MAL UM_Target_ID Nicotinamide Adenine Dinucleotide oxidized 10897651 C00003 NAD UM_Target_ID nicotinamide adenine dinucleotide phosphate oxidized 5886 C00006 NADP UM_Target_ID nicotinamide adenine dinucleotide phosphate reduced 5886 C00006 NADPH UM_Target_ID Nicotinamide Adenine Dinucleotide reduced 439153 C00004 NADH UM_Target_ID Phosphoenolpyruvate 1005 C00074 PEP UM_Target_ID Ribose-5-phosphate or xylulose 5-phosphate 77982 C00117 R5P/X5P UM_Target_ID sedoheptulose 102926 SED UM_Target_ID Sedoheptulose 7-phosphate 165007 C05382 S7P UM_Target_ID Sucrose 5988 C00089 SUC UM_Target_ID METABOLITES_END #END