#METABOLOMICS WORKBENCH araskind_20150313_9045041_mwtab.txt DATATRACK_ID:222 STUDY_ID:ST000143 ANALYSIS_ID:AN000226 PROJECT_ID:PR000219 VERSION 1 CREATED_ON 01-15-2019 #PROJECT PR:PROJECT_TITLE Metabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fibroblasts and Human PR:PROJECT_TITLE IPF & Normal Lung Fibroblasts PR:PROJECT_TYPE Glycolysis/TCA/Nucleotide analysis (tissue/cells) PR:PROJECT_SUMMARY Hedgehog signaling plays important roles in cell development and PR:PROJECT_SUMMARY differentiation. In this study, the ability of Sonic Hedgehog (SHH) to induce PR:PROJECT_SUMMARY myofibroblast differentiation was analyzed in isolated human lung fibroblasts, PR:PROJECT_SUMMARY and its in vivo significance was evaluated in rodent bleomycin-induced pulmonary PR:PROJECT_SUMMARY fibrosis. The results showed that SHH could induce myofibroblast differentiation PR:PROJECT_SUMMARY in human lung fibroblasts in a Smo- and Gli1-dependent manner. Gel shift PR:PROJECT_SUMMARY analysis, chromatin immunoprecipitation assay, and site-directed mutagenesis PR:PROJECT_SUMMARY revealed that a Gli1 binding consensus in the ?-SMA gene promoter was important PR:PROJECT_SUMMARY for mediating SHH-induced myofibroblast differentiation. Analysis of Hedgehog PR:PROJECT_SUMMARY reemergence in vivo revealed that of all three Hedgehog isoforms, only SHH was PR:PROJECT_SUMMARY significantly induced in bleomycin-injured lung along with Gli1. The induction PR:PROJECT_SUMMARY of SHH was only noted in epithelial cells, and its expression was undetectable PR:PROJECT_SUMMARY in lung fibroblasts or macrophages. Transforming growth factor (TGF)-? induced PR:PROJECT_SUMMARY SHH significantly in cultured alveolar epithelial cells, whereas SHH induced PR:PROJECT_SUMMARY TGF-? in lung fibroblasts. Pulmonary fibrosis and ?-smooth muscle actin (?-SMA) PR:PROJECT_SUMMARY expression were significantly reduced in mice that were Smo deficient only in PR:PROJECT_SUMMARY type I collagen–expressing cells. Thus, the reemergence of SHH in epithelial PR:PROJECT_SUMMARY cells could result in induction of myofibroblast differentiation in a PR:PROJECT_SUMMARY Smo-dependent manner and subsequent Gli1 activation 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 PR:DOI http://dx.doi.org/10.21228/M8359Z #STUDY ST:STUDY_TITLE Metabolic analysis of Normal Mouse Lung Fiboblasts with/without TGFbeta ST:STUDY_TITLE treatment (Part 1) ST:STUDY_TYPE Glycolysis/TCA/Nucleotide analysis (tissue/cells) ST:STUDY_SUMMARY This study is a part of series performed for the same researcher through ST:STUDY_SUMMARY pilot/feasibility grant program, so the publication is relevant reference for ST:STUDY_SUMMARY other studies, see the project for this study. This specific experiment is a ST:STUDY_SUMMARY small pilot study to establish method performance, it includes four biological ST:STUDY_SUMMARY replicas of identical cell cultures after the identical treatment and a single ST:STUDY_SUMMARY tissue sample. ST:INSTITUTE University of Michigan ST:DEPARTMENT Biomedical Research Core Facilities ST:LABORATORY Metabolomics core ST:LAST_NAME Kachman ST:FIRST_NAME Maureen ST:ADDRESS 6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714 ST:EMAIL mkachman@umich.edu ST:PHONE - #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 SU0003983 S00014557 Genotype:parp1 ko | Treatment:bleomycin SUBJECT_SAMPLE_FACTORS SU0003984 S00014558 Genotype:parp1 ko | Treatment:bleomycin SUBJECT_SAMPLE_FACTORS SU0003985 S00014559 Genotype:parp1 ko | Treatment:bleomycin SUBJECT_SAMPLE_FACTORS SU0003994 S00014568 Genotype:parp1 ko | Treatment:bleomycin SUBJECT_SAMPLE_FACTORS SU0003995 S00014569 Genotype:parp1 ko | Treatment:bleomycin SUBJECT_SAMPLE_FACTORS SU0004004 S00014578 Genotype:parp1 ko | Treatment:bleomycin SUBJECT_SAMPLE_FACTORS SU0004005 S00014579 Genotype:parp1 ko | Treatment:bleomycin SUBJECT_SAMPLE_FACTORS SU0004006 S00014580 Genotype:parp1 ko | Treatment:bleomycin SUBJECT_SAMPLE_FACTORS SU0003980 S00014554 Genotype:parp1 ko | Treatment:saline SUBJECT_SAMPLE_FACTORS SU0003981 S00014555 Genotype:parp1 ko | Treatment:saline SUBJECT_SAMPLE_FACTORS SU0003982 S00014556 Genotype:parp1 ko | Treatment:saline SUBJECT_SAMPLE_FACTORS SU0003992 S00014566 Genotype:parp1 ko | Treatment:saline SUBJECT_SAMPLE_FACTORS SU0003993 S00014567 Genotype:parp1 ko | Treatment:saline SUBJECT_SAMPLE_FACTORS SU0004001 S00014575 Genotype:parp1 ko | Treatment:saline SUBJECT_SAMPLE_FACTORS SU0004002 S00014576 Genotype:parp1 ko | Treatment:saline SUBJECT_SAMPLE_FACTORS SU0004003 S00014577 Genotype:parp1 ko | Treatment:saline SUBJECT_SAMPLE_FACTORS SU0003989 S00014563 Genotype:parp1 wt | Treatment:bleomycin SUBJECT_SAMPLE_FACTORS SU0003990 S00014564 Genotype:parp1 wt | Treatment:bleomycin SUBJECT_SAMPLE_FACTORS SU0003991 S00014565 Genotype:parp1 wt | Treatment:bleomycin SUBJECT_SAMPLE_FACTORS SU0003998 S00014572 Genotype:parp1 wt | Treatment:bleomycin SUBJECT_SAMPLE_FACTORS SU0003999 S00014573 Genotype:parp1 wt | Treatment:bleomycin SUBJECT_SAMPLE_FACTORS SU0004000 S00014574 Genotype:parp1 wt | Treatment:bleomycin SUBJECT_SAMPLE_FACTORS SU0003986 S00014560 Genotype:parp1 wt | Treatment:saline SUBJECT_SAMPLE_FACTORS SU0003987 S00014561 Genotype:parp1 wt | Treatment:saline SUBJECT_SAMPLE_FACTORS SU0003988 S00014562 Genotype:parp1 wt | Treatment:saline SUBJECT_SAMPLE_FACTORS SU0003996 S00014570 Genotype:parp1 wt | Treatment:saline SUBJECT_SAMPLE_FACTORS SU0003997 S00014571 Genotype:parp1 wt | Treatment:saline SUBJECT_SAMPLE_FACTORS SU0004007 S00014581 Genotype:parp1 wt | Treatment:saline SUBJECT_SAMPLE_FACTORS SU0004008 S00014582 Genotype:parp1 wt | Treatment:saline SUBJECT_SAMPLE_FACTORS SU0004009 S00014583 Genotype:parp1 wt | Treatment:saline #COLLECTION CO:SAMPLE_TYPE Tissues CO:COLLECTION_SUMMARY - #TREATMENT TR:TREATMENT_SUMMARY - #SAMPLEPREP SP:SAMPLEPREP_PROTOCOL_FILENAME Gly-TCA-nucleotides_analysis_protocol-2015-03-09.docx SP:SAMPLEPREP_SUMMARY - #CHROMATOGRAPHY CH:METHODS_ID AQM020 CH:METHODS_FILENAME QTOF-002-HILIC-35min-1mm.m.zip CH:INSTRUMENT_NAME Agilent 1260 CH:COLUMN_NAME Phenomenex Luna NH2 (150 x 1mm, 3um) CH:CHROMATOGRAPHY_TYPE HILIC #ANALYSIS AN:LABORATORY_NAME MRC2 (University of Michigan) AN:ANALYSIS_TYPE MS AN:ACQUISITION_PARAMETERS_FILE QTOF-002-HILIC-35min-1mm.m.zip AN:PROCESSING_PARAMETERS_FILE EX00294-MassHunterQuant-GlyTCA-LCMS-DataAnalysis-Method.m.zip #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Agilent 6520 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE NEGATIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS uM MS_METABOLITE_DATA_START Samples S00014557 S00014558 S00014559 S00014568 S00014569 S00014578 S00014579 S00014580 S00014554 S00014555 S00014556 S00014566 S00014567 S00014575 S00014576 S00014577 S00014563 S00014564 S00014565 S00014572 S00014573 S00014574 S00014560 S00014561 S00014562 S00014570 S00014571 S00014581 S00014582 S00014583 Factors Genotype:parp1 ko | Treatment:bleomycin Genotype:parp1 ko | Treatment:bleomycin Genotype:parp1 ko | Treatment:bleomycin Genotype:parp1 ko | Treatment:bleomycin Genotype:parp1 ko | Treatment:bleomycin Genotype:parp1 ko | Treatment:bleomycin Genotype:parp1 ko | Treatment:bleomycin Genotype:parp1 ko | Treatment:bleomycin Genotype:parp1 ko | Treatment:saline Genotype:parp1 ko | Treatment:saline Genotype:parp1 ko | Treatment:saline Genotype:parp1 ko | Treatment:saline Genotype:parp1 ko | Treatment:saline Genotype:parp1 ko | Treatment:saline Genotype:parp1 ko | Treatment:saline Genotype:parp1 ko | Treatment:saline Genotype:parp1 wt | Treatment:bleomycin Genotype:parp1 wt | Treatment:bleomycin Genotype:parp1 wt | Treatment:bleomycin Genotype:parp1 wt | Treatment:bleomycin Genotype:parp1 wt | Treatment:bleomycin Genotype:parp1 wt | Treatment:bleomycin Genotype:parp1 wt | Treatment:saline Genotype:parp1 wt | Treatment:saline Genotype:parp1 wt | Treatment:saline Genotype:parp1 wt | Treatment:saline Genotype:parp1 wt | Treatment:saline Genotype:parp1 wt | Treatment:saline Genotype:parp1 wt | Treatment:saline Genotype:parp1 wt | Treatment:saline 2 or 3-phosphoglycerate 2.6535 2.0613 3.4885 2.0597 1.4678 2.6674 1.6227 2.3605 1.2658 1.5084 2.1407 1.1526 1.3969 0.9749 0.7920 0.6063 1.9297 2.0073 2.1112 2.3264 2.2204 1.9894 1.2577 1.2413 0.4635 0.7224 1.0548 0.9298 0.5405 0.9217 6-Phosphogluconate 4.4931 4.4477 6.1817 3.8803 5.6457 1.5795 4.1915 3.8326 1.4187 1.4955 1.7618 1.7909 1.5738 2.0787 1.3548 1.1566 4.8474 3.8897 4.5157 5.4485 5.3370 4.3964 1.9149 1.8588 1.2201 0.9488 1.4814 1.2173 1.4377 1.3430 Acetyl-CoA 0.0083 0.0038 0.0014 0.0023 0.0007 0.0122 0.0096 0.0258 0.0068 0.0032 0.0012 0.0068 0.0016 0.0075 0.0018 0.0014 0.0026 0.0044 0.0132 0.0182 0.0059 0.0011 0.0015 0.0037 0.0005 0.0095 Adenosine diphosphate 1.5043 1.3182 2.2288 1.0972 1.8997 0.9749 1.4813 1.4879 1.5453 1.6803 1.8477 1.5318 1.5064 1.4959 1.4833 1.2623 1.8099 1.3163 1.3220 1.3622 1.7721 1.9270 1.7836 1.4980 1.6737 1.1938 1.4039 1.4743 1.0745 1.4563 Adenosine monophosphate 1.6004 1.1696 2.5563 0.6832 2.2546 0.5653 1.3007 2.4826 5.7147 7.4824 9.4457 2.3780 2.6396 3.0478 1.8936 3.6544 1.4514 0.8905 1.6877 1.0157 1.2305 1.1501 7.1108 5.0456 6.2726 2.2226 4.8690 3.1170 1.8647 2.8844 Adenosine triphosphate 0.2960 0.4852 0.2939 0.3022 0.1828 0.1881 0.2920 0.2660 0.1786 0.1647 0.2412 0.2686 0.1406 0.1295 0.2168 0.0752 0.5363 0.3583 0.4748 0.4689 0.3590 0.3466 0.2391 0.2742 0.1440 0.0987 0.0953 0.1639 0.1270 0.2378 Citrate or Isocitrate 21.6376 24.8690 21.6895 18.6761 19.9247 5.9272 11.6287 2.8338 8.8642 9.8332 7.0618 4.5750 5.6280 2.7569 1.6949 4.5562 18.2101 24.3097 21.3533 33.5082 35.4784 24.0798 7.7515 6.3965 6.5852 2.5077 3.5781 2.7033 2.2886 6.9790 Dihydronicotinamide-adenine dinucleotide phosphate 0.0499 0.3726 0.0894 0.0513 0.2645 0.1647 0.0911 0.2148 0.0730 0.1754 0.1770 0.0973 0.1354 0.2307 0.6056 0.2585 0.3638 0.3451 0.6220 0.1539 0.2182 0.1495 0.3020 0.2050 Flavin adenine dinucleotide 0.5990 0.3316 0.4890 0.3669 0.4189 0.3078 0.3673 0.3592 0.3551 0.4215 0.2035 0.2763 0.4089 0.5784 0.5253 0.6139 0.2711 0.3665 0.3792 0.5129 0.5134 0.3900 0.3400 0.1886 0.4497 0.5521 0.5944 0.5291 0.4261 0.3036 Fructose 1_6-bisphosphate 25.0851 26.1479 36.2161 21.6454 23.3500 7.6780 28.7395 21.1193 9.8760 15.7658 13.5273 12.7714 13.9415 12.2076 20.3809 7.3286 43.2561 21.0847 22.0443 23.7357 26.1368 31.3087 22.8418 18.9541 11.4802 11.2469 8.3555 12.9183 11.1033 12.7600 Glucose 6-phosphate or fructose-6-phosphate 91.3921 61.6863 85.4174 74.0206 87.1447 32.1643 83.8421 77.2553 37.2074 36.4412 26.6717 31.9985 40.4244 42.1510 38.0537 38.2250 84.1244 58.8614 65.1091 77.1580 97.6283 82.1395 41.5557 32.3720 39.0162 39.4828 40.7271 40.6188 31.5745 37.8240 Malate 33.4035 20.3296 27.2059 16.5010 28.4614 18.6191 23.9477 22.0698 7.3584 12.4476 5.3983 4.9672 13.5272 16.5580 18.4317 16.7952 19.2067 23.8915 21.3513 38.2673 34.8500 26.6794 7.7006 6.0771 11.6278 19.2600 22.2865 16.3916 14.3772 8.5986 Nicotinamide Adenine Dinucleotide oxidized Nicotinamide adenine dinucleotide phosphate 0.0847 0.1390 0.1924 0.0849 0.2144 0.1342 0.1396 0.1592 0.0908 0.1117 0.0408 0.0770 0.1406 0.3104 0.2714 0.1905 0.0760 0.0454 0.0890 0.2511 0.2390 0.1678 0.0942 0.0796 0.1640 0.2159 0.4128 0.2358 0.1517 0.2797 Nicotinamide Adenine Dinucleotide reduced 0.8459 0.5629 0.7203 0.5805 0.7433 0.6758 0.7004 0.7199 0.3567 Phosphoenolpyruvate 0.3049 0.2640 0.6811 0.1236 0.1124 0.1460 0.1141 0.0772 0.1410 0.0854 0.1686 0.1628 0.0706 0.0138 0.0109 0.0368 0.1517 0.1815 0.2246 0.2316 0.3506 0.3780 0.0957 0.1168 0.0110 0.0181 0.0144 0.0128 Sucrose 0.8662 1.5334 1.3334 0.6055 0.5992 0.7760 0.3400 0.6868 1.0186 0.6744 0.7134 0.7194 1.0530 0.6965 0.6743 0.4772 1.2556 0.9773 0.7177 1.9864 1.1077 0.9898 0.8599 1.0669 0.9653 0.5819 0.8536 0.7786 0.6326 0.8365 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name pubchem_id inchi_key kegg_id other_id other_id_type ri ri_type moverz_quant 2 or 3-phosphoglycerate 724 C00597 2PG/3PG UM_Target_ID 6-Phosphogluconate 91493 C00345 6PG UM_Target_ID Acetyl-CoA 444493 C00024 aCoA UM_Target_ID Adenosine diphosphate 6022 C00008 ADP UM_Target_ID Adenosine monophosphate 6083 C00020 AMP UM_Target_ID Adenosine triphosphate 5957 C00002 ATP UM_Target_ID Citrate or Isocitrate 311 C00158 CIT/ICIT UM_Target_ID Dihydronicotinamide-adenine dinucleotide phosphate 5884 C00005 NADPH 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 F6P/G6P UM_Target_ID Malate 222656 C00149 MAL UM_Target_ID Nicotinamide Adenine Dinucleotide oxidized 10897651 C00003 NAD UM_Target_ID Nicotinamide adenine dinucleotide phosphate 5886 C00006 NADP UM_Target_ID Nicotinamide Adenine Dinucleotide reduced 439153 C00004 NADH UM_Target_ID Phosphoenolpyruvate 1005 C00074 PEP UM_Target_ID Sucrose 5988 C00089 SUC UM_Target_ID METABOLITES_END #END