#METABOLOMICS WORKBENCH M_Sasaki_20230421_000842 DATATRACK_ID:3879 STUDY_ID:ST002584 ANALYSIS_ID:AN004256 PROJECT_ID:PR001664 VERSION 1 CREATED_ON April 26, 2023, 11:57 am #PROJECT PR:PROJECT_TITLE Metabolomics analysis of ALDH1L1-expressing HuH-7 cell line. PR:PROJECT_SUMMARY Quantitative metabolomics study of the effect of the folate metabolizing enzyme PR:PROJECT_SUMMARY ALDH1L1 on the HuH-7 cell line. PR:INSTITUTE Tohoku Medical and Pharmaceutical University PR:LAST_NAME Sasaki PR:FIRST_NAME Masato PR:ADDRESS 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan PR:EMAIL msasaki@tohoku-mpu.ac.jp PR:PHONE +81-22-727-0132 #STUDY ST:STUDY_TITLE Metabolomics analysis of ALDH1L1-expressing HuH7 cell lines. ST:STUDY_SUMMARY One-carbon metabolism is utilized for the de novo synthesis of purines. Given ST:STUDY_SUMMARY that tumor cells require large amounts of nucleotides, they are highly dependent ST:STUDY_SUMMARY on one-carbon metabolism. Among the one-carbon-metabolizing enzymes, the ST:STUDY_SUMMARY aldehyde dehydrogenase 1 family member L1 (ALDH1L1), which catalyzes ST:STUDY_SUMMARY 10-formyltetrahydrofolate to trahydrofolate, is considered a tumor suppressor ST:STUDY_SUMMARY gene, as its expression is reported to be attenuated or diminished in ST:STUDY_SUMMARY hepatocellular carcinoma. To clarify the effect of ALDH1L1 expression, we ST:STUDY_SUMMARY generated control and ALDH1L1-expressing HuH-7 (H7-1L1) cells, and measured the ST:STUDY_SUMMARY amounts of intracellular metabolites in both control and ALDH1L1-expressing by ST:STUDY_SUMMARY CE-TOFMS analysis. ST:INSTITUTE Tohoku Medical and Pharmaceutical University ST:LAST_NAME Sasaki ST:FIRST_NAME Masato ST:ADDRESS 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan ST:EMAIL msasaki@tohoku-mpu.ac.jp ST:PHONE +81-22-727-0132 #SUBJECT SU:SUBJECT_TYPE Cultured cells SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #FACTORS #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS L1-1 L1-1 Transgene:ALDH1L1 RAW_FILE_NAME=L1-1 SUBJECT_SAMPLE_FACTORS L1-2 L1-2 Transgene:ALDH1L1 RAW_FILE_NAME=L1-2 SUBJECT_SAMPLE_FACTORS L1-3 L1-3 Transgene:ALDH1L1 RAW_FILE_NAME=L1-3 SUBJECT_SAMPLE_FACTORS C-1 C-1 Transgene:empty RAW_FILE_NAME=C-1 SUBJECT_SAMPLE_FACTORS C-2 C-2 Transgene:empty RAW_FILE_NAME=C-2 SUBJECT_SAMPLE_FACTORS C-3 C-3 Transgene:empty RAW_FILE_NAME=C-3 #COLLECTION CO:COLLECTION_SUMMARY ALDH1L1-expressing cells or control (empty vector) cells were cultured in DMEM CO:COLLECTION_SUMMARY medium containing 5% fetal bovine serum and metabolites were collected during CO:COLLECTION_SUMMARY growing phase. CO:SAMPLE_TYPE HuH-7 cells #TREATMENT TR:TREATMENT_SUMMARY No treatment in this study. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Cells were washed with 5%(w/w) mannitol solution, and then extracted with SP:SAMPLEPREP_SUMMARY methanol. Extracts were filtered through a 5-kDa cut-off filter SP:SAMPLEPREP_SUMMARY (Ultrafree-MC-PLHCC, Human Metabolome Technologies) at 9,100 × g for 2 h at SP:SAMPLEPREP_SUMMARY 4 °C, dried in a centrifugal evaporator at 1,500 rpm at 1,000 Pa, and SP:SAMPLEPREP_SUMMARY resuspended in 50 μl of ultrapure water before metabolome analysis. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY CE-TOFMS (ESI negative) CH:CHROMATOGRAPHY_TYPE CE CH:INSTRUMENT_NAME Agilent CE CH:COLUMN_NAME Agilent Fused silica capillary (80cm x 50um) CH:SOLVENT_A 50 mM ammonium acetate CH:SOLVENT_B - CH:FLOW_GRADIENT - CH:FLOW_RATE −30 kV CH:COLUMN_TEMPERATURE 20 #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent CE-TOFMS MS:INSTRUMENT_TYPE Other MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS The spectrometer was scanned from m/z 50 to 1,000. Peaks were extracted using MS:MS_COMMENTS automatic integration software MasterHands (ver.2.16.0.15 Keio University). MS:MS_COMMENTS Signal peaks corresponding to isotopomers, adduct ions, and other product ions MS:MS_COMMENTS of known metabolites were excluded, and remaining peaks were annotated with MS:MS_COMMENTS putative metabolites from the HMT metabolite database based on their migration MS:MS_COMMENTS time and m/z values. Peak areas were normalized to internal standards and sample MS:MS_COMMENTS amounts. #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS Relative Area MS_METABOLITE_DATA_START Samples L1-1 L1-2 L1-3 C-1 C-2 C-3 Factors Transgene:ALDH1L1 Transgene:ALDH1L1 Transgene:ALDH1L1 Transgene:empty Transgene:empty Transgene:empty Urea 2.4E-01 2.4E-01 1.8E-01 2.3E-01 1.9E-01 1.9E-01 Ethanolamine N.D. N.D. N.D. 3.9E-03 3.2E-03 2.9E-03 Aminoacetone 1.9E-02 1.6E-02 1.9E-02 2.2E-02 2.0E-02 1.9E-02 Gly 5.6E+00 5.8E+00 5.6E+00 4.9E+00 5.0E+00 5.1E+00 Trimethylamine N-oxide 3.7E-03 3.8E-03 3.8E-03 3.9E-03 4.2E-03 3.5E-03 Putrescine 1.2E-02 1.0E-02 1.0E-02 1.2E-02 1.2E-02 1.1E-02 β-Ala 1.2E+00 1.3E+00 1.2E+00 1.2E+00 1.3E+00 1.3E+00 Ala 6.5E+00 7.0E+00 7.0E+00 6.4E+00 6.8E+00 6.8E+00 Glycerol 1.3E+00 1.8E+00 1.4E+00 1.3E+00 1.5E+00 1.6E+00 1-Aminocyclopropane-1-carboxylic acid / Homoserinelactone 7.0E-03 7.4E-03 6.3E-03 8.2E-03 6.2E-03 6.0E-03 3-Aminoisobutyric acid 1.3E-02 1.4E-02 2.0E-02 1.4E-02 1.9E-02 1.7E-02 2-Aminoisobutyric acid / 2-Aminobutyric acid 8.2E-02 7.8E-02 7.9E-02 8.3E-02 9.1E-02 8.3E-02 GABA 1.7E-01 2.0E-01 2.1E-01 2.3E-01 2.4E-01 2.5E-01 Choline 1.2E-01 1.2E-01 1.2E-01 1.2E-01 1.3E-01 1.2E-01 Ser 1.6E+00 1.6E+00 1.4E+00 2.3E+00 2.3E+00 2.3E+00 Diethanolamine 1.7E-02 1.7E-02 1.8E-02 3.3E-01 3.4E-02 2.9E-02 Hypotaurine 2.7E-01 3.0E-01 3.0E-01 2.5E-01 2.9E-01 2.6E-01 1-Pyrroline 5-carboxylic acid 5.4E-02 7.6E-02 7.5E-02 5.6E-02 8.4E-02 8.3E-02 Creatinine 2.9E-02 2.8E-02 2.7E-02 2.9E-02 2.8E-02 2.9E-02 Pro 4.0E-01 4.5E-01 4.3E-01 4.1E-01 4.3E-01 4.4E-01 5-Aminovaleric acid 1.9E-02 1.9E-02 1.8E-02 1.8E-02 1.9E-02 1.9E-02 Betaine 1.0E-01 1.2E-01 1.1E-01 1.1E-01 1.1E-01 1.1E-01 Val 4.8E+00 4.7E+00 4.1E+00 4.8E+00 4.5E+00 4.6E+00 Thr 7.1E+00 7.4E+00 7.0E+00 7.5E+00 7.5E+00 7.4E+00 Homoserine 4.2E-03 5.2E-03 N.D. 6.0E-03 5.3E-03 5.3E-03 Cys 1.4E-02 2.8E-02 8.4E-03 1.9E-02 8.0E-03 2.6E-02 Nicotinamide 3.8E-02 4.3E-02 4.8E-02 4.0E-02 3.4E-02 4.1E-02 Taurine 4.3E-02 4.0E-02 4.3E-02 4.1E-02 4.2E-02 4.2E-02 Imidazole-4-acetic acid N.D. N.D. N.D. N.D. N.D. N.D. 1-Aminocyclopentanecarboxylic acid 8.2E-03 8.3E-03 7.3E-03 7.5E-03 7.6E-03 7.4E-03 Pipecolic acid 2.4E-03 2.3E-03 2.2E-03 N.D. 2.3E-03 2.6E-03 trans-Glutaconic acid 1.1E-02 1.4E-02 1.3E-02 1.3E-02 1.3E-02 1.3E-02 N-Acetylputrescine 2.5E-03 2.9E-03 2.2E-03 3.3E-03 3.0E-03 1.8E-03 Hydroxyproline 1.7E-01 1.9E-01 1.9E-01 1.8E-01 1.9E-01 1.8E-01 cis-4-Hydroxyproline 2.6E-02 3.9E-02 3.7E-02 3.0E-02 3.8E-02 4.0E-02 Creatine 3.4E-01 4.2E-01 4.7E-01 3.4E-01 3.8E-01 3.9E-01 Ile 5.6E+00 5.3E+00 4.8E+00 5.7E+00 5.4E+00 5.3E+00 Leu 6.2E+00 6.0E+00 5.6E+00 6.5E+00 6.3E+00 6.2E+00 Asn 4.9E-01 5.2E-01 5.0E-01 4.4E-01 4.6E-01 4.7E-01 Gly-Gly 2.3E-02 2.6E-02 2.4E-02 2.7E-02 2.6E-02 2.7E-02 Ornithine 1.9E-01 2.0E-01 2.3E-01 2.1E-01 2.4E-01 2.3E-01 Thiaproline 1.9E-02 1.5E-02 9.1E-03 2.4E-02 1.2E-02 1.6E-02 Asp 7.3E+00 7.7E+00 7.2E+00 7.5E+00 7.6E+00 7.5E+00 Adenine 5.2E-03 4.4E-03 5.5E-03 5.1E-03 4.8E-03 4.4E-03 1-Methylnicotinamide 2.9E-02 3.2E-02 3.0E-02 3.4E-02 3.4E-02 3.2E-02 Urocanic acid N.D. N.D. N.D. N.D. N.D. N.D. 1-Methyl-4-imidazoleacetic acid 2.0E-03 2.6E-03 2.0E-03 2.1E-03 N.D. 2.1E-03 1H-Imidazole-4-propionic acid 2.4E-03 2.7E-03 2.7E-03 N.D. 2.6E-03 2.0E-03 γ-Butyrobetaine 3.9E-02 4.4E-02 4.2E-02 4.2E-02 4.4E-02 4.2E-02 Spermidine 2.9E-02 3.9E-02 3.7E-02 2.8E-02 3.7E-02 3.8E-02 Lys 1.2E+00 1.2E+00 1.1E+00 1.4E+00 1.2E+00 1.1E+00 N-Acetylserine 6.1E-02 5.7E-02 5.4E-02 5.4E-02 5.1E-02 5.6E-02 Gln 6.8E-01 6.4E-01 5.9E-01 6.7E-01 6.2E-01 6.2E-01 Glu 1.3E+00 1.4E+00 1.3E+00 1.3E+00 1.4E+00 1.4E+00 Met 8.9E-01 9.8E-01 1.0E+00 9.7E-01 1.1E+00 9.1E-01 Octopamine / Dopamine 4.0E-03 3.7E-03 3.4E-03 4.5E-03 3.4E-03 3.2E-03 His 1.4E+00 1.4E+00 1.3E+00 1.4E+00 1.4E+00 1.3E+00 O-Acetylhomoserine / 2-Aminoadipic acid 5.7E-02 6.3E-02 5.1E-02 6.3E-02 6.7E-02 6.6E-02 Carnitine 1.1E-01 1.2E-01 1.3E-01 1.2E-01 1.4E-01 1.3E-01 5-Hydroxylysine N.D. 9.5E-04 1.2E-03 N.D. N.D. 8.9E-04 Methionine sulfoxide 4.6E-02 3.9E-02 2.3E-02 4.0E-02 2.2E-02 3.6E-02 Phe 4.5E+00 4.4E+00 4.1E+00 4.3E+00 4.3E+00 4.1E+00 Pyridoxal 6.0E-03 6.6E-03 9.5E-03 5.2E-03 8.5E-03 7.5E-03 Pyridoxine 5.6E-02 4.9E-02 3.8E-02 6.1E-02 4.1E-02 4.2E-02 1-Methylhistidine / 3-Methylhistidine 2.9E-02 3.2E-02 3.1E-02 3.1E-02 3.1E-02 3.2E-02 N5-Ethylglutamine 1.4E-02 1.3E-02 1.4E-02 1.4E-02 1.5E-02 1.5E-02 Arg 5.9E-01 5.5E-01 4.8E-01 5.9E-01 5.5E-01 5.0E-01 Diethylaminomalonic acid 9.4E-03 9.8E-03 7.6E-03 9.3E-03 1.0E-02 9.6E-03 Citrulline 6.5E-02 6.7E-02 6.1E-02 6.4E-02 6.5E-02 6.8E-02 Cys-Gly 1.7E-03 2.1E-03 N.D. 1.8E-03 N.D. 4.3E-03 Gluconolactone 1.8E-02 1.5E-02 1.4E-02 1.5E-02 1.3E-02 1.4E-02 Galactosamine / Glucosamine N.D. 9.7E-04 N.D. 1.1E-03 N.D. N.D. N-Methylnorsalsolinol 3.0E-03 2.6E-03 3.0E-03 2.4E-03 3.1E-03 4.1E-03 Tyr 2.9E+00 3.0E+00 2.7E+00 2.9E+00 2.9E+00 2.8E+00 Phosphorylcholine 6.0E+00 5.8E+00 5.3E+00 4.8E+00 4.6E+00 4.6E+00 N8-Acetylspermidine 1.1E-02 1.2E-02 9.4E-03 7.5E-03 8.1E-03 8.4E-03 Gly-Leu N.D. N.D. 3.3E-03 N.D. 3.4E-03 N.D. N-Acetyllysine 3.8E-03 5.1E-03 4.1E-03 3.8E-03 5.7E-03 5.2E-03 N6-Acetyllysine N.D. 2.9E-03 3.9E-03 2.9E-03 N.D. 3.9E-03 Homocitrulline N.D. N.D. 3.1E-03 2.9E-03 3.5E-03 N.D. Gly-Asp 6.5E-02 6.7E-02 6.6E-02 6.3E-02 6.7E-02 7.0E-02 Tyrosine methyl ester 1.3E-03 1.4E-03 1.4E-03 N.D. 1.3E-03 1.5E-03 DOPA N.D. N.D. N.D. N.D. N.D. 3.3E-03 SDMA 1.7E-03 2.2E-03 2.1E-03 3.4E-03 2.6E-03 2.4E-03 ADMA 6.0E-03 7.1E-03 6.6E-03 7.0E-03 8.3E-03 8.4E-03 Spermine 2.0E-02 2.5E-02 3.0E-02 1.7E-02 2.7E-02 2.5E-02 O-Acetylcarnitine 1.2E-01 1.2E-01 1.1E-01 1.1E-01 1.1E-01 1.1E-01 Trp 3.4E-01 3.2E-01 2.8E-01 3.2E-01 3.0E-01 3.2E-01 Carboxymethyllysine 1.8E-03 2.3E-03 2.4E-03 2.1E-03 2.5E-03 2.4E-03 Kynurenine 6.8E-03 7.1E-03 8.2E-03 6.0E-03 6.5E-03 6.7E-03 β-Ala-Lys N.D. N.D. 1.4E-03 N.D. N.D. N.D. N-Acetylgalactosamine/N-Acetylmannosamine/N-Acetylglucosamine 9.2E-03 9.9E-03 9.1E-03 8.8E-03 7.8E-03 8.2E-03 Cystathionine 1.1E+00 1.3E+00 1.3E+00 1.2E+00 1.3E+00 1.2E+00 Carnosine 2.8E-03 2.2E-03 2.0E-03 2.7E-03 2.5E-03 1.8E-03 2'-Deoxycytidine 7.3E-04 6.3E-04 5.7E-04 9.2E-04 8.3E-04 8.0E-04 Butyrylcarnitine 8.1E-02 7.8E-02 7.5E-02 7.7E-02 8.4E-02 7.8E-02 Thr-Asp 3.5E-03 4.1E-03 3.8E-03 4.9E-03 4.8E-03 4.3E-03 Ser-Glu 8.4E-03 7.1E-03 7.4E-03 8.3E-03 8.0E-03 7.6E-03 7,8-Dihydrobiopterin 7.1E-04 1.1E-03 1.0E-03 6.2E-04 9.2E-04 8.4E-04 Ribavirin 2.1E-03 N.D. N.D. N.D. N.D. N.D. Isovalerylcarnitine 1.1E-02 1.1E-02 1.0E-02 1.1E-02 1.2E-02 1.1E-02 γ-Glu-Cys 1.1E-02 1.3E-02 1.2E-02 9.9E-03 1.2E-02 1.1E-02 Glycerophosphocholine 1.0E-01 1.1E-01 9.6E-02 8.8E-02 9.2E-02 8.2E-02 Thiamine 9.8E-02 1.0E-01 9.6E-02 9.7E-02 9.0E-02 8.9E-02 Adenosine 3.4E-02 3.3E-02 3.8E-02 2.5E-02 2.8E-02 3.4E-02 Inosine N.D. 1.5E-03 1.8E-03 N.D. 1.2E-03 2.0E-03 Saccharopine 9.2E-03 1.0E-02 8.7E-03 1.4E-02 1.5E-02 1.4E-02 1-Methyladenosine 8.7E-04 8.7E-04 7.1E-04 1.1E-03 6.5E-04 9.1E-04 Guanosine 1.6E-03 2.2E-03 2.3E-03 1.1E-03 1.6E-03 2.2E-03 His-Glu 9.7E-04 1.2E-03 1.2E-03 1.2E-03 1.6E-03 9.3E-04 Ophthalmic acid 4.2E-03 4.9E-03 4.0E-03 4.9E-03 4.4E-03 5.0E-03 Argininosuccinic acid 4.8E-02 5.4E-02 5.0E-02 5.0E-02 5.2E-02 5.4E-02 5'-Deoxy-5'-methylthioadenosine 7.9E-03 8.4E-03 8.7E-03 1.1E-02 8.4E-03 5.9E-03 Arg-Glu 2.1E-03 2.0E-03 1.7E-03 2.1E-03 1.6E-03 1.7E-03 Glutathione (GSSG)_divalent 2.9E+00 2.0E+00 1.9E+00 2.5E+00 1.9E+00 1.7E+00 Glutathione (GSH) 8.2E+00 1.0E+01 9.7E+00 8.6E+00 9.6E+00 9.8E+00 S-Methylglutathione 1.0E-02 1.1E-02 1.4E-02 1.0E-02 6.0E-03 5.1E-03 S-Nitrosoglutathione 2.1E-03 9.6E-04 1.2E-03 2.4E-03 2.2E-03 9.4E-04 Thiamine phosphate 5.3E-04 6.1E-04 6.8E-04 4.4E-04 5.4E-04 8.4E-04 Gibberellic acid 5.3E-03 5.9E-03 4.6E-03 5.5E-03 5.5E-03 5.5E-03 S-Lactoylglutathione 2.9E-03 4.1E-03 5.7E-03 3.0E-03 3.4E-03 2.0E-03 S-Adenosylhomocysteine 4.2E-03 5.3E-03 6.2E-03 5.0E-03 2.4E-03 2.2E-03 S-Adenosylmethionine 9.7E-02 1.0E-01 9.5E-02 9.5E-02 1.1E-01 1.0E-01 Cysteine glutathione disulfide 6.2E-03 4.3E-03 1.7E-03 5.0E-03 1.9E-03 3.8E-03 Folic acid 3.8E-03 3.7E-03 3.5E-03 2.1E-03 1.9E-03 2.1E-03 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name Urea Ethanolamine Aminoacetone Gly Trimethylamine N-oxide Putrescine β-Ala Ala Glycerol 1-Aminocyclopropane-1-carboxylic acid / Homoserinelactone 3-Aminoisobutyric acid 2-Aminoisobutyric acid / 2-Aminobutyric acid GABA Choline Ser Diethanolamine Hypotaurine 1-Pyrroline 5-carboxylic acid Creatinine Pro 5-Aminovaleric acid Betaine Val Thr Homoserine Cys Nicotinamide Taurine Imidazole-4-acetic acid 1-Aminocyclopentanecarboxylic acid Pipecolic acid trans-Glutaconic acid N-Acetylputrescine Hydroxyproline cis-4-Hydroxyproline Creatine Ile Leu Asn Gly-Gly Ornithine Thiaproline Asp Adenine 1-Methylnicotinamide Urocanic acid 1-Methyl-4-imidazoleacetic acid 1H-Imidazole-4-propionic acid γ-Butyrobetaine Spermidine Lys N-Acetylserine Gln Glu Met Octopamine / Dopamine His O-Acetylhomoserine / 2-Aminoadipic acid Carnitine 5-Hydroxylysine Methionine sulfoxide Phe Pyridoxal Pyridoxine 1-Methylhistidine / 3-Methylhistidine N5-Ethylglutamine Arg Diethylaminomalonic acid Citrulline Cys-Gly Gluconolactone Galactosamine / Glucosamine N-Methylnorsalsolinol Tyr Phosphorylcholine N8-Acetylspermidine Gly-Leu N-Acetyllysine N6-Acetyllysine Homocitrulline Gly-Asp Tyrosine methyl ester DOPA SDMA ADMA Spermine O-Acetylcarnitine Trp Carboxymethyllysine Kynurenine β-Ala-Lys N-Acetylgalactosamine/N-Acetylmannosamine/N-Acetylglucosamine Cystathionine Carnosine 2'-Deoxycytidine Butyrylcarnitine Thr-Asp Ser-Glu 7,8-Dihydrobiopterin Ribavirin Isovalerylcarnitine γ-Glu-Cys Glycerophosphocholine Thiamine Adenosine Inosine Saccharopine 1-Methyladenosine Guanosine His-Glu Ophthalmic acid Argininosuccinic acid 5'-Deoxy-5'-methylthioadenosine Arg-Glu Glutathione (GSSG)_divalent Glutathione (GSH) S-Methylglutathione S-Nitrosoglutathione Thiamine phosphate Gibberellic acid S-Lactoylglutathione S-Adenosylhomocysteine S-Adenosylmethionine Cysteine glutathione disulfide Folic acid METABOLITES_END #END