{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001075","ANALYSIS_ID":"AN001757","VERSION":"1","CREATED_ON":"October 17, 2018, 11:38 am"},

"PROJECT":{"PROJECT_TITLE":"Integrated metabolome and transcriptome analyses provide novel insight into colon cancer modulation by the gut microbiota","PROJECT_SUMMARY":"Colon cancer onset and progression is strongly associated with the presence, absence, or relative abundances of certain microbial taxa in the gastrointestinal tract. However, specific mechanisms affecting disease susceptibility related to complex commensal bacterial mixtures are poorly understood. We used a multi-omics approach to determine how differences in the complex gut microbiome (GM) influence the metabolome and host transcriptome and ultimately affect susceptibility to adenoma development. Fecal samples collected from a preclinical rat model of colon cancer harboring distinct complex GMs were analyzed using ultra-high performance liquid chromatography mass spectrometry (UHPLC-MS). We collected samples prior to observable disease onset and identified putative metabolite profiles that predicted future disease severity, independent of GM status. Transcriptome analyses performed after disease onset from normal epithelium and tumor tissues between the high and low tumor GMs suggests that the GM is also correlated with altered host gene expression. Integrated pathway (IP) analyses of the metabolome and transcriptome based on putatively identified metabolic features indicate that bile acid biosynthesis was enriched in rats with high tumors (GM:F344) along with increased fatty acid metabolism and mucin biosynthesis. These data emphasize the utility of using untargeted metabolomics to reveal signatures of susceptibility and resistance and integrated analysis reveals common pathways that are likely to be universal targets for intervention.","INSTITUTE":"University of Missouri","DEPARTMENT":"Veterinary Pathobiology","LABORATORY":"Amos-Landgraf","LAST_NAME":"Busi","FIRST_NAME":"Susheel Bhanu","ADDRESS":"4011 Discovery Drive, N121","EMAIL":"sb6f4@mail.missouri.edu","PHONE":"2404094390","CONTRIBUTORS":"Zhentian Lei, James Amos-Landgraf, Lloyd W. Sumner,"},

"STUDY":{"STUDY_TITLE":"Integrated metabolome and transcriptome analyses provide novel insight into colon cancer modulation by the gut microbiota","STUDY_SUMMARY":"Colon cancer onset and progression is strongly associated with the presence, absence, or relative abundances of certain microbial taxa in the gastrointestinal tract. However, specific mechanisms affecting disease susceptibility related to complex commensal bacterial mixtures are poorly understood. We used a multi-omics approach to determine how differences in the complex gut microbiome (GM) influence the metabolome and host transcriptome and ultimately affect susceptibility to adenoma development. Fecal samples collected from a preclinical rat model of colon cancer harboring distinct complex GMs were analyzed using ultra-high performance liquid chromatography mass spectrometry (UHPLC-MS). We collected samples prior to observable disease onset and identified putative metabolite profiles that predicted future disease severity, independent of GM status. Transcriptome analyses performed after disease onset from normal epithelium and tumor tissues between the high and low tumor GMs suggests that the GM is also correlated with altered host gene expression. Integrated pathway (IP) analyses of the metabolome and transcriptome based on putatively identified metabolic features indicate that bile acid biosynthesis was enriched in rats with high tumors (GM:F344) along with increased fatty acid metabolism and mucin biosynthesis. These data emphasize the utility of using untargeted metabolomics to reveal signatures of susceptibility and resistance and integrated analysis reveals common pathways that are likely to be universal targets for intervention.","INSTITUTE":"UNIVERSITY OF MISSOURI - COLUMBIA","LAST_NAME":"Busi","FIRST_NAME":"Susheel Bhanu","ADDRESS":"4011 Discovery Drive N121","EMAIL":"SB6F4@MAIL.MISSOURI.EDU","PHONE":"2404094390","NUM_GROUPS":"3","TOTAL_SUBJECTS":"13"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Rattus norvegicus","TAXONOMY_ID":"10116","GENOTYPE_STRAIN":"F344/Ntac-Apc-+/Pirc","AGE_OR_AGE_RANGE":"30","ANIMAL_ANIMAL_SUPPLIER":"Taconic and Envigo","ANIMAL_HOUSING":"Conventional,","ANIMAL_FEED":"Labdiet 5058","ANIMAL_WATER":"Autoclaved, purified with sulfuric acid"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"SB1",
"Factors":{"Group":"GM;F344"},
"Additional sample data":{"ColonicTumors":"11"}
},
{
"Subject ID":"-",
"Sample ID":"SB2",
"Factors":{"Group":"GM;F344"},
"Additional sample data":{"ColonicTumors":"8"}
},
{
"Subject ID":"-",
"Sample ID":"SB3",
"Factors":{"Group":"GM;F344"},
"Additional sample data":{"ColonicTumors":"34"}
},
{
"Subject ID":"-",
"Sample ID":"SB4",
"Factors":{"Group":"GM;F344"},
"Additional sample data":{"ColonicTumors":"19"}
},
{
"Subject ID":"-",
"Sample ID":"SB5",
"Factors":{"Group":"GM;LEW"},
"Additional sample data":{"ColonicTumors":"11"}
},
{
"Subject ID":"-",
"Sample ID":"SB6",
"Factors":{"Group":"GM;LEW"},
"Additional sample data":{"ColonicTumors":"10"}
},
{
"Subject ID":"-",
"Sample ID":"SB7",
"Factors":{"Group":"GM;LEW"},
"Additional sample data":{"ColonicTumors":"6"}
},
{
"Subject ID":"-",
"Sample ID":"SB8",
"Factors":{"Group":"GM;LEW"},
"Additional sample data":{"ColonicTumors":"10"}
},
{
"Subject ID":"-",
"Sample ID":"SB9",
"Factors":{"Group":"GM;SD"},
"Additional sample data":{"ColonicTumors":"10"}
},
{
"Subject ID":"-",
"Sample ID":"SB10",
"Factors":{"Group":"GM;SD"},
"Additional sample data":{"ColonicTumors":"15"}
},
{
"Subject ID":"-",
"Sample ID":"SB11",
"Factors":{"Group":"GM;SD"},
"Additional sample data":{"ColonicTumors":"20"}
},
{
"Subject ID":"-",
"Sample ID":"SB12",
"Factors":{"Group":"GM;SD"},
"Additional sample data":{"ColonicTumors":"10"}
},
{
"Subject ID":"-",
"Sample ID":"SB13",
"Factors":{"Group":"GM;SD"},
"Additional sample data":{"ColonicTumors":"6"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Fecal samples collected at 1 month of age, prior to any observable disease onset. F344 refers to Fisher (F344) rats, whereas as GM:SD refers to the GM from Sprague-Dawley rats, while GM:LEW refers to the gut microbiota (GM) from Lewis rats","COLLECTION_PROTOCOL_ID":"8732","SAMPLE_TYPE":"Feces","COLLECTION_METHOD":"Sterile, asceptic method. Animals were placed in clean, sterile cages and feces were speared with sterile, autoclaved toothpicks.","COLLECTION_LOCATION":"Discovery Ridge, Columbia MO","STORAGE_CONDITIONS":"-80℃","COLLECTION_VIALS":"Glass","STORAGE_VIALS":"Glass"},

"TREATMENT":{"TREATMENT_SUMMARY":"Pirc rats were rederived using 3 surrogate dams, each with distinct gut microbiota profiles","TREATMENT_PROTOCOL_ID":"8732"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Fecal samples were lyophilized at -20 ˚C using 0.1 millibar of vacuum pressure, following which dried samples (30 mg) were extracted sequentially for both UHPLC-MS and GC-MS. The dried samples were first treated with 1.0 mL of 80% MeOH containing 18 µg/mL umbelliferone, sonicated for 5 minutes and centrifuged for 40 minutes at 3000 g at 10 ºC. 0.5 mL of supernatant was used for UHPLC-MS analysis after a subsequent spin at 5000 g at 10 ºC for 20 minutes and transferring 250 µL of the sample into glass autosampler vials with inserts. For GC-MS (Gas Chromatography-Mass Spectrometry) analyses of primary polar metabolites, 0.5 mL water was added the remaining extract used above for the UHPLC preparation, sonicated for 5 min, extracted for 30min, and centrifuged at 3000 g. 0.5 mL of the polar extract was subsequently dried under nitrogen and derivatized using previously established protocols (84). Briefly, N-Methyl-N-(trimethylsilyl) trifluoroacetamide (MSTFA) with 1 % TMCS (2,2,2-Trifluoro-N-methyl-N-(trimethylsilyl)-acetamide, Chlorotrimethylsilane) was used to derivatize the polar metabolites, after treatment with methoxyamine-HCl-pyridine."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1290","COLUMN_NAME":"Waters Acquity BEH C18 (150 x 2.1mm, 1.7um)"},

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

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Bruker maXis Impact qTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_RESULTS_FILE":"ST001075_AN001757_Results.txt UNITS:Peak Area"}

}