Summary of Study ST000956

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000657. The data can be accessed directly via it's Project DOI: 10.21228/M8RD64 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST000956
Study TitleDetermine metabolomics signatures important for the ability of Streptococus gallolyticus to promote colon cancer cell proliferation
Study SummaryHT29 cells were treated with Sg TX20005 stationary phase, Sg TX20005 exponential phase (negative control), and Sg TX20008 stationary phase (negative control), and media only (baseline control). The cells were washed and aliquoted. One aliquot was pelleted and stored at -80C for metabolomics analysis. DNA was also extracted from the other aliquot for DNA methylation studies.
Institute
University of Florida
DepartmentSECIM
Last NameXu
First NameYi
Address2121 W. Holcombe Blvd., Houston, TX 77030
Emailyxu@ibt.tamhsc.edu
PhoneNA
Submit Date2018-04-14
Num Groups4
Total Subjects40
Study CommentsSECIM pilot and feasibility, NIH U24 DK097209
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2019-05-15
Release Version1
Yi Xu Yi Xu
https://dx.doi.org/10.21228/M8RD64
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000657
Project DOI:doi: 10.21228/M8RD64
Project Title:Determine metabolomics signatures important for the ability of Streptococus gallolyticus to promote colon cancer cell proliferation
Project Summary:It is now known that intestinal microbiota influences the development of colorectal cancer (CRC). This microbe-CRC connection suggests a potential paradigm shift in the way CRC is detected, treated and managed. Knowledge of specific microbial components involved in the development of CRC is critical to moving this field forward. Among the bacterial species known to associate with CRC, Streptococcus gallolyticus subsp. gallolyticus (Sg), previously known as S. bovis biotype I, stands out as having a strong and well-documented clinical association supported by numerous case reports and surveys over the past several decades. We and others also found that Sg is present in a substantial percentage of CRC patients (up to ~ 74%). We further demonstrated that Sg actively promotes colon tumor growth. These exciting discoveries underscore the importance of Sg in CRC with respect to both function and clinical relevance. Further investigation into the molecular details of the Sg-CRC relationship should have a high priority. Going forward, the key question is how Sg promotes colon tumor development. Data from our lab led us to hypothesize that Sg produces certain metabolites that contribute to its ability to promote cell proliferation. We propose to identify the metabolites important for promoting colon cancer cell proliferation. Our approach is based on two recent findings. We discovered that there are variations among Sg strains in the ability to stimulate host cell proliferation. We also observed that the ability of Sg to promote cell proliferation is bacterial growth phase regulated. Thus by comparing the metabolomics profiles of different Sg strains, and Sg strains from different growth phase co-cultured with colon cancer cells, respectively, we will identify metabolomics signatures that correlate with the ability of Sg to promote cell proliferation. These metabolites will then be investigated in more detail in future studies. In addition, DNA methylation pattern in cells treated with Sg, negative control bacteria and media only will also be compared.
Institute:Texas A&M Health Science Center, Institute of Biosciences and Technology
Department:Center for Infectious and Inflammatory Diseases
Last Name:Xu
First Name:Yi
Address:2121 W. Holcombe Blvd., Houston, TX 77030
Email:yxu@ibt.tamhsc.edu
Phone:NA

Subject:

Subject ID:SU000995
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Genotype Strain:HT29 cell line (colorectal cancer)

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA057251HT29-TX08-5Condition-1
SA057252HT29-TX08-4Condition-1
SA057253HT29-TX08-1Condition-1
SA057254HT29-TX08-6Condition-1
SA057255HT29-TX08-3Condition-1
SA057256HT29-TX08-7Condition-1
SA057257HT29-TX08-10Condition-1
SA057258HT29-TX08-9Condition-1
SA057259HT29-TX08-8Condition-1
SA057260HT29-TX08-2Condition-1
SA057261HT29-TX05-S-3Condition-2
SA057262HT29-TX05-S-8Condition-2
SA057263HT29-TX05-S-9Condition-2
SA057264HT29-TX05-S-10Condition-2
SA057265HT29-TX05-S-7Condition-2
SA057266HT29-TX05-S-6Condition-2
SA057267HT29-TX05-S-4Condition-2
SA057268HT29-TX05-S-5Condition-2
SA057269HT29-TX05-S-2Condition-2
SA057270HT29-TX05-S-1Condition-2
SA057271HT29-TX05-E-5Condition-3
SA057272HT29-TX05-E-4Condition-3
SA057273HT29-TX05-E-3Condition-3
SA057274HT29-TX05-E-6Condition-3
SA057275HT29-TX05-E-7Condition-3
SA057276HT29-TX05-E-10Condition-3
SA057277HT29-TX05-E-9Condition-3
SA057278HT29-TX05-E-8Condition-3
SA057279HT29-TX05-E-2Condition-3
SA057280HT29-TX05-E-1Condition-3
SA057281HT29-8Control
SA057282HT29-9Control
SA057283HT29-10Control
SA057284HT29-2Control
SA057285HT29-7Control
SA057286HT29-6Control
SA057287HT29-3Control
SA057288HT29-4Control
SA057289HT29-5Control
SA057290HT29-1Control
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Collection:

Collection ID:CO000989
Collection Summary:HT29 cells were treated with Sg TX20005 stationary phase, Sg TX20005 exponential phase (negative control), and Sg TX20008 stationary phase (negative control), and media only (baseline control). The cells were washed and aliquoted. One aliquot was pelleted and stored at -80C for metabolomics analysis. DNA was also extracted from the other aliquot for DNA methylation studies.
Sample Type:Cultured cells

Treatment:

Treatment ID:TR001009
Treatment Summary:HT29 cells were co-cultured with S. streptococcus gallolyticus strains TX20008 (stationary phase), TX20005 (Stationary phase) and TX20005 (Exponential phase). Cell storage: After collection ells were stored at -80 C Cell growth container:10 cm plates Cell percent confluence:80% Cell media: F12/DMEM 1:1 + 10% FBS Cell harvesting: Trypisinization

Sample Preparation:

Sampleprep ID:SP001002
Sampleprep Summary:No details provided. HT29 cells
Sampleprep Protocol Filename:GMetabolomics_LCMS_Protocol_092117.pdf
Appendix_A_Internal_Standard_Prep_GLCMS.pdf

Combined analysis:

Analysis ID AN001568 AN001569
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units peak height peak height

Chromatography:

Chromatography ID:CH001099
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
Flow Rate:350ul/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS001446
Analysis ID:AN001568
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS001447
Analysis ID:AN001569
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
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