Summary of Study ST001087

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 PR000726. The data can be accessed directly via it's Project DOI: 10.21228/M8TX0N 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 IDST001087
Study TitleMetabolomics and 16S rRNA sequencing of human colorectal cancers and adjacent mucosa
Study SummaryColorectal cancer (CRC) is ranked the third most common cancer in human worldwide. However, the exact mechanisms of CRC are not well established. Furthermore, there may be differences between mechanisms of CRC in the Asian and in the Western populations. In the present study, we utilized a liquid chromatography-mass spectrometry (LC-MS) metabolomic approach supported by the 16S rRNA next-generation sequencing to investigate the functional and taxonomical differences between paired tumor and unaffected (normal) surgical biopsy tissues from 17 Malaysian patients. Metabolomic differences associated with steroid biosynthesis, terpenoid biosynthesis and bile metabolism could be attributed to microbiome differences between normal and tumor sites. The relative abundances of Anaerotruncus, Intestinimonas and Oscillibacter displayed significant relationships with both steroid biosynthesis and terpenoid and triterpenoid biosynthesis pathways. Metabolites involved in serotonergic synapse/ tryptophan metabolism (Serotonin and 5-Hydroxy-3-indoleacetic acid [5-HIAA]) were only detected in normal tissue samples. On the other hand, S-Adenosyl-L-homocysteine (SAH), a metabolite involves in methionine metabolism and methylation, was frequently increased in tumor relative to normal tissues. In conclusion, this study suggests that local microbiome dysbiosis may contribute to functional changes at the cancer sites. Results from the current study also contributed to the list of metabolites that are found to differ between normal and tumor sites in CRC and supported our quest for understanding the mechanisms of carcinogenesis.
Institute
University of Malaya
Last NameLoke
First NameMun Fai
AddressDepartment of Medical Microbiology, Faculty of Medicine, Kuala Lumpur, Federal Territory, 50603, Malaysia
Emaillmunfai@gmail.com
Phone83880014
Submit Date2018-10-28
Num Groups4
Total Subjects17
Num Males7
Num Females10
Analysis Type DetailLC-MS
Release Date2018-12-11
Release Version1
Mun Fai Loke Mun Fai Loke
https://dx.doi.org/10.21228/M8TX0N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000726
Project DOI:doi: 10.21228/M8TX0N
Project Title:Metabolomics of Colorectal Cancer in Malaysia
Project Summary:Colorectal cancer (CRC) is one of the major leading cause of death in humans worldwide. In Malaysia, CRC is the fourth leading cause of death, covered 13.2% of new cancer diagnoses in Peninsular Malaysia in 2006. Causable factors are remaining unknown. Changes in dietary may alter colonic microbiome and mucosal immune microenvironment inducing colon oncogenesis. Previous investigation focused on mutagen production by colonic bacteria or their conversion of dietary procarcinogens into DNA-damaging molecules. Yet, no direct links between the metabolic activities of bacteria and sporadic CRC were identified. The objective of this study was to prospectively characterize the human colonic microbiome in CRC using metabolomic approache in Kuala Lumpur, Malaysia and to understand the functionality of the colonic microbiome and host-microbial interactions in CRC.
Institute:University of Malaya
Department:Medical Microbiology
Laboratory:Helicobacter Research Laboratory, UM Marshall Centre
Last Name:Loke
First Name:Mun Fai
Address:Department of Medical Microbiology, Faculty of Medicine, Kuala Lumpur, Federal Territory, 50603, Malaysia
Email:lmunfai@gmail.com
Phone:83880014

Subject:

Subject ID:SU001131
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:41-84 years old
Gender:Male and female
Human Race:Chinese, Malay, Indian
Human Exclusion Criteria:Individuals who have received pre-operative radiation, chemotherapy treatment or had a past history of CRC or inflammatory bowel disease. Standard pre-operative intravenous antibiotics (cefotetan, clindamycin/ gentamicin or cefoperazone/ metronidazole) were administered in all cases and none of the patients received any pre-operative oral antibiotics.

Factors:

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

mb_sample_id local_sample_id Site Condition
SA073438n35NLLeft Normal
SA073439p36NLLeft Normal
SA073440p37NLLeft Normal
SA073441n58NLLeft Normal
SA073442n57NLLeft Normal
SA073443n48NLLeft Normal
SA073444n53NLLeft Normal
SA073445p38NLLeft Normal
SA073446p40NLLeft Normal
SA073447p57NLLeft Normal
SA073448p58NLLeft Normal
SA073449p53NLLeft Normal
SA073450p48NLLeft Normal
SA073451p43NLLeft Normal
SA073452p46NLLeft Normal
SA073453n46NLLeft Normal
SA073454p35NLLeft Normal
SA073455n36NLLeft Normal
SA073456n38NLLeft Normal
SA073457n37NLLeft Normal
SA073458n43NLLeft Normal
SA073459n40NLLeft Normal
SA073460p57TLLeft Tumor
SA073461p40TLLeft Tumor
SA073462p38TLLeft Tumor
SA073463n35TLLeft Tumor
SA073464p53TLLeft Tumor
SA073465p37TLLeft Tumor
SA073466n38TLLeft Tumor
SA073467p43TLLeft Tumor
SA073468p48TLLeft Tumor
SA073469n46TLLeft Tumor
SA073470n37TLLeft Tumor
SA073471p46TLLeft Tumor
SA073472n36TLLeft Tumor
SA073473p36TLLeft Tumor
SA073474n48TLLeft Tumor
SA073475n43TLLeft Tumor
SA073476n57TLLeft Tumor
SA073477n40TLLeft Tumor
SA073478n58TLLeft Tumor
SA073479n53TLLeft Tumor
SA073480p35TLLeft Tumor
SA073481p58TLLeft Tumor
SA073482p60NRRight Normal
SA073483n56NRRight Normal
SA073484p56NRRight Normal
SA073485n45NRRight Normal
SA073486p51NRRight Normal
SA073487p44NRRight Normal
SA073488p39NRRight Normal
SA073489n51NRRight Normal
SA073490n60NRRight Normal
SA073491n39NRRight Normal
SA073492p45NRRight Normal
SA073493n44NRRight Normal
SA073494p60TRRight Tumor
SA073495p56TRRight Tumor
SA073496p39TRRight Tumor
SA073497n56TRRight Tumor
SA073498n44TRRight Tumor
SA073499n51TRRight Tumor
SA073500n60TRRight Tumor
SA073501n39TRRight Tumor
SA073502p45TRRight Tumor
SA073503p44TRRight Tumor
SA073504n45TRRight Tumor
SA073505p51TRRight Tumor
Showing results 1 to 68 of 68

Collection:

Collection ID:CO001125
Collection Summary:Tissue from the proximal colon through the hepatic flexure is considered as right (ascending) colon, whereas distal to the hepatic flexure as left (descending) colon. During surgery, excess colon tumor (adenomas and cancers) and paired tumor-free (herein referred to as “normal”) tissues were collected for analysis.
Sample Type:Colon
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001145
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP001138
Sampleprep Summary:The tissue, disposable pestle and 1.5 ml-centrifuge tube in liquid nitrogen were chilled in liquid nitrogen. The tissue was pulverized in the presence of liquid nitrogen to fine powder. Metabolites were extracted from tissue samples by the Bligh and Dyer extraction method.

Combined analysis:

Analysis ID AN001772
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 1260
Column Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um)
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6540 QTOF
Ion Mode UNSPECIFIED
Units peak area

Chromatography:

Chromatography ID:CH001252
Instrument Name:Agilent 1260
Column Name:Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um)
Column Temperature:30
Flow Gradient:t= 0 min, 5% B; t=2 min, 5% B; t=15 min, 98% B; t=18min, 98%; t=20 min, 5% B and the final stop time, t=25 min, 5% B
Flow Rate:0.45 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS001638
Analysis ID:AN001772
Instrument Name:Agilent 6540 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:UNSPECIFIED
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