Study Data
| Project uploaded by: | Neel Sarovar |
| Project ID: | IMP_100003 |
| Title: | NMR based metabolomics studies on human saliva from oral cancer patients and individuals that abuse tobacco |
| Project Description: | Background: Oral squamous cell carcinoma (OSCC) contribute about 95% of head and neck cancer with increasing prevalence in recent times. This type of cancer has been widely attributed to tobacco and alcohol. Early diagnosis increases the survival rate thus biomarker might be germane in its management. Metabolic profiling has the potential to understand the molecular mechanism of carcinogenesis and help to demystify the potential biomarkers for the early diagnosis of OSCC because metabolites are most informative proxies of the biochemical activity of an organism. Saliva metabolic profiling of OSCC and tobacco user were sought, using nuclear magnetic resonance (NMR) spectroscopy. Methods: We reported metabolic profiling of saliva from OSCC (n = 22), tobacco users (n = 21) and healthy control (n = 21) based on 1H NMR with multivariate, univariate, Chemometrics, cluster analyses (PCA, PLS-DA, OPLS-DA, ANOVA, T-test, fold change and heatmap). While perturbed metabolic pathways due to OSCC was also elucidated. Results: Both PLS-DA and OPLS-DA validated models showed adequate discrimination in OSCC as compared with tobacco user and healthy control. A total of 44 endogenous discriminating/distinguishing metabolites (FDR and p < 0.05) were identified, 19, 12 were upregulated and downregulated respectively while 8 were upregulated in tobacco user and 5 upregulated in healthy control. More so, some metabolites were dysregulated in OSCC vs. healthy control, OSCC vs. tobacco user and tobacco user vs., healthy control. Consequently, these perturbed metabolites revealed disturbance in glycolysis, TCA, fatty acid metabolism, amino acids and choline metabolism, which were correlated with the occurrence and development of OSCC. Conclusion: There is distinct saliva metabolite perturbation in OSCC and tobacco user, these results suggested that the metabolic profiling of OSCC has great potential in detecting this disease and helping to understand its underlying metabolic mechanisms. Saliva might be a good bio-fluid for NMR metabolomics as reported in this study. |
| Research Area: | Biological Sciences |
| Funding Source: | DBT and ICGEB |
| Project Contributors: | DBT and ICGEB |
| Study uploaded by: | Neel Sarovar |
| Study ID: | IMS_100003 |
| Title: | NMR analysis of the human saliva metabolic profiling distinguishes oral cancer patients from tobacco user |
| Summary: | Background: Oral squamous cell carcinoma (OSCC) contribute about 95% of head and neck cancer with increasing prevalence in recent times. This type of cancer has been widely attributed to tobacco and alcohol. Early diagnosis increases the survival rate thus biomarker might be germane in its management. Metabolic profiling has the potential to understand the molecular mechanism of carcinogenesis and help to demystify the potential biomarkers for the early diagnosis of OSCC because metabolites are most informative proxies of the biochemical activity of an organism. Saliva metabolic profiling of OSCC and tobacco user were sought, using nuclear magnetic resonance (NMR) spectroscopy. Methods: We reported metabolic profiling of saliva from OSCC (n = 22), tobacco users (n = 21) and healthy control (n = 21) based on 1H NMR with multivariate, univariate, Chemometrics, cluster analyses (PCA, PLS-DA, OPLS-DA, ANOVA, T-test, fold change and heatmap). While perturbed metabolic pathways due to OSCC was also elucidated. Results: Both PLS-DA and OPLS-DA validated models showed adequate discrimination in OSCC as compared with tobacco user and healthy control. A total of 44 endogenous discriminating/distinguishing metabolites (FDR and p < 0.05) were identified, 19, 12 were upregulated and downregulated respectively while 8 were upregulated in tobacco user and 5 upregulated in healthy control. More so, some metabolites were dysregulated in OSCC vs. healthy control, OSCC vs. tobacco user and tobacco user vs., healthy control. Consequently, these perturbed metabolites revealed disturbance in glycolysis, TCA, fatty acid metabolism, amino acids and choline metabolism, which were correlated with the occurrence and development of OSCC. Conclusion: There is distinct saliva metabolite perturbation in OSCC and tobacco user, these results suggested that the metabolic profiling of OSCC has great potential in detecting this disease and helping to understand its underlying metabolic mechanisms. Saliva might be a good bio-fluid for NMR metabolomics as reported in this study. |
| Keywords: | Oral squamous cell carcinoma, Metabolic profiling, 1H NMR |
| Publication: | https://doi.org/10.1039/D5MO00058K |
| Release Date: | July 2, 2025 |
| Study Type: | Nuclear Magnetic Resonance (NMR) |
| Data Type: | Untargeted |
| IEC/IBSC Approval Number : | IEC/SJH/VMMC/PROJECT/JULY-2016/611, ICGEB/IEC/2017/03 and ICGEB/IEC/2018/01 |
| Sr.No | Sample ID | Sample Name | Organism | Source | Sample Preparation Protocol | Sample Type | Experimental Condition | Time of treatment | Variant/Variety | Gender | Age | Replicates | Storage Conditions | Extraction Protocol | Number of files per sample |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | IMSM_100002 | C1 | Homo sapiens | NA | Saliva | NMR sample preparation in phosphase buffer | Healthy | NA | NA | NA | NA |
NA |
||||
| 2 | IMSM_100003 | C2 | Homo sapiens | NA | Saliva | NMR sample preparation in phosphase buffer | Healthy | NA | NA | NA | NA |
NA |
||||
| 3 | IMSM_100004 | C3 | Homo sapiens | NA | Saliva | NMR sample preparation in phosphase buffer | Healthy | NA | NA | NA | NA |
NA |
||||
| 4 | IMSM_100005 | C4 | Homo sapiens | NA | Saliva | NMR sample preparation in phosphase buffer | Healthy | NA | NA | NA | NA |
NA |
||||
| 5 | IMSM_100006 | C5 | Homo sapiens | NA | Saliva | NMR sample preparation in phosphase buffer | Healthy | NA | NA | NA | NA |
NA |
||||
| 6 | IMSM_100007 | C6 | Homo sapiens | NA | Saliva | NMR sample preparation in phosphase buffer | Healthy | NA | NA | NA | NA |
NA |
||||
| 7 | IMSM_100008 | C7 | Homo sapiens | NA | Saliva | NMR sample preparation in phosphase buffer | Healthy | NA | NA | NA | NA |
NA |
||||
| 8 | IMSM_100009 | C8 | Homo sapiens | NA | Saliva | NMR sample preparation in phosphase buffer | Healthy | NA | NA | NA | NA |
NA |
||||
| 9 | IMSM_100010 | C9 | Homo sapiens | NA | Saliva | NMR sample preparation in phosphase buffer | Healthy | NA | NA | NA | NA |
NA |
||||
| 10 | IMSM_100011 | C10 | Homo sapiens | NA | Saliva | NMR sample preparation in phosphase buffer | Healthy | NA | NA | NA | NA |
NA |
| Sr.No | NMR Exp ID | Sample Name/ID | Reference Standard | NMR Instrument Name | NMR Instrument Type | NMR Experiment Type | NMR Spectrometer Frequency | NMR Probe | NMR Probe temperature | NMR Solvent | NMR tube size | Data Transformation (Software/s Used) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 11 | IME_100013 | C11 / IMSM_100012 | 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS). | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500MHz | 15 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298K | D2O | 5mm | TopSpin |
| 12 | IME_100014 | C12 / IMSM_100013 | 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS). | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500MHz | 16 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298K | D2O | 5mm | TopSpin |
| 13 | IME_100015 | C13 / IMSM_100014 | 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS). | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500MHz | 17 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298K | D2O | 5mm | TopSpin |
| 14 | IME_100016 | C14 / IMSM_100015 | 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS). | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500MHz | 18 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298K | D2O | 5mm | TopSpin |
| 15 | IME_100017 | C15 / IMSM_100016 | 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS). | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500MHz | 19 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298K | D2O | 5mm | TopSpin |
| 16 | IME_100018 | C16 / IMSM_100017 | 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS). | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500MHz | 20 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298K | D2O | 5mm | TopSpin |
| 17 | IME_100019 | C17 / IMSM_100018 | 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS). | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500MHz | 21 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298K | D2O | 5mm | TopSpin |
| 18 | IME_100020 | C18 / IMSM_100019 | 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS). | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500MHz | 22 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298K | D2O | 5mm | TopSpin |
| 19 | IME_100021 | C19 / IMSM_100020 | 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS). | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500MHz | 23 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298K | D2O | 5mm | TopSpin |
| 20 | IME_100022 | C20 / IMSM_100021 | 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS). | Bruker Avance III 500MHz | Solution NMR | 1D 1H | 500MHz | 24 mm triple-resonance CPTCI cryogenic cooled probehead equipped with z-gradient | 298K | D2O | 5mm | TopSpin |
| Sr.No | First name | Last name | Organization | Designation |
|---|
| Sr.No | ftprun ID | NMR Exp ID | NMR Data Files |
|---|---|---|---|
| 21 | IMR_100022 | IME_100023 | C21.zip |
| 22 | IMR_100023 | IME_100024 | OC1.zip |
| 23 | IMR_100024 | IME_100025 | OC2.zip |
| 24 | IMR_100025 | IME_100026 | OC3.zip |
| 25 | IMR_100026 | IME_100027 | OC4.zip |
| 26 | IMR_100027 | IME_100028 | OC5.zip |
| 27 | IMR_100028 | IME_100029 | OC6.zip |
| 28 | IMR_100029 | IME_100030 | OC7.zip |
| 29 | IMR_100030 | IME_100031 | OC8.zip |
| 30 | IMR_100031 | IME_100032 | OC9.zip |
Download Metabolite/Compound
| Sr.No | Structure | Details |
|---|