Summary of Study ST001981
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 PR001257. The data can be accessed directly via it's Project DOI: 10.21228/M87986 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001981 |
| Study Title | Non-destructive characterization of Mesenchymal stem cells |
| Study Summary | Culture media from the growth of three different MSC cell lines (two bone marrow, one iPSC) were sampled daily for NMR metabolomics analysis. T cell proliferation and IDO assays were used as surrogates of anti-inflammatory function. Linear regression was used to assess the media metabolic changes over time, and partial least squares regression (PLSR) was then used to obtain predictive media markers (PMMs) based on variable importance in projection (VIP) scores. In addition, pathway analysis was performed to show the relations between media metabolites (MMs) and cell metabolites (CMs). |
| Institute | University of Georgia |
| Last Name | Shen |
| First Name | Xunan |
| Address | 315 riverbend road |
| xs41379@uga.edu | |
| Phone | 7858407009 |
| Submit Date | 2021-09-16 |
| Raw Data Available | Yes |
| Analysis Type Detail | NMR |
| Release Date | 2021-12-01 |
| Release Version | 1 |
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Project:
| Project ID: | PR001257 |
| Project DOI: | doi: 10.21228/M87986 |
| Project Title: | Non-destructive characterization of Mesenchymal stem cells |
| Project Summary: | Background: Mesenchymal stem cells (MSCs) have shown promising results in clinical trials for their anti-inflammatory function. However, MSC therapy isn’t licensed by FDA, in part because of the heterogeneity of MSCs. The lack of predictive markers also makes it difficult to both manufacture and translate MSCs into clinic. Indoleamine 2,3-Dioxygenase (IDO) assay and T cell suppression assays correlate with MSCs function. We previously showed that cellular metabolites can be used to predict IDO assay and T cell suppression results. Although these methods are promising, they are all destructive and time-consuming and therefore cannot easily translate to a cell manufacturing setting. A non-destructive, in-process method to evaluate cell quality would be extremely valuable. Methods: Culture media from the growth of three different MSC cell lines (two bone marrow, one iPSC) were sampled daily for NMR metabolomics analysis. T cell proliferation and IDO assays were used as surrogates of anti-inflammatory function. Linear regression was used to assess the media metabolic changes over time, and partial least squares regression (PLSR) was then used to obtain predictive media markers (PMMs) based on variable importance in projection (VIP) scores. In addition, pathway analysis was performed to show the relations between media metabolites (MMs) and cell metabolites (CMs). Results: Depending on the time of sampling, PLSR of culture media regressed against a composite score resulted in R2 values between 0.73 and 0.86. Several amnio acids and organic acids were useful PMMs at different time periods. Correlation and pathway analyses related the consumption of valine and aspartate to the release of glycine and alanine during culture. Discussion: The work described here used PLSR models to identify PMMs that can predict MSC function. This method is relatively simple, non-destructive and can could in the future be used in a manufacturing setting to help predict MSC function. |
| Institute: | University of Georgia |
| Last Name: | Shen |
| First Name: | Xunan |
| Address: | 315 riverbend road |
| Email: | xs41379@uga.edu |
| Phone: | 7858407009 |
Subject:
| Subject ID: | SU002062 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | experimental factor |
|---|---|---|
| SA185586 | iMSCp1 | p1 |
| SA185580 | BM182P1 | P1 |
| SA185581 | BM71P1 | P1 |
| SA185587 | iMSCp2 | p2 |
| SA185582 | BM182P2 | P2 |
| SA185583 | BM71P2 | P2 |
| SA185588 | iMSCp3 | p3 |
| SA185584 | BM182P3 | P3 |
| SA185585 | BM71P3 | P3 |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO002055 |
| Collection Summary: | Each cell line has 10 replicates. Two bone marrow-derived MSC lines (RoosterBio, Frederick MD) lot #0071 (F, 18-30) and #0182 (F, 26) (which the manufacturer has both research and clinical-grade lots available), and one induced pluripotent stem cell derived MSC cell-line (Cellular Dynamics International, Madison WI) (Lot #0003, also prequalified) were used and referred here as BM71, BM182, and iMSC, respectively. iMSC were cultured for 25 days, BM71 were cultured for 21 days and BM182 were cultured for 23 days. 100 µl media was sampled daily from each sample and stored at -80◦C for further analysis. |
| Sample Type: | Bone marrow |
Treatment:
| Treatment ID: | TR002074 |
| Treatment Summary: | Each cell line has 10 replicates. Two bone marrow-derived MSC lines (RoosterBio, Frederick MD) lot #0071 (F, 18-30) and #0182 (F, 26) (which the manufacturer has both research and clinical-grade lots available), and one induced pluripotent stem cell derived MSC cell-line (Cellular Dynamics International, Madison WI) (Lot #0003, also prequalified) were used and referred here as BM71, BM182, and iMSC, respectively. iMSC were cultured for 25 days, BM71 were cultured for 21 days and BM182 were cultured for 23 days. 100 µl media was sampled daily from each sample and stored at -80◦C for further analysis. |
Sample Preparation:
| Sampleprep ID: | SP002068 |
| Sampleprep Summary: | One hundred µl culture media was thawed on ice and then centrifuged at 14,000 x g for 15 min at 4◦C. For each sample, 54 µl of media supernatant was transferred to a new Eppendorf tube. 30 µl of remaining media in each sample from the same cell line was pooled together to generate six 54 µl internal quality control (QC) samples. 6 µl of 10/3 mM DSS-D6 (Cambridge Isotope Laboratory) in D2O (Cambridge Isotope Laboratory) was then added into each sample. In addition, six buffer blanks (6 µl of 10/3 mM DSS-D6 in 54 µl D2O) samples were added in each cell line for quality assurance purpose. We had 10 replicates for each cell line and time point. A total of 262 samples including 250 experimental samples, 6 pooled samples and 6 buffer blanks were generated for the iMSC group. A total of 222 samples including 210 experimental samples, 6 pooled samples and 6 buffer blanks were generated for BM71. A total of 242 samples including 230 experimental samples, 6 pooled samples and 6 buffer blanks were generated for BM182. All samples were randomized to reduce technical variance. |
Analysis:
| Analysis ID: | AN003231 |
| Analysis Type: | NMR |
| Num Factors: | 6 |
| Num Metabolites: | 50 |
| Units: | change rate |
NMR:
| NMR ID: | NM000222 |
| Analysis ID: | AN003231 |
| Instrument Name: | bruker800 |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| Spectrometer Frequency: | 800 |
