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Evaluating the Effect of Cell Culture on Gene Expression in Primary Tissue Samples Using Microfluidic-Based Single Cell Transcriptional Analysis
Significant transcriptional heterogeneity is an inherent property of complex tissues such as tumors and healing wounds. Traditional methods of high-throughput analysis rely on pooling gene expression data from hundreds of thousands of cells and reporting a population-wide average that is unable to c...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996408/ https://www.ncbi.nlm.nih.gov/pubmed/27600239 http://dx.doi.org/10.3390/microarrays4040540 |
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author | Januszyk, Michael Rennert, Robert C. Sorkin, Michael Maan, Zeshaan N. Wong, Lisa K. Whittam, Alexander J. Whitmore, Arnetha Duscher, Dominik Gurtner, Geoffrey C. |
author_facet | Januszyk, Michael Rennert, Robert C. Sorkin, Michael Maan, Zeshaan N. Wong, Lisa K. Whittam, Alexander J. Whitmore, Arnetha Duscher, Dominik Gurtner, Geoffrey C. |
author_sort | Januszyk, Michael |
collection | PubMed |
description | Significant transcriptional heterogeneity is an inherent property of complex tissues such as tumors and healing wounds. Traditional methods of high-throughput analysis rely on pooling gene expression data from hundreds of thousands of cells and reporting a population-wide average that is unable to capture differences within distinct cell subsets. Recent advances in microfluidic technology have permitted the development of large-scale single cell analytic methods that overcome this limitation. The increased granularity afforded by such approaches allows us to answer the critical question of whether expansion in cell culture significantly alters the transcriptional characteristics of cells isolated from primary tissue. Here we examine an established population of human adipose-derived stem cells (ASCs) using a novel, microfluidic-based method for high-throughput transcriptional interrogation, coupled with advanced bioinformatic analysis, to evaluate the dynamics of single cell gene expression among primary, passage 0, and passage 1 stem cells. We find significant differences in the transcriptional profiles of cells from each group, as well as a considerable shift in subpopulation dynamics as those subgroups better able to adhere and proliferate under these culture conditions gradually emerge as dominant. Taken together, these findings reinforce the importance of using primary or very early passage cells in future studies. |
format | Online Article Text |
id | pubmed-4996408 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-49964082016-09-06 Evaluating the Effect of Cell Culture on Gene Expression in Primary Tissue Samples Using Microfluidic-Based Single Cell Transcriptional Analysis Januszyk, Michael Rennert, Robert C. Sorkin, Michael Maan, Zeshaan N. Wong, Lisa K. Whittam, Alexander J. Whitmore, Arnetha Duscher, Dominik Gurtner, Geoffrey C. Microarrays (Basel) Article Significant transcriptional heterogeneity is an inherent property of complex tissues such as tumors and healing wounds. Traditional methods of high-throughput analysis rely on pooling gene expression data from hundreds of thousands of cells and reporting a population-wide average that is unable to capture differences within distinct cell subsets. Recent advances in microfluidic technology have permitted the development of large-scale single cell analytic methods that overcome this limitation. The increased granularity afforded by such approaches allows us to answer the critical question of whether expansion in cell culture significantly alters the transcriptional characteristics of cells isolated from primary tissue. Here we examine an established population of human adipose-derived stem cells (ASCs) using a novel, microfluidic-based method for high-throughput transcriptional interrogation, coupled with advanced bioinformatic analysis, to evaluate the dynamics of single cell gene expression among primary, passage 0, and passage 1 stem cells. We find significant differences in the transcriptional profiles of cells from each group, as well as a considerable shift in subpopulation dynamics as those subgroups better able to adhere and proliferate under these culture conditions gradually emerge as dominant. Taken together, these findings reinforce the importance of using primary or very early passage cells in future studies. MDPI 2015-11-04 /pmc/articles/PMC4996408/ /pubmed/27600239 http://dx.doi.org/10.3390/microarrays4040540 Text en © 2015 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Januszyk, Michael Rennert, Robert C. Sorkin, Michael Maan, Zeshaan N. Wong, Lisa K. Whittam, Alexander J. Whitmore, Arnetha Duscher, Dominik Gurtner, Geoffrey C. Evaluating the Effect of Cell Culture on Gene Expression in Primary Tissue Samples Using Microfluidic-Based Single Cell Transcriptional Analysis |
title | Evaluating the Effect of Cell Culture on Gene Expression in Primary Tissue Samples Using Microfluidic-Based Single Cell Transcriptional Analysis |
title_full | Evaluating the Effect of Cell Culture on Gene Expression in Primary Tissue Samples Using Microfluidic-Based Single Cell Transcriptional Analysis |
title_fullStr | Evaluating the Effect of Cell Culture on Gene Expression in Primary Tissue Samples Using Microfluidic-Based Single Cell Transcriptional Analysis |
title_full_unstemmed | Evaluating the Effect of Cell Culture on Gene Expression in Primary Tissue Samples Using Microfluidic-Based Single Cell Transcriptional Analysis |
title_short | Evaluating the Effect of Cell Culture on Gene Expression in Primary Tissue Samples Using Microfluidic-Based Single Cell Transcriptional Analysis |
title_sort | evaluating the effect of cell culture on gene expression in primary tissue samples using microfluidic-based single cell transcriptional analysis |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996408/ https://www.ncbi.nlm.nih.gov/pubmed/27600239 http://dx.doi.org/10.3390/microarrays4040540 |
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