The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq
| Autor: | Wills, QF, Mellado-Gomez, E, Nolan, R, Warner, D, Sharma, E, Broxholme, J, Wright, B, Lockstone, H, James, W, Lynch, M, Gonzales, M, West, J, Leyrat, A, Padilla-Parra, S, Filippi, S, Holmes, C, Moore, MD, Bowden, R |
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| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
08 Information And Computing Sciences
Bioinformatics Sequence Analysis RNA Methodology Article Macrophages 11 Medical And Health Sciences 06 Biological Sciences Single-cell imaging Single-cell culture Signaling microenvironment SAM Domain and HD Domain-Containing Protein 1 Gene Knockout Techniques Phenotype Single-cell sequencing Genetics Humans Gene-Environment Interaction Single-Cell Analysis Macrophage heterogeneity Biotechnology |
| Zdroj: | BMC Genomics |
| ISSN: | 1471-2164 |
| Popis: | Background Single-cell RNA-Seq can be a valuable and unbiased tool to dissect cellular heterogeneity, despite the transcriptome’s limitations in describing higher functional phenotypes and protein events. Perhaps the most important shortfall with transcriptomic ‘snapshots’ of cell populations is that they risk being descriptive, only cataloging heterogeneity at one point in time, and without microenvironmental context. Studying the genetic (‘nature’) and environmental (‘nurture’) modifiers of heterogeneity, and how cell population dynamics unfold over time in response to these modifiers is key when studying highly plastic cells such as macrophages. Results We introduce the programmable Polaris™ microfluidic lab-on-chip for single-cell sequencing, which performs live-cell imaging while controlling for the culture microenvironment of each cell. Using gene-edited macrophages we demonstrate how previously unappreciated knockout effects of SAMHD1, such as an altered oxidative stress response, have a large paracrine signaling component. Furthermore, we demonstrate single-cell pathway enrichments for cell cycle arrest and APOBEC3G degradation, both associated with the oxidative stress response and altered proteostasis. Interestingly, SAMHD1 and APOBEC3G are both HIV-1 inhibitors (‘restriction factors’), with no known co-regulation. Conclusion As single-cell methods continue to mature, so will the ability to move beyond simple ‘snapshots’ of cell populations towards studying the determinants of population dynamics. By combining single-cell culture, live-cell imaging, and single-cell sequencing, we have demonstrated the ability to study cell phenotypes and microenvironmental influences. It’s these microenvironmental components - ignored by standard single-cell workflows - that likely determine how macrophages, for example, react to inflammation and form treatment resistant HIV reservoirs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3445-0) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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