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BMC Genomics. 2017 Jan 7;18(1):53. doi: 10.1186/s12864-016-3445-0.

The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq.

Author information

1
Wellcome Trust Centre for Human Genetics (WTCHG), University of Oxford, Oxford, OX3 7BN, UK. qilin@well.ox.ac.uk.
2
Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, Oxford, OX3 9DS, UK. qilin@well.ox.ac.uk.
3
Wellcome Trust Centre for Human Genetics (WTCHG), University of Oxford, Oxford, OX3 7BN, UK.
4
Division of Structural Biology, University of Oxford, Oxford, OX3 7BN, UK.
5
Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
6
Fluidigm Corporation, 7000 Shoreline Ct Ste 100, South San Francisco, CA, 94080-7603, USA.
7
Department of Statistics, University of Oxford, Oxford, OX3 3LB, UK.
8
Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK. kenny.moore@path.ox.ac.uk.
9
Wellcome Trust Centre for Human Genetics (WTCHG), University of Oxford, Oxford, OX3 7BN, UK. rbowden@well.ox.ac.uk.

Abstract

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.

KEYWORDS:

Macrophage heterogeneity; Signaling microenvironment; Single-cell culture; Single-cell imaging; Single-cell sequencing

PMID:
28061811
PMCID:
PMC5219790
DOI:
10.1186/s12864-016-3445-0
[Indexed for MEDLINE]
Free PMC Article

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