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

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Title: The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq.
Authors: 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
Item Type: Journal Article
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.
Issue Date: 7-Jan-2017
Date of Acceptance: 20-Dec-2016
URI: http://hdl.handle.net/10044/1/44690
DOI: https://dx.doi.org/10.1186/s12864-016-3445-0
ISSN: 1471-2164
Publisher: BioMed Central
Journal / Book Title: BMC Genomics
Volume: 18
Issue: 1
Copyright Statement: © 2017 The Author(s). Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Keywords: Macrophage heterogeneity
Signaling microenvironment
Single-cell culture
Single-cell imaging
Single-cell sequencing
06 Biological Sciences
11 Medical And Health Sciences
08 Information And Computing Sciences
Publication Status: Published
Conference Place: England
Article Number: 53
Appears in Collections:School of Public Health