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

BMC Genomics

Methodology Article

Sarah Filippi¹  Mark Lynch²  Michael Gonzales²  Jay West²  Anne Leyrat²  William James³  Damien Warner³  Michael D. Moore³  John Broxholme⁴  Benjamin Wright⁴  Esther Mellado-Gomez⁴  Eshita Sharma⁴  Helen Lockstone⁴  Rory Bowden⁴  Chris Holmes⁵  Rory Nolan⁶  Sergi Padilla-Parra⁶  Quin F. Wills⁷ 

[1] Department of Statistics, University of Oxford, OX3 3LB, Oxford, UK;Fluidigm Corporation, 7000 Shoreline Ct Ste 100, 94080-7603, South San Francisco, CA, USA;Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK;Wellcome Trust Centre for Human Genetics (WTCHG), University of Oxford, OX3 7BN, Oxford, UK;Wellcome Trust Centre for Human Genetics (WTCHG), University of Oxford, OX3 7BN, Oxford, UK;Department of Statistics, University of Oxford, OX3 3LB, Oxford, UK;Wellcome Trust Centre for Human Genetics (WTCHG), University of Oxford, OX3 7BN, Oxford, UK;Division of Structural Biology, University of Oxford, OX3 7BN, Oxford, UK;Wellcome Trust Centre for Human Genetics (WTCHG), University of Oxford, OX3 7BN, Oxford, UK;Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, OX3 9DS, Oxford, UK;

关键词: Single-cell sequencing;    Single-cell culture;    Single-cell imaging;    Macrophage heterogeneity;    Signaling microenvironment;   

DOI  :  10.1186/s12864-016-3445-0

 received in 2016-08-27, accepted in 2016-12-20,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundSingle-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.ResultsWe 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.ConclusionAs 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.

【 授权许可】

CC BY   
© The Author(s). 2017