PT  - JOURNAL ARTICLE
AU  - Robert J. Kimmerling
AU  - Sanjay M. Prakadan
AU  - Alejandro J. Gupta
AU  - Nicholas L. Calistri
AU  - Mark M. Stevens
AU  - Selim Olcum
AU  - Nathan Cermak
AU  - Riley S. Drake
AU  - Alex K. Shalek
AU  - Scott R. Manalis
TI  - Linking single-cell measurements of mass, growth rate, and gene expression
AID  - 10.1101/331686
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 331686
4099  - http://biorxiv.org/content/early/2018/06/07/331686.short
4100  - http://biorxiv.org/content/early/2018/06/07/331686.full
AB  - We introduce a microfluidic platform that enables single-cell mass and growth rate measurements upstream of single-cell RNA-sequencing (scRNA-seq) to generate paired single-cell biophysical and transcriptional data sets. Biophysical measurements are collected with a serial suspended microchannel resonator platform (sSMR) that utilizes automated fluidic state switching to load individual cells at fixed intervals, achieving a throughput of 120 cells per hour. Each single-cell is subsequently captured downstream for linked molecular analysis using an automated collection system. From linked measurements of a murine leukemia (L1210) and pro-B cell line (FL5.12), we identify gene expression signatures that correlate significantly with cell mass and growth rate. In particular, we find that both cell lines display a cell-cycle signature that correlates with cell mass, with early and late cell-cycle signatures significantly enriched amongst genes with negative and positive correlations with mass, respectively. FL5.12 cells also show a significant correlation between single-cell growth efficiency and a G1-S transition signature, providing additional transcriptional evidence for a phenomenon previously observed through biophysical measurements alone. Importantly, the throughput and speed of our platform allows for the characterization of phenotypes in dynamic cellular systems. As a proof-of-principle, we apply our system to characterize activated murine CD8+ T cells and uncover two unique features of CD8+ T cells as they become proliferative in response to activation: i) the level of coordination between cell cycle gene expression and cell mass increases, and ii) translation-related gene expression increases and shows a correlation with single-cell growth efficiency. Overall, our approach provides a new means of characterizing the transcriptional mechanisms of normal and dysfunctional cellular mass and growth rate regulation across a range of biological contexts.scRNA-seq: single-cell RNA-sequencing;sSMR: serial suspended microchannel resonator;MAR: mass accumulation rate;FDR: false discovery rate