Correlating Morphology and Gene Expression in Single Cells with Coherent Raman Imaging and RNA Sequencing
Aaron M Streets1,2, Yanyi Huang2,3,4
1Department of Bioengineering, University of California Berkeley, Berkeley, CA; 2Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China;
3College of Engineering, Peking University; 4Peking-Tsinghua Center for Life Sciences, Peking University
Phenotype classification of single cells reveals biological variation that is masked in ensemble measurement. This heterogeneity is found in gene expression as well as in cell morphology. Many techniques are available to probe phenotypic heterogeneity at the single cell level, for example quantitative imaging and single-cell RNA sequencing, but it is difficult to perform multiple assays on the same single cell. In order to directly quantify correlation between morphology and gene expression at the single-cell level, we developed a microfluidic platform for coherent Raman imaging and immediate RNA sequencing (RNA-Seq) of single cells. With this device we actively sort and trap cells for analysis with stimulated Raman scattering microscopy (SRS). The cells are then processed in parallel pipelines for lysis, and preparation of cDNA for high-throughput transcriptome sequencing. SRS microscopy offers three-dimensional imaging with chemical specificity for quantitative analysis of protein and lipid distribution in single cells. Meanwhile, the microfluidic platform facilitates single-cell manipulation, minimizes contamination, and furthermore, provides improved RNA-Seq detection sensitivity and measurement precision, which is necessary for differentiating biological variability from technical noise. We used this platform to image and sequence single adipocytes and uncover correlations between lipid droplet formation and gene expression dynamics during adipogenesis. By combining SRS microscopy with RNA sequencing, we can better understand the relationship between cellular morphology and gene expression at the single-cell level.
 Cao C et al., Analytical Chemistry, 88(9), 4931-4939 (2016)
Streets AM et al., PNAS, 111(19) 7048-7053 (2014)
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