smFISH in chips: a microfluidic-based pipeline to quantify in situ gene expression in whole organisms

Gene expression and genetic regulatory networks in multi-cellular organisms control complex physiological processes ranging from cellular differentiation to development to aging. Traditional methods to investigate gene expression relationships rely on using bulk, pooled-population assays (e.g. RNA-s...

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Bibliographic Details
Published in:Lab on a chip 2020-01, Vol.20 (2), p.266-273
Main Authors: Wan, Jason, Sun, Gongchen, Dicent, Jocelyn, Patel, Dhaval S, Lu, Hang
Format: Article
Language:English
Subjects:
Animals
Biological models (mathematics)
Caenorhabditis elegans
Caenorhabditis elegans Proteins - genetics
Cellular communication
Differentiation (biology)
Exchanging
Fluorescence
Gene Expression
Gene sequencing
GTP-Binding Protein alpha Subunits, Gi-Go - genetics
In Situ Hybridization, Fluorescence
Lab-On-A-Chip Devices
Microfluidic devices
Mutation
Pipelines
Reagents
Tissue Culture Techniques
Toxicology
Transforming Growth Factor beta - genetics
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Summary:Gene expression and genetic regulatory networks in multi-cellular organisms control complex physiological processes ranging from cellular differentiation to development to aging. Traditional methods to investigate gene expression relationships rely on using bulk, pooled-population assays (e.g. RNA-sequencing and RT-PCR) to compare gene expression levels in hypo- or hyper-morphic mutant animals (e.g. gain-of-function or knockout). This approach is limited, especially in complex gene networks, as these genetic mutations may affect the expressions of related genes in unforseen ways. In contrast, we developed a microfluidic-based pipeline to discover gene relationships in a single genetic background. The microfluidic device provides efficient reagent exchange and the ability to track individual animals. By automating a robust microfluidic reagent exchange strategy, we adapted and validated single molecule fluorescent in situ hybridization (smFISH) on-chip and combined this technology with live-imaging of fluorescent transcriptional reporters. Together, this multi-level information enabled us to quantify a gene expression relationship with single-animal resolution. While this microfluidic-based pipeline is optimized for live-imaging and smFISH C. elegans studies, the strategy is highly-adaptable to other biological models as well as combining other live and end-point biological assays, such as behavior-based toxicology screening and immunohistochemistry.
ISSN:1473-0197
1473-0189
DOI:10.1039/c9lc00896a