Single-cell nanobiopsy reveals compartmentalization of mRNAs within neuronal cells

Eszter N. Tóth, Akshar Lohith, Manas Mondal, Jia Guo, Akiyoshi Fukamizu, Nader Pourmand

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

In highly polarized cells such as neurons, compartmentalization of mRNA and of local protein synthesis enables remarkably fast, precise, and local responses to external stimuli. These responses are highly important for neuron growth cone guidance, synapse formation, and regeneration following injury. Because an altered spatial distribution of mRNA can result in mental retardation or neurodegenerative diseases, subcellular transcriptome analysis of neurons could be a useful tool for studying these conditions, but current techniques, such as in situ hybridization, bulk microarray, and RNA-Seq, impose tradeoffs between spatial resolution and multiplexing. To obtain a comprehensive analysis of the cell body versus neurite transcriptome from the same neuron, we have recently developed a label-free, single-cell nanobiopsy platform based on scanning ion conductance microscopy that uses electrowetting within a quartz nanopipette to extract cellular material from living cells with minimal disruption of the cellular membrane and milieu. In this study, we used this platform to collect samples from the cell bodies and neurites of human neurons and analyzed the mRNA pool with multiplex RNA sequencing. The minute volume of a nanobiopsy sample allowed us to extract samples from several locations in the same cell and to map the various mRNA species to specific subcellular locations. In addition to previously identified transcripts, we discovered new sets of mRNAs localizing to neurites, including nuclear genes such as Eomes and Hmgb3. In summary, our single-neuron nanobiopsy analysis provides opportunities to improve our understanding of intracellular mRNA transport and local protein composition in neuronal growth, connectivity, and function.

Original languageEnglish (US)
Pages (from-to)4940-4951
Number of pages12
JournalJournal of Biological Chemistry
Volume293
Issue number13
DOIs
StatePublished - Jan 1 2018

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Neurons
Messenger RNA
Neurites
Cells
Electrowetting
RNA
Neurodegenerative diseases
RNA Sequence Analysis
Growth Cones
Quartz
Gene Expression Profiling
Microarrays
Multiplexing
Transcriptome
Intellectual Disability
Neurodegenerative Diseases
Synapses
Spatial distribution
In Situ Hybridization
Cones

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Single-cell nanobiopsy reveals compartmentalization of mRNAs within neuronal cells. / Tóth, Eszter N.; Lohith, Akshar; Mondal, Manas; Guo, Jia; Fukamizu, Akiyoshi; Pourmand, Nader.

In: Journal of Biological Chemistry, Vol. 293, No. 13, 01.01.2018, p. 4940-4951.

Research output: Contribution to journalArticle

Tóth, Eszter N. ; Lohith, Akshar ; Mondal, Manas ; Guo, Jia ; Fukamizu, Akiyoshi ; Pourmand, Nader. / Single-cell nanobiopsy reveals compartmentalization of mRNAs within neuronal cells. In: Journal of Biological Chemistry. 2018 ; Vol. 293, No. 13. pp. 4940-4951.
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