A Method to Analyze Gene Expression Profiles from Hippocampal Neurons Electrophysiologically Recorded

Overview

Journal Front Neurosci

Date 2024 May 2

PMID 38694898

Authors

Haruya Yagishita

Yasuhiro Go

Kazuki Okamoto

Nariko Arimura

Yuji Ikegaya

Takuya Sasaki

Affiliations

Soon will be listed here.

Abstract

Hippocampal pyramidal neurons exhibit diverse spike patterns and gene expression profiles. However, their relationships with single neurons are not fully understood. In this study, we designed an electrophysiology-based experimental procedure to identify gene expression profiles using RNA sequencing of single hippocampal pyramidal neurons whose spike patterns were recorded in living mice. This technique involves a sequence of experiments consisting of juxtacellular recording and labeling, brain slicing, cell collection, and transcriptome analysis. We demonstrated that the expression levels of a subset of genes in individual hippocampal pyramidal neurons were significantly correlated with their spike burstiness, submillisecond-level spike rise times or spike rates, directly measured by electrophysiological recordings. Because this methodological approach can be applied across a wide range of brain regions, it is expected to contribute to studies on various neuronal heterogeneities to understand how physiological spike patterns are associated with gene expression profiles.

References

Westenbroek R, Merrick D, Catterall W . Differential subcellular localization of the RI and RII Na+ channel subtypes in central neurons. Neuron. 1989; 3(6):695-704. DOI: 10.1016/0896-6273(89)90238-9. View

Thome C, Kelly T, Yanez A, Schultz C, Engelhardt M, Cambridge S . Axon-carrying dendrites convey privileged synaptic input in hippocampal neurons. Neuron. 2014; 83(6):1418-30. DOI: 10.1016/j.neuron.2014.08.013. View

Csicsvari J, Hirase H, MAMIYA A, Buzsaki G . Ensemble patterns of hippocampal CA3-CA1 neurons during sharp wave-associated population events. Neuron. 2001; 28(2):585-94. DOI: 10.1016/s0896-6273(00)00135-5. View

Arimura N, Okada M, Taya S, Dewa K, Tsuzuki A, Uetake H . DSCAM regulates delamination of neurons in the developing midbrain. Sci Adv. 2020; 6(36). PMC: 7467692. DOI: 10.1126/sciadv.aba1693. View

Ishikawa T, Sato A, Marcou C, Tester D, Ackerman M, Crotti L . A novel disease gene for Brugada syndrome: sarcolemmal membrane-associated protein gene mutations impair intracellular trafficking of hNav1.5. Circ Arrhythm Electrophysiol. 2012; 5(6):1098-107. DOI: 10.1161/CIRCEP.111.969972. View

Jarsky T, Mady R, Kennedy B, Spruston N . Distribution of bursting neurons in the CA1 region and the subiculum of the rat hippocampus. J Comp Neurol. 2007; 506(4):535-47. DOI: 10.1002/cne.21564. View

Hempel C, Sugino K, Nelson S . A manual method for the purification of fluorescently labeled neurons from the mammalian brain. Nat Protoc. 2007; 2(11):2924-9. DOI: 10.1038/nprot.2007.416. View

Cortada E, Brugada R, Verges M . Trafficking and Function of the Voltage-Gated Sodium Channel β2 Subunit. Biomolecules. 2019; 9(10). PMC: 6843408. DOI: 10.3390/biom9100604. View

Graves A, Moore S, Bloss E, Mensh B, Kath W, Spruston N . Hippocampal pyramidal neurons comprise two distinct cell types that are countermodulated by metabotropic receptors. Neuron. 2012; 76(4):776-89. PMC: 3509417. DOI: 10.1016/j.neuron.2012.09.036. View

10.

Mallet N, Ballion B, Le Moine C, Gonon F . Cortical inputs and GABA interneurons imbalance projection neurons in the striatum of parkinsonian rats. J Neurosci. 2006; 26(14):3875-84. PMC: 6674115. DOI: 10.1523/JNEUROSCI.4439-05.2006. View

11.

Sasaki T, Matsuki N, Ikegaya Y . Action-potential modulation during axonal conduction. Science. 2011; 331(6017):599-601. DOI: 10.1126/science.1197598. View

12.

Xu S, Yang H, Menon V, Lemire A, Wang L, Henry F . Behavioral state coding by molecularly defined paraventricular hypothalamic cell type ensembles. Science. 2020; 370(6514). DOI: 10.1126/science.abb2494. View

13.

Bruce F, Brown S, Smith J, Fuerst P, Erskine L . DSCAM promotes axon fasciculation and growth in the developing optic pathway. Proc Natl Acad Sci U S A. 2017; 114(7):1702-1707. PMC: 5321013. DOI: 10.1073/pnas.1618606114. View

14.

Nishimura Y, Fukuda Y, Okonogi T, Yoshikawa S, Karasuyama H, Osakabe N . Dual real-time in vivo monitoring system of the brain-gut axis. Biochem Biophys Res Commun. 2020; 524(2):340-345. DOI: 10.1016/j.bbrc.2020.01.090. View

15.

Rodriques S, Stickels R, Goeva A, Martin C, Murray E, Vanderburg C . Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science. 2019; 363(6434):1463-1467. PMC: 6927209. DOI: 10.1126/science.aaw1219. View

16.

Pinault D . A novel single-cell staining procedure performed in vivo under electrophysiological control: morpho-functional features of juxtacellularly labeled thalamic cells and other central neurons with biocytin or Neurobiotin. J Neurosci Methods. 1996; 65(2):113-36. DOI: 10.1016/0165-0270(95)00144-1. View

17.

Carbon S, Ireland A, Mungall C, Shu S, Marshall B, Lewis S . AmiGO: online access to ontology and annotation data. Bioinformatics. 2008; 25(2):288-9. PMC: 2639003. DOI: 10.1093/bioinformatics/btn615. View

18.

Ruhl D, Bomba-Warczak E, Watson E, Bradberry M, Peterson T, Basu T . Synaptotagmin 17 controls neurite outgrowth and synaptic physiology via distinct cellular pathways. Nat Commun. 2019; 10(1):3532. PMC: 6684635. DOI: 10.1038/s41467-019-11459-4. View

19.

Oyama K, Ohara S, Sato S, Karube F, Fujiyama F, Isomura Y . Long-lasting single-neuron labeling by in vivo electroporation without microscopic guidance. J Neurosci Methods. 2013; 218(2):139-47. DOI: 10.1016/j.jneumeth.2013.06.004. View

20.

Saunders A, Macosko E, Wysoker A, Goldman M, Krienen F, de Rivera H . Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain. Cell. 2018; 174(4):1015-1030.e16. PMC: 6447408. DOI: 10.1016/j.cell.2018.07.028. View