{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T03:10:53Z","timestamp":1778555453903,"version":"3.51.4"},"reference-count":46,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,6,30]],"date-time":"2022-06-30T00:00:00Z","timestamp":1656547200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Synaptic Neurosci."],"abstract":"<jats:p>Acute regulation of CO<jats:sub>2<\/jats:sub> and pH homeostasis requires sensory feedback from peripheral (carotid body) and central (central) CO<jats:sub>2<\/jats:sub>\/pH sensitive cells \u2013 so called respiratory chemoreceptors. Subsets of brainstem serotonin (5-HT) neurons in the medullary raphe are CO<jats:sub>2<\/jats:sub> sensitive or insensitive based on differences in embryonic origin, suggesting these functionally distinct subpopulations may have unique transcriptional profiles. Here, we used Patch-to-Seq to determine if the CO<jats:sub>2<\/jats:sub> responses in brainstem 5-HT neurons could be correlated to unique transcriptional profiles and\/or unique molecular markers and pathways. First, firing rate changes with hypercapnic acidosis were measured in fluorescently labeled 5-HT neurons in acute brainstem slices from transgenic, Dahl SS (SSMcwi) rats expressing T2\/ePet-eGFP transgene in Pet-1 expressing (serotonin) neurons (SS<jats:sup><jats:italic>ePet<\/jats:italic>1\u2013eGFP<\/jats:sup> rats). Subsequently, the transcriptomic and pathway profiles of CO<jats:sub>2<\/jats:sub> sensitive and insensitive 5-HT neurons were determined and compared by single cell RNA (scRNAseq) and bioinformatic analyses. Low baseline firing rates were a distinguishing feature of CO<jats:sub>2<\/jats:sub> sensitive 5-HT neurons. scRNAseq of these recorded neurons revealed 166 differentially expressed genes among CO<jats:sub>2<\/jats:sub> sensitive and insensitive 5-HT neurons. Pathway analyses yielded novel predicted upstream regulators, including the transcription factor <jats:italic>Egr2<\/jats:italic> and <jats:italic>Leptin<\/jats:italic>. Additional bioinformatic analyses identified 6 candidate gene markers of CO<jats:sub>2<\/jats:sub> sensitive 5-HT neurons, and 2 selected candidate genes (<jats:italic>CD46<\/jats:italic> and <jats:italic>Iba57<\/jats:italic>) were both expressed in 5-HT neurons determined via <jats:italic>in situ<\/jats:italic> mRNA hybridization. Together, these data provide novel insights into the transcriptional control of cellular chemoreception and provide unbiased candidate gene markers of CO<jats:sub>2<\/jats:sub> sensitive 5-HT neurons. Methodologically, these data highlight the utility of the patch-to-seq technique in enabling the linkage of gene expression to specific functions, like CO<jats:sub>2<\/jats:sub> chemoreception, in a single cell to identify potential mechanisms underlying functional differences in otherwise similar cell types.<\/jats:p>","DOI":"10.3389\/fnsyn.2022.910820","type":"journal-article","created":{"date-parts":[[2022,6,30]],"date-time":"2022-06-30T10:43:00Z","timestamp":1656585780000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Patch-to-Seq and Transcriptomic Analyses Yield Molecular Markers of Functionally Distinct Brainstem Serotonin Neurons"],"prefix":"10.3389","volume":"14","author":[{"suffix":"Jr.","given":"Gary C.","family":"Mouradian","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pengyuan","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pablo","family":"Nakagawa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erin","family":"Duffy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Javier","family":"Gomez Vargas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kirthikaa","family":"Balapattabi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Justin L.","family":"Grobe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Curt D.","family":"Sigmund","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew R.","family":"Hodges","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2022,6,30]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/j.lfs.2015.01.019","article-title":"Control of respiratory and cardiovascular functions by leptin.","volume":"125","author":"Bassi","year":"2015","journal-title":"Life Sci."},{"key":"B2","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1007\/s00424-012-1111-1","article-title":"Central leptin replacement enhances chemorespiratory responses in leptin-deficient mice independent of changes in body weight.","volume":"464","author":"Bassi","year":"2012","journal-title":"Pfl\u00fcgers Arch."},{"key":"B3","doi-asserted-by":"publisher","first-page":"2152","DOI":"10.1016\/j.celrep.2014.11.027","article-title":"Functional and developmental identification of a molecular subtype of brain serotonergic neuron specialized to regulate breathing dynamics.","volume":"9","author":"Brust","year":"2014","journal-title":"Cell Rep."},{"key":"B4","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1016\/j.tins.2019.02.002","article-title":"Impaired CO2-Induced Arousal in SIDS and SUDEP.","volume":"42","author":"Buchanan","year":"2019","journal-title":"Trends Neurosci."},{"key":"B5","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1016\/s0034-5687(01)00289-4","article-title":"Contributions of chemosensitive serotonergic neurons to interactions between the sleep-wake cycle and respiratory control","author":"Buchanan","year":"2008","journal-title":"Serotonin and Sleep: Molecular, Functional and Clinical Aspects."},{"key":"B6","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1038\/nbt.3445","article-title":"Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq.","volume":"34","author":"Cadwell","year":"2016","journal-title":"Nat Biotechnol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.neuroscience.2016.09.002","article-title":"Medullary 5-HT neurons: Switch from tonic respiratory drive to chemoreception during postnatal development.","volume":"344","author":"Cerpa","year":"2017","journal-title":"Neuroscience."},{"key":"B8","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1007\/s13238-016-0247-8","article-title":"Coupled electrophysiological recording and single cell transcriptome analyses revealed molecular mechanisms underlying neuronal maturation.","volume":"7","author":"Chen","year":"2016","journal-title":"Protein Cell."},{"key":"B9","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/j.resp.2009.04.014","article-title":"Medullary serotonin neurons and central CO2 chemoreception.","volume":"168","author":"Corcoran","year":"2009","journal-title":"Respir. 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