In psychiatric disorders, mismatches between disease states and therapeutic strategies are highly pronounced, largely because of unanswered questions regarding specific vulnerabilities of different cell types and therapeutic responses. Which cellular events (housekeeping or salient) are most affected? Which cell types succumb first to challenges, and which exhibit the strongest response to drugs? Are these events coordinated between cell types? How does disease and drug effect this coordination? To address these questions, we analyzed single-nucleus-RNAseq (sn-RNAseq) data from the human anterior cingulate cortex—a region involved in many psychiatric disorders. Density index, a metric for quantifying similarities and dissimilarities across functional profiles, was employed to identify common or salient functional themes across cell types. Cell-specific signatures were integrated with existing disease and drug-specific signatures to determine cell-type-specific vulnerabilities, druggabilities, and responsiveness. Clustering of functional profiles revealed cell types jointly participating in these events. SST and VIP interneurons were found to be most vulnerable, whereas pyramidal neurons were least. Overall, the disease state is superficial layer-centric, influences cell-specific salient themes, strongly impacts disinhibitory neurons, and influences astrocyte interaction with a subset of deep-layer pyramidal neurons. In absence of disease, drugs profiles largely recapitulate disease profiles, offering a possible explanation for drug side effects. However, in presence of disease, drug activities, are deep layer-centric and involve activating a distinct subset of deep-layer pyramidal neurons to circumvent the disease state’s disinhibitory circuit malfunction. These findings demonstrate a novel application of sn-RNAseq data to explain drug and disease action at a systems level.
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Pankevich DE, Altevogt BM, Dunlop J, Gage FH, Hyman SE. Improving and accelerating drug development for nervous system disorders. Neuron. 2014;84:546–53.
Gribkoff VK, Kaczmarek LK. The need for new approaches in CNS drug discovery: why drugs have failed, and what can be done to improve outcomes. Neuro pharmacology. 2017;120:11–9.
Tatti R, Maffei A. Synaptic dynamics: how network activity affects neuron communication. Curr Biol. 2015;25:R278–R280.
Shukla R, Prevot TD, French L, Isserlin R, Rocco BR, Banasr M, et al. The Relative Contributions of Cell-Dependent Cortical Microcircuit Aging to Cognition and Anxiety. Biol Psychiatry. 2019;85:257–67.
Darmanis S, Sloan SA, Zhang Y, Enge M, Caneda C, Shuer LM, et al. A survey of human brain transcriptome diversity at the single cell level. Proc Natl Acad Sci U S A. 2015;112:7285–90.
Lake BB, Ai R, Kaeser GE, Salathia NS, Yung YC, Liu R, et al. Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science. 2016;352:1586.
Hodge RD, Bakken TE, Miller JA, Smith KA, Barkan ER, Graybuck LT, et al. Conserved cell types with divergent features in human versus mouse cortex. Nature. 2019;573:61–68.
Nagy C, Maitra M, Tanti A, Suderman M, Théroux J-F, Davoli MA, et al. Single-nucleus transcriptomics of the prefrontal cortex in major depressive disorder implicates oligodendrocyte precursor cells and excitatory neurons. Nature Neuroscience. 2020;23:771–81.
Velmeshev D, Schirmer L, Jung D, Haeussler M, Perez Y, Mayer S, et al. Single-cell genomics identifies cell type–specific molecular changes in autism. Science. 2019;364:685.
Pfisterer U, Petukhov V, Demharter S, Meichsner J, Thompson JJ, Batiuk MY, et al. Identification of epilepsy-associated neuronal subtypes and gene expression underlying epileptogenesis. Nat Commun. 2020;11:5038.
Pinero J, Ramirez-Anguita JM, Sauch-Pitarch J, Ronzano F, Centeno E, Sanz F, et al. The DisGeNET knowledge platform for disease genomics: 2019 update. Nucleic Acids Res. 2020;48:D845–55.
Davis AP, Grondin CJ, Johnson RJ, Sciaky D, Wiegers J, Wiegers TC, et al. Comparative Toxicogenomics Database (CTD): update 2021. Nucleic Acids Res. 2021;49:D1138–43.
Subramanian A, Narayan R, Corsello SM, Peck DD, Natoli TE, Lu X, et al. A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. Cell. 2017;171:1437–52 e1417.
Smail MA, Wu X, Henkel ND, Eby HM, Herman JP, McCullumsmith RE, et al. Similarities and dissimilarities between psychiatric cluster disorders. Mol Psychiatry. 2021;26:4853–3.
Barthas F, Sellmeijer J, Hugel S, Waltisperger E, Barrot M, Yalcin I. The anterior cingulate cortex is a critical hub for pain-induced depression. Biol Psychiatry. 2015;77:236–45.
Sanders GS, Gallup GG, Heinsen H, Hof PR, Schmitz C. Cognitive deficits, schizophrenia, and the anterior cingulate cortex. Trends Cogn Sci. 2002;6:190–2.
Simms ML, Kemper TL, Timbie CM, Bauman ML, Blatt GJ. The anterior cingulate cortex in autism: heterogeneity of qualitative and quantitative cytoarchitectonic features suggests possible subgroups. Acta Neuropathol. 2009;118:673–84.
Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, et al. Integrated analysis of multimodal single-cell data. Cell. 2021;184:3573–87. e3529
Markram H, Toledo-Rodriguez M, Wang Y, Gupta A, Silberberg G, Wu C. Inter-neurons of the neocortical inhibitory system. Nat Rev Neurosci. 2004;5:793–807.
Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013;14:128.
Piñero J, Bravo À, Queralt-Rosinach N, Gutiérrez-Sacristán A, Deu-Pons J, Centeno E, et al. DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. Nucleic Acids Research. 2016;45:D833–39.
Yoo M, Shin J, Kim J, Ryall KA, Lee K, Lee S, et al. DSigDB: drug signatures database for gene set analysis. Bioinformatics. 2015;31:3069–71.
Pfeffer CK. Inhibitory neurons: vip cells hit the brake on inhibition. Curr Biol. 2014;24:R18–r20.
Pi HJ, Hangya B, Kvitsiani D, Sanders JI, Huang ZJ, Kepecs A. Cortical interneurons that specialize in disinhibitory control. Nature. 2013;503:521–4.
Letzkus JJ, Wolff SB. Lüthi A. Disinhibition, a circuit mechanism for associative learning and memory. Neuron. 2015;88:264–76.
Tremblay R, Lee S, Rudy B. GABAergic interneurons in the neocortex: from cellular properties to circuits. Neuron. 2016;91:260–92.
Naskar S, Qi J, Pereira F, Gerfen CR, Lee S. Cell-type-specific recruitment of GABAergic interneurons in the primary somatosensory cortex by long-range inputs. Cell Rep. 2021;34:108774.
Eckenstein F, Baughman RW. Two types of cholinergic innervation in cortex, one co-localized with vasoactive intestinal polypeptide. Nature. 1984;309:153–5.
Chu J, Anderson SA. Development of cortical interneurons. Neuropsycho pharmacology. 2015;40:16–23.
Takada N, Pi HJ, Sousa VH, Waters J, Fishell G, Kepecs A, et al. A developmental cell-type switch in cortical interneurons leads to a selective defect in cortical oscillations. Nature Communications. 2014;5:5333.
Poorthuis RB, Muhammad K, Wang M, Verhoog MB, Junek S, Wrana A, et al. Rapid Neuromodulation of Layer 1 Interneurons in Human Neocortex. Cell Rep. 2018;23:951–8.
Leong ATL, Chan RW, Gao PP, Chan Y-S, Tsia KK, Yung W-H, et al. Long-range projections coordinate distributed brain-wide neural activity with a specific spatiotemporal profile. Proceedings of the National Academy of Sciences. 2016;113:E8306.
Gerfen CR, Economo MN, Chandrashekar J. Long distance projections of cortical pyramidal neurons. J Neurosci Res. 2018;96:1467–75.
Baker A, Kalmbach B, Morishima M, Kim J, Juavinett A, Li N, et al. Specialized Subpopulations of Deep-Layer Pyramidal Neurons in the Neocortex: Bridging Cellular Properties to Functional Consequences. The Journal of Neuroscience. 2018;38:5441.
Cauli B, Tong XK, Rancillac A, Serluca N, Lambolez B, Rossier J, et al. Cortical GABA interneurons in neurovascular coupling: relays for subcortical vasoactive pathways. J Neurosci. 2004;24:8940–9.
Dong Y, Benveniste EN. Immune function of astrocytes. Glia. 2001;36:180–90.
Norris GT, Kipnis J. Immune cells and CNS physiology: microglia and beyond. J Exp Med. 2019;216:60–70.
Huang Y, Xu Z, Xiong S, Sun F, Qin G, Hu G, et al. Repopulated microglia are solely derived from the proliferation of residual microglia after acute depletion. Nature Neuroscience. 2018;21:530–40.
Wang H, Azuaje F, Bodenreider O, Dopazo J. Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships. Proc IEEE Symp Comput Intell Bioinforma Comput Biol. 2004;2004:25–31.
Rangaraju S, Solis GM, Thompson RC, Gomez-Amaro RL, Kurian L, Encalada SE, et al. Suppression of transcriptional drift extends C. elegans lifespan by postponing the onset of mortality. Elife. 2015;4:e08833.
Kamme F, Salunga R, Yu J, Tran DT, Zhu J, Luo L, et al. Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity. J Neurosci. 2003;23:3607–15.
Lee S, Kruglikov I, Huang ZJ, Fishell G, Rudy B. A disinhibitory circuit mediates motor integration in the somatosensory cortex. Nat Neurosci. 2013;16:1662–70.
Griemsmann S, Höft SP, Bedner P, Zhang J, von Staden E, Beinhauer A, et al. Characterization of Panglial Gap Junction Networks in the Thalamus, Neocortex, and Hippocampus Reveals a Unique Population of Glial Cells. Cerebral Cortex. 2014;25:3420–33.
Philippot C, Griemsmann S, Jabs R, Seifert G, Kettenmann H, Steinhäuser C. Astrocytes and oligodendrocytes in the thalamus jointly maintain synaptic activity by supplying metabolites. Cell Reports. 2021;34:108642.
Park K, Lee SJ. Deciphering the star codings: astrocyte manipulation alters mouse behavior. Experimental & Molecular Medicine. 2020;52:1028–38.
Min R, Nevian T. Astrocyte signaling controls spike timing-dependent depression at neocortical synapses. Nat Neurosci. 2012;15:746–53.
Heuser K, Nome CG, Pettersen KH, Åbjørsbråten KS, Jensen V, Tang W, et al. Ca2+ Signals in Astrocytes Facilitate Spread of Epileptiform Activity. Cereb Cortex. 2018;28:4036–48.
Voskuhl RR, Peterson RS, Song B, Ao Y, Morales LB, Tiwari-Woodruff S, et al. Reactive astrocytes form scar-like perivascular barriers to leukocytes during adaptive immune inflammation of the CNS. J Neurosci. 2009;29:11511–22.
Horchar MJ, Wohleb ES. Glucocorticoid receptor antagonism prevents microgliamediated neuronal remodeling and behavioral despair following chronic unpredictable stress. Brain Behav Immun. 2019;81:329–40.
Xu Z-X, Kim GH, Tan J-W, Riso AE, Sun Y, Xu EY, et al. Elevated protein synthesis in microglia causes autism-like synaptic and behavioral aberrations. Nature Communications. 2020;11:1797.
Urrego D, Troncoso J, Múnera A. Layer 5 pyramidal neurons’ dendritic remodeling and increased microglial density in primary motor cortex in a murine model of facial paralysis. Biomed Res Int. 2015;2015:482023.
Shukla R, Henkel ND, Alganem K, Hamoud AR, Reigle J, Alnafisah RS, et al. Signature-based approaches for informed drug repurposing: targeting CNS disorders. Neuropsychopharmacology. 2021;46:116–30.
Chiu CQ, Lur G, Morse TM, Carnevale NT, Ellis-Davies GC, Higley MJ. Compartmentalization of GABAergic inhibition by dendritic spines. Science. 2013;340:759–62.
Schulz JM, Knoflach F, Hernandez M-C, Bischofberger J. Dendrite-targeting interneurons control synaptic NMDA-receptor activation via nonlinear α5-GABAA receptors. Nat Commun. 2018;9:3576.
Karnani MM, Jackson J, Ayzenshtat I, Hamzehei Sichani A, Manoocheri K, Kim S, et al. Opening Holes in the Blanket of Inhibition: Localized Lateral Disinhibition by VIP Interneurons. J Neurosci. 2016;36:3471–80.
Pardi MB, Abs E, Letzkus JJ. Disinhibition goes spatial. Neuron. 2019;101:994–6.
Turi GF, Li WK, Chavlis S, Pandi I, O'Hare J, Priestley JB, et al. Vasoactive Intestinal Polypeptide-Expressing Interneurons in the Hippocampus Support Goal-Oriented Spatial Learning. Neuron. 2019;101:1150-65.e1158.
Seasholtz A. Regulation of adrenocorticotropic hormone secretion: lessons from mice deficient in corticotropin-releasing hormone. J Clin Invest. 2000;105:1187–8.
Zhu Y, Zhu JJ. Rapid arrival and integration of ascending sensory information in layer 1 nonpyramidal neurons and tuft dendrites of layer 5 pyramidal neurons of the neocortex. J Neurosci. 2004;24:1272–9.
Hartung J, Letzkus JJ. Inhibitory plasticity in layer 1 -dynamic gatekeeper of neocortical associations. Curr Opin Neurobiol. 2021;67:26–33.
Koob GF, Markou A, Weiss F, Schulteis G. Opponent process and drug dependence: neurobiological mechanisms. Semin Neurosci. 1993;5:351–8.
Chen C, Jiang Z, Fu X, Yu D, Huang H, Tasker JG. Astrocytes Amplify Neuronal Dendritic Volume Transmission Stimulated by Norepinephrine. Cell Rep. 2019;29:4349-.e4344.
Shukla R, Newton DF, Sumitomo A, Zare H, McCullumsmith R, Lewis DA, et al. Molecular characterization of depression trait and state. Mol Psychiatry. 2021;27:1083–94.
Kuang Y, Walt DR. Monitoring “promiscuous” drug effects on single cells of multiple cell types. Anal Biochem. 2005;345:320–5.
Baker A, Kalmbach B, Morishima M, Kim J, Juavinett A, Li N, et al. Specialized Subpopulations of Deep-Layer Pyramidal Neurons in the Neocortex: Bridging Cellular Properties to Functional Consequences. J Neurosci. 2018;38:5441–55.
Rajkowska G, Stockmeier CA. Astrocyte pathology in major depressive disorder: insights from human postmortem brain tissue. Curr Drug Targets. 2013;14:1225–36.
Anderson KM, Collins MA, Kong R, Fang K, Li J, He T, et al. Convergent molecular, cellular, and cortical neuroimaging signatures of major depressive disorder. Proceedings of the National Academy of Sciences. 2020;117:25138.
Arion D, Corradi JP, Tang S, Datta D, Boothe F, He A, et al. Distinctive transcriptome alterations of prefrontal pyramidal neurons in schizophrenia and schizoaffective disorder. Molecular Psychiatry. 2015;20:1397–405.
Cotter D, Mackay D, Landau S, Kerwin R, Everall I. Reduced glial cell density and neuronal size in the anterior cingulate cortex in major depressive disorder. Arch Gen Psychiatry. 2001;58:545–53.
Cotter D, Mackay D, Chana G, Beasley C, Landau S, Everall IP. Reduced Neuronal Size and Glial Cell Density in Area 9 of the Dorsolateral Prefrontal Cortex in Subjects with Major Depressive Disorder. Cerebral Cortex. 2002;12:386–94.
Anderson EM, Gomez D, Caccamise A, McPhail D, Hearing M. Chronic unpredictable stress promotes cell-specific plasticity in prefrontal cortex D1 and D2 pyramidal neurons. Neurobiol Stress. 2019;10:100152.
Gee S, Ellwood I, Patel T, Luongo F, Deisseroth K, Sohal VS. Synaptic activity unmasks dopamine D2 receptor modulation of a specific class of layer V pyramidal neurons in prefrontal cortex. J Neurosci. 2012;32:4959–71.
Alnafisah RS, Reigle J, Eladawi MA, O’Donovan SM, Funk AJ, Meller J, et al. Assessing the effects of antipsychotic medications on schizophrenia functional analysis: a postmortem proteome study. Neuropsychopharmacology 2022.
Armstrong RA. When to use the Bonferroni correction. Ophthalmic Physiol Opt. 2014;34:502–8.
Reddy V, Sherif M, Shukla R. Integrating single-cell transcriptomics and microcircuit computer modeling. Curr Opin Pharmacol. 2021;60:34–39.
MAS is supported by the National Institute of Mental Health predoctoral fellowship F31MH125541.
The authors declare no competing interests.
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Smail, M.A., Chandrasena, S.S., Zhang, X. et al. Differential vulnerability of anterior cingulate cortex cell types to diseases and drugs. Mol Psychiatry (2022). https://doi.org/10.1038/s41380-022-01657-w