Abstract
Background
Adult hippocampal neurogenesis (AHN) is necessary for rodent memory and emotional resilience, which are disrupted with psychiatric illness. If AHN occurs in human remains debated, and knowledge on the transcriptomic characteristics of hippocampus cells is limited. Cell development and function is regulated by chromatin-accessible regions (CARs) controlling gene expression (GEX) through cis- and trans- regulatory networks and transcription factors (TF). Co-profiling CARs and GEX may help unravel molecular signatures of human hippocampus cell types including the neurogenic progeny. MDD memory and emotional deficits present with reduced hippocampus volume, cell number and neuroplasticity, possibly explained by reduced AHN, survival, or neuropil, which is unknown.
Aims & Objectives
We aimed to understand if adult neurogenesis occurs in the adult human hippocampus, and if the neurogenic trajectory is disrupted in MDD. We aimed to determine hippocampus cell type-specific and subfield-specific molecular alterations in MDD.
Method
We performed single-nucleus multiome sequencing, spatial transcriptomic and bulk shotgun proteomic in human hippocampus from neurotypical and MDD subjects. We queried neurogenic cells using machine learning, RNA Velocity and Palantir pseudotime trajectory inference.
Results
We simultaneously generated snRNA-seq and snATAC-seq data on over 600,000 nuclei from deeply clinically phenotyped sudden death subjects with high-quality brain tissue. Clusters included oligodendrocyte progenitor cells (OPC), oligodendrocytes (Olig), endothelial cells (Endo), pericytes (Peri), vascular leptomeningeal cells (VLMC), microglia (Micro), macrophages (Macro), T-cells (Tcell), choroid plexus cells (Ch.Pl), subventricular zone (SVZ) ependymal cells (Epe), Cajal Retzius cells (CR), three astrocyte (Astro1-3), nine inhibitory neuron (InN.SST, InN.LHX6, InN.PVALB, InN.VIP, InN.LAMP5, InN.SLC17A8, InN.PENK, InN.TUBB3, InN.PROX1), six non-granule excitatory neuron (ExN1-6), and two GN (GN1, GN2) clusters. Machine learning detected neural progenitor subtypes and immature granule neurons (GN).
We performed unsupervised clustering of Visium spots (55x55 μm in size) which provided a more detailed spot-type annotation than manual annotation of hippocampal subfields and delivered 13 clusters that expressed genes concordant with expected cell types based on spot location in the respective subfields. Unsupervised spot clusters included-: 2 hilus clusters (hilus1, hilus2), CA3 stratum pyramidales (ca3), stratum oriens-stratum lucidum (so-slu), so-slu of the CA3 (ca3-so-slu), stratum radiatum (sr), stratum oriens-stratum lacunosum (so-sla), stratum moleculare (ml), stratum granulosum (gcl), SGZ-polymorphic layer (sgz-pl), stratum moleculare (sgz-ml).
MDD-associated cell-type specific molecular alterations detected using GSEA, TF footprinting analysis, and WGCNA, included hyperexcitability of a GN subtype, reduced developmental pathways and synaptic function, activated inflammation and apoptosis.
Discussion & Conclusions
Overall, this comprehensive single-nuclei multi-omic and spatial transcriptomic profiling of brain tissue supports the presence of a neurogenic niche and identifies potential molecular underpinnings of hippocampal atrophy in MDD. Findings support sustained AHN and prolonged GN immaturity in human, with cell-type specific molecular dysregulations in MDD, pointing to potential treatment targets for drugs aimed at restoring hippocampal homeostasis.