About
Here, we have generated a combined single-nucleus RNA-sequencing (snRNA-seq) and single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) NHP brain atlas comprising around two million nuclei from eight brain regions of 23 cynomolgus monkeys (Macaca fascicularis), covering the entire adult lifespan. By integrative analysis of gene expression and chromatin accessibility dynamics, we have investigated the general and region-specific changes in cell type composition, cell state and niche multicellular interactions induced by aging, and the associations of these changes with human genetic risk variants linked to cognition, neurodegeneration, and others. We also highlight key differences between healthy brain aging and AD and uncover potential mechanisms exerting protective effects. Our NHP aging brain cell atlas (NHPABC) and its future expansions will assist in the development of therapeutic strategies aimed at promoting brain health in late life in primates including humans.
Explanation Notes
In the telencephalon, PFC Ex neurons (SLC17A7+) could be further subdivided into layer-specific subtypes including L2/3-IT (intratelencephalic; PDZD2+), L4/5-IT (RORB+), L5/6-IT-Car3 (claustrum-like; RGS12+), L5-IT (TSHZ2+), L5-ET (extratelencephalic; ADRA1A+), L5/6-NP (near-projecting; HTR2C+), L6-CT (corticothalamic; SEMA3E+) and L6-IT (ITGA8+)1,2. Hippocampal non-DG Ex neurons clustered according to their subanatomical location including the CA1/SUB (cornu ammonis subfields 1 and subiculum; PID1+), CA2/4 (cornu ammonis subfields 2 , 3 and 4; NRIP3+), and entorhinal cortex (EC) that was subdivided into upper layer (L2, CUX2+ RXFP1+; L3-5, TLL1+ PCP4+) and deep layer (L6, TLE4+ NXPH2+) neurons1,4. Additionally, the CA1/SUB subpopulations could be further subdivided according to the superficial-deep axis (CA1/SUB: superficial CCBE1+ and deep NDST4+). Among the Inh neurons, we identified subpopulations derived from the MGE (LHX6+), CGE (ADARB2+), and lateral ganglionic eminence (LGE; FOXP1+)5. MGE-derived Inh neurons were distributed in all telencephalic regions, CGE-derived Inh neurons were mainly in the PFC and hippocampal formation, and LGE-derived Inh neurons in the striatum. MGE-derived Inh neurons could be further subdivided into PVALB+ and SST+ in the PFC and hippocampal formation, as well as SST+, TAC3+ and CRABP1+ in the striatum. We also noticed a small cluster of MGE-derived UNC5B+ chandelier cells in the PFC. CGE-derived Inh neurons contained LAMP5+ and CNR1+. LGE-derived Inh neurons were composed of SPNs (MEIS2+) including subtypes expressing the D1-type (SPN-D1; TAC1+) or D2-type (SPN-D2; PENK+) dopamine receptor, and eccentric SPNs (RBM20+). SPN-D1 contained a cluster belonging to neurochemically unique domains in the accumbens and putamen (SPN-D1-NUDAP; RXFP1+). In addition, we identified granule cells from the islands of Calleja (ICj) in the ventral striatum (ICj Inh; CPNE4+)6.
In the thalamus, we observed TPH1+cells,and a cluster of Ex neurons (SLC17A6+) comprising RYR3+ and CBLN2+ subtypes. RYR3+ neurons correspond to cortex-projecting neurons distributed in the ventral lateral and ventral anterior thalamus7, while CBLN2 is highly expressed in motor-related nuclei8. We also noticed GAD2+ SST+ Inh neurons characteristic of the thalamic reticular nucleus9, and GAD2+ OTX2+ midbrain-derived Inh neurons in the thalamus,midbrain and pons and midbrain10. Likewise, there were A9 (SOX6+) and A10 (CALB1+) subtype dopaminergic (DA) neurons (TH+) in the midbrain11, and in the pons and medulla Ex neurons including upper rhombic lip and lower rhombic lip neuron10. In the cerebellum, besides cerebellar granule cells(GCs), we observed Purkinje cells (PPP1R17+), molecular layer interneuron (MLI1/2;LYPD6+; CALB1+), Purkinje layer Inh (PLI; KLHL1+) neurons and unipolar brush cells (UBC; EOMES+)12.
Notably, the mixed neuron were appeared in the non-telencephalic regions. To explore this population further, we combined those cells together and reclustered, obtaining a total of 18 clusters. These include: SLC24A2+ glutamatergiic neurons; SLC32A1+ GABAergic neurons; CALCR+ (calcitonin receptor) neurons; TAC1+ (encodes preprotachykinin-1) neurons; SST+ (encodes somatostatin) neurons; PENK+ (encodes proenkephalin) neurons; CRHBP+ (encodes corticotropin-releasing hormone-binding protein) neurons; CARTPT+ (encodes cocaine- and amphetamine-regulated transcript prepropeptide) neurons; TRH+ (encodes thyrotropin-releasing hormon) neurons; TRHR+ (encodes thyrotropin-releasing hormone receptor); CRH+ (encodes corticotropin-releasing hormone); POMC+ (encodes proopiomelanocortin) population; histaminergic neurons (HDC+) that are located in ventral posterior hypothalamus; TPH2+ (encodes tryptophan hydroxylase 2) neuron; PMCH+ (encodes pro-melanin concentrating hormone) neuron; AVP+ (encodes arginine vasopressin) neurons; HCRT+ (encodes hypocretin neuropeptide precursor) neurons; OXT+ (encodes oxytocin) neurons.
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6. Gokce, O., Stanley, G.M., Treutlein, B., Neff, N.F., Camp, J.G., Malenka, R.C., Rothwell, P.E., Fuccillo, M.V., Sudhof, T.C., and Quake, S.R. (2016). Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq. Cell Rep 16, 1126-1137. 10.1016/j.celrep.2016.06.059.
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8. Seigneur, E., Wang, J., Dai, J., Polepalli, J., and Sudhof, T.C. (2021). Cerebellin-2 regulates a serotonergic dorsal raphe circuit that controls compulsive behaviors. Mol Psychiatry 26, 7509-7521. 10.1038/s41380-021-01187-x.
9. Tran, M.N., Maynard, K.R., Spangler, A., Huuki, L.A., Montgomery, K.D., Sadashivaiah, V., Tippani, M., Barry, B.K., Hancock, D.B., Hicks, S.C., et al. (2021). Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain. Neuron 109, 3088-3103 e3085. 10.1016/j.neuron.2021.09.001.
10. Siletti, K., Hodge, R., Mossi Albiach, A., Lee, K.W., Ding, S.L., Hu, L., Lonnerberg, P., Bakken, T., Casper, T., Clark, M., et al. (2023). Transcriptomic diversity of cell types across the adult human brain. Science 382, eadd7046. 10.1126/science.add7046.
11. Kamath, T., Abdulraouf, A., Burris, S.J., Langlieb, J., Gazestani, V., Nadaf, N.M., Balderrama, K., Vanderburg, C., and Macosko, E.Z. (2022). Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson's disease. Nat Neurosci 25, 588-595. 10.1038/s41593-022-01061-1.
12. Kozareva, V., Martin, C., Osorno, T., Rudolph, S., Guo, C., Vanderburg, C., Nadaf, N., Regev, A., Regehr, W.G., and Macosko, E. (2021). A transcriptomic atlas of mouse cerebellar cortex comprehensively defines cell types. Nature 598, 214-219. 10.1038/s41586-021-03220-z.
Extended Figure
(A-D) Left: Schematic representation of major anatomical regions in a hemi-brain section (section H7) from a 6-year-old macaque monkey, alongside spatial visualization of astrocyte (Ast1-3), microglia (Mic1-3, Macrophage), oligodendrocyte (ODC1-2) and oligodendrocyte progenitor cells (OPC1-2, COP) subtypes, mapped to the same anatomical section using Stereo-seq data from Chen et al. Right: Bubble plots showing the expression levels of representative marker genes for each cell subtype. The colour scale represents scaled average gene expression, while dot size indicates the percentage of cells expressing a given marker within the corresponding cell population.
Accessions
CNP0004459
Contact
laiyiwei@genomics.cn; zhangxiao6@genomics.cn; laiguangyao@genomics.cn