SUMMARY Trisomy 21, or Down syndrome (DS), is the most common genetic cause of developmental delay and intellectual disability. To gain insight into the underlying molecular and cellular pathogenesis, we conducted a multi-region transcriptome analysis of DS and euploid control brains spanning from mid-fetal development to adulthood. We found genome-wide alterations in the expression of a large number of genes, many of which exhibited temporal and spatial specificity and were associated with distinct biological processes. In particular, we uncovered co-dysregulation of genes associated with oligodendrocyte differentiation and myelination that were validated via cross-species comparison to Ts65Dn trisomy mice. Furthermore, we show that hypomyelination present in Ts65Dn mice is in part due to cell-autonomous effects of trisomy on oligodendrocyte differentiation and results in slower neocortical action potential transmission. Together, these results identify defects in white matter development and function in DS and provide a transcriptional framework for further investigating DS neuropathogenesis.

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SummaryDopamine is critical for working memory. However, its effects throughout the large-scale primate cortex are poorly understood. Here we report that dopamine receptor density per neuron, measured by receptor autoradiography in the macaque monkey cortex, displays a macroscopic gradient along the cortical hierarchy. We developed a connectome- and biophysically-based model for distributed working memory that incorporates multiple neuron types and a dopamine gradient. The model captures an inverted U-shaped dependence of working memory on dopamine. The spatial distribution of mnemonic persistent activity matches that observed in over 90 experimental studies. We show that dopamine filters out irrelevant stimuli by enhancing inhibition of pyramidal cell dendrites. The level of cortical dopamine can also determine whether memory encoding is through persistent activity or an internal synaptic state. Taken together, our work represents a cross-level understanding that links molecules, cell types, recurrent circuit dynamics and a core cognitive function distributed across the cortex.

Based on quantitative cyto- and receptor architectonic analyses, we identified 35 prefrontal areas and introduced a novel subdivision of Walker’s areas 10, 9, 8B and 46. Statistical analysis of receptor densities revealed regional differences in lateral and ventrolateral prefrontal cortex. Since structural and functional organization of subdivisions encompassing areas 46 and 12 demonstrated significant differences in the interareal levels of α2 receptors. Furthermore, multivariate analysis included receptor fingerprints of previously identified 16 motor areas in the same macaque brains, and revealed five clusters encompassing frontal lobe areas. Based on the functional connectivity analysis, clustered areas showed similar connectivity distribution pattern. In particular, rostrally located areas (in clusters 1-2) were characterized by bigger fingerprints, i.e., higher receptor densities, and stronger regional interconnections. Whereas, more caudal areas (in clusters 3-5) had smaller fingerprints, but showed a widespread connectivity pattern with distant cortical regions. Taken together, present study provides a comprehensive insight into the molecular structure underlying the functional organization of the cortex and, thus, reconcile discrepancies between the structural and functional hierarchical organization of the primate frontal lobe. Finally, our data are publicly available via the EBRAINS and BALSA repositories for the entire scientific community.

RESULTS 104Transcriptomic diversity of hippocampal and entorhinal cells 105 To survey the transcriptomic diversity and functional specification of the mesial temporal 106 cortex, we used snRNA-seq to profile five subregions of the hippocampal-entorhinal system 107 6 collected from fresh frozen postmortem brains of clinically unremarkable human donors. These 108 specimens were selected from a larger pool of postmortem human brains based on the quality 109 of isolated nuclei and RNA. Taking into consideration dramatic cytoarchitectonic variations, 110 we microdissected the hippocampal formation (DG, CA2-4, CA1, and subiculum) and EC for 111 a total of five subregions (Fig. 1A). 112 Unbiased isolation of nuclei using our previously described protocol (Li et al., 2018; 113 Zhu et al., 2018) followed by snRNA barcoding, cDNA sequencing and quality filtering yielded 114 108,315 high-quality single-nucleus profiles from all five subregions ( Fig. 1A, S1A-D). 115 Analysis of the expression of genes known to be enriched in major cell subpopulations 116 suggested these included 44,697 neurons, of which 35,768 (80.02%) were glutamatergic 117 excitatory neurons (expressing the gene encoding the vesicular glutamate transporter SLC17A7) 118 and 8,929 (19.98%) were GABAergic inhibitory neurons (expressing the gene encoding the 119 GABA synthesis enzyme GAD1), reflecting the expected 80:20 ratio of these populations. In 120 addition, we identified 63,618 (58.73% of the total population) non-neuronal cells. 121 We next analyzed the transcriptomes of those nuclei on the Uniform Manifold 122 Approximation and Projection (UMAP) layout representing their similarities at cellular 123 granularity ( Fig. 1B-D). Iterative clustering defined 69 transcriptomically distinct cell clusters 124 representing presumptive cell types across all individuals (donors). These transcriptomically 125 diverse subpopulations were organized into a dendrogramatic taxonomy reflecting their gene 126 expression patterns and were subsequently assigned identities commensurate with predicted cell 127 types. This allowed us to identify 26 subtypes of excitatory neurons (Fig. 1E and S2A-B), 23 128 inhibitory neuron subtypes ( Fig. 1E and S2C-D), and 20 non-neuronal cell types and subtypes 129 ( Fig. 1E and S2E-F). Similar single nucleus approaches applied to human neocortical samples 130 7 yielded comparable numbers and distributions of cell populations in medial temporal gyrus 131 (MTG) (Hodge et al., 2019)and dorso-lateral prefrontal cortex (dlPFC) (Li et al., 2018)(Fig. 132 S1E-F). 133Within excitatory neuron subtypes, we found marked transcriptional diversity that 134 reflects differences in the cytoarchitectonic organization among the subregions of the HIP (DG, 135 CA2-4, CA1, and subiculum) and EC (Fig. 1E). For example, in addition to ADCYAP1-136 expressing mossy cells in DG, we found three distinct subclusters of PROX1-expressing granule 137 cells. We also identified excitatory neurons in CA1 and CA2-4 that could be deconstructe...