Molecular fingerprinting of principal neurons in the rodent hippocampus: A neuroinformatics approach

Abstract

Neurons are often classified by their morphological and molecular properties. The online knowledge base Hippocampome.org primarily defines neuron types from the rodent hippocampal formation based on their main neurotransmitter (glutamate or GABA) and the spatial distributions of their axons and dendrites. For each neuron type, this open-access resource reports any and all published information regarding the presence or absence of known molecular markers, including calcium-binding proteins, neuropeptides, receptors, channels, transcription factors, and other molecules of biomedical relevance. The resulting chemical profile is relatively sparse: even for the best studied neuron types, the expression or lack thereof of fewer than 70 molecules has been firmly established to date. The mouse genome-wide in situ hybridization mapping of the Allen Brain Atlas provides a wealth of data that, when appropriately analyzed, can substantially augment the molecular marker knowledge in Hippocampome.org. Here we focus on the principal cell layers of dentate gyrus (DG), CA3, CA2, and CA1, which together contain approximately 90% of hippocampal neurons. These four anatomical parcels are densely packed with somata of mostly excitatory projection neurons. Thus, gene expression data for those layers can be justifiably linked to the respective principal neuron types: granule cells in DG and pyramidal cells in CA3, CA2, and CA1. In order to enable consistent interpretation across genes and regions, we screened the whole-genome dataset against known molecular markers of those neuron types. The resulting threshold values allow over 6000 very-high confidence (>99.5%) expressed/not-expressed assignments, expanding the biochemical information content of Hippocampome.org more than five-fold. Many of these newly identified molecular markers are potential pharmacological targets for major neurological and psychiatric conditions. Furthermore, our approach yields reasonable expression/non-expression estimates for every single gene in each of these four neuron types with >90% average confidence, providing a considerably complete genetic characterization of hippocampal principal neurons.

Molecular Expression Profiles of Morphologically Defined Hippocampal Neuron Types: Empirical Evidence and Relational Inferences

“…From this literature, 237 papers showed data indicating expression or lack of expression via immunohistochemistry, in situ hybridization, or single cell RT-PCR in neurons matching the descriptions of Hippocampome.org types based on neurite location and putative neurotransmitter. In addition, we used data from the Allen Gene Expression Atlas as the basis for assigning the presence or absence of certain molecular markers in the principal neuron types DG Granule, CA1 Pyramidal, CA2 Pyramidal, and CA3 Pyramidal (Hamilton et al, 2017). All of these data are considered neuron type-specific evidence and lead to interpretations of positive or negative expression in Hippocampome.org.…”

Enzymatic dissociation induces transcriptional and proteotype bias in brain cell populations

“…Quality check for the scRNA-seq is provided in Figure S2. Clustering using specific gene-set enrichment for cell-type identification (Hamilton, White, Rees, Wheeler, & Ascoli, 2017; Saunders et al, 2018) (Figure 1b) revealed quantitative and qualitative differences in cellular subpopulations between ED and MD. It appears evident that in tissue processed at 37°C there is a higher extent of cell death among sensitive populations, e.g.…”

Operations Research Methods for Estimating the Population Size of Neuron Types

“…We defined dentate gyrus cell types based on the knowledge base Hippocampome.org, an online repository containing morphological, molecular, and physiological information on neurons of the rodent hippocampal formation (Wheeler et al 2015). Hippocampome.org classifies neurons primarily by neurotransmitter released and the presence of axons and dendrites in the distinct sub-regions and layers of the rodent hippocampus ( Figure 1), and also includes molecular biomarker (Hamilton et al 2017) and electrophysiological properties (e.g. Lubke et al 1998) for each type.…”

“…Therefore, the system was both underdetermined and inconsistent. 16 Buckmaster and Jongen-Relo 1999, Table 1 stereology 46, 734 = X 2 + X 4 + X 5 + X 6 + X 12 + X 14 + X 16 Buckmaster and Jongen-Relo 1999, Table 1 stereology 35, 900 = X 6 + X 7 + X 8 + X 9 + X 10 + X 11 + X 12 + X 13 +…”