New Approach for Untangling the Role of Uncommon Calcium-Binding Proteins in the Central Nervous System

Abstract

Although Ca²⁺ ion plays an essential role in cellular physiology, calcium-binding proteins (CaBPs) were long used for mainly as immunohistochemical markers of specific cell types in different regions of the central nervous system. They are a heterogeneous and wide-ranging group of proteins. Their function was studied intensively in the last two decades and a tremendous amount of information was gathered about them. Girard et al. compiled a comprehensive list of the gene-expression profiles of the entire EF-hand gene superfamily in the murine brain. We selected from this database those CaBPs which are related to information processing and/or neuronal signalling, have a Ca²⁺-buffer activity, Ca²⁺-sensor activity, modulator of Ca²⁺-channel activity, or a yet unknown function. In this way we created a gene function-based selection of the CaBPs. We cross-referenced these findings with publicly available, high-quality RNA-sequencing and in situ hybridization databases (Human Protein Atlas (HPA), Brain RNA-seq database and Allen Brain Atlas integrated into the HPA) and created gene expression heat maps of the regional and cell type-specific expression levels of the selected CaBPs. This represents a useful tool to predict and investigate different expression patterns and functions of the less-known CaBPs of the central nervous system.

Keywords: calcium-binding proteins; central nervous system; human protein atlas; in situ hybridisation database; transcriptome database.

Figure 1

The main types of calcium-binding proteins (CaBPs) [9].

Figure 2

The helix-loop-helix EF-hand Ca²⁺-binding motif based on Zhou et al., 2009 (Wikimedia commons licence). The conformation of the helixes resembles a spread thumb and forefinger of a human hand. In the representative 3D model of a typical canonical EF-hand motif from calmodulin, the Ca²⁺ ion is integrated within the loop, which includes seven oxygen atoms from the sidechain carboxyl or hydroxyl groups (loop sequence positions 1, 3, 5, 12), a main chain carbonyl group (position 7), and a bridged water (via position 9) [16]. Figure copyright permission obtained.

Figure 3

Regional expression levels of the selected CaBP genes. Mouse gene data from Human Protein Atlas (HPA) transcriptomics analysis is shown as NX values in different brain regions. Numerical data is presented in Supplementary Materials Table S1.

Figure 4

Transcript expression levels in 10 brain regions based on in situ hybridisation. RNA Allen mouse brain region gene data of the selected CaBPs from in situ hybridization (ISH) analysis is represented by the expression energy value. Numerical data are presented in Supplementary Materials Table S2.

Figure 5

Cell-type specific gene expression levels of selected CaBPs from the Brain RNA-seq database. Expression level estimation is reported as fragments per kilobase of transcript sequence per million mapped fragments (FPKM). Astro: astrocytes, OPC: oligodendrocyte progenitor cells, NFO: newly formed oligodendrocytes, Myelinating: myelinating oligodendrocyte, MGL: microglia/macrophage, Endo: endothelial. Numerical data are presented in Supplementary Materials Table S3.

Figure 6

Mouse regional gene data of CaBPs with lower expression in the CNS by Girard database. Transcriptomics analysis from HPA showing normalized expression (NX) values of genes in different brain regions. Numerical data are presented in Supplementary Materials Table S4.

Figure 7

Transcript expression levels of CaBPs with lower expression in the CNS by Girard database in 10 brain regions, based on in situ hybridisation. RNA Allen mouse brain region gene data is represented by the expression energy value. Note the different color scale from Figure 4. Numerical data are presented in Supplementary Materials Table S5.

Figure 8

Cell-type specific gene expression levels of CaBPs with lower expression in the CNS by Girard database. Expression level estimation from Brain RNA-seq database is reported as fragments per kilobase of transcript sequence per million mapped fragments (FPKM). Astro: astrocytes, OPC: oligodendrocyte progenitor cells, NFO: newly formed oligodendrocytes, Myelinating: myelinating oligodendrocyte, MGL: microglia/macrophage, Endo: endothelial. Numerical data are presented in Supplementary Materials Table S6.