Functional Genomics of Axons and Synapses to Understand Neurodegenerative Diseases

Abstract

Functional genomics studies through transcriptomics, translatomics and proteomics have become increasingly important tools to understand the molecular basis of biological systems in the last decade. In most cases, when these approaches are applied to the nervous system, they are centered in cell bodies or somatodendritic compartments, as these are easier to isolate and, at least in vitro, contain most of the mRNA and proteins present in all neuronal compartments. However, key functional processes and many neuronal disorders are initiated by changes occurring far away from cell bodies, particularly in axons (axopathologies) and synapses (synaptopathies). Both neuronal compartments contain specific RNAs and proteins, which are known to vary depending on their anatomical distribution, developmental stage and function, and thus form the complex network of molecular pathways required for neuron connectivity. Modifications in these components due to metabolic, environmental, and/or genetic issues could trigger or exacerbate a neuronal disease. For this reason, detailed profiling and functional understanding of the precise changes in these compartments may thus yield new insights into the still intractable molecular basis of most neuronal disorders. In the case of synaptic dysfunctions or synaptopathies, they contribute to dozens of diseases in the human brain including neurodevelopmental (i.e., autism, Down syndrome, and epilepsy) as well as neurodegenerative disorders (i.e., Alzheimer's and Parkinson's diseases). Histological, biochemical, cellular, and general molecular biology techniques have been key in understanding these pathologies. Now, the growing number of omics approaches can add significant extra information at a high and wide resolution level and, used effectively, can lead to novel and insightful interpretations of the biological processes at play. This review describes current approaches that use transcriptomics, translatomics and proteomic related methods to analyze the axon and presynaptic elements, focusing on the relationship that axon and synapses have with neurodegenerative diseases.

Keywords: axon; axopathologies; neurodegenerative diseases; presynaptic compartment; proteomics; synaptopathies; transcriptomics; translatomics.

FIGURE 1

Schemes of axoplasm isolation protocols compatible with omic approaches including (A) Campenot chambers, (B) Boyden modified chambers, (C) microfluidic device of two channels, (D) organoid microfluidics, (E) laser capture microdissection, and (F) in vivo axoplasm isolation systems (above the Koenig’s microdissection and below Fainzilber’s osmotic axoplasm isolation).

FIGURE 2

Schemes of synapse isolation protocols compatible with omic approaches including (A) synaptosome and synaptoneurosome, (B) neuropil, (C) axon TRAP, (D) FACS, (E) puromycin proximity ligation assay, (F) spatial transcriptomic example with ExSEQ protocol, (G) APEX and BioID protocols. SV, synaptic vesicle; HA, hemagglutinin; RGC, retinal ganglion cell; DEG, differentially expressed genes; SSC, side-scatter; FSC, forward scatter; RCA, rolling circle amplification; FISSEQ, fluorescent in situ sequencing of RNA.