Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility

Jerry C Wang,Gokul Ramaswami,Daniel H Geschwind

doi:10.1038/s41598-021-85061-4

Abstract

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease defined by motor neuron (MN) loss. Multiple genetic risk factors have been identified, implicating RNA and protein metabolism and intracellular transport, among other biological mechanisms. To achieve a systems-level understanding of the mechanisms governing ALS pathophysiology, we built gene co-expression networks using RNA-sequencing data from control human spinal cord samples, identifying 13 gene co-expression modules, each of which represents a distinct biological process or cell type. Analysis of four RNA-seq datasets from a range of ALS disease-associated contexts reveal dysregulation in numerous modules related to ribosomal function, wound response, and leukocyte activation, implicating astrocytes, oligodendrocytes, endothelia, and microglia in ALS pathophysiology. To identify potentially causal processes, we partitioned heritability across the genome, finding that ALS common genetic risk is enriched within two specific modules, SC.M4, representing genes related to RNA processing and gene regulation, and SC.M2, representing genes related to intracellular transport and autophagy and enriched in oligodendrocyte markers. Top hub genes of this latter module include ALS-implicated risk genes such as KPNA3, TMED2, and NCOA4, the latter of which regulates ferritin autophagy, implicating this process in ALS pathophysiology. These unbiased, genome-wide analyses confirm the utility of a systems approach to understanding the causes and drivers of ALS.

Highlights

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease defined by motor neuron (MN) loss
To help elucidate the biological mechanisms underlying ALS pathophysiology in an unbiased genome-wide manner, we generated co-expression networks using RNA-sequencing of control human cervical spinal cord samples from the Genotype-Tissue Expression (GTEx) Consortium
We find that ALS genetic risk factors are enriched in SC.M4, a co-expression module representing genes involved in RNA processing and epigenetics and SC.M2, which is enriched in oligodendrocyte markers and genes involved in intracellular transport, protein modification, and cellular catabolic processes

Summary

Introduction

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease defined by motor neuron (MN) loss. To investigate gene expression signatures associated with ALS in the spinal cord, we generated gene co-expression networks using RNA-sequencing of 62 neurotypical human cervical spinal cord samples from the GTEx consortium[18] We characterized these co-expression modules through gene ontology (GO) enrichment analysis, which reveals that the modules represent a diverse range of biological processes. We find enrichment of ALS common genetic risk variants in SC.M2, which represents genes involved in intracellular transport, protein modification, and cellular catabolic processes We extend these results by demonstrating the dysregulation of these modules in data from multiple published human ALS patient and animal model tissues[12,13,22,23]. The set of genes underlying these modules provides a rich set of targets for exploring new mechanisms for therapeutic development

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Conclusion