Burden of Rare Variants in ALS and Axonal Hereditary Neuropathy Genes Influence Survival in ALS: Insights from a Next Generation Sequencing Study of an Italian ALS Cohort

Abstract

Although the genetic architecture of amyotrophic lateral sclerosis (ALS) is incompletely understood, recent findings suggest a complex model of inheritance in ALS, which is consistent with a multistep pathogenetic process. Therefore, the aim of our work is to further explore the architecture of ALS using targeted next generation sequencing (NGS) analysis, enriched in motor neuron diseases (MND)-associated genes which are also implicated in axonal hereditary motor neuropathy (HMN), in order to investigate if disease expression, including the progression rate, could be influenced by the combination of multiple rare gene variants. We analyzed 29 genes in an Italian cohort of 83 patients with both familial and sporadic ALS. Overall, we detected 43 rare variants in 17 different genes and found that 43.4% of the ALS patients harbored a variant in at least one of the investigated genes. Of note, 27.9% of the variants were identified in other MND- and HMN-associated genes. Moreover, multiple gene variants were identified in 17% of the patients. The burden of rare variants is associated with reduced survival and with the time to reach King stage 4, i.e., the time to reach the need for percutaneous endoscopic gastrostomy (PEG) positioning or non-invasive mechanical ventilation (NIMV) initiation, independently of known negative prognostic factors. Our data contribute to a better understanding of the molecular basis of ALS supporting the hypothesis that rare variant burden could play a role in the multistep model of disease and could exert a negative prognostic effect. Moreover, we further extend the genetic landscape of ALS to other MND-associated genes traditionally implicated in degenerative diseases of peripheral axons, such as HMN and CMT2.

A common theme for axonopathies? The dependency cycle of local axon homeostasis

“…• Multiple sclerosis; dying back pathology (Cotsapas, Mitrovic, & Hafler, 2018;Dutta & Trapp, 2011;van den Berg, Hoogenraad, & Hintzen, 2017) • Carcinoma-associated paraneoplastic peripheral neuropathy; proximal-distal pathology (Dalmau, 1999) hereditary spastic paraplegias (HSPs), which primarily affect upper motorneurons, link to a disproportionately high number of genes associated with the formation or function of endomembrane organelles, preferentially the endoplasmic reticulum (Table S1B Fridman & Murphy, 2014;Gentile et al, 2019;Katz et al, 2020;Liu, Duan, Zhang, Sun, & Fan, 2020;Ma, Chen, Raskind, & Bird, 2020;Scarlino et al, 2020;Tian et al, 2020).…”

“…Third, many genes linked to one certain disease have further associations with other neurological disorders on OMIM® (Online Mendelian Inheritance in Man; last column in Table S1), and there is an increasing number of reported genetic associations that reach across different classes of axonopathy‐related disorders including CMT, distal hereditary motor neuropathy (dHMN), HSP, amyotrophic lateral sclerosis (ALS) and hereditary cerebellar ataxias (HCA); for example, Bis‐Brewer, Danzi, Wuchty, & Züchner, 2019; d'Ydewalle et al, 2011; Fridman & Murphy, 2014; Gentile et al, 2019; Katz et al, 2020; Liu, Duan, Zhang, Sun, & Fan, 2020; Ma, Chen, Raskind, & Bird, 2020; Scarlino et al, 2020; Tian et al, 2020).…”

High-Throughput Genetic Testing in ALS: The Challenging Path of Variant Classification Considering the ACMG Guidelines

“…It suggests that the pathological process underlying the disease could exist from birth, but the accumulation of variants, toxic effects of proteins, and environmental factors are needed to trigger the disease [ 169 , 170 , 171 ]. Variants in some genes, such as SOD1 and C9orf72 , could have a more severe effect, while multiple variants in other genes with a lower impact are needed to exceed the threshold [ 172 , 173 , 174 , 175 , 176 ].…”

SOD-1 Variants in Amyotrophic Lateral Sclerosis: Systematic Re-Evaluation According to ACMG-AMP Guidelines

“…Although a large number of genes have been related to ALS, other variants are to be discovered, which could play adjunct roles in increasing risk or susceptibility to the disease. Specific mutations not identifiable by GWAS or massive sequencing methods, such as repeated expansions [ 67 ] or variants in noncoding regions, could belong to this category [ 68 , 69 ].…”