Identification of let-7f and miR-338 as plasma-based biomarkers for sporadic amyotrophic lateral sclerosis using meta-analysis and empirical validation

Abstract

Amyotrophic lateral sclerosis (ALS) is a lethal neurodegenerative disease that in most cases occurs sporadic (sALS). The disease is not curable, and its pathogenesis mechanisms are not well understood yet. Given the intricacy of underlying molecular interactions and heterogeneity of ALS, the discovery of molecules contributing to disease onset and progression will open a new avenue for advancement in early diagnosis and therapeutic intervention. Here we conducted a meta-analysis of 12 circulating miRNA profiling studies using the robust rank aggregation (RRA) method, followed by enrichment analysis and experimental verification. We identified miR-451a and let-7f-5p as meta-signature miRNAs whose targets are involved in critical pathogenic pathways underlying ALS, including ‘FoxO signaling pathway’, ‘MAPK signaling pathway’, and ‘apoptosis’. A systematic review of 7 circulating gene profiling studies elucidated that 241 genes up-regulated in sALS circulation with concomitant being targets of the meta-signature miRNAs. Protein–protein interaction (PPI) network analysis of the candidate targets using MCODE algorithm revealed the main subcluster is involved in multiple cascades eventually leads apoptosis, including ‘positive regulation of neuron apoptosis. Besides, we validated the meta-analysis results using RT-qPCR. Indeed, relative expression analysis verified let-7f-5p and miR-338-3p as significantly down-regulated and up-regulated biomarkers in the plasma of sALS patients, respectively. Receiver operating characteristic (ROC) analysis also highlighted the let-7f-5p and miR-338-3p potential as robustness plasma biomarkers for diagnosis and potential therapeutic targets of sALS disease.

Identification of potentially functional modules and diagnostic genes related to amyotrophic lateral sclerosis based on the WGCNA and LASSO algorithms

“…The gene expression-based studies have improved our understanding about the genetic perturbation associated with ALS, nevertheless the findings are strongly affected by the disease heterogeneity and sample-specific variation, making the result inconsistent across independent studies. One solution to address the problem of heterogeneity involves meta-analysis of multiple independent studies that increase the sample size and statistical power 27 . Another approach involves the study of the interaction among groups of genes, i.e.…”

A Machine Learning Approach for Highlighting microRNAs as Biomarkers Linked to Amyotrophic Lateral Sclerosis Diagnosis and Progression

“…The latter is a biomarker present in the CSF and consequently in the blood; it is negatively associated with patient survival and is considered a clinically validated prognostic biomarker for ALS [83]. Lastly, the expression of miRNA-338-3p was found to be upregulated in several studies, and in different sample types from sALS patients, such as blood leukocytes, CSF, serum, and the spinal cord, thus supporting the hypothesis that it could represent a very interesting candidate diagnostic biomarker [71,84,85]. Other studies have shown that its expression is reduced in the leukocytes of ALS patients and that its decreased levels are correlated with shorter survival and a more aggressive disease course [73,86].…”

“…Elevated levels have been associated with disease progression and survival [71,84,85] ↓ miR-338-3p Blood leukocytes Microarray technology Decreased levels correlated with shorter survival and a more aggressive disease course [73,86] As mentioned above, this specific research field is still evolving; therefore, further validation and larger-scale studies are necessary to identify robust miRNA biomarkers useful for ALS diagnosis, prognosis, and monitoring of disease progression to establish their effective clinical utility.…”

Dysregulated miRNAs as Biomarkers and Therapeutical Targets in Neurodegenerative Diseases

“…In ALS, this miRNA was found differentially expressed in blood, CFS, serum, and spinal cord, and its use as an effective early biomarker has been considered [ 222 , 251 , 252 , 254 , 255 ] ( Table 3 ). From a functional point of view, miR-338 modulates the expression of COXIV and ATP synthase [ 281 ], as well as the ALS-related genes ARHGEF28 (involved in the aggregation of low molecular weight neurofilaments) and VAPB (involved in protein misfolding and ER-associated aggregates) [ 282 , 283 ]. Moreover, ectopic expression of miR-338 mediated by FoxO3a may play a critical role in reducing cell survival by directly suppressing the expression of NRP1 [ 284 ] ( Table 3 , Figure 2 ).…”