Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology

Abstract

Amyotrophic Lateral Sclerosis (ALS) causes motor neuron degeneration, with 97% of cases exhibiting TDP-43 proteinopathy. Elucidating pathomechanisms has been hampered by disease heterogeneity and difficulties accessing motor neurons. Human induced pluripotent stem cell-derived motor neurons (iPSMNs) offer a solution; however, studies have typically been limited to underpowered cohorts. Here, we present a comprehensive compendium of 429 iPSMNs from 15 datasets, and 271 post-mortem spinal cord samples. Using reproducible bioinformatic workflows, we identify robust upregulation of p53 signalling in ALS in both iPSMNs and post-mortem spinal cord. p53 activation is greatest with C9orf72 repeat expansions but is weakest with SOD1 and FUS mutations. TDP-43 depletion potentiates p53 activation in both post-mortem neuronal nuclei and cell culture, thereby functionally linking p53 activation with TDP-43 depletion. ALS iPSMNs and post-mortem tissue display enrichment of splicing alterations, somatic mutations, and gene fusions, possibly contributing to the DNA damage response.

Transcriptome-based screening in TARDBP/TDP-43 knock-in motor neurons identifies the NEDD8-activating enzyme inhibitor MLN4924

“…Sulpiride is a neuroleptic and all hit compounds of a previous large-scale chemical screen in TDP-43 A315T worms and TDP-43 G348C zebrafish were neuroleptics. 111 Additionally, while there is evidence of increased MAP kinase signaling in ALS patients as well as in animal and iPSC models, 57,112–115 two compounds identified here were MAP kinase inhibitors (XMD-892, XMD-885). Finally, XMD-892 116 and other compounds (tacedinaline, 117–119 MLN4924, 120 piperlongumine, 121,122 prunetin 123 ) have also been under investigation for their antioxidant, anti-inflammatory, anti-ischemic, neuroprotective, and/or antitumour properties.…”

Meta-analysis of differential gene expression in lower motor neurons isolated by laser capture microdissection from post-mortem ALS spinal cords

“…Few DEGs from this LCM meta-analysis were differentially expressed in prior studies of iPSC-MNs derived from ALS and CTL subjects ( Workman et al, 2023 ; Ziff et al, 2023 ). There was no significant overlap between DEG sets ( Figures 7C,D ) and less than two-thirds of DEGs identified by LCM were altered in the same direction in iPSC-MNs ( Figures 7C,D ); however, significant LCM/iPSC correspondence could be demonstrated using GSEA ( Figures 7K,L ).…”

“…There was no significant overlap between iPSC-MN and LCM DEGs based on the Wang semantic similarity of GO BP terms ( Figures 7I,J ) ( Wang et al, 2007 ), although some gene pairs had functional similarity based on the Wang measure ( Figures 7M,N ). These analyses were repeated based upon a limited set of DEGs (9 ALS-increased, 5 ALS-decreased) reported by an independent meta-analysis of iPSC-MN datasets (ALS vs. CTL samples) ( Ziff et al, 2023 ), but there was no significant genewise or functional overlap with meta-analysis DEGs from the current study ( Supplementary Figure S27 ).…”

“…An initial transcriptome comparison of 341 ALS and 92 control (CTL) iPSC lines from the Answer ALS project identified only 13 differentially expressed genes (DEGs) ( Workman et al, 2023 ). Similarly, meta-analysis of 15 transcriptome datasets generated from iPSC-derived motor neurons identified only 43 genes differentially expressed between ALS ( n = 323) and CTL ( n = 106) samples ( Ziff et al, 2023 ). Much larger numbers of differentially expressed genes, however, have been obtained from post-mortem tissue studies.…”

“…The study incorporates both microarray and RNA-seq data and applies a random effects meta-analysis model to define differentially expressed genes (DEGs). The identified DEGs are compared to those linked to ALS by genome-wide association (GWA) studies as well as to genes altered in iPSC-derived motor neurons ( Workman et al, 2023 ; Ziff et al, 2023 ) and bulk spinal cord segments ( Humphrey et al, 2023 ). A novel approach utilizing nearest neighbor statistics is applied to identify putative transcription factor (TF) binding sites near DEGs and to further identify ALS-associated SNPs that may disrupt such sites.…”