Premature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration

Abstract

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are associated with loss of nuclear TDP-43. Here we identify that TDP-43 regulates expression of the neuronal growth-associated factor stathmin-2. Lowered TDP-43 levels, which reduce its binding to sites within the first intron of stathmin-2 pre-mRNA, uncover a cryptic polyadenylation site whose utilization produces a truncated, non-functional mRNA. Reduced stathmin-2 expression is found in neurons trans-differentiated from patient fibroblasts expressing an ALS-causing TDP-43 mutation, in motor cortex and spinal motor neurons from sporadic ALS patients and familial ALS patients with expansion in C9orf72, and in induced pluripotent stem cell (iPSC)-derived motor neurons depleted of TDP-43. Remarkably, while reduction in TDP-43 is shown to inhibit axonal regeneration of iPSC-derived motor neurons, rescue of stathmin-2 expression restores axonal regenerative capacity. Thus, premature polyadenylation-mediated reduction in stathmin-2 is a hallmark of ALS/FTD that functionally links reduced nuclear TDP-43 function to enhanced neuronal vulnerability.

Single-cell RNA-seq analysis of human iPSC-derived motor neurons resolves early and predictive ALS signatures

“…Similarly, examination of downregulated genes overlapping among the Blue and Midnightblue modules in data set A, the Darkgreen module in data set B, and MNs highlighted genes previously implicated in ALS (Lederer et al, 2007;Saris et al, 2009;Umahara et al, 2016) ( Figure 5D). The GO term regulation of neuronal projection development was significantly represented among the overlapping, downregulated genes ( Figure 5D), consistent with recent models suggesting that deficiencies in maintaining axonal projections may underlie ALS (Klim et al, 2019;Melamed et al, 2019).…”

“…The most recent iPSC-based transcriptomic reports performed RNA profiling at time points during differentiation concomitant with various observed ALS phenotypes which include nuclear RNA foci (Sareen et al, 2013), decreased neurite length (Fujimori et al, 2018), reduced neurite repair after injury (Klim et al, 2019;Melamed et al, 2019), and MN death (Kiskinis et al, 2014;Shi et al, 2018). Several of these protocols differentiated iPSCs for over 30 days, and many required a relatively prolonged maturation phase, the presence of glia, and additional stressor conditions in order to yield a disease phenotype.…”

“…Of note, recent literature has characterized convergent and divergent aspects of ALS pathways and mechanisms across subject lines and subsets of ALS conditions, often delineated by genotype (including familial ALS mutations in C9orf72, SOD1, hnRNPA1, TARDBP, FUS, and CHMP2B as well as sporadic ALS), site of symptom onset, disease progression, or treatment response (Chen et al, 2014;Fujimori et al, 2018;Kiskinis et al, 2014;Klim et al, 2019;Melamed et al, 2019;Sareen et al, 2013;Shi et al, 2018). We noted that bulk transcriptomic analysis may contribute to discrepancies in pathway discoveries, and thus sought to characterize these commonalities and distinctions using higher resolution, single-cell analysis.…”

TDP-43 and HSP70 phase separate into anisotropic, intranuclear liquid spherical annuli

“…We recently reported that TDP-43 naturally de-mixes in the nucleus, and shuttles to the cytoplasm in response to multiple stresses (21). Loss of nuclear TDP-43 causes usage of cryptic splice (22)(23)(24) and polyadenylation sites (24), dysregulating many important neuronal genes such as HDAC6 (25) and stathmin-2 (22,24).…”

Optogenetic modulation of TDP-43 oligomerization fast-forwards ALS-related pathologies in the spinal motor neurons

“…TDP-43 can associate with more than 6,000 RNA targets 41–44 , and RNA-binding is antagonistic to toxic TDP-43 oligomerization in an optogenetic cellular model 28 , implying that light-dependent opTDP-43 oligomerization would profoundly affect its RNA-binding capacity, thereby influencing the expression of a myriad of genes. In terms of the axon outgrowth defect, whether toxicity is ascribable to dysregulation of specific key proteins 39, 45 or to a widespread translational abnormality 46 , which could lead to stress-inducing misfolded protein accumulation, remains to be investigated. Nevertheless, the normal motor axon pathfinding and unaffected branching frequency suggest a certain specificity of opTDP-43 toxicity and would favor the idea that the cellular growth pathway is primarily affected by the toxicity.…”