ELAVL4, splicing, and glutamatergic dysfunction precede neuron loss in MAPT mutation cerebral organoids

In the paper

“In iPSC-derived induced neurons, tau-V337M disrupts neuronal activity regulation and excitability (Sohn et al., 2019), spurring further studies in more complex models.”

What the sources say

• Supported

  The Results sections on AIS plasticity and homeostatic control of neuronal excitability report that tau-V337M impairs activity-dependent AIS plasticity and alters activity patterns in human iPSC-derived neurons. The Discussion likewise states that the mutation disrupts homeostatic AIS rearrangement and leads to neuronal dysfunction. (LLM, conf=0.94)

  cites Sohn et al., 2019 source

In the paper

“FTD-tau is associated with glutamatergic neuronal loss in frontal and temporal cortices (Benussi et al., 2019).”

What the sources say

• Partly supported

  The Abstract reports depletion of glutamatergic pyramidal neurons in the frontal and temporal cortices of patients with FTD. It does not specify that this finding applies to FTD-tau; the Introduction identifies tau as one of several FTD pathologies. (LLM, conf=0.88)

  cites Benussi et al., 2019 sourceExperimental — accuracy not yet measured

In the paper

“Increasing evidence showing that early alterations in brain development contribute to later manifestation of neurodegenerative diseases (Faravelli et al., 2020) further encourages use of iPSC-based organoid systems to study FTD-tau.”

What the sources say

• Supported

  The Introduction states that premature alterations during brain development have been related to late manifestations of neurodegenerative disease. The Conclusions further explain how mutations could disrupt neural progenitor maturation and increase vulnerability to later triggers, supporting the claim's qualified account of contribution. (LLM, conf=0.92)

  cites Faravelli et al., 2020 source

In the paper

“Pathologic studies reveal accumulation of filamentous, hyperphosphorylated tau protein (P-tau) in cerebral cortical and hippocampal neurons and glia, and tau redistribution from axons to the somatodendritic compartment.”

What the sources say

• Supported

  The ‘Tau phosphorylation and neurofibrillary tangle formation’ section describes hyperphosphorylated tau deposits that form filaments and reports tau inclusions in glia. ‘Spreading of tau pathology’ places inclusions in the hippocampus and neocortex, while the Figure 3 caption in ‘Conclusions and perspectives’ contrasts tau’s normal axonal concentration with its pathological accumulation in the neuronal soma and dendrites. Pages are not specified in our copy. (LLM, conf=0.88)

  cites Bodea et al., 2016 source
• ?Could not verify

  The 'Synaptic Proteins and AD' section mentions neurons containing neurofibrillary tangles, but does not identify their composition or describe tau pathology. Searches for hyperphosphorylated tau and its redistribution from axons to the somatodendritic compartment found no passage addressing the claim in our copy; page numbers were unavailable. (LLM, conf=0.72)

  cites Clare et al., 2010 sourceExperimental — accuracy not yet measured

In the paper

“Brain organoids derived from iPSCs develop in culture along a trajectory mimicking key features of fetal brain development and can be patterned toward specific brain regions affected in tauopathy (Camp et al., 2015; Lancaster et al., 2017; Paşca et al., 2015; Velasco et al., 2019; Yoon et al., 2019).”

What the sources say

• ?Not checked — no full text of the sourcecites Camp et al., 2015 source
• Partly supported

  The Online Methods (Preparation of EBs and enCORs) include an iPS cell line, and the main text reports that engineered organoids form forebrain tissue, including regions consistent with hippocampal identity. It also finds that 60-day organoids most closely match early-gestation human forebrain gene expression. The copy does not establish a developmental trajectory matching fetal brain development or connect the patterned regions to tauopathy. (LLM, conf=0.86)

  cites Lancaster et al., 2017 sourceExperimental — accuracy not yet measured
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Paşca et al., 2015

In the paper

“These changes correlate with degeneration of synapses and neuronal loss in frontal and temporal cortices (Bodea et al., 2016; Clare et al., 2010).”

What the sources say

• Partly supported

  The section ‘Role of tau in dendritic spines and synaptic impairment’ links pathological tau to synaptic degeneration and reports neuronal loss in a tau mouse model. The paper also describes frontal and temporal cortical atrophy in FTLD, but it does not establish that the tau changes correlate with both synaptic degeneration and neuronal loss specifically in those cortices. The mouse-model comparison distinguishes tau changes associated with synaptic loss from those associated with neuronal loss. (LLM, conf=0.85)

  cites Bodea et al., 2016 sourceExperimental — accuracy not yet measured
• Partly supported

  The ‘Synaptic Proteins and AD’ section reports a correlation between synapse loss and neurons containing neurofibrillary tangles, but also notes that another synaptic marker showed no correlation with tangle density. The FTLD section reports synaptic reductions in frontal and temporal regions. Neither section establishes that tau changes correlate with neuronal loss in those cortices. (LLM, conf=0.86)

  cites Clare et al., 2010 sourceExperimental — accuracy not yet measured

In the paper

“The tau-V337M mutation selected for this study is located in MAPT exon 12, expressed in iPSC-derived neurons, and associated with FTD with abundant neurofibrillary tangles in frontal and temporal cortices and the cingulate gyrus and atrophy throughout the hippocampus and amygdala (Spillantini et al., 1996; Spina et al., 2017; Sumi et al., 1992).”

What the sources say

• ?Not checked — no full text of the sourcecites Spillantini et al., 1996 source
• Partly supported

  Split into 2 atoms — 0 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 1 unverifiable. Expand the claim to see per-atom verdicts.

  cites Spina et al., 2017 sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites Sumi et al., 1992 source

In the paper

“Disruption of the autophagy-lysosomal pathway (ALP) is another pathological hallmark in human tauopathy brain (Bain et al., 2019; Piras et al., 2016; Wang et al., 2009).”

What the sources say

• Partly supported

  The Discussion reports lower LAMP-1 levels in human FTLD-tau cases and suggests that deficient lysosomes or defective vesicular transport may impair tau clearance. This supports disruption of the pathway in the FTLD-tau cases studied, but the paper does not establish it as a pathological hallmark across human tauopathies; its mechanistic conclusion is hedged. (LLM, conf=0.84)

  cites Bain et al., 2019 sourceExperimental — accuracy not yet measured
• Supported

  The Discussion reports abnormal accumulation of autophagy-lysosomal markers as a common feature of the tauopathies studied. The Conclusions likewise state that the autophagosomal-lysosomal clearance pathway is compromised in all three, supporting the citing sentence’s broad paraphrase. (LLM, conf=0.92)

  cites Piras et al., 2016 source
• Partly supported

  The Discussion (page unavailable) states that the autophagy–lysosomal system is disturbed in Alzheimer disease brain, and the Introduction says lysosomal alterations in Alzheimer disease are well established. The paper does not establish that this disruption is a pathological hallmark across human tauopathies; its own tauopathy experiments use a cell model. (LLM, conf=0.84)

  cites Wang et al., 2009 sourceExperimental — accuracy not yet measured

In the paper

“glutamate levels, and neuronal excitability (Ince-Dunn et al., 2012; Jung and Lee, 2021)”

What the sources say

• Partly supported

  The Results section, “A new role for nElavl in regulating glutamate in the brain” (page not provided), reports reduced glutamate in mice lacking both Elavl3 and Elavl4. The Results section, “Seizures in Elavl3-/- Mice” (page not provided), links abnormal cortical activity to loss of Elavl3. These findings support a role for the neuronal Elav-like proteins collectively, but do not establish that ELAVL4 alone regulates both glutamate levels and neuronal excitability. (LLM, conf=0.86)

  cites Ince-Dunn et al., 2012 sourceExperimental — accuracy not yet measured
• Partly supported

  The Introduction identifies HuD as ELAVL4. Section 4.1 reports that mice lacking neuronal ELAV proteins had impaired splicing of genes regulating cellular glutamate levels and spontaneous epileptic seizures. That supports a link to glutamate regulation and excitability, but the passage concerns the neuronal ELAV group, not ELAVL4 individually. (LLM, conf=0.85)

  cites Jung and Lee, 2021 sourceExperimental — accuracy not yet measured

In the paper

“ELAVL4 expression decreases self-renewal of neural progenitor cells and promotes deep-layer glutamatergic neuronal differentiation (Akamatsu et al., 2005; DeBoer et al., 2014; Popovitchenko et al., 2020).”

What the sources say

• Partly supported

  The Results (page not provided) show increased self-renewal and reduced neuronal differentiation in neural stem/progenitor cells from HuD-deficient mice, supporting a role for HuD in limiting self-renewal and promoting neuronal differentiation. The paper does not establish that the neurons are specifically deep-layer or glutamatergic, and it tests HuD loss rather than experimentally increasing its expression. (LLM, conf=0.88)

  cites Akamatsu et al., 2005 sourceExperimental — accuracy not yet measured
• Partly supported

  The Results section, “HuD is critical for the balanced expression of Tle4 in lower layer neocortical neurons” (page unavailable), reports fewer Tle4-positive lower-layer neurons after HuD deletion and suggests a role in their specification and/or maintenance. That supports a connection to deep-layer neuronal identity, but does not establish that ELAVL4 expression promotes differentiation specifically. Our copy does not report that ELAVL4 decreases neural progenitor self-renewal. (LLM, conf=0.86)

  cites DeBoer et al., 2014 sourceExperimental — accuracy not yet measured
• Partly supported

  The Results section, “Elavl4-v3 promotes lower layer (LL) identity when not repressed in RG” (page unavailable), reports that premature Elavl4-v3 expression in radial glia increased a lower-layer neuronal identity marker, supporting the differentiation part of the claim. It does not establish that ELAVL4 expression decreases neural progenitor self-renewal; the Results section, “Celf1 regulates the balance of glutamatergic neurons” (page unavailable), instead reports greater progenitor retention in a condition with increased Elavl4 protein. (LLM, conf=0.86)

  cites Popovitchenko et al., 2020 sourceExperimental — accuracy not yet measured

In the paper

“binds to the glutamatergic receptor GRM5 and other genes within the long-term potentiation (LTP) pathway (Bolognani et al., 2010)”

What the sources say

• Supported

  The Results (Gene ontology analysis of HuD targets; page unavailable) state that the long-term potentiation pathway contains a number of HuD targets. The Discussion (page unavailable) identifies metabotropic glutamate receptor 5 (mGluR5, encoded by GRM5) as another HuD target and names other targets involved in long-term potentiation. (LLM, conf=0.91)

  cites Bolognani et al., 2010 source

In the paper

“ELAVL4 is a target of FUS activity”

What the sources say

• ?Could not verify

  The Discussion describes FUS as a regulator of neuronal mRNA transport and stability, and separately discusses HuD and other ELAV-family proteins in relation to TDP-43 aggregates. Searches for ELAVL4 as a FUS target and for FUS regulation of HuD found no passage connecting them in our copy. (LLM, conf=0.75)

  cites Fallini et al., 2012 sourceExperimental — accuracy not yet measured
• Supported

  The Results section, “FUS Regulates ELAVL4 Expression by Binding the 3′ UTR of Its mRNA,” identifies ELAVL4 as a target of FUS regulation. It reports increased ELAVL4 expression in FUS-mutant motor neurons and increased ELAVL4 3′ UTR reporter activity in the presence of mutant FUS; the demonstrated effect is chiefly for mutant FUS. (LLM, conf=0.93)

  cites De Santis et al., 2019 source

In the paper

“tau-TIA1 interaction can lead to formation and stabilization of toxic tau oligomers (Ash et al., 2021).”

What the sources say

• Supported

  The Results section reports that adding TIA1 and RNA increases formation of tau oligomers, and that the resulting oligomeric tau is neurotoxic. The Discussion says TIA1 inhibits conversion of oligomers into fibrils, promoting their accumulation—supporting the claim that the interaction helps form and stabilize toxic oligomers. (LLM, conf=0.93)

  cites Ash et al., 2021 source

In the paper

“ELAVL4 binds the 3′ UTR of MAPT RNA in rat primary neurons and in mouse P19 cells”

What the sources say

• ?Not checked — no full text of the sourcecites Atlas et al., 2007 source
• ?Not checked — no full text of the sourcecites Behar et al., 1995 source
• Partly supported

  The Introduction identifies HuD as ELAVL4, and §3.1 says HuD regulates tau expression. A reference listed in the paper concerns tau mRNA and HuD protein in differentiated P19 neuronal cells, but our copy does not establish direct binding to the MAPT 3′ UTR in either P19 cells or rat primary neurons. (LLM, conf=0.84)

  cites Jung and Lee, 2021 sourceExperimental — accuracy not yet measured

In the paper

“ELAVL4 regulates RNA splicing (Scheckel et al., 2016)”

What the sources say

• Partly supported

  The Results section, “nELAVL regulates splicing of human brain targets” (page unavailable), reports altered exon splicing after nELAVL depletion. But the depletion targeted ELAVL2, ELAVL3, and ELAVL4 together, as specified in “nELAVL proteins regulate mRNA abundance of human brain targets” (page unavailable). The paper therefore supports a role for the neuronal ELAVL proteins in splicing, not an independently established role for ELAVL4 alone. (LLM, conf=0.85)

  cites Scheckel et al., 2016 sourceExperimental — accuracy not yet measured

In the paper

“is present in TAR DNA-binding protein 43 (TDP-43) inclusions (Fallini et al., 2012; De Santis et al., 2019).”

What the sources say

• Supported

  Figure 7 reports that HuD co-aggregated with TDP-43 C-terminal-fragment-positive cytoplasmic inclusions in transfected primary motor neurons. The Discussion says it remains unknown whether HuD is present in pathological aggregates in animal models or ALS patients; the cited finding concerns experimentally induced inclusions. (LLM, conf=0.88)

  cites Fallini et al., 2012 source
• Supported

  The Results section, “ELAVL4 Is a Component of Pathological Inclusions in ALS Patients’ Specimens,” reports ELAVL4 in phosphorylated TDP-43-positive cytoplasmic inclusions in sporadic ALS specimens. The Figure 6 caption likewise identifies inclusions positive for both pTDP-43 and ELAVL4. (LLM, conf=0.94)

  cites De Santis et al., 2019 source

In the paper

“Tau influences stress granule formation in neurons”

What the sources say

• Partly supported

  The Discussion (page unavailable) says tau selectively associates with TIA1-containing stress granules. The paper examines TIA1’s effects on tau phase separation and tests tau toxicity in cultured neurons, but the passages do not show that tau influences stress granule formation in neurons. (LLM, conf=0.82)

  cites Ash et al., 2021 sourceExperimental — accuracy not yet measured

In the paper

“PIKFYVE inhibition increases the number of EEA1-positive endosomes and LAMP1-positive lysosomes”

What the sources say

• Partly supported

  The section on small-molecule regulators of endosomal trafficking (page not provided) reports that PIKFYVE inhibition increased the size of EEA1-positive endosomes, not their number. The lysosomal-biogenesis section attributes restored numbers of LAMP1-positive lysosomes to forced C9ORF72 expression; our copy does not report that PIKFYVE inhibition increased their number. (LLM, conf=0.88)

  cites Shi et al., 2018 sourceExperimental — accuracy not yet measured
• Supported

  The Main text reports that apilimod, a PIKFYVE inhibitor, increased EEA1-positive vesicles in hippocampal neurons and astrocytes of C9orf72-deficient mice. It also reports increased LAMP1-positive vesicles in hippocampal neurons after treatment. The claim omits that experimental setting but accurately summarizes the reported effects. (LLM, conf=0.92)

  cites Staats et al., 2019 source

In the paper

“humans and mice haplodeficient for PIKFYVE are normal”

What the sources say

• Partly supported

  The Results section (page unavailable) reports that heterozygous PIKfyve WT/KO mice developed without ostensible defects. But the Discussion (page unavailable) says humans with heterozygous PIKFYVE mutations can have fleck corneal dystrophy, a pathology not seen in the mice. The claim that affected humans are normal is therefore not supported. (LLM, conf=0.90)

  cites Ikonomov et al., 2011 sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites Sands et al., 2010 source

In the paper

“It would be of interest to include microglia in the model, given their contribution to tau pathology, spread, and synaptic degeneration (Vogels et al., 2019).”

What the sources say

• Supported

  The section on the effects of tau pathology on microglia says dysfunctional glial cells can contribute to neuronal tau pathology. The introduction identifies microglial involvement in tau-induced synapse loss and tau spreading, and the section on synaptic spreading describes reduced tau spread after microglial depletion. No page numbers are provided in our copy. (LLM, conf=0.91)

  cites Vogels et al., 2019 source

In the paper

“The false discovery rate (FDR) of the differential expression test was estimated using the Benjamini-Hochberg (BH) method (Reiner et al., 2003).”

What the sources say

• Supported

  The section “The linear step-up procedure (BH)” describes BH as a procedure for controlling FDR. “Resampling FDR adjustments” explains how the paper obtains a BH point estimate, and “Results of multiple testing on the original data” reports using that estimator for differential-expression tests. The citation supports identifying BH as the method, though it does not verify what the citing authors did in their own analysis. (LLM, conf=0.90)

  cites Reiner et al., 2003 source

In the paper

“Data from different sequencing runs, batches and ages were integrated and scaled using SCTransform (Hafemeister and Satija, 2019), while regressing out the following covariates; percentage of mitochondrial genes, the number of cells collected per parent organoid, the number of genes per cell and the number of reads per cell.”

What the sources say

• Supported

  The Discussion identifies sctransform as the authors’ method for normalization and variance stabilization and says its model can include covariates such as mitochondrial percentage and experimental batch. The citation identifies the method used; the particular runs, ages, organoids, and covariates listed in the citing sentence describe the citing authors’ own analysis, not results attributed to this paper. (LLM, conf=0.90)

  cites Hafemeister and Satija, 2019 source

In the paper

“Differential gene expression between MAPT mutation organoids and isogenic controls was predicted by linear mixed model analysis using the variancePartition package (v1.14.1) in the R programming environment (Hoffman and Roussos, 2021) to account for sample correlations within isogenic lines and differentiation batches.”

What the sources say

• Supported

  The Software section identifies dream as a function in the variancePartition package. The Dream model section describes differential-expression analysis using a linear mixed model with multiple random effects, which supports citing it as the method used to account for sample correlations. The MAPT organoid analysis is the citing authors’ application, not a result attributed to this source. (LLM, conf=0.91)

  cites Hoffman and Roussos, 2021 source

In the paper

“Overtime, the proportion of upper cortical layer-enriched (ExM-U) neurons increased, as did inhibitory neurons, astrocytes, and oligodendrocytes (all p < 2.2 × 10−16; Figures 1B–1D).”

In the paper

“These differences were validated by immunohistochemistry (IHC) analysis, which showed a reduction in neuronal nuclear protein+ (NeuN+) neurons at 4 and 6 months (Figures 2B and 2C) and in MAP2+ neurons at 6 months (Figures S2A and S2B).”

In the paper

“Lysosome-related multi-membrane lamellar bodies were rare in healthy neurons (Figure 2E) but more frequent in tau-V337M neurons, including those showing early signs of apoptosis (Figure 2F), suggesting ALP dysfunction.”

In the paper

“In contrast, pro-CTSD was increased significantly at 6 months in the absence of increased active CTSD, whereas sequestosome 1 (p62) and microtubule-associated protein 1A/1B-light chain 3 (LC3-II) were reduced significantly at the same time point (Figures 2H and 2I), suggesting defects in proteolytic cleavage and activity.”

In the paper

“Tau-V337M organoids showed no genotype-dependent differences at 2 months (Figure 2J), but a significant increase in total tau and the P-tau S396/total tau ratio emerged between 4 and 6 months compared with isogenic controls (Figures 2J–2L).”

In the paper

“Figure 7K: nisogenic+nc = 120, nisogenic+ASO = 120, Chi-sq = 0.3814, p = 0.5369.”

In the paper

“for Figures 7B: nisogenic = 80, nmutant = 80, Chi-sq = 3.723, p = 0.0537;”

In the paper

“There was no batch-specific effect on differentiation over three replicates assessed by uniform manifold approximation and projection (UMAP) (Figure S1B) and no clustering because of mutation at 2 or 4 months (Figure S1C).”

In the paper

“Transcriptional signatures in the human frontal cortex at this age correlate highly with gene expression profiles of organoids (Qian et al., 2016).”

What the sources say

• ?Not checked — no full text of the sourcecites Qian et al., 2016 source

In the paper

“Therefore, PIKFYVE inhibition may rescue glutamate-induced neurodegeneration by correcting ALP dysfunction, increasing turnover of misfolded tau, and favoring elimination of internalized NMDA and AMPA receptors over recycling back to the synapse.”

In the paper

“These findings demonstrate that iPSC-tau-V337M organoids phenocopy aspects of ALP dysfunction seen in the FTD brain, which may be triggered by expression of mutant tau protein in neurons early in disease development.”

In the paper

“High-molecular-weight (HMW) ubiquitinated species were increased significantly in tau-V337M organoids at 2 months, suggesting disrupted degradation and accumulation of poly-ubiquitinated proteins and, thus, increased proteostasis stress in mutant organoids.”

In the paper

“Additionally, dysfunctional proteostasis may result in increased levels of tau and ELAVL4 because of impaired protein clearance, promoting their cytosolic accumulation.”

In the paper

“Given its pleiotropic functions, our observation of perturbed ELAVL4 expression and localization could contribute to several phenotypes observed in tau-V337M organoids, including aberrant MAPT/tau expression, early neuronal maturation, aberrant glutamate signaling, and dysregulated splicing.”

In the paper

“All presented differential expression, GSEA, pathway enrichment and splicing analyses p values were adjusted for multiple test correction.”

In the paper

“Two organoids were excluded from further analysis due to inconsistent positioning away from the remaining samples by principal components analysis”

In the paper

“Given the low 4R tau expression in these organoid models, additional effects of the mutant 4R protein may be missed.”

In the paper

“The resulting dataset for analysis included 379,064 cells (V337M n = 161,706, V337V n = 217,358).”

In the paper

“Protein bands’ densitometry (pixel mean intensity in arbitrary units, a.u.) was measured with ImageJ and normalized to the respective internal control (GAPDH) band.”

In the paper

“Data was also corrected for differentiation batch.”

In the paper

“resulting in a final dataset consisting of 239 organoids (V337M n = 99, V337V n = 140).”

In the paper

“In our working model, the MAPT mutation results in accumulation of mutant tau”

In the paper

“All reported p values were adjusted for multiple test correction; Significance was defined as adjusted p < 0.05.”

In the paper

“For every set of slides stained, a neuropathologically confirmed severe AD case and healthy control case was included as a batch control.”

In the paper

“Pathological changes assessed using semiquantitative analysis were scored by two researchers (JFC and KW) blinded to mutational and control conditions using a semiquantitative scoring system”

In the paper

“of which 339 passed quality control, determined by samples containing detectable cells with clear HTO identities.”

In the paper

“Our data characterizing glutamatergic signaling in tau-V337M organoids require additional validation by comprehensive electrophysiological assessment to confirm our hypothesized mechanism.”

In the paper

“Although these changes are initially accommodated by plasticity, over time they result in glutamatergic neuron death.”

In the paper

“Band intensity was analyzed using GeneTools, normalized against total protein by Ponceau S staining of each blot, and band intensity was expressed relative to the normalized control within each blot.”

In the paper

“and second by impaired proteostasis, preventing recycling of receptors away from the synapse and promoting further tau accumulation.”