Biology subjects

Sinha, I. R.

Publications and source records attributed to Sinha, I. R..

7 recordsLinked to original sources

bioRxiv2026

Prevention of Unc13a cryptic splicing is sufficient to preserve memory

TDP-43 dysfunction is thought to underlie frontotemporal dementia and limbic-predominant age-related TDP-43 encephalopathy, neurodegenerative dementias currently without effective therapy. Therapeutic strategies are designed to correct individual cryptic targets of TDP-43, such as UNC13A, whereby its cryptic splicing compromises synaptic function, yet the sufficiency of such an approach to prevent memory deficits is unclear. Using a forebrain neuron-specific TDP-43 knockout mouse model that recapitulates TDP-43 dysfunction occurring during early stages of human disorders, we found here that prevention of cryptic splicing to include that of Unc13a attenuated memory deficits. We show that genetic ablation of Unc13a cryptic exon solely in such TDP-43 knockout mice is sufficient to preserve cognition, supporting the clinical value of targeting UNC13A to mitigate memory deficits. Prevention of cryptic splicing of multiple targets of TDP-43 additionally attenuate neuron loss. For optimal outcomes in TDP-43 related dementias, these findings thus strongly support strategies designed to repress cryptic splicing of multiple targets of TDP-43, including UNC13A.

pathology↗

bioRxiv2025

Brain Iron as a Surrogate Biomarker of Pathological TDP-43 Identifies Brain Region-Specific Signatures in Ageing, Alzheimer's Disease and Amyotrophic Lateral Sclerosis

BackgroundTDP-43 pathology is a defining feature of several neurodegenerative diseases, but its prevalence and regional distribution in ageing and disease are not well characterised. We investigated the burden of brain TDP-43 pathology across ageing, Alzheimers disease (AD), and amyotrophic lateral sclerosis (ALS), and examined ferritin as a region-specific correlate of TDP-43 pathology. MethodsPathological TDP-43 was detected using an HDGFL2 cryptic exon in situ hybridisation probe and a TDP-43 RNA aptamer, providing greater sensitivity and specificity than antibody-based approaches. Amygdala, hippocampus, and frontal cortex tissue was analysed from non-neurological controls (ages 40-80), AD cases, and ALS cases. Ferritin (as a proxy for iron accumulation) was quantified in parallel to assess its association with TDP-43 pathology. FindingsTDP-43 pathology was detectable from the fourth decade of life, with a 4.5-fold increase in hippocampal involvement after age 60 years. In AD, pathology was present in 90% of cases and distinguished from ageing by selective amygdala involvement. In ALS, TDP-43 pathology was nearly ubiquitous across all regions studied. Regional ferritin strongly predicted TDP-43 burden: amygdala ferritin explained 87% of TDP-43 variance in ALS and 66% in AD, while hippocampal ferritin differentiated AD from controls. Across AD, ferritin explained between 43-81% of regional TDP-43 variance. InterpretationTDP-43 brain pathology emerges in midlife with increased involvement after age 60 years, exhibits disease-specific regional signatures in AD and ALS, and is closely linked to ferritin accumulation. As TDP-43 confers a worse prognosis in AD, the capacity of ferritin, detectable with iron-sensitive MRI, to serve as a proxy for regional TDP-43 burden highlights its promise as a biomarker for disease stratification and prognosis. Short AbstractHere we show that pathological TDP-43 emerges during normal ageing from the fourth decade of life, with a 4.5-fold increase in hippocampal involvement after 60 years. In Alzheimers disease (AD), TDP-43 pathology was present in 90% of cases and distinguished from ageing by disproportionate amygdala involvement, while in amyotrophic lateral sclerosis (ALS) it was nearly ubiquitous across hippocampus, amygdala, and frontal cortex. Using sensitive detection tools, we demonstrate that region-specific ferritin strongly predicts TDP-43 burden: amygdala ferritin explained 87% of variance in ALS and 66% in AD, while hippocampal ferritin differentiated AD from controls. Across AD, ferritin levels in all three regions explained 43-81% of TDP-43 variance. As TDP-43 pathology confers a worse prognosis in AD, the ability of ferritin, quantifiable with iron-sensitive MRI, to serve as a proxy for regional TDP-43 burden highlights its potential as a biomarker for disease stratification and prognostic assessment. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/680028v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@9c54b3org.highwire.dtl.DTLVardef@17cb415org.highwire.dtl.DTLVardef@12dabeorg.highwire.dtl.DTLVardef@1d72f95_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITDP-43 brain pathology occurs in normal ageing from early in the fourth decade, characterised by a 4.5-fold increase in hippocampus pathology from the sixth decade. C_LIO_LITDP-43 brain pathology is detectable in 90% of AD cases, with a disease-signature of increased amygdala pathology relative to age-matched controls. C_LIO_LIIn ALS, TDP-43 is nearly ubiquitous in amygdala, hippocampus and frontal cortex. C_LIO_LIHippocampus high brain ferritin distinguishes AD from and age-matched controls C_LIO_LIBrain ferritin is a brain region-specific marker of TDP-43 pathology in ageing and disease, with amygdala ferritin explaining 87% of the variance in amygdala TDP-43 pathology in ALS, and 66% of amygdala TDP-43 pathology in AD C_LIO_LIIn AD, ferritin levels for all three brain regions explain between 43-81% of variance in their TDP-43 pathology levels C_LI

neuroscience↗

bioRxiv2025

Broad brain biodistribution conferred by an AAV to restore TDP-43 function mitigates Frontotemporal Demenia-like deficits

TDP-43 dysfunction is an early pathogenic determinant of frontotemporal lobar degeneration with TDP-43 pathology (FTLD-TDP), a devastating disorder currently without effective therapy. Here, we exploit a blood-brain-barrier (BBB)-permeable AAV (AAV-PHP.eB) that confers broad brain biodistribution to restore TDP-43 function in a TDP-43 deficient model (CamKIIa-CreER;Tardbp mice) that mimics the early stage of TDP-43 dysfunction occurring in FTLD-TDP. Intracerebroventricular delivery by AAV-PHP.eB of CTR, our previously characterized splicing repressor, revealed its accumulation in [~]40% of adult hippocampal neurons. Remarkably, treatment of adult CamKIIa-CreER;Tardbpf/fmice with AAV-PHP.eB-CTR restored TDP-43 function, attenuated neuronal aberrant activity and memory deficits, and rescued neuron loss. Importantly, we showed that TDP-43s autoregulatory element restricts CTR expression to a physiological range. No overt phenotype was observed after long-term exposure to AAV-PHP.eB-CTR in aged mice, highlighting a favorable safety profile for this gene therapy. These results validate that BBB-crossing AAVs can deliver CTR with a biodistribution in the adult brain that is broad enough to rescue FTD-like phenotypes, supporting clinical testing of this gene therapy for FTLD-TDP.

neuroscience↗

bioRxiv2025

Symptomatic treatment by a BBB-permeable AAV engineered to restore TDP-43 function slows motor neuron disease and prevents paralysis

TAR DNA-binding protein 43kDa (TDP-43) dysfunction is an early pathogenic mechanism that underlies amyotrophic lateral sclerosis (ALS), a devastating neurodegenerative disorder that lacks disease modifying therapies. We previously developed a mouse model in which TDP-43 is selectively deleted from motor neurons (ChAT-Cre;Tardbpf/f) that mimics the early stages of ALS. Here, we demonstrate that intravenous delivery of a blood-brain-barrier (BBB) permeable AAV capsid expressing our rationally designed splicing repressor CTR (AAV-PHP.eB-CTR) in symptomatic ChAT-Cre;Tardbpf/f mice markedly slowed disease progression and prevented paralysis. Systemic delivery of AAV-PHP.eB-CTR led to transduction of [~]80% of spinal motor neurons, repression of TDP-43-associated cryptic exons within motor neurons expressing CTR, and attenuation of motor neuron loss. Notably, the addition of the TARDBP 3UTR autoregulatory element to CTR maintained its expression within a physiological range. In control littermates that received AAV-PHP.eB-CTR and were monitored for >20 months, grip strength and body weight remained normal, and no histopathological abnormalities were observed, underscoring a favorable safety profile for this gene therapy. These results provide preclinical proof-of-concept that BBB-crossing AAV delivery of CTR can rescue motor neuron disease through the restoration of TDP-43 function, offering a promising mechanism-based therapeutic strategy for ALS.

neuroscience↗

bioRxiv2025

5-ethynyluridine perturbs nuclear RNA metabolism to promote the nuclear accumulation of TDP-43 and other RNA binding proteins

TDP-43, an essential nucleic acid binding protein and splicing regulator, is broadly disrupted in neurodegeneration. TDP-43 nuclear localization and function depend on the abundance of its nuclear RNA targets and its recruitment into large ribonucleoprotein complexes, which restricts TDP-43 nuclear efflux. To further investigate the interplay between TDP-43 and nascent RNAs, we aimed to employ 5-ethynyluridine (5EU), a widely used uridine analog for click chemistry labeling of newly transcribed RNAs. Surprisingly, 5EU induced the nuclear accumulation of TDP-43 and other RNA-binding proteins and attenuated TDP-43 mislocalization caused by disruption of the nuclear transport apparatus. RNA FISH demonstrated 5EU-induced nuclear accumulation of polyadenylated and GU-repeat-rich RNAs, suggesting increased retention of both processed and intronic RNAs. TDP-43 eCLIP confirmed that 5EU preserved TDP-43 binding at predominantly GU-rich intronic sites. RNAseq revealed significant 5EU-induced changes in alternative splicing, accompanied by an overall reduction in splicing diversity, without any major changes in RNA stability or TDP-43 splicing regulatory function. These data suggest that 5EU may impede RNA splicing efficiency and subsequent nuclear RNA processing and export. Our findings have important implications for studies utilizing 5EU and offer unexpected confirmation that the accumulation of endogenous nuclear RNAs promotes TDP-43 nuclear localization.

cell biology↗

bioRxiv2024

Large-scale RNA-seq mining reveals ciclopirox triggers TDP-43 cryptic exons

Nuclear clearance and cytoplasmic aggregation of TDP-43 in neurons, initially identified in ALS-FTD, are hallmark pathological features observed across a spectrum of neurodegenerative diseases. We previously found that TDP-43 loss-of-function leads to the transcriptome-wide inclusion of deleterious cryptic exons in brains and biofluids post-mortem as well as during the presymptomatic stage of ALS-FTD, but upstream mechanisms that lead to TDP-43 dysregulation remain unclear. Here, we developed a web-based resource (SnapMine) to determine the levels of TDP-43 cryptic exon inclusion across hundreds of thousands of publicly available RNA sequencing datasets. We established cryptic exon inclusion across a variety of human cells and tissues to provide ground truth references for future studies on TDP-43 dysregulation. We then explored studies that were entirely unrelated to TDP-43 or neurodegeneration and found that ciclopirox olamine (CPX), an FDA-approved antifungal, can trigger the inclusion of TDP-43-associated cryptic exons in a variety of mouse and human primary cells. CPX induction of cryptic exon occurs via heavy metal toxicity and oxidative stress, suggesting that similar vulnerabilities could play a role in neurodegeneration. Our work demonstrates how diverse datasets can be linked through common biological features and underscores that public archives of sequencing data represent a vastly underutilized resource with tremendous potential for uncovering novel insights into complex biological mechanisms and diseases.

neuroscience↗

bioRxiv2023

Elevated nuclear TDP-43 induces constitutive exon skipping

Cytoplasmic inclusions and loss of nuclear TDP-43 are key pathological features found in several neurodegenerative disorders, suggesting both gain- and loss-of-function mechanisms of disease. To study gain-of-function, TDP-43 overexpression has been used to generate in vitro and in vivo model systems. Our study shows that excessive levels of nuclear TDP-43 protein lead to constitutive exon skipping that is largely species-specific. Furthermore, while aberrant exon skipping is detected in some human brains, it is not correlated with disease, unlike the incorporation of cryptic exons that occurs after loss of TDP-43. Our findings emphasize the need for caution in interpreting TDP-43 overexpression data, and stress the importance of controlling for exon skipping when generating models of TDP-43 proteinopathy. Understanding the subtle aspects of TDP-43 toxicity within different subcellular locations is essential for the development of therapies targeting neurodegenerative disease.

neuroscience↗