Biology subjects

Sandal, P. S.

Publications and source records attributed to Sandal, P. S..

3 recordsLinked to original sources

bioRxiv2026

Fine-tuning genomic models on rare splicing events identifies a novel biomarker of TDP-43 pathology

Genomic foundation models (GFMs) are pretrained on large genomic datasets, but their ability to predict rare disease-associated events after fine-tuning remains unclear. We tested this using TDP-43 cryptic exons, well characterized splicing events linked to neurodegenerative disease that are poorly represented in standard annotations. We compared the state-of-the-art GFM AlphaGenome with OpenSpliceAI, a specialized splice site prediction model. Fine-tuned OpenSpliceAI detected held-out cryptic exons in human and mouse and captured allele-specific splicing effects at the disease-associated UNC13A locus. In contrast, a splicing prediction head trained on AlphaGenome's frozen pretrained backbone failed to predict cryptic exons. Unfreezing and fine-tuning all model weights, however, enabled AlphaGenome to generalize to held-out data. To investigate cryptic splicing in cell types that are difficult to study experimentally, we applied fine-tuned OpenSpliceAI across the genome to study cell type-specific genes. This led to the identification of new cryptic splicing events in CLDN11 and ARHGAP23, which were subsequently validated in FTLD-TDP brain tissue. Notably, the cryptic exon in CLDN11 is predicted to generate a neoepitope that could serve as an oligodendrocyte-specific biomarker of TDP-43 pathology. Our results show that even a state-of-the-art GFM can fail to generalize to rare splicing events, even with substantial pretraining. However, both foundation and specialized models that learn to generalize to rare biological events can have broad applications in biological discovery and medicine.

genomics↗

bioRxiv2025

Inhibition of nonsense-mediated decay in TDP-43 deficient neurons reveals novel cryptic exons

TAR DNA-binding protein 43 kDa (TDP-43) is an essential splicing repressor whose loss of function underlies the pathophysiology of amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). Nuclear clearance of TDP-43 disrupts its function and leads to the inclusion of aberrant cryptic exons. These cryptic exons frequently introduce premature termination codons resulting in the degradation of affected transcripts through nonsense-mediated mRNA decay (NMD). Conventional RNA sequencing approaches thus may fail to detect cryptic exons that are efficiently degraded by NMD, precluding identification of potential therapeutic targets. We generated a comprehensive set of neuronal targets of TDP-43 in human iPSC-derived i3Neurons (i3N) by combining TDP-43 knockdown with inhibition of multiple factors essential for NMD, revealing novel cryptic targets. We then restored expression of selected NMD targets in TDP-43 deficient i3Ns and determined which genes improved neuronal viability. Our findings highlight the role of NMD in masking cryptic splicing events and identify novel potential therapeutic targets for TDP-43-related neurodegenerative disorders.

neuroscience↗

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↗