Faura Júlia, Heeman Bavo, Pottier Cyril, Baker Matthew C, DeJesus-Hernandez Mariely, Küçükali Fahri, Heiß Laura, Wynants Sarah, Van den Broeck Marleen, De Rijk Peter, De Pooter Tim, Joris Geert, Finch NiCole A, Asmann Yan, Strazisar Mojca, Murray Melissa E, Petrucelli Leonard, Oskarsson Björn, Sleegers Kristel, Josephs Keith A, Nguyen Aivi T, Reichard R Ross, Petersen Ronald C, Boeve Bradley F, Graff-Radford Neill R, Dickson Dennis W, van Blitterswijk Marka, Rademakers Rosa
Applied and Translational Neurogenomics, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.
Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
Acta Neuropathol. 2025 Jun 6;149(1):59. doi: 10.1007/s00401-025-02901-7.
Dysregulation of TDP-43 as seen in TDP-43 proteinopathies leads to specific RNA splicing dysfunction. While discovery studies have explored novel TDP-43-driven splicing events in induced pluripotent stem cell (iPSC)-derived neurons and TDP-43 negative neuronal nuclei, transcriptome-wide investigations in frontotemporal lobar degeneration with TDP-43 aggregates (FTLD-TDP) brains remain unexplored. Such studies hold promise for identifying widespread novel and relevant splicing alterations in FTLD-TDP patient brains. We conducted the largest differential splicing analysis (DSA) using bulk short-read RNAseq data from frontal cortex (FCX) tissue of 127 FTLD-TDP (A, B, C, GRN and C9orf72 carriers) and 22 control subjects (Mayo Clinic Brain Bank), using Leafcutter. In addition, long-read bulk cDNA sequencing data were generated from FCX of 9 FTLD-TDP and 7 controls and human TARDBP wildtype and knock-down iPSC-derived neurons. Publicly available RNAseq data (MayoRNAseq, MSBB and ROSMAP studies) from Alzheimer's disease patients (AD) was also analyzed. Our DSA revealed extensive splicing alterations in FTLD-TDP patients with 1881 differentially spliced events, in 892 unique genes. When evaluating differences between FTLD-TDP subtypes, we found that C9orf72 repeat expansion carriers carried the most splicing alterations after accounting for differences in cell-type proportions. Focusing on cryptic splicing events, we identified STMN2 and ARHGAP32 as genes with the most abundant and differentially expressed cryptic exons between FTLD-TDP patients and controls in the brain, and we uncovered a set of 17 cryptic events consistently observed across studies, highlighting their potential relevance as biomarkers for TDP-43 proteinopathies. We also identified 16 cryptic events shared between FTLD-TDP and AD brains, suggesting potential common splicing dysregulation pathways in neurodegenerative diseases. Overall, this study provides a comprehensive map of splicing alterations in FTLD-TDP brains, revealing subtype-specific differences and identifying promising candidates for biomarker development and potential common pathogenic mechanisms between FTLD-TDP and AD.
在TDP-43蛋白病中所见的TDP-43失调会导致特定的RNA剪接功能障碍。虽然探索性研究已在诱导多能干细胞（iPSC）衍生的神经元和TDP-43阴性神经元核中研究了新型TDP-43驱动的剪接事件，但对伴有TDP-43聚集的额颞叶痴呆（FTLD-TDP）患者大脑进行的全转录组研究仍未开展。此类研究有望识别FTLD-TDP患者大脑中广泛存在的新型且相关的剪接改变。我们使用Leafcutter软件，对来自127例FTLD-TDP（A、B、C、GRN和C9orf72携带者）患者及22例对照受试者（梅奥诊所脑库）额叶皮质（FCX）组织的批量短读长RNA测序数据进行了规模最大的差异剪接分析（DSA）。此外，还从9例FTLD-TDP患者和7例对照受试者以及人TARDBP野生型和敲低的iPSC衍生神经元的FCX中生成了长读长批量cDNA测序数据。我们还分析了来自阿尔茨海默病（AD）患者的公开可用RNA测序数据（MayoRNAseq、MSBB和ROSMAP研究）。我们的DSA显示，FTLD-TDP患者存在广泛的剪接改变，有1881个差异剪接事件，涉及892个独特基因。在评估FTLD-TDP各亚型之间的差异时，我们发现，在考虑细胞类型比例差异后，C9orf72重复扩增携带者的剪接改变最多。聚焦于隐蔽剪接事件，我们确定STMN2和ARHGAP32是FTLD-TDP患者与对照受试者大脑中隐蔽外显子最丰富且差异表达的基因，并且我们发现了一组在各项研究中均一致观察到的17个隐蔽事件，突出了它们作为TDP-43蛋白病生物标志物的潜在相关性。我们还确定了FTLD-TDP与AD大脑之间共有的16个隐蔽事件，提示神经退行性疾病中可能存在共同的剪接失调途径。总体而言，本研究提供了FTLD-TDP患者大脑中剪接改变的全面图谱，揭示了亚型特异性差异，并确定了生物标志物开发的有前景候选物以及FTLD-TDP与AD之间潜在的共同致病机制。
