A multi-faceted approach to unravel coding and non-coding gene fusions and target chimeric proteins in ataxia

Ataxia represents a heterogeneous group of neurodegenerative disorders characterized by a loss of balance and coordination, often resulting from mutations in genes vital for cerebellar function and maintenance. Recent advances in genomics have identified gene fusion events as critical contributors to various cancers and neurodegenerative diseases. However, their role in ataxia pathogenesis remains largely unexplored. Our study Hdelved into this possibility by analyzing RNA sequencing data from 1443 diverse samples, including cell and mouse models, patient samples, and healthy controls. We identified 7067 novel gene fusions, potentially pivotal in disease onset. These fusions, notably in-frame, could produce chimeric proteins, disrupt gene regulation, or introduce new functions. We observed conservation of specific amino acids at fusion breakpoints and identified potential aggregate formations in fusion proteins, known to contribute to ataxia. Through AI-based protein structure prediction, we identified topological changes in three high-confidence fusion proteins—TEN1-ACOX1, PEX14-NMNAT1, and ITPR1-GRID2—which could potentially alter their functions. Subsequent virtual drug screening identified several molecules and peptides with high-affinity binding to fusion sites. Molecular dynamics simulations confirmed the stability of these protein-ligand complexes at fusion breakpoints. Additionally, we explored the role of non-coding RNA fusions as miRNA sponges. One such fusion, <i>RP11-547P4-FLJ33910</i>, showed strong interaction with hsa-miR-504-5p, potentially acting as its sponge. This interaction correlated with the upregulation of hsa-miR-504-5p target genes, some previously linked to ataxia. In conclusion, our study unveils new aspects of gene fusions in ataxia, suggesting their significant role in pathogenesis and opening avenues for targeted therapeutic interventions.

共济失调(Ataxia)是一组异质性神经退行性疾病，以平衡与协调能力丧失为核心特征，其发病通常与对小脑功能维持至关重要的基因突变相关。近年来基因组学领域的研究进展表明，基因融合(gene fusion)事件是多种癌症及神经退行性疾病的关键致病因素，但其在共济失调发病机制中的作用仍未得到充分探索。本研究针对这一研究空白，对1443份多样化样本的RNA测序(RNA sequencing)数据展开深入分析，样本涵盖细胞模型、小鼠模型、患者样本及健康对照。我们共鉴定出7067个全新基因融合事件，这类事件可能在疾病发生过程中发挥关键作用。其中尤以框内(in-frame)融合事件最为显著，它们可编码产生嵌合蛋白、破坏内源基因调控网络或引入全新蛋白功能。我们观察到融合断点(fusion breakpoints)处存在特定氨基酸保守性特征，并发现融合蛋白可能形成聚集体，这类聚集体已被证实与共济失调的病理进程密切相关。通过基于人工智能(AI)的蛋白质结构预测技术，我们在三种高置信度(high-confidence)融合蛋白——TEN1-ACOX1、PEX14-NMNAT1及ITPR1-GRID2中鉴定到拓扑结构改变，这类结构改变可能会影响其蛋白功能。后续的虚拟药物筛选(virtual drug screening)实验发现了多个可与融合位点高亲和力结合的小分子与肽类物质。分子动力学模拟(molecular dynamics simulations)进一步证实了这些蛋白-配体复合物在融合断点处的结构稳定性。此外，我们还探索了非编码RNA融合(non-coding RNA fusions)作为miRNA海绵(miRNA sponges)的调控功能。其中一例融合产物<i>RP11-547P4-FLJ33910</i>可与hsa-miR-504-5p发生强相互作用，可能作为其miRNA海绵发挥调控作用。该相互作用与hsa-miR-504-5p靶基因(target genes)的上调表达显著相关，其中部分靶基因此前已被证实与共济失调存在关联。综上，本研究揭示了共济失调中基因融合的全新生物学层面，表明其在发病机制中具有重要作用，并为靶向治疗干预提供了全新的研究方向。