Distinct circular DNA profile in hSOD1G93A ALS that intersects with ALS proteome changes

Numerous genes mutated in amyotrophic lateral sclerosis (ALS) share a role in DNA damage and repair, emphasizing genome disintegration in ALS. DNA instability and repair mechanisms segregate extrachromosomal circular DNAs (ec/eccDNAs) that can modulate gene expression somatically. Here, circulome profiling in a hSOD1G93A genotoxicity model of ALS revealed a 6-fold enrichment of small-size eccDNAs relative to controls. DifCir-based differential analysis identified 189 genes with patterned segregation of differentially produced per gene circles (DPpGCs) from ALS but not from control samples, implicating an inter-sample recurrence rate of at least 89% for the top 6 DPpGCs. Mass spectrometry-based ALS circulome-proteome cross-referencing revealed 31 corresponding differentially expressed proteins (DEPs), with 12 DPpGC-DEP pairs being itemized in ALS risk GWAS databases. DPpGC-DEP hotspots mainly convey neuron-specific functions counteracting ALS detriments. This is unanticipated evidence for non-random, profiled eccDNA accumulation in ALS neurodegeneration, involving putative interactions with their gene products as well as biomarker perspectives. The data C (Control,C57BL/6J) is performed with 10 replicates. The data A (ALS,B6.Cg-Tg(SOD1*G93A)1Gur/J) is performed with 9 replicates.诸多在肌萎缩侧索硬化症（amyotrophic lateral sclerosis, ALS）中发生突变的基因，均在DNA损伤与修复通路中发挥作用，这凸显了ALS患者体内的基因组崩解现象。DNA不稳定及修复机制会对染色体外环状DNA（extrachromosomal circular DNAs, ec/eccDNAs）进行分选，此类环状DNA可调控体细胞的基因表达。本研究针对ALS的hSOD1G93A遗传毒性模型开展循环组分析，结果显示小尺寸ec/eccDNAs的富集程度较对照组提升6倍。基于DifCir的差异分析鉴定出189个基因，这些基因的每基因环状DNA差异生成量（differentially produced per gene circles, DPpGCs）在ALS样本中呈现特征性分选模式，而对照组样本则无此现象；其中排名前6的DPpGCs在样本间的重现率至少达89%。基于质谱的ALS循环组-蛋白质组交叉比对共鉴定出31个对应的差异表达蛋白（differentially expressed proteins, DEPs），其中12个DPpGC-DEP配对条目被收录于ALS风险全基因组关联分析（GWAS）数据库。DPpGC-DEP热点区域主要承载拮抗ALS损伤的神经元特异性功能。本研究为ALS神经退行性变过程中存在非随机、特征性ec/eccDNA积累提供了意料之外的证据，该过程涉及ec/eccDNA与其基因产物的潜在相互作用，同时具备生物标志物应用前景。本研究中对照组（C组，C57BL/6J品系）设置10次生物学重复，ALS模型组（A组，B6.Cg-Tg(SOD1*G93A)1Gur/J品系）设置9次生物学重复。