A distinct circular DNA profile intersects with proteome changes in the genotoxic stress-related hSOD1G93A model of ALS
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Numerous genes, including SOD1, mutated in familial and sporadic amyotrophic lateral sclerosis (f/sALS) share a role in DNA damage and repair, emphasizing genome disintegration in ALS. One possible outcome of chromosomal instability and repair processes is extrachromosomal circular DNA (eccDNA) formation. Therefore, eccDNA might accumulate in f/sALS with yet unknown function.
Methods
We combined rolling circle amplification with linear DNA digestion to purify eccDNA from the cervical spinal cord of 9 co-isogenic symptomatic hSOD1G93A mutants and 10 controls, followed by deep short-read sequencing. We mapped the eccDNAs and performed differential analysis based on the split read signal of the eccDNAs, referred as DifCir, between the ALS and control specimens, to find differentially produced per gene circles (DPpGC) in the two groups. Compared were eccDNA abundances, length distributions and genic profiles. We further assessed proteome alterations in ALS by mass spectrometry, and matched the DPpGCs with differentially expressed proteins (DEPs) in ALS. Additionally, we aligned the ALS-specific DPpGCs to ALS risk gene databases.
Results
We found a six-fold enrichment in the number of unique eccDNAs in the genotoxic ALS-model relative to controls. We uncovered a distinct genic circulome profile characterized by 225 up-DPpGCs, i.e., genes that produced more eccDNAs from distinct gene sequences in ALS than under control conditions. The inter-sample recurrence rate was at least 89% for the top 6 up-DPpGCs. ALS proteome analyses revealed 42 corresponding DEPs, of which 19 underlying genes were itemized for an ALS risk in GWAS databases. The up-DPpGCs and their DEP tandems mainly impart neuron-specific functions, and gene set enrichment analyses indicated an overrepresentation of the adenylate cyclase modulating G protein pathway.
Conclusions
We prove, for the first time, a significant enrichment of eccDNA in the ALS-affected spinal cord. Our triple circulome, proteome and genome approach provide indication for a potential importance of certain eccDNAs in ALS neurodegeneration and a yet unconsidered role as ALS biomarkers. The related functional pathways might open up new targets for therapeutic intervention.
| Originalsprog | Engelsk |
|---|---|
| Artikelnummer | 170 |
| Tidsskrift | Cell and Bioscience |
| Vol/bind | 13 |
| Udgave nummer | 1 |
| Antal sider | 25 |
| ISSN | 2045-3701 |
| DOI | |
| Status | Udgivet - 2023 |
Bibliografisk note
Funding Information:
We gratefully acknowledge support from the Core Facility Proteomics of the Leibniz Institute on Aging—Fritz Lipmann Institute, Jena, Germany, for the acquisition of the proteomics data. The next-generation sequencing of eccDNA libraries were supported by Jie Ma at BGI Research-Qingdao. We thank the Qingdao-Europe Advanced Institute for Life Sciences for the support in executing the project. We thank Svetlana Würl and Ina Ingrisch at UKJ, and Sefa Alizadeh at UCH, for technical assistance and genotyping analyses. We thank Diane Wengerodt for animal scoring and tissue extraction, and Sathish Venkataramanappa for DNA isolation. We are grateful for the support by the animal facility at Jena University Hospital.
Funding Information:
We gratefully acknowledge support from the Core Facility Proteomics of the Leibniz Institute on Aging—Fritz Lipmann Institute, Jena, Germany, for the acquisition of the proteomics data. The next-generation sequencing of eccDNA libraries were supported by Jie Ma at BGI Research-Qingdao. We thank the Qingdao-Europe Advanced Institute for Life Sciences for the support in executing the project. We thank Svetlana Würl and Ina Ingrisch at UKJ, and Sefa Alizadeh at UCH, for technical assistance and genotyping analyses. We thank Diane Wengerodt for animal scoring and tissue extraction, and Sathish Venkataramanappa for DNA isolation. We are grateful for the support by the animal facility at Jena University Hospital.
Funding Information:
Open Access funding enabled and organized by Projekt DEAL. This work was supported by the ‘Else-Kröner-Fresenius-Stiftung’ (EKFS), the German Research Foundation (DFG) [WI 830/12-1], the Ministry for Economics, Sciences and Digital Society of Thuringia (TMWWDG) under the framework of the ProExcellence Initiative RegenerAging (RegenerAging-52-5581-413-FSU-I-03/14 to AK) and the Interdisciplinary Center for Clinical Research (IZKF) Jena [FF01 to AK]. D.G. and M.J.A.-B. were supported by the Circular Vision project with funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 899417, by Ministerio de Ciencia e Innovación, Spain Grant No. PID2020-119715 GB-I00/AEI/10.13039/501100011033, and by Instituto de Salud Carlos III, Infrastructure of Precision Medicine associated with Science and Technology (IMPaCT) of the Strategic Action in Health (iDATA-MP). J.B.N. and Y.Q. were funded by Innovation Fund Denmark (8088-00049B), the Carlsberg Foundation (CF21-0167) and the Novo Nordisk Foundation (NNF21OC0072023). Study design, and data collection, analyses and interpretation were not influenced by any of the funding sources.
Publisher Copyright:
© 2023, Society of Chinese Bioscientists in America (SCBA).
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