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In the work we present here, we test the hypothesis that differentially expressed TEs in blood could be used as biomarkers of cognitive decline and development of AD. To this aim, we used a sample of aging subjects (age\u2009&gt;\u200970) that developed late-onset Alzheimer\u2019s disease (LOAD) over a relatively short period of time (12\u201348\u00a0months), for which blood was available before and after their <jats:italic>pheno<\/jats:italic>conversion, and a group of cognitive stable subjects as controls. We applied our developed and validated customized pipeline that allows the identification, characterization, and quantification of the differentially expressed (DE) TEs before and after the onset of manifest LOAD, through analyses of RNA-Seq data. We compared the level of DE TEs within more than 600,000 TE-mapping RNA transcripts from 25 individuals, whose specimens we obtained before and after their <jats:italic>phenotypic<\/jats:italic> conversion (<jats:italic>pheno<\/jats:italic>conversion) to LOAD, and discovered that 1790 TE transcripts showed significant expression differences between these two timepoints (logFC\u2009\u00b1\u20091.5, logCMP\u2009&gt;\u20095.3, nominal <jats:italic>p<\/jats:italic> value\u2009&lt;\u20090.01). These DE transcripts mapped both over- and under-expressed TE elements. Occurring before the clinical <jats:italic>pheno<\/jats:italic>conversion, this TE storm features significant increases in DE transcripts of LINEs, LTRs, and SVAs, while those for SINEs are significantly depleted. These dysregulations end with signs of manifest LOAD. This set of highly DE transcripts generates a TE transcriptional profile that accurately discriminates the before and after <jats:italic>pheno<\/jats:italic>conversion states of these subjects. Our findings suggest that a storm of DE TEs occurs before <jats:italic>pheno<\/jats:italic>conversion from normal cognition to manifest LOAD in risk individuals compared to controls, and may provide useful blood-based biomarkers for heralding such a clinical transition, also suggesting that TEs can indeed participate in the complex process of neurodegeneration.<\/jats:p>","DOI":"10.1007\/s11357-022-00580-w","type":"journal-article","created":{"date-parts":[[2022,5,19]],"date-time":"2022-05-19T03:37:26Z","timestamp":1652931446000},"page":"1525-1550","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":36,"title":["A retrotransposon storm marks clinical phenoconversion to late-onset Alzheimer\u2019s disease"],"prefix":"10.1007","volume":"44","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0537-4266","authenticated-orcid":false,"given":"Fabio","family":"Macciardi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria","family":"Giulia Bacalini","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ricardo","family":"Miramontes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessio","family":"Boattini","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cristian","family":"Taccioli","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giorgia","family":"Modenini","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rond","family":"Malhas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laura","family":"Anderlucci","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuriy","family":"Gusev","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas J.","family":"Gross","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert M.","family":"Padilla","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Massimo S.","family":"Fiandaca","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elizabeth","family":"Head","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guia","family":"Guffanti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Howard J.","family":"Federoff","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Mapstone","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,5,19]]},"reference":[{"key":"580_CR1","doi-asserted-by":"publisher","unstructured":"Ibanez L, Cruchaga C, Fernandez MV. 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