Locus specific endogenous retroviral expression associated with Alzheimer’s disease
IntroductionHuman endogenous retroviruses (HERVs) are transcriptionally-active remnants of ancient retroviral infections that may play a role in Alzheimer’s disease.MethodsWe combined two, publicly available RNA-Seq datasets with a third, novel dataset for a total cohort of 103 patients with Alzheim...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-07-01
|
| Series: | Frontiers in Aging Neuroscience |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fnagi.2023.1186470/full |
| _version_ | 1797785631757172736 |
|---|---|
| author | Tyson Dawson Tyson Dawson Uzma Rentia Jessie Sanford Carlos Cruchaga John S. K. Kauwe Keith A. Crandall Keith A. Crandall |
| author_facet | Tyson Dawson Tyson Dawson Uzma Rentia Jessie Sanford Carlos Cruchaga John S. K. Kauwe Keith A. Crandall Keith A. Crandall |
| author_sort | Tyson Dawson |
| collection | DOAJ |
| description | IntroductionHuman endogenous retroviruses (HERVs) are transcriptionally-active remnants of ancient retroviral infections that may play a role in Alzheimer’s disease.MethodsWe combined two, publicly available RNA-Seq datasets with a third, novel dataset for a total cohort of 103 patients with Alzheimer’s disease and 45 healthy controls. We use telescope to perform HERV quantification for these samples and simultaneously perform gene expression analysis.ResultsWe identify differentially expressed genes and differentially expressed HERVs in Alzheimer’s disease patients. Differentially expressed HERVs are scattered throughout the genome; many of them are members of the HERV-K superfamily. A number of HERVs are correlated with the expression of dysregulated genes in Alzheimer’s and are physically proximal to genes which drive disease pathways.DiscussionDysregulated expression of ancient retroviral insertions in the human genome are present in Alzheimer’s disease and show localization patterns that may explain how these elements drive pathogenic gene expression. |
| first_indexed | 2024-03-13T00:56:46Z |
| format | Article |
| id | doaj.art-1852eb2d44514d08ae2e4b85e874498f |
| institution | Directory Open Access Journal |
| issn | 1663-4365 |
| language | English |
| last_indexed | 2024-03-13T00:56:46Z |
| publishDate | 2023-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Aging Neuroscience |
| spelling | doaj.art-1852eb2d44514d08ae2e4b85e874498f2023-07-06T16:26:20ZengFrontiers Media S.A.Frontiers in Aging Neuroscience1663-43652023-07-011510.3389/fnagi.2023.11864701186470Locus specific endogenous retroviral expression associated with Alzheimer’s diseaseTyson Dawson0Tyson Dawson1Uzma Rentia2Jessie Sanford3Carlos Cruchaga4John S. K. Kauwe5Keith A. Crandall6Keith A. Crandall7Computational Biology Institute, The George Washington University, Washington, DC, United StatesDepartment of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United StatesComputational Biology Institute, The George Washington University, Washington, DC, United StatesDepartment of Psychiatry, Washington University School of Medicine, St. Louis, MO, United StatesDepartment of Psychiatry, Washington University School of Medicine, St. Louis, MO, United StatesDepartment of Biology, Brigham Young University, Provo, UT, United StatesComputational Biology Institute, The George Washington University, Washington, DC, United StatesDepartment of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United StatesIntroductionHuman endogenous retroviruses (HERVs) are transcriptionally-active remnants of ancient retroviral infections that may play a role in Alzheimer’s disease.MethodsWe combined two, publicly available RNA-Seq datasets with a third, novel dataset for a total cohort of 103 patients with Alzheimer’s disease and 45 healthy controls. We use telescope to perform HERV quantification for these samples and simultaneously perform gene expression analysis.ResultsWe identify differentially expressed genes and differentially expressed HERVs in Alzheimer’s disease patients. Differentially expressed HERVs are scattered throughout the genome; many of them are members of the HERV-K superfamily. A number of HERVs are correlated with the expression of dysregulated genes in Alzheimer’s and are physically proximal to genes which drive disease pathways.DiscussionDysregulated expression of ancient retroviral insertions in the human genome are present in Alzheimer’s disease and show localization patterns that may explain how these elements drive pathogenic gene expression.https://www.frontiersin.org/articles/10.3389/fnagi.2023.1186470/fullAlzheimer’s diseaseHERVendogenous retrovirusRNA-Seqgene expression |
| spellingShingle | Tyson Dawson Tyson Dawson Uzma Rentia Jessie Sanford Carlos Cruchaga John S. K. Kauwe Keith A. Crandall Keith A. Crandall Locus specific endogenous retroviral expression associated with Alzheimer’s disease Frontiers in Aging Neuroscience Alzheimer’s disease HERV endogenous retrovirus RNA-Seq gene expression |
| title | Locus specific endogenous retroviral expression associated with Alzheimer’s disease |
| title_full | Locus specific endogenous retroviral expression associated with Alzheimer’s disease |
| title_fullStr | Locus specific endogenous retroviral expression associated with Alzheimer’s disease |
| title_full_unstemmed | Locus specific endogenous retroviral expression associated with Alzheimer’s disease |
| title_short | Locus specific endogenous retroviral expression associated with Alzheimer’s disease |
| title_sort | locus specific endogenous retroviral expression associated with alzheimer s disease |
| topic | Alzheimer’s disease HERV endogenous retrovirus RNA-Seq gene expression |
| url | https://www.frontiersin.org/articles/10.3389/fnagi.2023.1186470/full |
| work_keys_str_mv | AT tysondawson locusspecificendogenousretroviralexpressionassociatedwithalzheimersdisease AT tysondawson locusspecificendogenousretroviralexpressionassociatedwithalzheimersdisease AT uzmarentia locusspecificendogenousretroviralexpressionassociatedwithalzheimersdisease AT jessiesanford locusspecificendogenousretroviralexpressionassociatedwithalzheimersdisease AT carloscruchaga locusspecificendogenousretroviralexpressionassociatedwithalzheimersdisease AT johnskkauwe locusspecificendogenousretroviralexpressionassociatedwithalzheimersdisease AT keithacrandall locusspecificendogenousretroviralexpressionassociatedwithalzheimersdisease AT keithacrandall locusspecificendogenousretroviralexpressionassociatedwithalzheimersdisease |