Linking the association between circRNAs and Alzheimer’s disease progression by multi-tissue circular RNA characterization

References

• Hyman BT, Van Hoesen GW, Damasio AR, et al. Alzheimer’s disease: cell-specific pathology isolates the hippocampal formation. Sci (New York) 1984;225(4667):1168–1170.
   Google Scholar
• Pagani M, Giuliani A, Oberg J, et al. Progressive disintegration of brain networking from normal aging to Alzheimer disease: analysis of independent components of (18)F-FDG PET data. J Nucl Med. 2017;58(7):1132–1139.
   PubMed Web of Science ®Google Scholar
• Fang -X-X, Sun G-L, Zhou Y, et al. TGF-beta1 protection against Abeta1-42-induced hippocampal neuronal inflammation and apoptosis by TbetaR-I. Neuroreport. 2018;29(2):141–146.
   PubMed Web of Science ®Google Scholar
• Rupaimoole R, Slack FJ. MicroRNA therapeutics: towards a new era for the management of cancer and other diseases. Nat Rev Drug Discov. 2017;16(3):203–222.
   PubMed Web of Science ®Google Scholar
• Maass PG, Glažar P, Memczak S, et al. A map of human circular RNAs in clinically relevant tissues. J Mol Med. 2017;95(11):1179–1189.
   PubMed Web of Science ®Google Scholar
• Han B, Chao J, Yao H. Circular RNA and its mechanisms in disease: from the bench to the clinic. Pharmacol Ther. 2018;187:31–44.
   PubMed Web of Science ®Google Scholar
• Chen G, Shi Y, Zhang Y, et al. CircRNA_100782 regulates pancreatic carcinoma proliferation through the IL6-STAT3 pathway. Onco Targets Ther. 2017;10:5783–5794.
   PubMed Web of Science ®Google Scholar
• Zhao Y, Alexandrov PN, Jaber V, et al. Deficiency in the ubiquitin conjugating enzyme UBE2A in Alzheimer’s Disease (AD) is linked to deficits in a natural circular miRNA-7 sponge (circRNA; ciRS-7). Genes (Basel). 2016;7(12):116.
   PubMed Web of Science ®Google Scholar
• Gu Y, Ke G, Wang L, et al. Altered expression profile of circular RNAs in the serum of patients with diabetic retinopathy revealed by microarray. Ophthalmic Res. 2017;58(3):176–184.
   PubMed Web of Science ®Google Scholar
• Holdt LM, Stahringer A, Sass K, et al. Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans. Nat Commun. 2016;7:12429.
   PubMed Web of Science ®Google Scholar
• Kristensen LS, Andersen MS, Stagsted LVW, et al. The biogenesis, biology and characterization of circular RNAs. Nat Rev Genet. 2019;20(11):675–691.
   PubMed Web of Science ®Google Scholar
• Enuka Y, Lauriola M, Feldman ME, et al. Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor. Nucleic Acids Res. 2016;44(3):1370–1383.
   PubMed Web of Science ®Google Scholar
• You X, Vlatkovic I, Babic A, et al. Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity. Nat Neurosci. 2015;18(4):603–610.
   PubMed Web of Science ®Google Scholar
• Gruner H, Cortes-Lopez M, Cooper DA, et al. CircRNA accumulation in the aging mouse brain. Sci Rep. 2016;6:38907.
   PubMed Web of Science ®Google Scholar
• Dube U, Del-Aguila JL, Li Z, et al. An atlas of cortical circular RNA expression in Alzheimer disease brains demonstrates clinical and pathological associations. Nat Neurosci. 2019;22(11):1903–1912.
   PubMed Web of Science ®Google Scholar
• Wang M, Beckmann ND, Roussos P, et al. The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer’s disease. Sci Data. 2018;5:1–16.
   PubMed Web of Science ®Google Scholar
• Ranganath C, Heller AS, Wilding EL. Dissociable correlates of two classes of retrieval processing in prefrontal cortex. NeuroImage. 2007;35(4):1663–1673.
   PubMed Web of Science ®Google Scholar
• Costa A, Oliveri M, Barban F, et al. The right frontopolar cortex is involved in visual-spatial prospective memory. PloS One. 2013;8(2):e56039.
   PubMed Web of Science ®Google Scholar
• Grossman M, Cooke A, DeVita C, et al. Sentence processing strategies in healthy seniors with poor comprehension: an fMRI study. Brain Lang. 2002;80(3):296–313.
   PubMed Web of Science ®Google Scholar
• Li M, Lu S, Zhong N. The parahippocampal cortex mediates contextual associative memory: evidence from an fMRI study. Biomed Res Int. 2016;2016:9860604.
   PubMed Web of Science ®Google Scholar
• Morris JC. Clinical dementia rating: a reliable and valid diagnostic and staging measure for dementia of the Alzheimer type. Int Psychogeriatr. 1997;9(S1):173–176.
   PubMedGoogle Scholar
• Mirra SS, Heyman A, McKeel D, et al. The consortium to establish a registry for Alzheimer’s disease (CERAD). Part II. Standardization of the neuropathologic assessment of Alzheimer’s disease. Neurology. 1991;41(4):479–486.
   PubMed Web of Science ®Google Scholar
• Wang M, Roussos P, McKenzie A, et al. Integrative network analysis of nineteen brain regions identifies molecular signatures and networks underlying selective regional vulnerability to Alzheimer’s disease. Genome Med. 2016;8(1):104.
   PubMedGoogle Scholar
• Gu Y, Scarmeas N, Cosentino S, et al. Change in body mass index before and after Alzheimer’s disease onset. Curr Alzheimer Res. 2014;11(4):349–356.
   PubMed Web of Science ®Google Scholar
• Echávarri C, Aalten P, Uylings HBM, et al. Atrophy in the parahippocampal gyrus as an early biomarker of Alzheimer’s disease. Brain Struct Funct. 2011;215(3–4):265–271.
   PubMed Web of Science ®Google Scholar
• Krumm S, Kivisaari SL, Probst A, et al. Neurobiology of Aging Cortical thinning of parahippocampal subregions in very early Alzheimer’s disease. Neurobiol Aging. 2016;38:188–196.
   PubMed Web of Science ®Google Scholar
• Xu H, Guo S, Li W, et al. The circular RNA Cdr1as, via miR-7 and its targets, regulates insulin transcription and secretion in islet cells. Nat Publishing Group. 2015;July:1–12. DOI:10.1038/srep12453
   Google Scholar
• Nativio R, Donahue G, Berson A, et al. Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease. Nat Neurosci. 2018;21(4):497–505.
   PubMed Web of Science ®Google Scholar
• Picard Tools - By Broad Institute. n.d. [cited 2018 Dec 17]. Available from: http://broadinstitute.github.io/picard/
   Google Scholar
• Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013. https://arxiv.org/abs/1303.3997
   Google Scholar
• Gao Y, Zhang J, Zhao F. Circular RNA identification based on multiple seed matching. Brief Bioinform. 2018;19(5):803–810.
   PubMed Web of Science ®Google Scholar
• Carlson M. org.Hs.eg.db: genome wide annotation for Human. 2018. Available from: https://bioconductor.statistik.tu-dortmund.de/packages/3.8/data/annotation/html/org.Hs.eg.db.html.
   Google Scholar
• Carlson M, Maintainer BP. TxDb.Hsapiens.UCSC.hg19.knownGene: annotation package for TxDb object(s). 2015. Available from: https://bioconductor.org/packages/release/data/annotation/html/TxDb.Hsapiens.UCSC.hg19.knownGene.html .
   Google Scholar
• Smedley D, Haider S, Durinck S, et al. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res. 2015;43(W1):W589–98.
   PubMed Web of Science ®Google Scholar
• Glažar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs. RNA (New York). 2014;20(11):1666–1670.
   PubMed Web of Science ®Google Scholar
• Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.
   PubMed Web of Science ®Google Scholar
• Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Phipson B, Wu D, et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47.
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504.
   PubMed Web of Science ®Google Scholar
• Yu G, Wang L-G, Han Y, et al. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics. 2012;16(5):284–287.
   PubMed Web of Science ®Google Scholar
• Yu G, Wang L-G, Yan G-R, et al. DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis. Bioinformatics. 2015;31(4):608–609.
   PubMed Web of Science ®Google Scholar
• Kuhn M. Building predictive models in R using the caret package. J Stat Softw. 2008;1(5):1–26. Available from: www.jstatsoft.org/v028/i05.
   Google Scholar
• Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Stat Softw. 2010;33(1):1–22.
   PubMed Web of Science ®Google Scholar