Improved nanopore direct RNA sequencing of cardiac myocyte samples by selective mt-RNA depletion

Journal of Molecular and Cellular Cardiology - Tập 163 - Trang 175-186 - 2022
Isabel S. Naarmann-de Vries1,2,3, Jessica Eschenbach1,2, Christoph Dieterich1,2,3
1Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Germany
2Department of Internal Medicine III, University Hospital Heidelberg, Germany
3German Center for Cardiovascular Research (DZHK), partner site, Heidelberg/Mannheim, Germany

Tài liệu tham khảo

Casamassimi, 2017, Transcriptome profiling in human diseases: new advances and perspectives, Int. J. Mol. Sci., 18, 10.3390/ijms18081652 Tang, 2020, A roadmap for fixing the heart: RNA regulatory networks in cardiac disease, Mol. Ther. Nucleic Acids., 20, 673, 10.1016/j.omtn.2020.04.007 Sweet, 2018, Transcriptome analysis of human heart failure reveals dysregulated cell adhesion in dilated cardiomyopathy and activated immune pathways in ischemic heart failure, BMC Genomics, 19, 812, 10.1186/s12864-018-5213-9 Roth, 2018, Global, regional, and national age-sex-specific mortality for 282 causes of death in 195 countries and territories, 1980–2017: a systematic analysis for the Global Burden of Disease Study 2017, Lancet, 392, 1736, 10.1016/S0140-6736(18)32203-7 Song, 2012, Deep RNA sequencing reveals novel cardiac transcriptomic signatures for physiological and pathological hypertrophy, PLoS One, 7 Heinig, 2017, Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy, Genome Biol., 18, 170, 10.1186/s13059-017-1286-z Thomas, 2014, Bench To Basinet Cv DCIS. Long-read sequencing of chicken transcripts and identification of new transcript isoforms, PLoS One, 9, 10.1371/journal.pone.0094650 Muller, 2021, Updated and enhanced pig cardiac transcriptome based on long-read RNA sequencing and proteomics, J. Mol. Cell. Cardiol., 150, 23, 10.1016/j.yjmcc.2020.10.005 Garalde, 2018, Highly parallel direct RNA sequencing on an array of nanopores, Nat. Methods, 15, 201, 10.1038/nmeth.4577 Workman, 2019, Nanopore native RNA sequencing of a human poly(A) transcriptome, Nat. Methods, 16, 1297, 10.1038/s41592-019-0617-2 Liu, 2019, Accurate detection of m(6)A RNA modifications in native RNA sequences, Nat. Commun., 10, 4079, 10.1038/s41467-019-11713-9 Smith, 2019, Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing, PLoS One, 14 Jenjaroenpun, 2021, Decoding the epitranscriptional landscape from native RNA sequences, Nucleic Acids Res., 49, 10.1093/nar/gkaa620 Mercer, 2011, The human mitochondrial transcriptome, Cell., 146, 645, 10.1016/j.cell.2011.06.051 Yang, 2014, Deep RNA sequencing reveals dynamic regulation of myocardial noncoding RNAs in failing human heart and remodeling with mechanical circulatory support, Circulation, 129, 1009, 10.1161/CIRCULATIONAHA.113.003863 Molenaar, 2018, Single-cell sequencing of the mammalian heart, Circ. Res., 123, 1033, 10.1161/CIRCRESAHA.118.313531 Slomovic, 2005, Polyadenylation and degradation of human mitochondrial RNA: the prokaryotic past leaves its mark, Mol. Cell. Biol., 25, 6427, 10.1128/MCB.25.15.6427-6435.2005 Hershberger, 2013, Dilated cardiomyopathy: the complexity of a diverse genetic architecture, Nat. Rev. Cardiol., 10, 531, 10.1038/nrcardio.2013.105 Jordan, 2021, An evidence-based assessment of genes in dilated cardiomyopathy, Circulation, 144, 7, 10.1161/CIRCULATIONAHA.120.053033 Siede, 2017, Identification of circular RNAs with host gene-independent expression in human model systems for cardiac differentiation and disease, J. Mol. Cell. Cardiol., 109, 48, 10.1016/j.yjmcc.2017.06.015 Hafezqorani, 2020, Trans-NanoSim characterizes and simulates nanopore RNA-sequencing data, Gigascience, 9, 10.1093/gigascience/giaa061 Sheffield, 2001, The molecular genetics of Bardet-Biedl syndrome, Curr. Opin. Genet. Dev., 11, 317, 10.1016/S0959-437X(00)00196-9 Elbedour, 1994, Cardiac abnormalities in the Bardet-Biedl syndrome: echocardiographic studies of 22 patients, Am. J. Med. Genet., 52, 164, 10.1002/ajmg.1320520208 Slavotinek AM. McKusick-Kaufman Syndrome. In: Adam MP, Ardinger HH, Pagon RA, Wallace SE, Bean LJH, Mirzaa G, et al., GeneReviews(R). Seattle (WA) 1993–2021. Montano, 2013, Inducible re-expression of HEXIM1 causes physiological cardiac hypertrophy in the adult mouse, Cardiovasc. Res., 99, 74, 10.1093/cvr/cvt086 Collins, 2015, EPLIN: a fundamental actin regulator in cancer metastasis?, Cancer Metastasis Rev., 34, 753, 10.1007/s10555-015-9595-8 Demal, 2019, A familial congenital heart disease with a possible multigenic origin involving a mutation in BMPR1A, Sci. Rep., 9, 2959, 10.1038/s41598-019-39648-7 Redwood, 2013, Alpha-tropomyosin mutations in inherited cardiomyopathies, J. Muscle Res. Cell Motil., 34, 285, 10.1007/s10974-013-9358-5 Ingles, 2019, Evaluating the clinical validity of hypertrophic cardiomyopathy genes, Circ. Genom. Precis. Med., 12, 10.1161/CIRCGEN.119.002460 Knoll, 2007, Laminin-alpha4 and integrin-linked kinase mutations cause human cardiomyopathy via simultaneous defects in cardiomyocytes and endothelial cells, Circulation, 116, 515, 10.1161/CIRCULATIONAHA.107.689984 Li, 2020, Mitochondrial dynamics in adult cardiomyocytes and heart diseases, Front. Cell Dev. Biol., 8, 584800, 10.3389/fcell.2020.584800 Baldwin, 2021, An easy, cost-effective, and scalable method to deplete human ribosomal RNA for RNA-seq, Curr. Protoc., 1, 10.1002/cpz1.176 Temperley, 1797, Human mitochondrial mRNAs--like members of all families, similar but different, Biochim. Biophys. Acta, 2010, 1081 Mandegar, 2016, CRISPR interference efficiently induces specific and reversible gene silencing in human iPSCs, Cell Stem Cell, 18, 541, 10.1016/j.stem.2016.01.022 Burridge, 2014, Chemically defined generation of human cardiomyocytes, Nat. Methods, 11, 855, 10.1038/nmeth.2999 Lian, 2013, Directed cardiomyocyte differentiation from human pluripotent stem cells by modulating Wnt/beta-catenin signaling under fully defined conditions, Nat. Protoc., 8, 162, 10.1038/nprot.2012.150 Tohyama, 2013, Distinct metabolic flow enables large-scale purification of mouse and human pluripotent stem cell-derived cardiomyocytes, Cell Stem Cell, 12, 127, 10.1016/j.stem.2012.09.013 Schmittgen, 2008, Analyzing real-time PCR data by the comparative C(T) method, Nat. Protoc., 3, 1101, 10.1038/nprot.2008.73 Huang, 2009, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat. Protoc., 4, 44, 10.1038/nprot.2008.211 Huang, 2009, Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists, Nucleic Acids Res., 37, 1, 10.1093/nar/gkn923