Spatial detection of fetal marker genes expressed at low level in adult human heart tissue
Michaela Asp, Fredrik Salmén, Patrik L Ståhl, Sanja Vickovic, Ulrika Felldin, Marie Löfling, José Fernandez Navarro, Jonas Maaskola, Maria J Eriksson, Bengt Persson, Matthias Corbascio, Hans Persson, Cecilia Linde, Joakim Lundeberg, Michaela Asp, Fredrik Salmén, Patrik L Ståhl, Sanja Vickovic, Ulrika Felldin, Marie Löfling, José Fernandez Navarro, Jonas Maaskola, Maria J Eriksson, Bengt Persson, Matthias Corbascio, Hans Persson, Cecilia Linde, Joakim Lundeberg
Abstract
Heart failure is a major health problem linked to poor quality of life and high mortality rates. Hence, novel biomarkers, such as fetal marker genes with low expression levels, could potentially differentiate disease states in order to improve therapy. In many studies on heart failure, cardiac biopsies have been analyzed as uniform pieces of tissue with bulk techniques, but this homogenization approach can mask medically relevant phenotypes occurring only in isolated parts of the tissue. This study examines such spatial variations within and between regions of cardiac biopsies. In contrast to standard RNA sequencing, this approach provides a spatially resolved transcriptome- and tissue-wide perspective of the adult human heart, and enables detection of fetal marker genes expressed by minor subpopulations of cells within the tissue. Analysis of patients with heart failure, with preserved ejection fraction, demonstrated spatially divergent expression of fetal genes in cardiac biopsies.
Conflict of interest statement
P.L.S. and J.L. are founders of a company that holds IP rights to the presented technology.
Figures
References
- Roger VL. Epidemiology of heart failure. Circ. Res. 2013;113:646–659. doi: 10.1161/CIRCRESAHA.113.300268.
- Chowdhury A, et al. Expression of fibulin-6 in failing hearts and its role for cardiac fibroblastmigration. Cardiovasc. Res. 2014;103:509–520. doi: 10.1093/cvr/cvu161.
- Mearini G, et al. Atrogin-1 and MuRF1 regulate cardiac MyBP-C levels via different mechanisms. Cardiovasc. Res. 2010;85:357–366. doi: 10.1093/cvr/cvp348.
- Karamanlidis G, et al. Mitochondrial complex I deficiency increases protein acetylation and accelerates heart failure. Cell Metab. 2013;18:239–50. doi: 10.1016/j.cmet.2013.07.002.
- Akat KM, et al. Comparative RNA-sequencing analysis of myocardial and circulating small RNAs in human heart failure and their utility as biomarkers. Proc. Natl. Acad. Sci. USA. 2014;111:11151–6. doi: 10.1073/pnas.1401724111.
- Yang KC, et al. Deep RNA sequencing reveals dynamic regulation of myocardial noncoding RNAs in failing human heart and remodeling with mechanical circulatory support. Circulation. 2014;129:1009–1021. doi: 10.1161/CIRCULATIONAHA.113.003863.
- Ståhl PL, Salmén F, et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science. 2016;353:78–82. doi: 10.1126/science.aaf2403.
- Lonsdale J, et al. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 2013;45:580–5. doi: 10.1038/ng.2653.
- Gaborit B, et al. Human epicardial adipose tissue has a specific transcriptomic signature depending on its anatomical peri-atrial, peri-ventricular, or peri-coronary location. Cardiovasc. Res. 2015;108:62–73. doi: 10.1093/cvr/cvv208.
- Braas K, et al. Expression of peptidylglycine alpha-amidating monooxygenase: an in situ hybridization and immunocytochemical study. Endocrinology. 1992;130:2778–88. doi: 10.1210/endo.130.5.1572293.
- Bodine SC, et al. Identification of ubiquitin ligases required for skeletal muscle atrophy. Science. 2001;294:1704–8. doi: 10.1126/science.1065874.
- Zidar, N. et al. Cyclooxygenase in normal human tissues - is COX-1 really a constitutive isoform, and COX-2 an inducible isoform? J. Cell. Mol. Med. 10.1111/j.1582-4934.2008.00430.x (2009).
- Jain R, et al. Integration of Bmp and Wnt signaling by Hopx specifies commitment of cardiomyoblasts. Science. 2015;348:aaa6071. doi: 10.1126/science.aaa6071.
- Dirkx E, da Costa Martins PA, De Windt LJ. Regulation of fetal gene expression in heart failure. Biochim. Biophys. Acta - Mol. Basis Dis. 2013;1832:2414–2424. doi: 10.1016/j.bbadis.2013.07.023.
- Rajabi M, Kassiotis C, Razeghi P, Taegtmeyer H. Return to the fetal gene program protects the stressed heart: A strong hypothesis. Heart Fail. Rev. 2007;12:331–343. doi: 10.1007/s10741-007-9034-1.
- Taegtmeyer H, Sen S, Vela D. Return to the fetal gene program: A suggested metabolic link to gene expression in the heart. Ann. N. Y. Acad. Sci. 2010;1188:191–198. doi: 10.1111/j.1749-6632.2009.05100.x.
- Coles JG, et al. Cardioprotective stress response in the human fetal heart. J. Thorac. Cardiovasc. Surg. 2005;129:1128–1136. doi: 10.1016/j.jtcvs.2004.11.055.
- Bedada FB, et al. Acquisition of a quantitative, stoichiometrically conserved ratiometric marker of maturation status in stem cell-derived cardiac myocytes. Stem Cell Reports. 2014;3:594–605. doi: 10.1016/j.stemcr.2014.07.012.
- Ahuja P, et al. Divergent mitochondrial biogenesis responses in human cardiomyopathy. Circulation. 2013;127:1957–1967. doi: 10.1161/CIRCULATIONAHA.112.001219.
- Linde, C. et al. Rationale and design of the PREFERS (Preserved and Reduced Ejection Fraction Epidemiological Regional Study) Stockholm heart failure study: an epidemiological regional study in Stockholm county of 2. 1 million inhabitants. Eur. J. Heart Fail. 1–11, 10.1002/ejhf.599 (2016).
- Vickovic S, et al. Massive and parallel expression profiling using microarrayed single-cell sequencing. Nat. Commun. 2016;7:1–9. doi: 10.1038/ncomms13182.
- Jemt, A. et al. An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries. Sci. Rep. (2016).
- Lundin S, et al. Increased throughput by parallelization of library preparation for massive sequencing. PLoS One. 2010;5:e10029. doi: 10.1371/journal.pone.0010029.
- Dobin A, et al. STAR: ultrafast universal RNA-seq aligne≥r. Bioinformatics. 2013;29:15–21. doi: 10.1093/bioinformatics/bts635.
- Anders S, Pyl PT, Huber W. HTSeq - A Python framework to work with high-throughput sequencing data. Bioinformatics. 2014;31:166–169. doi: 10.1093/bioinformatics/btu638.
- Sjöstrand, J. & Fernandez Navarro, J. TagGD.
- Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq. 2. Genome Biol. 2014;15:550. doi: 10.1186/s13059-014-0550-8.
- Li, H. seqtk. (2013).
- Warnes, G. R. et al. gplots: Various R programming tools for plotting data. R Packag. version2 (2009).
Source: PubMed