CoChat
Sign Up
PreprintCited by 59Single-cell and spatial transcriptomicsPluripotent Stem Cells ResearchCell Image Analysis Techniques

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Cell states beyond transcriptomics: integrating structural organization and gene expression in hiPSC-derived cardiomyocytes

Open access
Gerbin, Kaytlyn A., Grancharova, Tanya, Donovan-Maiye, Rory, Hendershott, Melissa C., Brown, Jackson, Dinh, Stephanie Q., Gehring, Jamie L., Hirano, Matthew, Johnson, Gregory R., Nath, Aditya, Nelson, Angelique, Roco, Charles M., Rosenberg, Alexander B., Filip Sluzewski, M., Viana, Matheus P., Yan, Calysta, Zaunbrecher, Rebecca J., Cordes Metzler, Kimberly R., Menon, Vilas, Palecek, Sean P., Seelig, Georg, Gaudreault, Nathalie, Knijnenburg, Theo, Rafelski, Susanne M., Theriot, Julie A., Gunawardane, Ruwanthi N.·2020·Cell Systems
DOI 10.1101/2020.05.26.081083

Preprint — published as 10.1016/j.cels.2021.05.001 · Paper page

Open this paper in CoChat — free accountOpen PDF

Abstract

Summary: We present a quantitative co-analysis of RNA abundance and sarcomere organization in single cells and an integrated framework to predict subcellular organization states from gene expression. We used human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes expressing mEGFP-tagged alpha-actinin-2 to develop quantitative image analysis tools for systematic and automated classification of subcellular organization. This captured a wide range of sarcomeric organization states within cell populations that were previously difficult to quantify. We performed RNA FISH targeting genes identified by single cell RNA sequencing to simultaneously assess the relationship between transcript abundance and structural states in single cells. Co-analysis of gene expression and sarcomeric patterns in the same cells revealed biologically meaningful correlations that could be used to predict organizational states. This study establishes a framework for multi-dimensional analysis of single cells to study the relationships between gene expression and subcellular organization and to develop a more nuanced description of cell states. Graphical Abstract: Transcriptional profiling and structural classification was performed on human induced pluripotent stem cell-derived cardiomyocytes to characterize the relationship between transcript abundance and subcellular organization.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2020.05.26.081083

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

  • Global quantification of mammalian gene expression control

    Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · cited 1×

    “Ribosomal proteins, for example, show only a weak correlation between RNA expression and protein abundance due to their relative stability and highly regulated post-translational assembly into stoichiometric complexes (Schwanhausser et al., 2011).”
    Background

Flagged first, then by citations

Research works printed but not linked: 132

  1. 1916, The Causal Relations between Structure and Function in Biology, The American Journal of Psychology, 27, 245, 10.2307/1413176 · DOI
  2. 2018, Following hearts, one cell at a time: recent applications of single-cell RNA sequencing to the understanding of heart disease, Nat Commun, 9, 4434, 10.1038/s41467-018-06894-8 · DOI
  3. 2018, Identifying cell populations with scRNASeq, Mol Aspects Med, 59, 114, 10.1016/j.mam.2017.07.002 · DOI
  4. 10.1016/j.cell.2015.11.018 · DOI · Paper page
  5. 2019, Single-Cell RNA-Sequencing and Optical Electrophysiology of Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Reveal Discordance Between Cardiac Subtype-Associated Gene Expression Patterns and Electrophysiological Phenotypes, Stem Cells Dev, 28, 659, 10.1089/scd.2019.0030 · DOI · Paper page
  6. 10.1016/j.scr.2013.09.003 · DOI
  7. 10.3390/cells2020294 · DOI
  8. 10.1161/01.RES.61.3.329 · DOI
  9. 10.1002/cm.20290 · DOI · Paper page
  10. 10.1038/nbt.4096 · DOI · Paper page
  11. 10.1038/nrm3918 · DOI
  12. 10.1242/dev.130534 · DOI
  13. 10.1016/j.tcb.2016.07.004 · DOI · Paper page
  14. 2019, Single-Cell RNA Sequencing of the Cardiovascular System: New Looks for Old Diseases, Front Cardiovasc Med, 6, 173, 10.3389/fcvm.2019.00173 · DOI
  15. Chen, J. , Ding, L. , Viana, M.P. , Hendershott, M.C. , Yang, R. , Mueller, I.A. , and Rafelski, S.M. (2018). The Allen Cell Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures influorescence microscopy images. bioRxiv. · DOI · Paper page
  16. Chen, K.H. , Boettiger, A.N. , Moffitt, J.R. , Wang, S. , and Zhuang, X . (2015). RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090. · DOI · Paper page
  17. Choi, H.M.T. , Schwarzkopf, M. , Fornace, M.E. , Acharya, A. , Artavanis, G. , Stegmaier, J. , Cunha, A. , and Pierce, N.A . (2018). Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust. Development 145. · DOI · Paper page
  18. 10.1016/j.devcel.2017.12.012 · DOI
  19. 2018, Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis, Nat Commun, 9, 4906, 10.1038/s41467-018-07333-4 · DOI · Paper page
  20. Cui, M. , Wang, Z. , Bassel-Duby, R. , and Olson, E.N . (2018). Genetic and epigenetic regulation of cardiomyocytes in development, regeneration and disease. Development 145. · DOI · Paper page
  21. 10.1016/j.celrep.2019.01.079 · DOI
  22. 10.1096/fj.201500096R · DOI
  23. 10.1016/j.devcel.2016.10.001 · DOI
  24. 10.1016/j.bbamcr.2015.10.014 · DOI · Paper page
  25. 10.1093/bioinformatics/bts635 · DOI · Paper page
  26. 2019, Coculture of Endothelial Cells with Human Pluripotent Stem Cell-Derived Cardiac Progenitors Reveals a Differentiation Stage-Specific Enhancement of Cardiomyocyte Maturation, Biotechnol J, 14, e1800725, 10.1002/biot.201800725 · DOI
  27. 10.15252/msb.20167144 · DOI · Paper page
  28. 1979, Bootstrap Methods: Another Look at the Jackknife, The Annals of Statistics, 7, 1
  29. 2019, Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+, Nature, 568, 235, 10.1038/s41586-019-1049-y · DOI · Paper page
  30. 10.1038/onc.2008.347 · DOI
  31. Fenix, A.M. , Neininger, A.C. , Taneja, N. , Hyde, K. , Visetsouk, M.R. , Garde, R.J. , Liu, B. , Nixon, B.R. , Manalo, A.E. , Becker, J.R. , et al. (2018). Muscle-specific stress fibers give rise to sarcomeres in cardiomyocytes. Elife 7. · DOI
  32. 2018, Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation, Cell Stem Cell, 23, 586, 10.1016/j.stem.2018.09.009 · DOI · Paper page
  33. 10.18637/jss.v033.i01 · DOI · Paper page
  34. 10.1186/s13059-016-1045-6 · DOI · Paper page
  35. 10.1161/01.RES.54.6.694 · DOI
  36. 2014, Validation of noise models for single-cell transcriptomics, Nature Methods, 11, 637, 10.1038/nmeth.2930 · DOI · Paper page
  37. 10.1126/science.aax0249 · DOI · Paper page
  38. Gut, G. , Herrmann, M.D. , and Pelkmans, L . (2018). Multiplexed protein maps link subcellular organization to cellular states. Science 361, eaar7042. · DOI · Paper page
  39. 10.1038/173971a0 · DOI · Paper page
  40. 10.1038/173973a0 · DOI
  41. Judge, L.M. , Perez-Bermejo, J.A. , Truong, A. , Ribeiro, A.J. , Yoo, J.C. , Jensen, C.L. , Mandegar, M.A. , Huebsch, N. , Kaake, R.M. , So, P.L. , et al. (2017). A BAG3 chaperone complex maintains cardiomyocyte function during proteotoxic stress. JCI Insight 2. · DOI
  42. 10.1253/circj.CJ-12-0987 · DOI · Paper page
  43. 10.1093/bioinformatics/btr095 · DOI
  44. Kandel, E.R. , Schwartz, J.H. , Jessell, T.M. , Siegelbaum, S.A. , and Hudspeth, A.J. (2012). Principles of Nueral Science, 5 edn (McGraw-Hill Education).
  45. Karbassi, E. , Fenix, A. , Marchiano, S. , Muraoka, N. , Nakamura, K. , Yang, X. , and Murry, C.E . (2020). Cardiomyocyte maturation: advances in knowledge and implications for regenerative medicine. Nat Rev Cardiol. · DOI
  46. 10.1161/CIRCRESAHA.110.231514 · DOI
  47. 2014, Bayesian approach to single-cell differential expression analysis, Nature Methods, 11, 740, 10.1038/nmeth.2967 · DOI · Paper page
  48. 2015, Single-Cell Expression Profiling Reveals a Dynamic State of Cardiac Precursor Cells in the Early Mouse Embryo, PLoS One, 10, e0140831, 10.1371/journal.pone.0140831 · DOI
  49. 2013, A robust method to derive functional neural crest cells from human pluripotent stem cells, Am J Stem Cells, 2, 119
  50. 2019, HIMF (Hypoxia-Induced Mitogenic Factor)-IL (Interleukin)-6 Signaling Mediates Cardiomyocyte-Fibroblast Crosstalk to Promote Cardiac Hypertrophy and Fibrosis, Hypertension, 73, 1058, 10.1161/HYPERTENSIONAHA.118.12267 · DOI
  51. 10.1038/nprot.2014.191 · DOI · Paper page
  52. 10.1126/science.aao4174 · DOI
  53. 10.1177/0963689718779346 · DOI
  54. 2018, Localization of transcripts, translation, and degradation for spatiotemporal sarcomere maintenance, J Mol Cell Cardiol, 116, 16, 10.1016/j.yjmcc.2018.01.012 · DOI
  55. 10.1016/j.devcel.2016.10.014 · DOI
  56. 10.1073/pnas.1200250109 · DOI · Paper page
  57. 10.1038/nnano.2013.34 · DOI
  58. Liu, J. , Huang, Y. , Singh, R. , Vert, J.-P. , and Noble, W.S. (2019). Jointly embedding multiple single-cell omics measurements. bioRxiv. · DOI
  59. 10.1038/nbt.4162 · DOI
  60. Lopez, R. , Nazaret, A. , Langevin, M. , Samaran, J. , Regier, J. , Jordan, M.I. , and Yosef, N. (2019). A joint model of unpaired data from scRNA-seq and spatial transcriptomics for imputing missing gene expression measurements. In arXiv e-prints.
  61. 10.1038/msb.2010.106 · DOI · Paper page
  62. 10.1089/scd.2012.0490 · DOI · Paper page
  63. 10.1073/pnas.1103216108 · DOI
  64. 10.1038/316696a0 · DOI
  65. 10.1016/j.cell.2015.05.002 · DOI · Paper page
  66. Mann, H.B. , and Whitney, D.R . (1947). On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other. In The Annals of Mathematical Statistics, pp. 50–60. · DOI · Paper page
  67. 10.1006/bbrc.1999.0531 · DOI
  68. 10.1093/nar/gks042 · DOI · Paper page
  69. McDermott-Roe, C. , Lv, W. , Maximova, T. , Wada, S. , Bukowy, J. , Marquez, M. , Lai, S. , Shehu, A. , Benjamin, I. , Geurts, A. , et al. (2019). Investigation of a dilated cardiomyopathy-associated variant in BAG3 using genome-edited iPSC-derived cardiomyocytes. JCI Insight 4. · DOI
  70. McInnes, L. , Healy, J. , and Melville, J. (2018). UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction. In arXiv e-prints. · DOI · Paper page
  71. McKinney, W. , and others (2010). Data structures for statistical computing in python. In In Proceedings of the 9th Python in Science Conference (Austin, TX), pp. 51–56. · DOI
  72. McQuin C, G.A. , Chernyshev V , Kamentsky L , Cimini BA , Karhohs KW , Doan M , Ding L , Rafelski SM , Thirstrup D , Wiegraebe W , Singh S , Becker T , Caicedo JC , Carpenter AE (2018). CellProfiler 3.0: Next-generation image processing for biology. PLoS Biology 16. · DOI
  73. 10.1073/pnas.1612826113 · DOI
  74. 2020, Striated myocyte structural integrity: Automated analysis of sarcomeric z-discs, PLoS Comput Biol, 16, e1007676, 10.1371/journal.pcbi.1007676 · DOI
  75. 10.1016/j.cell.2019.12.023 · DOI · Paper page
  76. 10.3181/00379727-4-96 · DOI
  77. 10.1016/j.molcel.2015.03.005 · DOI
  78. Paik, D.T. , Cho, S. , Tian, L. , Chang, H.Y. , and Wu, J.C . (2020). Single-cell RNA sequencing in cardiovascular development, disease and medicine. Nat Rev Cardiol. · DOI
  79. 10.1242/dev.117010 · DOI
  80. 10.1016/j.celrep.2011.12.009 · DOI
  81. Paszke, A. , Gross, S. , Massa, F. , Lerer, A. , Bradbury, J. , Chanan, G. , Killeen, T. , Lin, Z. , Gimelshein, N. , Antiga, L ., et al. (2019). PyTorch: An Imperative Style, High-Performance Deep Learning Library. In (Curran Associates, Inc.), pp. 8024–8035.
  82. 2011, Scikit-learn: Machine Learning in Python, Journal of Machine Learning Research, 12, 2825
  83. 2018, The developmental transcriptome of the human heart, Sci Rep, 8, 15362, 10.1038/s41598-018-33837-6 · DOI
  84. 10.1038/nbt.3973 · DOI · Paper page
  85. 2016, Isolation and Mechanical Measurements of Myofibrils from Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes, Stem Cell Reports, 6, 885, 10.1016/j.stemcr.2016.04.006 · DOI
  86. Piquereau, J. , and Ventura-Clapier, R . (2018). Maturation of Cardiac Energy Metabolism During Perinatal Development. Frontiers in Physiology 9. · DOI
  87. 2018, Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells, Cell Syst, 7, 398, 10.1016/j.cels.2018.09.001 · DOI
  88. 10.1038/nprot.2013.067 · DOI
  89. 2015, Contractile properties of developing human fetal cardiac muscle, J Physiol, 594, 437
  90. 10.1038/nmeth.1253 · DOI · Paper page
  91. 10.1038/s41467-019-08388-7 · DOI
  92. 10.1152/ajpheart.2001.280.4.H1814 · DOI · Paper page
  93. 10.1091/mbc.E17-03-0209 · DOI · Paper page
  94. 2019, Fluorescent Gene Tagging of Transcriptionally Silent Genes in hiPSCs, Stem Cell Reports, 12, 1145, 10.1016/j.stemcr.2019.03.001 · DOI
  95. 10.1093/bioinformatics/btp616 · DOI · Paper page
  96. 10.1115/1.4027145 · DOI
  97. 2018, Advanced maturation of human cardiac tissue grown from pluripotent stem cells, Nature, 556, 239, 10.1038/s41586-018-0016-3 · DOI · Paper page
  98. 10.1126/science.aam8999 · DOI · Paper page
  99. 1991, Topical steroid induced chronic demodicidosis, J Med Assoc Thai, 74, 116
  100. 10.1007/s10974-005-9016-7 · DOI
  101. 10.1038/nmeth.2019 · DOI · Paper page
  102. 2018, Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry, Cell Syst, 6, 25, 10.1016/j.cels.2017.12.001 · DOI
  103. 10.1038/s41467-018-02891-z · DOI
  104. 10.1242/dev.138560 · DOI
  105. 2019, Identification of Cell Types from Single-Cell Transcriptomic Data, Methods Mol Biol, 1935, 45, 10.1007/978-1-4939-9057-3_4 · DOI
  106. 10.1016/j.celrep.2017.12.072 · DOI
  107. 10.1152/ajpheart.00020.2003 · DOI
  108. 10.1073/pnas.0905729106 · DOI
  109. Spearman, C . (1904). The Proof and Measurement of Association between Two Things. The American Journal of Psychology 15. · DOI · Paper page
  110. Suryawanshi, H. , Clancy, R. , Morozov, P. , Halushka, M.K. , Buyon, J.P. , and Tuschl, T . (2019). Cell atlas of the fetal human heart and implications for autoimmune-mediated congenital heart block. Cardiovasc Res. · DOI
  111. 2018, High content analysis identifies unique morphological features of reprogrammed cardiomyocytes, Scientific Reports, 8, 1258, 10.1038/s41598-018-19539-z · DOI
  112. 2015, Where does the pulmonary artery catheter float: transesophageal echocardiography evaluation, Ann Card Anaesth, 18, 491, 10.4103/0971-9784.166450 · DOI
  113. 2019, SarcTrack, Circ Res, 124, 1172, 10.1161/CIRCRESAHA.118.314505 · DOI
  114. 2018, Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH, Cell Syst, 6, 171, 10.1016/j.cels.2018.01.014 · DOI
  115. 2018, Pingouin: statistics in Python, Journal of Open Source Software, 3, 1026, 10.21105/joss.01026 · DOI · Paper page
  116. 10.7717/peerj.453 · DOI
  117. 10.1002/stem.2403 · DOI
  118. 2018, Altair: Interactive Statistical Visualizations for Python, Journal of Open Source Software, 3, 1057, 10.21105/joss.01057 · DOI
  119. 10.1089/scd.2014.0533 · DOI
  120. 2020, SciPy 1.0: fundamental algorithms for scientific computing in Python, Nat Methods, 17, 261, 10.1038/s41592-019-0686-2 · DOI · Paper page
  121. 10.1038/s41598-018-22297-7 · DOI
  122. Wasserman, L . (2006). All of Nonparametric Statistics, 1 edn (New York: Springer-Verlag).
  123. Weber, N. , Kowalski, K. , Holler, T. , Radocaj, A. , Fischer, M. , Thiemann, S. , de la Roche, J. , Schwanke, K. , Piep, B. , Peschel, N. , et al. (2020). Advanced Single-Cell Mapping Reveals that in hESC Cardiomyocytes Contraction Kinetics and Action Potential Are Independent of Myosin Isoform. Stem Cell Reports. · DOI
  124. 10.1007/s00395-016-0587-9 · DOI
  125. Wickham, H . (2016). ggplot2: Elegant Graphics for Data Analysis, 2 edn (New York: Springer-Verlag New York).
  126. 10.1186/s13059-017-1382-0 · DOI · Paper page
  127. 10.1016/j.devcel.2018.03.019 · DOI
  128. 2012, Differentiation and enrichment of cardiomyocytes from human pluripotent stem cells, J Mol Cell Cardiol, 52, 1203, 10.1016/j.yjmcc.2012.03.012 · DOI
  129. 10.1002/stem.166 · DOI
  130. 10.1161/CIRCRESAHA.114.300558 · DOI · Paper page
  131. 10.1093/bioinformatics/btv053 · DOI
  132. 10.1111/j.1467-9868.2005.00503.x · DOI · Paper page

Cited by

Sorted by citations

Metadata

Authors
Gerbin, K. A., Grancharova, T., Donovan-Maiye, R., Hendershott, M. C., Brown, J., Dinh, S. Q., Gehring, J. L., Hirano, M., Johnson, G. R., Nath, A., Nelson, A., Roco, C. M., Rosenberg, A. B., Filip Sluzewski, M., Viana, M. P., Yan, C., Zaunbrecher, R. J., Cordes Metzler, K. R., Menon, V., Palecek, S. P., Seelig, G., Gaudreault, N., Knijnenburg, T., Rafelski, S. M., Theriot, J. A., & Gunawardane, R. N.
Affiliations
  • Allen Institute for Cell Science (US)
  • University of Washington (US)
  • Columbia University Irving Medical Center (US)
  • University of Wisconsin–Madison (US)
  • Howard Hughes Medical Institute (US)
Corresponding author
Gunawardane, Ruwanthi N.
ORCID
Venue
Cell Systems
Publisher
openRxiv
Published
2020-05-27
Volume
12
Issue
6
Pages
670-687.e10
ISSN
2405-4712 (ISSN-L)
DOI
10.1101/2020.05.26.081083
OpenAlex
W3164615498
Cited by
59
References
1
Citations by year
2026: 5 · 2025: 10 · 2024: 12 · 2023: 13 · 2022: 11 · 2021: 7 · 2020: 1
FWCI
3.37
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell Systems (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
Funders
  • Howard Hughes Medical Institute
  • Gladstone Institutes
  • University of California, San Francisco
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
Keywords
cell states, human induced pluripotent stem cell-derived cardiomyocytes, subcellular organization, sarcomere organization, single-cell imaging, gene expression, mRNA levels, beta-myosin heavy chain, MYH7, cellular heterogeneity, single-cell classification
MeSH terms
Cell Differentiation, Humans, Myocytes, Cardiac, Induced Pluripotent Stem Cells, Transcriptome

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review