Multi-Cellular Transcriptional Analysis of Mammalian Heart Regeneration

Gregory A Quaife-Ryan, Choon Boon Sim, Mark Ziemann, Antony Kaspi, Haloom Rafehi, Mirana Ramialison, Assam El-Osta, James E. Hudson, Enzo R Porrello

Research output: Contribution to journalArticleResearchpeer-review

Abstract

BACKGROUND—: The inability of the adult mammalian heart to regenerate following injury represents a major barrier in cardiovascular medicine. In contrast, the neonatal mammalian heart retains a transient capacity for regeneration, which is lost shortly after birth. Defining the molecular mechanisms that govern regenerative capacity in the neonatal period remains a central goal in cardiac biology. Here, we assemble a transcriptomic framework of multiple cardiac cell populations during postnatal development and following injury, which enables comparative analyses of the regenerative (neonatal) versus non-regenerative (adult) state for the first time. METHODS—: Cardiomyocytes, fibroblasts, leukocytes and endothelial cells from infarcted and non-infarcted neonatal (P1) and adult (P56) mouse hearts were isolated by enzymatic dissociation and FACS at day 3 following surgery. RNA sequencing (RNA-seq) was performed on these cell populations to generate the transcriptome of the major cardiac cell populations during cardiac development, repair and regeneration. To complement our transcriptomic data, we also surveyed the epigenetic landscape of cardiomyocytes during postnatal maturation by performing deep sequencing of accessible chromatin regions using the Assay for Transposase-Accessible Chromatin (ATAC-seq) from purified mouse cardiomyocyte nuclei (P1, P14 and P56). RESULTS—: Profiling of cardiomyocyte and non-myocyte transcriptional programs uncovered several injury-responsive genes across regenerative and non-regenerative time points. However, the majority of transcriptional changes in all cardiac cell types resulted from developmental maturation from neonatal stages to adulthood rather than activation of a distinct regeneration-specific gene program. Furthermore, adult leukocytes and fibroblasts were characterized by the expression of a proliferative gene expression network following infarction, which mirrored the neonatal state. In contrast, cardiomyocytes failed to re-activate the neonatal proliferative network following infarction, which was associated with loss of chromatin accessibility around cell cycle genes during postnatal maturation. CONCLUSIONS—: This work provides a comprehensive framework and transcriptional resource of multiple cardiac cell populations during cardiac development, repair and regeneration. Our findings define a regulatory program underpinning the neonatal regenerative state and identify alterations in the chromatin landscape that could limit re-induction of the regenerative program in adult cardiomyocytes.

Original languageEnglish
Pages (from-to)1123-1139
Number of pages17
JournalCirculation
Volume136
Issue number12
DOIs
Publication statusPublished - 19 Sep 2017

Keywords

  • ATAC-seq
  • cell proliferation
  • epigenomics
  • muscle cells
  • myocardial infarction
  • regeneration
  • transcriptional profiling

Cite this

Quaife-Ryan, G. A., Sim, C. B., Ziemann, M., Kaspi, A., Rafehi, H., Ramialison, M., ... Porrello, E. R. (2017). Multi-Cellular Transcriptional Analysis of Mammalian Heart Regeneration. Circulation, 136(12), 1123-1139. https://doi.org/10.1161/CIRCULATIONAHA.117.028252
Quaife-Ryan, Gregory A ; Sim, Choon Boon ; Ziemann, Mark ; Kaspi, Antony ; Rafehi, Haloom ; Ramialison, Mirana ; El-Osta, Assam ; Hudson, James E. ; Porrello, Enzo R. / Multi-Cellular Transcriptional Analysis of Mammalian Heart Regeneration. In: Circulation. 2017 ; Vol. 136, No. 12. pp. 1123-1139.
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abstract = "BACKGROUND—: The inability of the adult mammalian heart to regenerate following injury represents a major barrier in cardiovascular medicine. In contrast, the neonatal mammalian heart retains a transient capacity for regeneration, which is lost shortly after birth. Defining the molecular mechanisms that govern regenerative capacity in the neonatal period remains a central goal in cardiac biology. Here, we assemble a transcriptomic framework of multiple cardiac cell populations during postnatal development and following injury, which enables comparative analyses of the regenerative (neonatal) versus non-regenerative (adult) state for the first time. METHODS—: Cardiomyocytes, fibroblasts, leukocytes and endothelial cells from infarcted and non-infarcted neonatal (P1) and adult (P56) mouse hearts were isolated by enzymatic dissociation and FACS at day 3 following surgery. RNA sequencing (RNA-seq) was performed on these cell populations to generate the transcriptome of the major cardiac cell populations during cardiac development, repair and regeneration. To complement our transcriptomic data, we also surveyed the epigenetic landscape of cardiomyocytes during postnatal maturation by performing deep sequencing of accessible chromatin regions using the Assay for Transposase-Accessible Chromatin (ATAC-seq) from purified mouse cardiomyocyte nuclei (P1, P14 and P56). RESULTS—: Profiling of cardiomyocyte and non-myocyte transcriptional programs uncovered several injury-responsive genes across regenerative and non-regenerative time points. However, the majority of transcriptional changes in all cardiac cell types resulted from developmental maturation from neonatal stages to adulthood rather than activation of a distinct regeneration-specific gene program. Furthermore, adult leukocytes and fibroblasts were characterized by the expression of a proliferative gene expression network following infarction, which mirrored the neonatal state. In contrast, cardiomyocytes failed to re-activate the neonatal proliferative network following infarction, which was associated with loss of chromatin accessibility around cell cycle genes during postnatal maturation. CONCLUSIONS—: This work provides a comprehensive framework and transcriptional resource of multiple cardiac cell populations during cardiac development, repair and regeneration. Our findings define a regulatory program underpinning the neonatal regenerative state and identify alterations in the chromatin landscape that could limit re-induction of the regenerative program in adult cardiomyocytes.",
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Quaife-Ryan, GA, Sim, CB, Ziemann, M, Kaspi, A, Rafehi, H, Ramialison, M, El-Osta, A, Hudson, JE & Porrello, ER 2017, 'Multi-Cellular Transcriptional Analysis of Mammalian Heart Regeneration', Circulation, vol. 136, no. 12, pp. 1123-1139. https://doi.org/10.1161/CIRCULATIONAHA.117.028252

Multi-Cellular Transcriptional Analysis of Mammalian Heart Regeneration. / Quaife-Ryan, Gregory A; Sim, Choon Boon; Ziemann, Mark; Kaspi, Antony; Rafehi, Haloom; Ramialison, Mirana; El-Osta, Assam; Hudson, James E.; Porrello, Enzo R.

In: Circulation, Vol. 136, No. 12, 19.09.2017, p. 1123-1139.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Multi-Cellular Transcriptional Analysis of Mammalian Heart Regeneration

AU - Quaife-Ryan, Gregory A

AU - Sim, Choon Boon

AU - Ziemann, Mark

AU - Kaspi, Antony

AU - Rafehi, Haloom

AU - Ramialison, Mirana

AU - El-Osta, Assam

AU - Hudson, James E.

AU - Porrello, Enzo R

PY - 2017/9/19

Y1 - 2017/9/19

N2 - BACKGROUND—: The inability of the adult mammalian heart to regenerate following injury represents a major barrier in cardiovascular medicine. In contrast, the neonatal mammalian heart retains a transient capacity for regeneration, which is lost shortly after birth. Defining the molecular mechanisms that govern regenerative capacity in the neonatal period remains a central goal in cardiac biology. Here, we assemble a transcriptomic framework of multiple cardiac cell populations during postnatal development and following injury, which enables comparative analyses of the regenerative (neonatal) versus non-regenerative (adult) state for the first time. METHODS—: Cardiomyocytes, fibroblasts, leukocytes and endothelial cells from infarcted and non-infarcted neonatal (P1) and adult (P56) mouse hearts were isolated by enzymatic dissociation and FACS at day 3 following surgery. RNA sequencing (RNA-seq) was performed on these cell populations to generate the transcriptome of the major cardiac cell populations during cardiac development, repair and regeneration. To complement our transcriptomic data, we also surveyed the epigenetic landscape of cardiomyocytes during postnatal maturation by performing deep sequencing of accessible chromatin regions using the Assay for Transposase-Accessible Chromatin (ATAC-seq) from purified mouse cardiomyocyte nuclei (P1, P14 and P56). RESULTS—: Profiling of cardiomyocyte and non-myocyte transcriptional programs uncovered several injury-responsive genes across regenerative and non-regenerative time points. However, the majority of transcriptional changes in all cardiac cell types resulted from developmental maturation from neonatal stages to adulthood rather than activation of a distinct regeneration-specific gene program. Furthermore, adult leukocytes and fibroblasts were characterized by the expression of a proliferative gene expression network following infarction, which mirrored the neonatal state. In contrast, cardiomyocytes failed to re-activate the neonatal proliferative network following infarction, which was associated with loss of chromatin accessibility around cell cycle genes during postnatal maturation. CONCLUSIONS—: This work provides a comprehensive framework and transcriptional resource of multiple cardiac cell populations during cardiac development, repair and regeneration. Our findings define a regulatory program underpinning the neonatal regenerative state and identify alterations in the chromatin landscape that could limit re-induction of the regenerative program in adult cardiomyocytes.

AB - BACKGROUND—: The inability of the adult mammalian heart to regenerate following injury represents a major barrier in cardiovascular medicine. In contrast, the neonatal mammalian heart retains a transient capacity for regeneration, which is lost shortly after birth. Defining the molecular mechanisms that govern regenerative capacity in the neonatal period remains a central goal in cardiac biology. Here, we assemble a transcriptomic framework of multiple cardiac cell populations during postnatal development and following injury, which enables comparative analyses of the regenerative (neonatal) versus non-regenerative (adult) state for the first time. METHODS—: Cardiomyocytes, fibroblasts, leukocytes and endothelial cells from infarcted and non-infarcted neonatal (P1) and adult (P56) mouse hearts were isolated by enzymatic dissociation and FACS at day 3 following surgery. RNA sequencing (RNA-seq) was performed on these cell populations to generate the transcriptome of the major cardiac cell populations during cardiac development, repair and regeneration. To complement our transcriptomic data, we also surveyed the epigenetic landscape of cardiomyocytes during postnatal maturation by performing deep sequencing of accessible chromatin regions using the Assay for Transposase-Accessible Chromatin (ATAC-seq) from purified mouse cardiomyocyte nuclei (P1, P14 and P56). RESULTS—: Profiling of cardiomyocyte and non-myocyte transcriptional programs uncovered several injury-responsive genes across regenerative and non-regenerative time points. However, the majority of transcriptional changes in all cardiac cell types resulted from developmental maturation from neonatal stages to adulthood rather than activation of a distinct regeneration-specific gene program. Furthermore, adult leukocytes and fibroblasts were characterized by the expression of a proliferative gene expression network following infarction, which mirrored the neonatal state. In contrast, cardiomyocytes failed to re-activate the neonatal proliferative network following infarction, which was associated with loss of chromatin accessibility around cell cycle genes during postnatal maturation. CONCLUSIONS—: This work provides a comprehensive framework and transcriptional resource of multiple cardiac cell populations during cardiac development, repair and regeneration. Our findings define a regulatory program underpinning the neonatal regenerative state and identify alterations in the chromatin landscape that could limit re-induction of the regenerative program in adult cardiomyocytes.

KW - ATAC-seq

KW - cell proliferation

KW - epigenomics

KW - muscle cells

KW - myocardial infarction

KW - regeneration

KW - transcriptional profiling

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U2 - 10.1161/CIRCULATIONAHA.117.028252

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JF - Circulation

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