The ribosomal prolyl-hydroxylase OGFOD1 decreases during cardiac differentiation and modulates translation and splicing

Stoehr, Andrea; Kennedy, Leslie; Yang, Yanqin; Patel, Sajni; Lin, Yongshun; Linask, Kaari L.; Fergusson, Marı́a M.; Jun, Zhu; Guček, Marjan; Zou, Jizhong; Murphy, Elizabeth

doi:10.1172/jci.insight.128496

Cited by 12 publications

(13 citation statements)

References 36 publications

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“…Cx43, which is a member of the connexin family, is the major protein expressed in the mammalian heart [42]. These markers are often used to evaluate the differentiation of CMs from iPS cells [43][44][45][46]. Therefore, we examined the expression of GATA4, cTnI, cTnT, and Cx43 mRNA by RT-PCR and the expression of the corresponding proteins by immunostaining.…”

Section: Discussionmentioning

confidence: 99%

Negative chronotropic and inotropic effects of lubiprostone on iPS cell-derived cardiomyocytes via activation of CFTR

Akita

Yoshie

Ishida

et al. 2020

BMC Complement Med Ther

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Background: Lubiprostone (LBP) is a novel chloride channel opener that has been reported to activate chloride channel protein 2 (ClC-2) and cystic fibrosis transmembrane conductance regulator (CFTR). LBP facilitates fluid secretion by activating CFTR in the intestine and is used as a drug for treating chronic constipation. While ClC-2 and CFTR expression has been confirmed in cardiomyocytes (CMs), the effect of LBP on CMs has not yet been investigated. Thus, the present study aimed to investigate the effect of LBP on CMs using mouse-induced pluripotent stem (iPS) cell-derived CMs (iPS-CMs). Methods: We induced mouse iPS cells into CMs through embryoid body (EB) formation. We compared the differentiated cells to CMs isolated from adult and fetal mice using gene expression, spontaneous beating rate, and contraction ratio analyses. Results: Gene expression analysis revealed that, in the iPS-CMs, the mRNA expression of the undifferentiated cell markers Rex1 and Nanog decreased, whereas the expression of the unique cardiomyocyte markers cardiac troponin I (cTnI) and cardiac troponin T (cTNT), increased. Immunostaining showed that the localization of cTnI and connexin-43 in the iPS-CMs was similar to that in the primary fetal CMs (FCMs) and adult CMs (ACMs). LBP decreased the spontaneous beating rate of the iPS-CMs and FCMs, and decreased the contraction ratio of the iPS-CMs and ACMs. The reduction in the beating rate and contraction ratio caused by LBP was inhibited by glycine hydrazide (GlyH), which is a CFTR inhibitor. Conclusion: These results suggest that LBP stimulates CFTR in CMs and that LBP has negative chronotropic and inotropic effects on CMs. LBP may be useful for treating cardiac diseases such as heart failure, ischemia, and arrhythmia.

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Section: Discussionmentioning

confidence: 99%

Negative chronotropic and inotropic effects of lubiprostone on iPS cell-derived cardiomyocytes via activation of CFTR

Akita

Yoshie

Ishida

et al. 2020

BMC Complement Med Ther

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“…The effect of Cas9-mediated homozygous knockout of OGFOD1 in cardiomyocytes was investigated by Stoehr et al. ( 11 ). The top 20 off-targets predicted by ( 45 ) were sequenced, without finding mutations attributable to off-target effects ( 11 ).…”

Section: Methodsmentioning

confidence: 99%

“…( 11 ). The top 20 off-targets predicted by ( 45 ) were sequenced, without finding mutations attributable to off-target effects ( 11 ). RNA-seq data was downloaded in four replicates for both knockout and wild-type cells.…”

Section: Methodsmentioning

confidence: 99%

`CRISPRroots`: on- and off-target assessment of RNA-seq data in CRISPR–Cas9 edited cells

Corsi

Gadekar

Gorodkin

et al. 2021

Nucleic Acids Research

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The CRISPR-Cas9 genome editing tool is used to study genomic variants and gene knockouts, and can be combined with transcriptomic analyses to measure the effects of such alterations on gene expression. But how can one be sure that differential gene expression is due to a successful intended edit and not to an off-target event, without performing an often resource-demanding genome-wide sequencing of the edited cell or strain? To address this question we developed CRISPRroots: CRISPR–Cas9-mediated edits with accompanying RNA-seq data assessed for on-target and off-target sites. Our method combines Cas9 and guide RNA binding properties, gene expression changes, and sequence variants between edited and non-edited cells to discover potential off-targets. Applied on seven public datasets, CRISPRroots identified critical off-target candidates that were overlooked in all of the corresponding previous studies. CRISPRroots is available via https://rth.dk/resources/crispr.

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“…4A, Table S3). [24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43] These protocols use combinations of signaling proteins and small molecules over a range of 7 days to 23 days to make the differentiated CMs. Therefore, the list of compiled protocols covered in our study includes a wide range of differentiation molecules and timelines ( Fig.…”

Section: Evaluating Pluripotent Stem Cell Differentiation Toward Cardmentioning

confidence: 99%

Integrated analysis of high throughput transcriptomic data revealed specific gene expression signature of cardiomyocytes

Omrani

Sharifi

Khazaei

et al. 2020

Preprint

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Tel: 001 438 985 2772 Funding: The authors have no support or funding to report. This research did not receive any external funding and was conducted using the authors' personal money. Abstract:Acquiring a specific transcriptomic signature of the human and mouse cardiomyocyte (CM) will greatly increase our understanding of their biology and associated diseases that remain the most deadly across the world. In this study, using comprehensive transcriptomic mining of 91 cell types over 877 samples from bulk RNA-sequencing, single cell RNA-sequencing, and microarray techniques, we describe a unique 118-gene signature of human and mouse primary CMs. Once we had access to this CM-specific gene signature, we investigated the spatial heterogeneity of CMs throughout the heart tissue. Moreover, we compared the CM-specific gene signature to that of CMs derived from 10 differentiation protocols, and we identified the protocols that generate cells most similar to primary CMs. Finally, we looked at the specific differences between primary and differentiated CMs and found that differentiated cells underexpress genes related to CM development and maturity. The differentiated cells conversely overexpressed cell cycle-related genes, resulting in the progenitor features that remain in differentiated CMs compared to primary adult CMs. The presence of histone post translational modification H3K27a from ChIP sequencing data sets were used to confirm transcriptomic findings. To the best of our knowledge, this is the most comprehensive study to date that unravels the unique transcrtipomic signature of primary and differentiated CMs. This study provides important insights into our understanding of CM biology and the moelcular mechanisms that make them such a unique cell type. Moreover, the specific transcritpomic signature of CMs could be used in developmental studies, stem cell therapy, regenerative medicine, and drug screening assays.

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The ribosomal prolyl-hydroxylase OGFOD1 decreases during cardiac differentiation and modulates translation and splicing

Cited by 12 publications

References 36 publications

Negative chronotropic and inotropic effects of lubiprostone on iPS cell-derived cardiomyocytes via activation of CFTR

Negative chronotropic and inotropic effects of lubiprostone on iPS cell-derived cardiomyocytes via activation of CFTR

`CRISPRroots`: on- and off-target assessment of RNA-seq data in CRISPR–Cas9 edited cells

Integrated analysis of high throughput transcriptomic data revealed specific gene expression signature of cardiomyocytes

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The ribosomal prolyl-hydroxylase OGFOD1 decreases during cardiac differentiation and modulates translation and splicing

Cited by 12 publications

References 36 publications

Negative chronotropic and inotropic effects of lubiprostone on iPS cell-derived cardiomyocytes via activation of CFTR

Negative chronotropic and inotropic effects of lubiprostone on iPS cell-derived cardiomyocytes via activation of CFTR

CRISPRroots: on- and off-target assessment of RNA-seq data in CRISPR–Cas9 edited cells

Integrated analysis of high throughput transcriptomic data revealed specific gene expression signature of cardiomyocytes

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Product

Resources

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`CRISPRroots`: on- and off-target assessment of RNA-seq data in CRISPR–Cas9 edited cells