1
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Chen EZ, Kannan S, Murphy S, Farid M, Kwon C. Protocol for quantifying stem-cell-derived cardiomyocyte maturity using transcriptomic entropy score. STAR Protoc 2024; 5:103083. [PMID: 38781077 PMCID: PMC11145390 DOI: 10.1016/j.xpro.2024.103083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/15/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
The inability to quantify cardiomyocyte (CM) maturation remains a significant barrier to evaluating the effects of ongoing efforts to produce adult-like CMs from pluripotent stem cells (PSCs). Here, we present a protocol to quantify stem-cell-derived CM maturity using a single-cell RNA sequencing-based metric "entropy score." We describe steps for generating an entropy score using customized R code. This tool can be used to quantify maturation levels of PSC-CMs and potentially other cell types. For complete details on the use and execution of this protocol, please refer to Kannan et al.1.
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Affiliation(s)
- Elaine Zhelan Chen
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA
| | - Suraj Kannan
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA
| | - Sean Murphy
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA
| | - Michael Farid
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA
| | - Chulan Kwon
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA.
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2
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Ochoa-Alejo N, Reyes-Valdés MH, Martínez O. Estimating Transcriptome Diversity and Specialization in Capsicum annuum L. PLANTS (BASEL, SWITZERLAND) 2024; 13:983. [PMID: 38611513 PMCID: PMC11013594 DOI: 10.3390/plants13070983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]
Abstract
Chili pepper fruits of the genus Capsicum represent excellent experimental models to study the growth, development, and ripening processes in a non-climacteric species at the physiological, biochemical, and molecular levels. Fruit growth, development, and ripening involve a complex, harmonious, and finely controlled regulation of gene expression. The purpose of this study was to estimate the changes in transcriptome diversity and specialization, as well as gene specificities during fruit development in this crop, and to illustrate the advantages of estimating these parameters. To achieve these aims, we programmed and made publicly available an R package. In this study, we applied these methods to a set of 179 RNA-Seq libraries from a factorial experiment that includes 12 different genotypes at various stages of fruit development. We found that the diversity of the transcriptome decreases linearly from the flower to the mature fruit, while its specialization follows a complex and non-linear behavior during this process. Additionally, by defining sets of genes with different degrees of specialization and applying Gene Ontology enrichment analysis, we identified processes, functions, and components that play a central role in particular fruit development stages. In conclusion, the estimation of diversity, specialization, and specificity summarizes the global properties of the transcriptomes, providing insights that are difficult to achieve by other means.
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Affiliation(s)
- Neftalí Ochoa-Alejo
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico;
| | - M. Humberto Reyes-Valdés
- Department of Plant Breeding, Universidad Autónoma Agraria Antonio Narro, Saltillo 25315, Coahuila, Mexico;
| | - Octavio Martínez
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Guanajuato, Mexico
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3
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Sehgal M, Ramu S, Vaz JM, Ganapathy YR, Muralidharan S, Venkatraghavan S, Jolly MK. Characterizing heterogeneity along EMT and metabolic axes in colorectal cancer reveals underlying consensus molecular subtype-specific trends. Transl Oncol 2024; 40:101845. [PMID: 38029508 PMCID: PMC10698572 DOI: 10.1016/j.tranon.2023.101845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023] Open
Abstract
Colorectal cancer (CRC) is highly heterogeneous with variable survival outcomes and therapeutic vulnerabilities. A commonly used classification system in CRC is the Consensus Molecular Subtypes (CMS) based on gene expression patterns. However, how these CMS categories connect to axes of phenotypic plasticity and heterogeneity remains unclear. Here, in our analysis of CMS-specific TCGA data and 101 bulk transcriptomic datasets, we found the epithelial phenotype score to be consistently positively correlated with scores of glycolysis, OXPHOS and FAO pathways, while PD-L1 activity scores positively correlated with mesenchymal phenotype scoring, revealing possible interconnections among plasticity axes. Single-cell RNA-sequencing analysis of patient samples revealed that that CMS2 and CMS3 subtype samples were relatively more epithelial as compared to CMS1 and CMS4. CMS1 revealed two subpopulations: one close to CMS4 (more mesenchymal) and the other closer to CMS2 or CMS3 (more epithelial), indicating a partial EMT-like behavior. Consistent observations were made in single-cell analysis of metabolic axes and PD-L1 activity scores. Together, our results quantify the patterns of two functional interconnected axes of phenotypic heterogeneity - EMT and metabolic reprogramming - in a CMS-specific manner in CRC.
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Affiliation(s)
- Manas Sehgal
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Soundharya Ramu
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Joel Markus Vaz
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India; School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, United States
| | | | - Srinath Muralidharan
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | | | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India.
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4
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Yang J, Daily N, Pullinger TK, Wakatsuki T, Sobie EA. Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.07.574577. [PMID: 38260376 PMCID: PMC10802448 DOI: 10.1101/2024.01.07.574577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) have gained traction as a powerful model in cardiac disease and therapeutics research, since iPSCs are self-renewing and can be derived from healthy and diseased patients without invasive surgery. However, current iPSC-CM differentiation methods produce cardiomyocytes with immature, fetal-like electrophysiological phenotypes, and the variety of maturation protocols in the literature results in phenotypic differences between labs. Heterogeneity of iPSC donor genetic backgrounds contributes to additional phenotypic variability. Several mathematical models of iPSC-CM electrophysiology have been developed to help understand the ionic underpinnings of, and to simulate, various cell responses, but these models individually do not capture the phenotypic variability observed in iPSC-CMs. Here, we tackle these limitations by developing a computational pipeline to calibrate cell preparation-specific iPSC-CM electrophysiological parameters. We used the genetic algorithm (GA), a heuristic parameter calibration method, to tune ion channel parameters in a mathematical model of iPSC-CM physiology. To systematically optimize an experimental protocol that generates sufficient data for parameter calibration, we created simulated datasets by applying various protocols to a population of in silico cells with known conductance variations, and we fitted to those datasets. We found that calibrating models to voltage and calcium transient data under 3 varied experimental conditions, including electrical pacing combined with ion channel blockade and changing buffer ion concentrations, improved model parameter estimates and model predictions of unseen channel block responses. This observation held regardless of whether the fitted data were normalized, suggesting that normalized fluorescence recordings, which are more accessible and higher throughput than patch clamp recordings, could sufficiently inform conductance parameters. Therefore, this computational pipeline can be applied to different iPSC-CM preparations to determine cell line-specific ion channel properties and understand the mechanisms behind variability in perturbation responses.
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Affiliation(s)
- Janice Yang
- Department of Pharmacological Sciences & Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Neil Daily
- InvivoSciences Inc., Madison, WI 53719, USA
| | - Taylor K Pullinger
- Department of Pharmacological Sciences & Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Eric A Sobie
- Department of Pharmacological Sciences & Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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5
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Li S, Yan B, Wu B, Su J, Lu J, Lam TW, Boheler KR, Poon ENY, Luo R. Integrated modeling framework reveals co-regulation of transcription factors, miRNAs and lncRNAs on cardiac developmental dynamics. Stem Cell Res Ther 2023; 14:247. [PMID: 37705079 PMCID: PMC10500942 DOI: 10.1186/s13287-023-03442-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 08/07/2023] [Indexed: 09/15/2023] Open
Abstract
AIMS Dissecting complex interactions among transcription factors (TFs), microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are central for understanding heart development and function. Although computational approaches and platforms have been described to infer relationships among regulatory factors and genes, current approaches do not adequately account for how highly diverse, interacting regulators that include noncoding RNAs (ncRNAs) control cardiac gene expression dynamics over time. METHODS To overcome this limitation, we devised an integrated framework, cardiac gene regulatory modeling (CGRM) that integrates LogicTRN and regulatory component analysis bioinformatics modeling platforms to infer complex regulatory mechanisms. We then used CGRM to identify and compare the TF-ncRNA gene regulatory networks that govern early- and late-stage cardiomyocytes (CMs) generated by in vitro differentiation of human pluripotent stem cells (hPSC) and ventricular and atrial CMs isolated during in vivo human cardiac development. RESULTS Comparisons of in vitro versus in vivo derived CMs revealed conserved regulatory networks among TFs and ncRNAs in early cells that significantly diverged in late staged cells. We report that cardiac genes ("heart targets") expressed in early-stage hPSC-CMs are primarily regulated by MESP1, miR-1, miR-23, lncRNAs NEAT1 and MALAT1, while GATA6, HAND2, miR-200c, NEAT1 and MALAT1 are critical for late hPSC-CMs. The inferred TF-miRNA-lncRNA networks regulating heart development and contraction were similar among early-stage CMs, among individual hPSC-CM datasets and between in vitro and in vivo samples. However, genes related to apoptosis, cell cycle and proliferation, and transmembrane transport showed a high degree of divergence between in vitro and in vivo derived late-stage CMs. Overall, late-, but not early-stage CMs diverged greatly in the expression of "heart target" transcripts and their regulatory mechanisms. CONCLUSIONS In conclusion, we find that hPSC-CMs are regulated in a cell autonomous manner during early development that diverges significantly as a function of time when compared to in vivo derived CMs. These findings demonstrate the feasibility of using CGRM to reveal dynamic and complex transcriptional and posttranscriptional regulatory interactions that underlie cell directed versus environment-dependent CM development. These results with in vitro versus in vivo derived CMs thus establish this approach for detailed analyses of heart disease and for the analysis of cell regulatory systems in other biomedical fields.
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Affiliation(s)
- Shumin Li
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Bin Yan
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Binbin Wu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Centre for Cardiovascular Genomics and Medicine, Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Junhao Su
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Jianliang Lu
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Tak-Wah Lam
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Kenneth R Boheler
- The Division of Cardiology, Department of Medicine and The Whiting School of Engineering, Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, 21205, USA.
| | - Ellen Ngar-Yun Poon
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Centre for Cardiovascular Genomics and Medicine, Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Hong Kong Hub of Paediatric Excellence (HK HOPE), The Chinese University of Hong Kong, Kowloon Bay, Hong Kong, China.
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China.
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6
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Cheng C, Nguyen TT, Tang M, Wang X, Jiang C, Liu Y, Gorlov I, Gorlova O, Iafrate J, Lanuti M, Christiani DC, Amos CI. Immune Infiltration in Tumor and Adjacent Non-Neoplastic Regions Codetermines Patient Clinical Outcomes in Early-Stage Lung Cancer. J Thorac Oncol 2023; 18:1184-1198. [PMID: 37146750 PMCID: PMC10528252 DOI: 10.1016/j.jtho.2023.04.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/07/2023]
Abstract
INTRODUCTION In recent years, the proportion of patients with NSCLC diagnosed at an early stage has increased continuously. METHODS In this study, we analyzed samples and data collected from 119 samples from 67 early stage patients with NSCLC, including 52 pairs of tumor and adjacent non-neoplastic samples, and performed RNA-sequencing analysis with high sequencing depth. RESULTS We found that immune-related genes were highly enriched among the differentially expressed genes and observed significantly higher inferred immune infiltration levels in adjacent non-neoplastic samples than in tumor samples. In survival analysis, the infiltration of certain immune cell types in tumor, but not adjacent non-neoplastic, samples were associated with overall patient survival, and excitingly, the differential infiltration between paired samples (tumor minus non-neoplastic) was more prognostic than expression in either non-neoplastic or tumor tissues. We also performed B cell receptor (BCR) and T cell receptor (TCR) repertoire analysis and observed more BCR/TCR clonotypes and increased BCR clonality in tumor than in non-neoplastic samples. Finally, we carefully quantified the fraction of the five histologic subtypes in our adenocarcinoma samples and found that higher histologic pattern complexity was associated with higher immune infiltration and low TCR clonality in the tumor-proximal regions. CONCLUSIONS Our results indicated significantly differential immune characteristics between tumor and adjacent non-neoplastic samples and suggested that the two regions provided complementary prognostic values in early-stage NSCLCs.
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Affiliation(s)
- Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, Texas; Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; The Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Thinh T Nguyen
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Mabel Tang
- Department of Biosciences, Rice University, Houston, Texas
| | - Xinan Wang
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Chongming Jiang
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Yanhong Liu
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Ivan Gorlov
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Olga Gorlova
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Michael Lanuti
- Department of Surgery, Thoracic Surgery Division, Massachusetts General Hospital, Boston, Massachusetts
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Pulmonary and Critical Care Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Christopher I Amos
- Department of Medicine, Baylor College of Medicine, Houston, Texas; Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; The Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.
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7
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Salameh S, Ogueri V, Posnack NG. Adapting to a new environment: postnatal maturation of the human cardiomyocyte. J Physiol 2023; 601:2593-2619. [PMID: 37031380 PMCID: PMC10775138 DOI: 10.1113/jp283792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/16/2023] [Indexed: 04/10/2023] Open
Abstract
The postnatal mammalian heart undergoes remarkable developmental changes, which are stimulated by the transition from the intrauterine to extrauterine environment. With birth, increased oxygen levels promote metabolic, structural and biophysical maturation of cardiomyocytes, resulting in mature muscle with increased efficiency, contractility and electrical conduction. In this Topical Review article, we highlight key studies that inform our current understanding of human cardiomyocyte maturation. Collectively, these studies suggest that human atrial and ventricular myocytes evolve quickly within the first year but might not reach a fully mature adult phenotype until nearly the first decade of life. However, it is important to note that fetal, neonatal and paediatric cardiac physiology studies are hindered by a number of limitations, including the scarcity of human tissue, small sample size and a heavy reliance on diseased tissue samples, often without age-matched healthy controls. Future developmental studies are warranted to expand our understanding of normal cardiac physiology/pathophysiology and inform age-appropriate treatment strategies for cardiac disease.
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Affiliation(s)
- Shatha Salameh
- Department of Pharmacology & Physiology, George Washington University, Washington, DC, USA
- Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, Washington, DC, USA
| | - Vanessa Ogueri
- Children’s National Heart Institute, Children’s National Hospital, Washington, DC, USA
| | - Nikki Gillum Posnack
- Department of Pharmacology & Physiology, George Washington University, Washington, DC, USA
- Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, Washington, DC, USA
- Children’s National Heart Institute, Children’s National Hospital, Washington, DC, USA
- Department of Pediatrics, George Washington University, Washington, DC, USA
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8
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Zhou P, VanDusen NJ, Zhang Y, Cao Y, Sethi I, Hu R, Zhang S, Wang G, Ye L, Mazumdar N, Chen J, Zhang X, Guo Y, Li B, Ma Q, Lee JY, Gu W, Yuan GC, Ren B, Chen K, Pu WT. Dynamic changes in P300 enhancers and enhancer-promoter contacts control mouse cardiomyocyte maturation. Dev Cell 2023; 58:898-914.e7. [PMID: 37071996 PMCID: PMC10231645 DOI: 10.1016/j.devcel.2023.03.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 02/16/2023] [Accepted: 03/05/2023] [Indexed: 04/20/2023]
Abstract
Cardiomyocyte differentiation continues throughout murine gestation and into the postnatal period, driven by temporally regulated expression changes in the transcriptome. The mechanisms that regulate these developmental changes remain incompletely defined. Here, we used cardiomyocyte-specific ChIP-seq of the activate enhancer marker P300 to identify 54,920 cardiomyocyte enhancers at seven stages of murine heart development. These data were matched to cardiomyocyte gene expression profiles at the same stages and to Hi-C and H3K27ac HiChIP chromatin conformation data at fetal, neonatal, and adult stages. Regions with dynamic P300 occupancy exhibited developmentally regulated enhancer activity, as measured by massively parallel reporter assays in cardiomyocytes in vivo, and identified key transcription factor-binding motifs. These dynamic enhancers interacted with temporal changes of the 3D genome architecture to specify developmentally regulated cardiomyocyte gene expressions. Our work provides a 3D genome-mediated enhancer activity landscape of murine cardiomyocyte development.
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Affiliation(s)
- Pingzhu Zhou
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Nathan J VanDusen
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yanchun Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Yangpo Cao
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Isha Sethi
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Shuo Zhang
- Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Guangyu Wang
- Cardiovascular Department, Houston Methodist, Weill Cornell Medical College, Houston, TX, USA
| | - Lincai Ye
- Department of Thoracic and Cardiovascular Surgery, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Neil Mazumdar
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Jian Chen
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Xiaoran Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Yuxuan Guo
- Peking University Health Science Center, Beijing, China
| | - Bin Li
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qing Ma
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Julianna Y Lee
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Weiliang Gu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pharmacology, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kaifu Chen
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA.
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA.
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9
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Kannan S, Miyamoto M, Zhu R, Lynott M, Guo J, Chen EZ, Colas AR, Lin BL, Kwon C. Trajectory reconstruction identifies dysregulation of perinatal maturation programs in pluripotent stem cell-derived cardiomyocytes. Cell Rep 2023; 42:112330. [PMID: 37014753 PMCID: PMC10545814 DOI: 10.1016/j.celrep.2023.112330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/12/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
A limitation in the application of pluripotent stem cell-derived cardiomyocytes (PSC-CMs) is the failure of these cells to achieve full functional maturity. The mechanisms by which directed differentiation differs from endogenous development, leading to consequent PSC-CM maturation arrest, remain unclear. Here, we generate a single-cell RNA sequencing (scRNA-seq) reference of mouse in vivo CM maturation with extensive sampling of previously difficult-to-isolate perinatal time periods. We subsequently generate isogenic embryonic stem cells to create an in vitro scRNA-seq reference of PSC-CM-directed differentiation. Through trajectory reconstruction, we identify an endogenous perinatal maturation program that is poorly recapitulated in vitro. By comparison with published human datasets, we identify a network of nine transcription factors (TFs) whose targets are consistently dysregulated in PSC-CMs across species. Notably, these TFs are only partially activated in common ex vivo approaches to engineer PSC-CM maturation. Our study can be leveraged toward improving the clinical viability of PSC-CMs.
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Affiliation(s)
- Suraj Kannan
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Matthew Miyamoto
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Renjun Zhu
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michaela Lynott
- Sanford Burham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Jason Guo
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Elaine Zhelan Chen
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Alexandre R Colas
- Sanford Burham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Brian Leei Lin
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chulan Kwon
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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10
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Chun YW, Miyamoto M, Williams CH, Neitzel LR, Silver-Isenstadt M, Cadar AG, Fuller DT, Fong DC, Liu H, Lease R, Kim S, Katagiri M, Durbin MD, Wang KC, Feaster TK, Sheng CC, Neely MD, Sreenivasan U, Cortes-Gutierrez M, Finn AV, Schot R, Mancini GMS, Ament SA, Ess KC, Bowman AB, Han Z, Bichell DP, Su YR, Hong CC. Impaired Reorganization of Centrosome Structure Underlies Human Infantile Dilated Cardiomyopathy. Circulation 2023; 147:1291-1303. [PMID: 36970983 PMCID: PMC10133173 DOI: 10.1161/circulationaha.122.060985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 02/22/2023] [Indexed: 03/29/2023]
Abstract
BACKGROUND During cardiomyocyte maturation, the centrosome, which functions as a microtubule organizing center in cardiomyocytes, undergoes dramatic structural reorganization where its components reorganize from being localized at the centriole to the nuclear envelope. This developmentally programmed process, referred to as centrosome reduction, has been previously associated with cell cycle exit. However, understanding of how this process influences cardiomyocyte cell biology, and whether its disruption results in human cardiac disease, remains unknown. We studied this phenomenon in an infant with a rare case of infantile dilated cardiomyopathy (iDCM) who presented with left ventricular ejection fraction of 18% and disrupted sarcomere and mitochondria structure. METHODS We performed an analysis beginning with an infant who presented with a rare case of iDCM. We derived induced pluripotent stem cells from the patient to model iDCM in vitro. We performed whole exome sequencing on the patient and his parents for causal gene analysis. CRISPR/Cas9-mediated gene knockout and correction in vitro were used to confirm whole exome sequencing results. Zebrafish and Drosophila models were used for in vivo validation of the causal gene. Matrigel mattress technology and single-cell RNA sequencing were used to characterize iDCM cardiomyocytes further. RESULTS Whole exome sequencing and CRISPR/Cas9 gene knockout/correction identified RTTN, the gene encoding the centrosomal protein RTTN (rotatin), as the causal gene underlying the patient's condition, representing the first time a centrosome defect has been implicated in a nonsyndromic dilated cardiomyopathy. Genetic knockdowns in zebrafish and Drosophila confirmed an evolutionarily conserved requirement of RTTN for cardiac structure and function. Single-cell RNA sequencing of iDCM cardiomyocytes showed impaired maturation of iDCM cardiomyocytes, which underlie the observed cardiomyocyte structural and functional deficits. We also observed persistent localization of the centrosome at the centriole, contrasting with expected programmed perinuclear reorganization, which led to subsequent global microtubule network defects. In addition, we identified a small molecule that restored centrosome reorganization and improved the structure and contractility of iDCM cardiomyocytes. CONCLUSIONS This study is the first to demonstrate a case of human disease caused by a defect in centrosome reduction. We also uncovered a novel role for RTTN in perinatal cardiac development and identified a potential therapeutic strategy for centrosome-related iDCM. Future study aimed at identifying variants in centrosome components may uncover additional contributors to human cardiac disease.
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Affiliation(s)
- Young Wook Chun
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland Medical Center, Baltimore, MD 21201
| | - Matthew Miyamoto
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland Medical Center, Baltimore, MD 21201
| | - Charles H. Williams
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland Medical Center, Baltimore, MD 21201
| | - Leif R. Neitzel
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland Medical Center, Baltimore, MD 21201
| | - Maya Silver-Isenstadt
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland Medical Center, Baltimore, MD 21201
| | - Adrian G. Cadar
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37201
| | - Daniela T. Fuller
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland Medical Center, Baltimore, MD 21201
| | - Daniel C. Fong
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland Medical Center, Baltimore, MD 21201
| | - Hanhan Liu
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland Medical Center, Baltimore, MD 21201
| | - Robert Lease
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sungseek Kim
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37201
| | - Mikako Katagiri
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37201
| | - Matthew D. Durbin
- Division of Neonatology-Perinatology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 26202
| | - Kuo-Chen Wang
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland Medical Center, Baltimore, MD 21201
| | - Tromondae K. Feaster
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37201
| | - Calvin C. Sheng
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37201
| | - M. Diana Neely
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37201
| | - Urmila Sreenivasan
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland Medical Center, Baltimore, MD 21201
| | - Marcia Cortes-Gutierrez
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Aloke V. Finn
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland Medical Center, Baltimore, MD 21201
| | - Rachel Schot
- Division of Neonatology-Perinatology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 26202
| | - Grazia M. S. Mancini
- Department of Clinical Genetics, Erasmus University Medical Center (Erasmus MC), P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Seth A. Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kevin C. Ess
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN37201
| | - Aaron B. Bowman
- School of Health Sciences, Purdue University, West Lafayette, IN 47906
| | - Zhe Han
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland Medical Center, Baltimore, MD 21201
| | - David P. Bichell
- Department of Pediatric Cardiac Surgery, Vanderbilt University Medical Center, Nashville, TN 37201
| | - Yan Ru Su
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37201
| | - Charles C. Hong
- Division of Cardiovascular Medicine, Department of Medicine, University of Maryland Medical Center, Baltimore, MD 21201
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11
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Cheng S, Brenière-Letuffe D, Ahola V, Wong AO, Keung HY, Gurung B, Zheng Z, Costa KD, Lieu DK, Keung W, Li RA. Single-cell RNA sequencing reveals maturation trajectory in human pluripotent stem cell-derived cardiomyocytes in engineered tissues. iScience 2023; 26:106302. [PMID: 36950112 PMCID: PMC10025988 DOI: 10.1016/j.isci.2023.106302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/04/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
Cardiac in vitro models have become increasingly obtainable and affordable with the optimization of human pluripotent stem cell-derived cardiomyocyte (hPSC-CM) differentiation. However, these CMs are immature compared to their in vivo counterparts. Here we study the cellular phenotype of hPSC-CMs by comparing their single-cell gene expression and functional profiles in three engineered cardiac tissue configurations: human ventricular (hv) cardiac anisotropic sheet, cardiac tissue strip, and cardiac organoid chamber (hvCOC), with spontaneously aggregated 3D cardiac spheroids (CS) as control. The CM maturity was found to increase with increasing levels of complexity of the engineered tissues from CS to hvCOC. The contractile components are the first function to mature, followed by electrophysiology and oxidative metabolism. Notably, the 2D tissue constructs show a higher cellular organization whereas metabolic maturity preferentially increases in the 3D constructs. We conclude that the tissue engineering models resembling configurations of native tissues may be reliable for drug screening or disease modeling.
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Affiliation(s)
- Shangli Cheng
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong SAR, China
| | - David Brenière-Letuffe
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong SAR, China
- Department of Clinical Sciences, Intervention and Technology, CLINTEC, Karolinska Institutet, 141 52 Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, 141 86 Stockholm, Sweden
| | - Virpi Ahola
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong SAR, China
| | | | - Hoi Yee Keung
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong SAR, China
| | - Bimal Gurung
- Novoheart, Irvine, CA 92617, USA
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zongli Zheng
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong SAR, China
| | - Kevin D. Costa
- Novoheart, Irvine, CA 92617, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deborah K. Lieu
- Novoheart, Irvine, CA 92617, USA
- Institute for Regenerative Cures and Stem Cell Program, University of California, Davis, Sacramento, CA 95817, USA
| | - Wendy Keung
- Novoheart, Irvine, CA 92617, USA
- Dr. Li Dak Sum Research Centre, The University of Hong Kong, Hong Kong SAR, China
| | - Ronald A. Li
- Novoheart, Irvine, CA 92617, USA
- Corresponding author
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12
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Vanderkruk B, Maeshima N, Pasula DJ, An M, McDonald CL, Suresh P, Luciani DS, Lynn FC, Hoffman BG. Methylation of histone H3 lysine 4 is required for maintenance of beta cell function in adult mice. Diabetologia 2023; 66:1097-1115. [PMID: 36912927 PMCID: PMC10163146 DOI: 10.1007/s00125-023-05896-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 02/08/2023] [Indexed: 03/14/2023]
Abstract
AIMS/HYPOTHESIS Beta cells control glucose homeostasis via regulated production and secretion of insulin. This function arises from a highly specialised gene expression programme that is established during development and then sustained, with limited flexibility, in terminally differentiated cells. Dysregulation of this programme is seen in type 2 diabetes but mechanisms that preserve gene expression or underlie its dysregulation in mature cells are not well resolved. This study investigated whether methylation of histone H3 lysine 4 (H3K4), a marker of gene promoters with unresolved functional importance, is necessary for the maintenance of mature beta cell function. METHODS Beta cell function, gene expression and chromatin modifications were analysed in conditional Dpy30 knockout mice, in which H3K4 methyltransferase activity is impaired, and in a mouse model of diabetes. RESULTS H3K4 methylation maintains expression of genes that are important for insulin biosynthesis and glucose responsiveness. Deficient methylation of H3K4 leads to a less active and more repressed epigenome profile that locally correlates with gene expression deficits but does not globally reduce gene expression. Instead, developmentally regulated genes and genes in weakly active or suppressed states particularly rely on H3K4 methylation. We further show that H3K4 trimethylation (H3K4me3) is reorganised in islets from the Leprdb/db mouse model of diabetes in favour of weakly active and disallowed genes at the expense of terminal beta cell markers with broad H3K4me3 peaks. CONCLUSIONS/INTERPRETATION Sustained methylation of H3K4 is critical for the maintenance of beta cell function. Redistribution of H3K4me3 is linked to gene expression changes that are implicated in diabetes pathology.
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Affiliation(s)
- Ben Vanderkruk
- Diabetes Research Group, British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Nina Maeshima
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Daniel J Pasula
- Diabetes Research Group, British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Meilin An
- Diabetes Research Group, British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Cassandra L McDonald
- Diabetes Research Group, British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Priya Suresh
- Diabetes Research Group, British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Dan S Luciani
- Diabetes Research Group, British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Francis C Lynn
- Diabetes Research Group, British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Brad G Hoffman
- Diabetes Research Group, British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada.
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13
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Ogata N, Konishi S, Yokoyama T. In vivo-like Culture of Monophagous Animal Organ using Dietary Components. JOURNAL OF BIOTECHNOLOGY AND BIOMEDICINE 2023; 6:42-48. [PMID: 36874218 PMCID: PMC9983661 DOI: 10.26502/jbb.2642-91280070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Animals depend on other species to live, with monophagy being an extreme mode. Monophagous animals depend on their diet not only for nutritients but also for developmental and reproductive controls. Thus, dietary components may be useful in culturing tissues from monophagous animals. We hypothesized that a dedifferentiated tissue from the monophagous silkworm, Bombyx mori, would re-differentiate when cultured in a medium containing an extract of mulberry (Morus alba) leaves, the only food of B. mori. Over 40 fat-body transcriptomes were sequenced, and we concluded that it is possible to establish in vivo-like silkworm tissue cultures using their diet.
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Affiliation(s)
- Norichika Ogata
- Nihon BioData Corporation, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Shogo Konishi
- Nihon BioData Corporation, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Takeshi Yokoyama
- Laboratory of Sericultural Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8, Saiwai-cho, Fuchu, Tokyo, 183-8501, Japan
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14
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Ogata N. Transcriptome Dedifferentiation Observed in Animal Primary Cultures is Essential to Plant Reprogramming. JOURNAL OF BIOINFORMATICS AND SYSTEMS BIOLOGY : OPEN ACCESS 2022; 5:116-118. [PMID: 36397740 PMCID: PMC9668052 DOI: 10.26502/jbsb.5107039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Tissue culture environment liberate cells from ordinary laws of multi-cellular organisms. This liberation enables cells several behaviors, such as growth, dedifferentiation, acquisition of pluripotency, immortalization and reprogramming. Each phenomenon is relating to each other and hardly to determine. Recently, dedifferentiation of animal cell was quantified as increasing liberality which is information entropy of transcriptome. The increasing liberality induced by tissue culture may reappear in plant cells too. Here we corroborated it. Measuring liberality during reprogramming of plant cells suggested that reprogramming is a combined phenomenon of dedifferentiation and re-differentiation.
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15
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Kambhampati S, Murphy S, Uosaki H, Kwon C. Cross-Organ Transcriptomic Comparison Reveals Universal Factors During Maturation. J Comput Biol 2022; 29:1031-1044. [PMID: 35802489 PMCID: PMC9499449 DOI: 10.1089/cmb.2021.0349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Various cell types can be derived from stem cells. However, these cells are immature and do not match their adult counterparts in functional capabilities, limiting their use in disease modeling and cell therapies. Thus, it is crucial to understand the mechanisms of maturation in vivo. However, it is unknown if there are genes and pathways conserved across organs during maturation. To address this, we performed a time-series analysis of the transcriptome of the mouse heart, brain, liver, and kidney and analyzed their trajectories over time. In addition, gene regulatory networks were reconstructed to determine overlapping expression patterns. Based on these, we identified commonly upregulated and downregulated pathways across all four organs. Key upstream regulators were also predicted based on the temporal expression of downstream genes. These findings suggest the presence of universal regulators during organ maturation, which may help us develop a general strategy to mature stem cell-derived cells in vitro.
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Affiliation(s)
- Sandeep Kambhampati
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sean Murphy
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hideki Uosaki
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Chulan Kwon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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16
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Hamledari H, Asghari P, Jayousi F, Aguirre A, Maaref Y, Barszczewski T, Ser T, Moore E, Wasserman W, Klein Geltink R, Teves S, Tibbits GF. Using human induced pluripotent stem cell-derived cardiomyocytes to understand the mechanisms driving cardiomyocyte maturation. Front Cardiovasc Med 2022; 9:967659. [PMID: 36061558 PMCID: PMC9429949 DOI: 10.3389/fcvm.2022.967659] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Cardiovascular diseases are the leading cause of mortality and reduced quality of life globally. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) provide a personalized platform to study inherited heart diseases, drug-induced cardiac toxicity, and cardiac regenerative therapy. However, the immaturity of CMs obtained by current strategies is a major hurdle in utilizing hiPSC-CMs at their fullest potential. Here, the major findings and limitations of current maturation methodologies to enhance the utility of hiPSC-CMs in the battle against a major source of morbidity and mortality are reviewed. The most recent knowledge of the potential signaling pathways involved in the transition of fetal to adult CMs are assimilated. In particular, we take a deeper look on role of nutrient sensing signaling pathways and the potential role of cap-independent translation mediated by the modulation of mTOR pathway in the regulation of cardiac gap junctions and other yet to be identified aspects of CM maturation. Moreover, a relatively unexplored perspective on how our knowledge on the effects of preterm birth on cardiovascular development can be actually utilized to enhance the current understanding of CM maturation is examined. Furthermore, the interaction between the evolving neonatal human heart and brown adipose tissue as the major source of neonatal thermogenesis and its endocrine function on CM development is another discussed topic which is worthy of future investigation. Finally, the current knowledge regarding transcriptional mediators of CM maturation is still limited. The recent studies have produced the groundwork to better understand CM maturation in terms of providing some of the key factors involved in maturation and development of metrics for assessment of maturation which proves essential for future studies on in vitro PSC-CMs maturation.
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Affiliation(s)
- Homa Hamledari
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Cellular and Regenerative Medicine Centre, BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Parisa Asghari
- Department of Cellular and Physiological Sciences, University of British Colombia, Vancouver, BC, Canada
| | - Farah Jayousi
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Cellular and Regenerative Medicine Centre, BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Alejandro Aguirre
- Department of Medical Genetics, University of British Colombia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Yasaman Maaref
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Cellular and Regenerative Medicine Centre, BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Tiffany Barszczewski
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Cellular and Regenerative Medicine Centre, BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Terri Ser
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Colombia, Vancouver, BC, Canada
| | - Edwin Moore
- Department of Cellular and Physiological Sciences, University of British Colombia, Vancouver, BC, Canada
| | - Wyeth Wasserman
- Department of Medical Genetics, University of British Colombia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Ramon Klein Geltink
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Colombia, Vancouver, BC, Canada
| | - Sheila Teves
- Department of Biochemistry and Molecular Biology, University of British Colombia, Vancouver, BC, Canada
| | - Glen F. Tibbits
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Cellular and Regenerative Medicine Centre, BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
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17
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Zhang F, Yang C, Wang Y, Jiao H, Wang Z, Shen J, Li L. FitDevo: accurate inference of single-cell developmental potential using sample-specific gene weight. Brief Bioinform 2022; 23:6649289. [PMID: 35870444 PMCID: PMC9487676 DOI: 10.1093/bib/bbac293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/11/2022] [Accepted: 06/29/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
The quantification of developmental potential is critical for determining developmental stages and identifying essential molecular signatures in single-cell studies. Here, we present FitDevo, a novel method for inferring developmental potential using scRNA-seq data. The main idea of FitDevo is first to generate sample-specific gene weight (SSGW) and then infer developmental potential by calculating the correlation between SSGW and gene expression. SSGW is generated using a generalized linear model that combines sample-specific information and gene weight learned from a training dataset covering scRNA-seq data of 17 previously published datasets. We have rigorously validated FitDevo’s effectiveness using a testing dataset with scRNA-seq data from 28 existing datasets and have also demonstrated its superiority over current methods. Furthermore, FitDevo’s broad application scope has been illustrated using three practical scenarios: deconvolution analysis of epidermis, spatial transcriptomic data analysis of hearts and intestines, and developmental potential analysis of breast cancer. The source code and related data are available at https://github.com/jumphone/fitdevo.
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Affiliation(s)
- Feng Zhang
- Department of Histoembryology , Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, , Shanghai 200025 , China
- Shanghai Jiao Tong University School of Medicine , Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, , Shanghai 200025 , China
| | - Chen Yang
- Department of Histoembryology , Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, , Shanghai 200025 , China
- Shanghai Jiao Tong University School of Medicine , Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, , Shanghai 200025 , China
| | - Yihao Wang
- Department of Ophthalmology , Ninth People’s Hospital, , Shanghai 200025 , China
- Shanghai Jiao Tong University School of Medicine , Ninth People’s Hospital, , Shanghai 200025 , China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology , Shanghai 200025 , China
- Institute of Translational Medicine , National Facility for Translational Medicine, , Shanghai 201109 , China
- Shanghai Jiao Tong University , National Facility for Translational Medicine, , Shanghai 201109 , China
| | - Huiyuan Jiao
- Department of Histoembryology , Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, , Shanghai 200025 , China
- Shanghai Jiao Tong University School of Medicine , Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, , Shanghai 200025 , China
| | - Zhiming Wang
- Department of Histoembryology , Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, , Shanghai 200025 , China
- Shanghai Jiao Tong University School of Medicine , Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, , Shanghai 200025 , China
| | - Jianfeng Shen
- Department of Ophthalmology , Ninth People’s Hospital, , Shanghai 200025 , China
- Shanghai Jiao Tong University School of Medicine , Ninth People’s Hospital, , Shanghai 200025 , China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology , Shanghai 200025 , China
- Institute of Translational Medicine , National Facility for Translational Medicine, , Shanghai 201109 , China
- Shanghai Jiao Tong University , National Facility for Translational Medicine, , Shanghai 201109 , China
| | - Lingjie Li
- Department of Histoembryology , Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, , Shanghai 200025 , China
- Shanghai Jiao Tong University School of Medicine , Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, , Shanghai 200025 , China
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18
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Brooks IR, Garrone CM, Kerins C, Kiar CS, Syntaka S, Xu JZ, Spagnoli FM, Watt FM. Functional genomics and the future of iPSCs in disease modeling. Stem Cell Reports 2022; 17:1033-1047. [PMID: 35487213 PMCID: PMC9133703 DOI: 10.1016/j.stemcr.2022.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 10/28/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) are valuable in disease modeling because of their potential to expand and differentiate into virtually any cell type and recapitulate key aspects of human biology. Functional genomics are genome-wide studies that aim to discover genotype-phenotype relationships, thereby revealing the impact of human genetic diversity on normal and pathophysiology. In this review, we make the case that human iPSCs (hiPSCs) are a powerful tool for functional genomics, since they provide an in vitro platform for the study of population genetics. We describe cutting-edge tools and strategies now available to researchers, including multi-omics technologies, advances in hiPSC culture techniques, and innovations in drug development. Functional genomics approaches based on hiPSCs hold great promise for advancing drug discovery, disease etiology, and the impact of genetic variation on human biology.
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Affiliation(s)
- Imogen R Brooks
- St John's Institute of Dermatology, King's College London, London, SE1 9RT, UK
| | - Cristina M Garrone
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK
| | - Caoimhe Kerins
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
| | - Cher Shen Kiar
- Peter Gorer Department of Immunobiology, King's College London, London, SE1 9RT, UK
| | - Sofia Syntaka
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK
| | - Jessie Z Xu
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK
| | - Francesca M Spagnoli
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK.
| | - Fiona M Watt
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK; Directors' Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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Deciphering Cardiac Biology and Disease by Single-Cell Transcriptomic Profiling. Biomolecules 2022; 12:biom12040566. [PMID: 35454155 PMCID: PMC9032111 DOI: 10.3390/biom12040566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 11/29/2022] Open
Abstract
By detecting minute molecular changes in hundreds to millions of single cells, single-cell RNA sequencing allows for the comprehensive characterization of the diversity and dynamics of cells in the heart. Our understanding of the heart has been transformed through the recognition of cellular heterogeneity, the construction of regulatory networks, the building of lineage trajectories, and the mapping of intercellular crosstalk. In this review, we introduce cardiac progenitors and their transcriptional regulation during embryonic development, highlight cellular heterogeneity and cell subtype functions in cardiac health and disease, and discuss insights gained from the study of pluripotent stem-cell-derived cardiomyocytes.
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