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Ma XR, Conley SD, Kosicki M, Bredikhin D, Cui R, Tran S, Sheth MU, Qiu WL, Chen S, Kundu S, Kang HY, Amgalan D, Munger CJ, Duan L, Dang K, Rubio OM, Kany S, Zamirpour S, DePaolo J, Padmanabhan A, Olgin J, Damrauer S, Andersson R, Gu M, Priest JR, Quertermous T, Qiu X, Rabinovitch M, Visel A, Pennacchio L, Kundaje A, Glass IA, Gifford CA, Pirruccello JP, Goodyer WR, Engreitz JM. Molecular convergence of risk variants for congenital heart defects leveraging a regulatory map of the human fetal heart. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.11.20.24317557. [PMID: 39606363 PMCID: PMC11601760 DOI: 10.1101/2024.11.20.24317557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Congenital heart defects (CHD) arise in part due to inherited genetic variants that alter genes and noncoding regulatory elements in the human genome. These variants are thought to act during fetal development to influence the formation of different heart structures. However, identifying the genes, pathways, and cell types that mediate these effects has been challenging due to the immense diversity of cell types involved in heart development as well as the superimposed complexities of interpreting noncoding sequences. As such, understanding the molecular functions of both noncoding and coding variants remains paramount to our fundamental understanding of cardiac development and CHD. Here, we created a gene regulation map of the healthy human fetal heart across developmental time, and applied it to interpret the functions of variants associated with CHD and quantitative cardiac traits. We collected single-cell multiomic data from 734,000 single cells sampled from 41 fetal hearts spanning post-conception weeks 6 to 22, enabling the construction of gene regulation maps in 90 cardiac cell types and states, including rare populations of cardiac conduction cells. Through an unbiased analysis of all 90 cell types, we find that both rare coding variants associated with CHD and common noncoding variants associated with valve traits converge to affect valvular interstitial cells (VICs). VICs are enriched for high expression of known CHD genes previously identified through mapping of rare coding variants. Eight CHD genes, as well as other genes in similar molecular pathways, are linked to common noncoding variants associated with other valve diseases or traits via enhancers in VICs. In addition, certain common noncoding variants impact enhancers with activities highly specific to particular subanatomic structures in the heart, illuminating how such variants can impact specific aspects of heart structure and function. Together, these results implicate new enhancers, genes, and cell types in the genetic etiology of CHD, identify molecular convergence of common noncoding and rare coding variants on VICs, and suggest a more expansive view of the cell types instrumental in genetic risk for CHD, beyond the working cardiomyocyte. This regulatory map of the human fetal heart will provide a foundational resource for understanding cardiac development, interpreting genetic variants associated with heart disease, and discovering targets for cell-type specific therapies.
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Affiliation(s)
- X Rosa Ma
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Stephanie D Conley
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michael Kosicki
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Danila Bredikhin
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ran Cui
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven Tran
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Maya U Sheth
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Wei-Lin Qiu
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sijie Chen
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Soumya Kundu
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Helen Y Kang
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Current address: PhD Program in Computational and Systems Biology, MIT, Cambridge, MA, USA
| | - Dulguun Amgalan
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Maternal and Child Health Research Institute, Stanford University, Stanford, CA, USA
| | - Chad J Munger
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Lauren Duan
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Katherine Dang
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Oriane Matthys Rubio
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Shinwan Kany
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Cardiology, University Heart and Vascular Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Siavash Zamirpour
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - John DePaolo
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arun Padmanabhan
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco School of Medicine, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jeffrey Olgin
- Division of Cardiology, Department of Medicine and Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Scott Damrauer
- Division of Vascular Surgery and Endovascular Therapy, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robin Andersson
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mingxia Gu
- Center for Stem Cell and Organoid Medicine, Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- University of Cincinnati School of Medicine, Cincinnati, OH, USA
| | - James R Priest
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Tenaya Therapeutics, South San Francisco, CA, USA
| | - Thomas Quertermous
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Xiaojie Qiu
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Maternal and Child Health Research Institute, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Bio-X, Stanford University, Stanford, CA, USA
| | - Marlene Rabinovitch
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University, Stanford, CA, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Natural Sciences, University of California, Merced, Merced, CA, USA
| | - Len Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ian A Glass
- Maternal and Child Health Research Institute, Stanford University, Stanford, CA, USA
- Department of Pediatrics and Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Casey A Gifford
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Maternal and Child Health Research Institute, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - James P Pirruccello
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Cardiology, Department of Medicine and Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Bakar Computation Health Sciences Institute, University of California, San Francisco, CA, USA
| | - William R Goodyer
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Maternal and Child Health Research Institute, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Jesse M Engreitz
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Maternal and Child Health Research Institute, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Vastrad B, Vastrad C. Screening and identification of key biomarkers associated with endometriosis using bioinformatics and next-generation sequencing data analysis. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2024; 25:116. [DOI: 10.1186/s43042-024-00572-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 08/23/2024] [Indexed: 01/04/2025] Open
Abstract
Abstract
Background
Endometriosis is a common cause of endometrial-type mucosa outside the uterine cavity with symptoms such as painful periods, chronic pelvic pain, pain with intercourse and infertility. However, the early diagnosis of endometriosis is still restricted. The purpose of this investigation is to identify and validate the key biomarkers of endometriosis.
Methods
Next-generation sequencing dataset GSE243039 was obtained from the Gene Expression Omnibus database, and differentially expressed genes (DEGs) between endometriosis and normal control samples were identified. After screening of DEGs, gene ontology (GO) and REACTOME pathway enrichment analyses were performed. Furthermore, a protein–protein interaction (PPI) network was constructed and modules were analyzed using the Human Integrated Protein–Protein Interaction rEference database and Cytoscape software, and hub genes were identified. Subsequently, a network between miRNAs and hub genes, and network between TFs and hub genes were constructed using the miRNet and NetworkAnalyst tool, and possible key miRNAs and TFs were predicted. Finally, receiver operating characteristic curve analysis was used to validate the hub genes.
Results
A total of 958 DEGs, including 479 upregulated genes and 479 downregulated genes, were screened between endometriosis and normal control samples. GO and REACTOME pathway enrichment analyses of the 958 DEGs showed that they were mainly involved in multicellular organismal process, developmental process, signaling by GPCR and muscle contraction. Further analysis of the PPI network and modules identified 10 hub genes, including vcam1, snca, prkcb, adrb2, foxq1, mdfi, actbl2, prkd1, dapk1 and actc1. Possible target miRNAs, including hsa-mir-3143 and hsa-mir-2110, and target TFs, including tcf3 (transcription factor 3) and clock (clock circadian regulator), were predicted by constructing a miRNA-hub gene regulatory network and TF-hub gene regulatory network.
Conclusions
This investigation used bioinformatics techniques to explore the potential and novel biomarkers. These biomarkers might provide new ideas and methods for the early diagnosis, treatment and monitoring of endometriosis.
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Zhu Y, Su SA, Shen J, Ma H, Le J, Xie Y, Xiang M. Recent advances of the Ephrin and Eph family in cardiovascular development and pathologies. iScience 2024; 27:110556. [PMID: 39188984 PMCID: PMC11345580 DOI: 10.1016/j.isci.2024.110556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024] Open
Abstract
Erythropoietin-producing hepatoma (Eph) receptors, comprising the largest family of receptor tyrosine kinases (RTKs), exert profound influence on diverse biological processes and pathological conditions such as cancer. Interacting with their corresponding ligands, erythropoietin-producing hepatoma receptor interacting proteins (Ephrins), Eph receptors regulate crucial events like embryonic development, tissue boundary formation, and tumor cell survival. In addition to their well-established roles in embryonic development and cancers, emerging evidence highlights the pivotal contribution of the Ephrin/Eph family to cardiovascular physiology and pathology. Studies have elucidated their involvement in cardiovascular development, atherosclerosis, postnatal angiogenesis, and, more recently, cardiac fibrosis and calcification, suggesting a promising avenue for therapeutic interventions in cardiovascular diseases. There remains a need for a comprehensive synthesis of their collective impact in the cardiovascular context. By exploring the intricate interactions between Eph receptors, ephrins, and cardiovascular system, this review aims to provide a holistic understanding of their roles and therapeutic potential in cardiovascular health and diseases.
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Affiliation(s)
- Yuan Zhu
- Department of Cardiology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou 310009, China
| | - Sheng-an Su
- Department of Cardiology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou 310009, China
| | - Jian Shen
- Department of Cardiology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou 310009, China
| | - Hong Ma
- Department of Cardiology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou 310009, China
| | - Jixie Le
- Department of Cardiology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou 310009, China
| | - Yao Xie
- Department of Cardiology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou 310009, China
| | - Meixiang Xiang
- Department of Cardiology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou 310009, China
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4
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Veiga RN, de Azevedo ALK, de Oliveira JC, Gradia DF. Targeting EphA2: a promising strategy to overcome chemoresistance and drug resistance in cancer. J Mol Med (Berl) 2024; 102:479-493. [PMID: 38393661 DOI: 10.1007/s00109-024-02431-x] [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: 03/29/2023] [Revised: 01/24/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024]
Abstract
Erythropoietin-producing hepatocellular A2 (EphA2) is a vital member of the Eph tyrosine kinase receptor family and has been associated with developmental processes. However, it is often overexpressed in tumors and correlates with cancer progression and worse prognosis due to the activation of its noncanonical signaling pathway. Throughout cancer treatment, the emergence of drug-resistant tumor cells is relatively common. Since the early 2000s, researchers have focused on understanding the role of EphA2 in promoting drug resistance in different types of cancer, as well as finding efficient and secure EphA2 inhibitors. In this review, the current knowledge regarding induced resistance by EphA2 in cancer treatment is summarized, and the types of cancer that lead to the most cancer-related deaths are highlighted. Some EphA2 inhibitors were also investigated. Regardless of whether the cancer treatment has reached a drug-resistance stage in EphA2-overexpressing tumors, once EphA2 is involved in cancer progression and aggressiveness, targeting EphA2 is a promising therapeutic strategy, especially in combination with other target-drugs for synergistic effect. For that reason, monoclonal antibodies against EphA2 and inhibitors of this receptor should be investigated for efficacy and drug toxicity.
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Affiliation(s)
- Rafaela Nasser Veiga
- Laboratory of Human Cytogenetics and Oncogenetics, Postgraduate Program in Genetics. Department of Genetics, Universidade Federal Do Paraná, Rua Coronel Francisco Heráclito Dos Santos, 100, Jardim das AméricasCuritiba, CEP, 81531-980, Brazil
| | - Alexandre Luiz Korte de Azevedo
- Laboratory of Human Cytogenetics and Oncogenetics, Postgraduate Program in Genetics. Department of Genetics, Universidade Federal Do Paraná, Rua Coronel Francisco Heráclito Dos Santos, 100, Jardim das AméricasCuritiba, CEP, 81531-980, Brazil
| | - Jaqueline Carvalho de Oliveira
- Laboratory of Human Cytogenetics and Oncogenetics, Postgraduate Program in Genetics. Department of Genetics, Universidade Federal Do Paraná, Rua Coronel Francisco Heráclito Dos Santos, 100, Jardim das AméricasCuritiba, CEP, 81531-980, Brazil
| | - Daniela Fiori Gradia
- Laboratory of Human Cytogenetics and Oncogenetics, Postgraduate Program in Genetics. Department of Genetics, Universidade Federal Do Paraná, Rua Coronel Francisco Heráclito Dos Santos, 100, Jardim das AméricasCuritiba, CEP, 81531-980, Brazil.
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5
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Ballester Roig MN, Roy PG, Hannou L, Delignat-Lavaud B, Sully Guerrier TA, Bélanger-Nelson E, Dufort-Gervais J, Mongrain V. Transcriptional regulation of the mouse EphA4, Ephrin-B2 and Ephrin-A3 genes by the circadian clock machinery. Chronobiol Int 2023; 40:983-1003. [PMID: 37551686 DOI: 10.1080/07420528.2023.2237580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 08/09/2023]
Abstract
Circadian rhythms originate from molecular feedback loops. In mammals, the transcription factors CLOCK and BMAL1 act on regulatory elements (i.e. E-boxes) to shape biological functions in a rhythmic manner. The EPHA4 receptor and its ligands Ephrins (EFN) are cell adhesion molecules regulating neurotransmission and neuronal morphology. Previous studies showed the presence of E-boxes in the genes of EphA4 and specific Ephrins, and that EphA4 knockout mice have an altered circadian rhythm of locomotor activity. We thus hypothesized that the core clock machinery regulates the gene expression of EphA4, EfnB2 and EfnA3. CLOCK and BMAL1 (or NPAS2 and BMAL2) were found to have transcriptional activity on distal and proximal regions of EphA4, EfnB2 and EfnA3 putative promoters. A constitutively active form of glycogen synthase kinase 3β (GSK3β; a negative regulator of CLOCK and BMAL1) blocked the transcriptional induction. Mutating the E-boxes of EphA4 distal promoter sequence reduced transcriptional induction. EPHA4 and EFNB2 protein levels did not show circadian variations in the mouse suprachiasmatic nucleus or prefrontal cortex. The findings uncover that core circadian transcription factors can regulate the gene expression of elements of the Eph/Ephrin system, which might contribute to circadian rhythmicity in biological processes in the brain or peripheral tissues.
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Affiliation(s)
- Maria Neus Ballester Roig
- Department of Neuroscience, Université de Montréal, Montreal, Quebec, Canada
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Recherche CIUSSS-NIM, Montreal, Quebec, Canada
| | - Pierre-Gabriel Roy
- Department of Neuroscience, Université de Montréal, Montreal, Quebec, Canada
- Recherche CIUSSS-NIM, Montreal, Quebec, Canada
- Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | | | | | | | | | | | - Valérie Mongrain
- Department of Neuroscience, Université de Montréal, Montreal, Quebec, Canada
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Recherche CIUSSS-NIM, Montreal, Quebec, Canada
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Lin Z, Garbern JC, Liu R, Li Q, Mancheño Juncosa E, Elwell HL, Sokol M, Aoyama J, Deumer US, Hsiao E, Sheng H, Lee RT, Liu J. Tissue-embedded stretchable nanoelectronics reveal endothelial cell-mediated electrical maturation of human 3D cardiac microtissues. SCIENCE ADVANCES 2023; 9:eade8513. [PMID: 36888704 PMCID: PMC9995081 DOI: 10.1126/sciadv.ade8513] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Clinical translation of stem cell therapies for heart disease requires electrical integration of transplanted cardiomyocytes. Generation of electrically matured human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) is critical for electrical integration. Here, we found that hiPSC-derived endothelial cells (hiPSC-ECs) promoted the expression of selected maturation markers in hiPSC-CMs. Using tissue-embedded stretchable mesh nanoelectronics, we achieved a long-term stable map of human three-dimensional (3D) cardiac microtissue electrical activity. The results revealed that hiPSC-ECs accelerated the electrical maturation of hiPSC-CMs in 3D cardiac microtissues. Machine learning-based pseudotime trajectory inference of cardiomyocyte electrical signals further revealed the electrical phenotypic transition path during development. Guided by the electrical recording data, single-cell RNA sequencing identified that hiPSC-ECs promoted cardiomyocyte subpopulations with a more mature phenotype, and multiple ligand-receptor interactions were up-regulated between hiPSC-ECs and hiPSC-CMs, revealing a coordinated multifactorial mechanism of hiPSC-CM electrical maturation. Collectively, these findings show that hiPSC-ECs drive hiPSC-CM electrical maturation via multiple intercellular pathways.
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Affiliation(s)
- Zuwan Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jessica C. Garbern
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Cardiology, Boston Children’s Hospital, Boston, MA, USA
| | - Ren Liu
- School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
| | - Qiang Li
- School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
| | | | - Hannah L.T. Elwell
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Morgan Sokol
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Junya Aoyama
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Undine-Sophie Deumer
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Emma Hsiao
- School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
| | - Hao Sheng
- School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
| | - Richard T. Lee
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Corresponding author. (J.L.), (R.T.L.)
| | - Jia Liu
- School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
- Corresponding author. (J.L.), (R.T.L.)
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7
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Nicin L, Schroeter SM, Glaser SF, Schulze-Brüning R, Pham MD, Hille SS, Yekelchyk M, Kattih B, Abplanalp WT, Tombor L, Müller OJ, Braun T, Meder B, Reich C, Arsalan M, Holubec T, Walther T, Emrich F, Krishnan J, Zeiher AM, John D, Dimmeler S. A human cell atlas of the pressure-induced hypertrophic heart. NATURE CARDIOVASCULAR RESEARCH 2022; 1:174-185. [PMID: 39195989 PMCID: PMC11357985 DOI: 10.1038/s44161-022-00019-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 01/05/2022] [Indexed: 08/29/2024]
Abstract
Pathological cardiac hypertrophy is a leading cause of heart failure, but knowledge of the full repertoire of cardiac cells and their gene expression profiles in the human hypertrophic heart is missing. Here, by using large-scale single-nucleus transcriptomics, we present the transcriptional response of human cardiomyocytes to pressure overload caused by aortic valve stenosis and describe major alterations in cardiac cellular crosstalk. Hypertrophied cardiomyocytes had reduced input from endothelial cells and fibroblasts. Genes encoding Eph receptor tyrosine kinases, particularly EPHB1, were significantly downregulated in cardiomyocytes of the hypertrophied heart. Consequently, EPHB1 activation by its ligand ephrin (EFN)B2, which is mainly expressed by endothelial cells, was reduced. EFNB2 inhibited cardiomyocyte hypertrophy in vitro, while silencing its expression in endothelial cells induced hypertrophy in co-cultured cardiomyocytes. Our human cell atlas of the hypertrophied heart highlights the importance of intercellular crosstalk in disease pathogenesis and provides a valuable resource.
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Affiliation(s)
- Luka Nicin
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), partner site Frankfurt Rhine-Main, Berlin, Germany
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Sam Michael Schroeter
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), partner site Frankfurt Rhine-Main, Berlin, Germany
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Simone Franziska Glaser
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), partner site Frankfurt Rhine-Main, Berlin, Germany
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Ralf Schulze-Brüning
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt, Germany
| | - Minh-Duc Pham
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
- Cardiac Metabolism Group, Department of Cardiology, Goethe University Frankfurt, Frankfurt, Germany
| | - Susanne S Hille
- Department of Internal Medicine III, University Hospital Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Berlin, Germany
| | - Michail Yekelchyk
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Badder Kattih
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), partner site Frankfurt Rhine-Main, Berlin, Germany
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Wesley Tyler Abplanalp
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), partner site Frankfurt Rhine-Main, Berlin, Germany
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Lukas Tombor
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), partner site Frankfurt Rhine-Main, Berlin, Germany
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Oliver J Müller
- Department of Internal Medicine III, University Hospital Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Berlin, Germany
| | - Thomas Braun
- German Center for Cardiovascular Research (DZHK), partner site Frankfurt Rhine-Main, Berlin, Germany
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Benjamin Meder
- Institute for Cardiomyopathies, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim, Berlin, Germany
| | - Christoph Reich
- Institute for Cardiomyopathies, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim, Berlin, Germany
| | - Mani Arsalan
- Department of Cardiovascular Surgery, Goethe University Hospital, Frankfurt, Germany
| | - Tomas Holubec
- Department of Cardiovascular Surgery, Goethe University Hospital, Frankfurt, Germany
| | - Thomas Walther
- German Center for Cardiovascular Research (DZHK), partner site Frankfurt Rhine-Main, Berlin, Germany
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
- Department of Cardiovascular Surgery, Goethe University Hospital, Frankfurt, Germany
| | - Fabian Emrich
- Department of Cardiovascular Surgery, Goethe University Hospital, Frankfurt, Germany
| | - Jaya Krishnan
- German Center for Cardiovascular Research (DZHK), partner site Frankfurt Rhine-Main, Berlin, Germany
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
- Cardiac Metabolism Group, Department of Cardiology, Goethe University Frankfurt, Frankfurt, Germany
| | - Andreas M Zeiher
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), partner site Frankfurt Rhine-Main, Berlin, Germany
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - David John
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), partner site Frankfurt Rhine-Main, Berlin, Germany
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt, Germany.
- German Center for Cardiovascular Research (DZHK), partner site Frankfurt Rhine-Main, Berlin, Germany.
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany.
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Evgeniou M, Sacnun JM, Kratochwill K, Perco P. A Meta-Analysis of Human Transcriptomics Data in the Context of Peritoneal Dialysis Identifies Novel Receptor-Ligand Interactions as Potential Therapeutic Targets. Int J Mol Sci 2021; 22:ijms222413277. [PMID: 34948074 PMCID: PMC8703997 DOI: 10.3390/ijms222413277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/01/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022] Open
Abstract
Peritoneal dialysis (PD) is one therapeutic option for patients with end-stage kidney disease (ESKD). Molecular profiling of samples from PD patients using different Omics technologies has led to the discovery of dysregulated molecular processes due to PD treatment in recent years. In particular, a number of transcriptomics (TX) datasets are currently available in the public domain in the context of PD. We set out to perform a meta-analysis of TX datasets to identify dysregulated receptor-ligand interactions in the context of PD-associated complications. We consolidated transcriptomics profiles from twelve untargeted genome-wide gene expression studies focusing on human cell cultures or samples from human PD patients. Gene set enrichment analysis was used to identify enriched biological processes. Receptor-ligand interactions were identified using data from CellPhoneDB. We identified 2591 unique differentially expressed genes in the twelve PD studies. Key enriched biological processes included angiogenesis, cell adhesion, extracellular matrix organization, and inflammatory response. We identified 70 receptor-ligand interaction pairs, with both interaction partners being dysregulated on the transcriptional level in one of the investigated tissues in the context of PD. Novel receptor-ligand interactions without prior annotation in the context of PD included BMPR2-GDF6, FZD4-WNT7B, ACKR2-CCL2, or the binding of EPGN and EREG to the EGFR, as well as the binding of SEMA6D to the receptors KDR and TYROBP. In summary, we have consolidated human transcriptomics datasets from twelve studies in the context of PD and identified sets of novel receptor-ligand pairs being dysregulated in the context of PD that warrant investigation in future functional studies.
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Affiliation(s)
- Michail Evgeniou
- Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria; (M.E.); (J.M.S.); (K.K.)
| | - Juan Manuel Sacnun
- Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria; (M.E.); (J.M.S.); (K.K.)
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
- Zytoprotec GmbH, 1090 Vienna, Austria
| | - Klaus Kratochwill
- Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria; (M.E.); (J.M.S.); (K.K.)
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Paul Perco
- Department of Internal Medicine IV, Medical University Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria
- Correspondence:
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