1
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Sun C, Feng Y. EPDRNA: A Model for Identifying DNA-RNA Binding Sites in Disease-Related Proteins. Protein J 2024; 43:513-521. [PMID: 38491248 DOI: 10.1007/s10930-024-10183-3] [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] [Accepted: 02/02/2024] [Indexed: 03/18/2024]
Abstract
Protein-DNA and protein-RNA interactions are involved in many biological processes and regulate many cellular functions. Moreover, they are related to many human diseases. To understand the molecular mechanism of protein-DNA binding and protein-RNA binding, it is important to identify which residues in the protein sequence bind to DNA and RNA. At present, there are few methods for specifically identifying the binding sites of disease-related protein-DNA and protein-RNA. In this study, so we combined four machine learning algorithms into an ensemble classifier (EPDRNA) to predict DNA and RNA binding sites in disease-related proteins. The dataset used in model was collated from UniProt and PDB database, and PSSM, physicochemical properties and amino acid type were used as features. The EPDRNA adopted soft voting and achieved the best AUC value of 0.73 at the DNA binding sites, and the best AUC value of 0.71 at the RNA binding sites in 10-fold cross validation in the training sets. In order to further verify the performance of the model, we assessed EPDRNA for the prediction of DNA-binding sites and the prediction of RNA-binding sites on the independent test dataset. The EPDRNA achieved 85% recall rate and 25% precision on the protein-DNA interaction independent test set, and achieved 82% recall rate and 27% precision on the protein-RNA interaction independent test set. The online EPDRNA webserver is freely available at http://www.s-bioinformatics.cn/epdrna .
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Affiliation(s)
- CanZhuang Sun
- College of Science, Inner Mongolia Agriculture University, Hohhot, 010018, People's Republic of China
| | - YongE Feng
- College of Science, Inner Mongolia Agriculture University, Hohhot, 010018, People's Republic of China.
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2
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Berkeley B, Tang MNH, Brittan M. Mechanisms regulating vascular and lymphatic regeneration in the heart after myocardial infarction. J Pathol 2023; 260:666-678. [PMID: 37272582 PMCID: PMC10953458 DOI: 10.1002/path.6093] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/14/2023] [Accepted: 04/27/2023] [Indexed: 06/06/2023]
Abstract
Myocardial infarction, caused by a thrombus or coronary vascular occlusion, leads to irreversible ischaemic injury. Advances in early reperfusion strategies have significantly reduced short-term mortality after myocardial infarction. However, survivors have an increased risk of developing heart failure, which confers a high risk of death at 1 year. The capacity of the injured neonatal mammalian heart to regenerate has stimulated extensive research into whether recapitulation of developmental regeneration programmes may be beneficial in adult cardiovascular disease. Restoration of functional blood and lymphatic vascular networks in the infarct and border regions via neovascularisation and lymphangiogenesis, respectively, is a key requirement to facilitate myocardial regeneration. An improved understanding of the endogenous mechanisms regulating coronary vascular and lymphatic expansion and function in development and in adult patients after myocardial infarction may inform future therapeutic strategies and improve translation from pre-clinical studies. In this review, we explore the underpinning research and key findings in the field of cardiovascular regeneration, with a focus on neovascularisation and lymphangiogenesis, and discuss the outcomes of therapeutic strategies employed to date. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Bronwyn Berkeley
- Centre for Cardiovascular Science, The Queen's Medical Research InstituteUniversity of EdinburghEdinburghUK
| | - Michelle Nga Huen Tang
- Centre for Cardiovascular Science, The Queen's Medical Research InstituteUniversity of EdinburghEdinburghUK
| | - Mairi Brittan
- Centre for Cardiovascular Science, The Queen's Medical Research InstituteUniversity of EdinburghEdinburghUK
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3
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Sun N, Chu B, Choi DH, Lim L, Song H. ETV2 Enhances CXCL5 Secretion from Endothelial Cells, Leading to the Promotion of Vascular Smooth Muscle Cell Migration. Int J Mol Sci 2023; 24:9904. [PMID: 37373052 DOI: 10.3390/ijms24129904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Abnormal communication between endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) promotes vascular diseases, including atherogenesis. ETS variant transcription factor 2 (ETV2) plays a substantial role in pathological angiogenesis and the reprogramming of ECs; however, the role of ETV2 in the communication between ECs and VSMCs has not been revealed. To investigate the interactive role of ETV2 in the EC to VSMC phenotype, we first showed that treatment with a conditioned medium from ETV2-overexpressed ECs (Ad-ETV2 CM) significantly increased VSMC migration. The cytokine array showed altered levels of several cytokines in Ad-ETV2 CM compared with those in normal CM. We found that C-X-C motif chemokine 5 (CXCL5) promoted VSMC migration using the Boyden chamber and wound healing assays. In addition, an inhibitor of C-X-C motif chemokine receptor 2 (CXCR2) (the receptor for CXCL5) significantly inhibited this process. Gelatin zymography showed that the activities of matrix metalloproteinase (MMP)-2 and MMP-9 increased in the media of VSMCs treated with Ad-ETV2 CM. Western blotting revealed a positive correlation between Akt/p38/c-Jun phosphorylation and CXCL5 concentration. The inhibition of Akt and p38-c-Jun effectively blocked CXCL5-induced VSMC migration. In conclusion, CXCL5 from ECs induced by ETV2 promotes VSMC migration via MMP upregulation and the activation of Akt and p38/c-Jun.
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Affiliation(s)
- Ningning Sun
- Department of Biochemistry and Molecular Biology, Chosun University School of Medicine, Gwangju 61452, Republic of Korea
| | - Beyongsam Chu
- Department of Medical Sciences, Chosun University Graduate School, Gwangju 61452, Republic of Korea
| | - Dong-Hyun Choi
- Department of Internal Medicine, Chosun University School of Medicine, Gwangju 61452, Republic of Korea
| | - Leejin Lim
- Advanced Cancer Controlling Research Center, Chosun University, Gwangju 61452, Republic of Korea
| | - Heesang Song
- Department of Biochemistry and Molecular Biology, Chosun University School of Medicine, Gwangju 61452, Republic of Korea
- Department of Medical Sciences, Chosun University Graduate School, Gwangju 61452, Republic of Korea
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4
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Kim TM, Lee RH, Kim MS, Lewis CA, Park C. ETV2/ER71, the key factor leading the paths to vascular regeneration and angiogenic reprogramming. Stem Cell Res Ther 2023; 14:41. [PMID: 36927793 PMCID: PMC10019431 DOI: 10.1186/s13287-023-03267-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
Extensive efforts have been made to achieve vascular regeneration accompanying tissue repair for treating vascular dysfunction-associated diseases. Recent advancements in stem cell biology and cell reprogramming have opened unforeseen opportunities to promote angiogenesis in vivo and generate autologous endothelial cells (ECs) for clinical use. We have, for the first time, identified a unique endothelial-specific transcription factor, ETV2/ER71, and revealed its essential role in regulating endothelial cell generation and function, along with vascular regeneration and tissue repair. Furthermore, we and other groups have demonstrated its ability to directly reprogram terminally differentiated non-ECs into functional ECs, proposing ETV2/ER71 as an effective therapeutic target for vascular diseases. In this review, we discuss the up-to-date status of studies on ETV2/ER71, spanning from its molecular mechanism to vasculo-angiogenic role and direct cell reprogramming toward ECs. Furthermore, we discuss future directions to deploy the clinical potential of ETV2/ER71 as a novel and potent target for vascular disorders such as cardiovascular disease, neurovascular impairment and cancer.
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Affiliation(s)
- Tae Min Kim
- Graduate School of International Agricultural Technology and Institutes of Green-Bio Science and Technology, Seoul National University, 1447 Pyeongchang-daero, Pyeongchang, Gangwon-do, 25354, Republic of Korea.
| | - Ra Ham Lee
- Department of Molecular and Cellular Physiology, Louisiana State University Health Science Center, 1501 Kings Highway, Shreveport, LA, 71103, USA
| | - Min Seong Kim
- Department of Molecular and Cellular Physiology, Louisiana State University Health Science Center, 1501 Kings Highway, Shreveport, LA, 71103, USA
| | - Chloe A Lewis
- Department of Molecular and Cellular Physiology, Louisiana State University Health Science Center, 1501 Kings Highway, Shreveport, LA, 71103, USA
| | - Changwon Park
- Department of Molecular and Cellular Physiology, Louisiana State University Health Science Center, 1501 Kings Highway, Shreveport, LA, 71103, USA.
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5
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Epigenetic impact of a 1-week intensive multimodal group program for adolescents with multiple adverse childhood experiences. Sci Rep 2022; 12:17177. [PMID: 36266402 PMCID: PMC9585146 DOI: 10.1038/s41598-022-21246-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/26/2022] [Indexed: 01/04/2023] Open
Abstract
Adverse childhood experiences (ACEs, i.e., abuse, neglect, household dysfunction) represent a potential risk factor for a wide range of long-lasting diseases and shorter life expectancy. We recently described a 1-week residential group program, based on mindfulness training, artistic expression and EMDR group therapy, that significantly reduced PTSD-related symptoms and increased attention/awareness-related outcomes in adolescent girls with multiple ACEs in a randomized controlled study. Since epigenetic mechanisms (i.e., DNA methylation) have been associated with the long-lasting effects of ACEs, the present report extends these prior findings by exploring genome-wide DNA methylation changes following the program. Saliva samples from all participants (n = 44) were collected and genomic DNA was extracted prior (T1) and following (T2) the intervention. Genome-wide DNA methylation analysis using the MethylationEPIC beadchip array (Illumina) revealed 49 differentially methylated loci (DML; p value < 0.001; methylation change > 10%) that were annotated to genes with roles in biological processes linked to early childhood adversity (i.e., neural, immune, and endocrine pathways, cancer and cardiovascular disease). DNA sequences flanking these DML showed significant enrichment of transcription factor binding sites involved in inflammation, cancer, cardiovascular disease, and brain development. Methylation changes in SIRT5 and TRAPPC2L genes showed associations with changes in trauma-related psychological measures. Results presented here suggest that this multimodal group program for adolescents with multiple victimization modulates the DNA methylome at sites of potential relevance for health and behavioral disorders associated with ACEs.
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6
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Abstract
Formation of the vasculature is a critical step within the developing embryo and its disruption causes early embryonic lethality. This complex process is driven by a cascade of signaling events that controls differentiation of mesodermal progenitors into primordial endothelial cells and their further specification into distinct subtypes (arterial, venous, hemogenic) that are needed to generate a blood circulatory network. Hemogenic endothelial cells give rise to hematopoietic stem and progenitor cells that generate all blood cells in the body during embryogenesis and postnatally. We focus our discussion on the regulation of endothelial cell differentiation, and subsequent hemogenic specification, and highlight many of the signaling pathways involved in these processes, which are conserved across vertebrates. Gaining a better understanding of the regulation of these processes will yield insights needed to optimize the treatment of vascular and hematopoietic disease and generate human stem cell-derived vascular and hematopoietic cells for tissue engineering and regenerative medicine.
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Affiliation(s)
- Jordon W Aragon
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, Virginia 22903, USA
- Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
| | - Karen K Hirschi
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, Virginia 22903, USA
- Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
- Departments of Medicine and Genetics, Yale University School of Medicine, Yale Cardiovascular Research Center, New Haven, Connecticut 06520, USA
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7
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Shrestha S, Lamattina A, Pacheco-Rodriguez G, Ng J, Liu X, Sonawane A, Imani J, Qiu W, Kosmas K, Louis P, Hentschel A, Steagall WK, Onishi R, Christou H, Henske EP, Glass K, Perrella MA, Moss J, Tantisira K, El-Chemaly S. ETV2 regulates PARP-1 binding protein to induce ER stress-mediated death in tuberin-deficient cells. Life Sci Alliance 2022; 5:5/5/e202201369. [PMID: 35181635 PMCID: PMC8860090 DOI: 10.26508/lsa.202201369] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 11/24/2022] Open
Abstract
Lymphangioleiomyomatosis (LAM) is a rare progressive disease, characterized by mutations in the tuberous sclerosis complex genes (TSC1 or TSC2) and hyperactivation of mechanistic target of rapamycin complex 1 (mTORC1). Here, we report that E26 transformation-specific (ETS) variant transcription factor 2 (ETV2) is a critical regulator of Tsc2-deficient cell survival. ETV2 nuclear localization in Tsc2-deficient cells is mTORC1-independent and is enhanced by spleen tyrosine kinase (Syk) inhibition. In the nucleus, ETV2 transcriptionally regulates poly(ADP-ribose) polymerase 1 binding protein (PARPBP) mRNA and protein expression, partially reversing the observed down-regulation of PARPBP expression induced by mTORC1 blockade during treatment with both Syk and mTORC1 inhibitors. In addition, silencing Etv2 or Parpbp in Tsc2-deficient cells induced ER stress and increased cell death in vitro and in vivo. We also found ETV2 expression in human cells with loss of heterozygosity for TSC2, lending support to the translational relevance of our findings. In conclusion, we report a novel ETV2 signaling axis unique to Syk inhibition that promotes a cytocidal response in Tsc2-deficient cells and therefore maybe a potential alternative therapeutic target in LAM.
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Affiliation(s)
- Shikshya Shrestha
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anthony Lamattina
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gustavo Pacheco-Rodriguez
- Division of Intramural Research, Pulmonary Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Julie Ng
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaoli Liu
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Abhijeet Sonawane
- Department of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School Boston, MA, USA
| | - Jewel Imani
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kosmas Kosmas
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Pierce Louis
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anne Hentschel
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Wendy K Steagall
- Division of Intramural Research, Pulmonary Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rieko Onishi
- Division of Intramural Research, Pulmonary Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Helen Christou
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth P Henske
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark A Perrella
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joel Moss
- Division of Intramural Research, Pulmonary Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kelan Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Division of Pediatric Pulmonary and Critical Care Medicine, University of California San Diego, La Jolla, CA, USA
| | - Souheil El-Chemaly
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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8
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Liu T, Shen J, He Q, Xu S. Identification of a Novel Immune-Related lncRNA CTD-2288O8.1 Regulating Cisplatin Resistance in Ovarian Cancer Based on Integrated Analysis. Front Genet 2022; 13:814291. [PMID: 35237300 PMCID: PMC8884246 DOI: 10.3389/fgene.2022.814291] [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: 11/13/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Ovarian cancer (OC) is the most lethal gynecological malignancy, in which chemoresistance is a crucial factor leading to the poor prognosis. Recently, immunotherapy has brought new light for the treatment of solid tumors. Hence, as a kind of immunologically active cancer, it is reasonably necessary to explore the potential mechanism between immune characteristics and cisplatin resistance in OC. Our study focused on the important role of cisplatin resistance-related lncRNAs on mediating the OC tumor immune microenvironment (TIME) using an integrative analysis based on the Cancer Genome Atlas (TCGA) database. First, the cisplatin resistance-related differentially expressed lncRNAs (DELs) and mRNAs (DEMs) were preliminarily screened to construct a DEL–DEM co-expression network. Next, the protein–protein interaction (PPI) network and pivot analysis were performed to reveal the relevance of these lncRNAs with tumor immune response. Second, the novel lncRNA CTD-2288O8.1 was identified as a key gene for the OC cisplatin resistance formation by qRT-PCR and survival analysis. Gain- and loss-of-function assays (Cell Counting Kit-8 (CCK-8) assay, wound-healing scratch assay, transwell assay, and colony formation assay) further verified the activity of CTD-2288O8.1 in OC progression as well. Third, gene set enrichment analysis (GSEA) was applied along with the correlation analyses of CTD-2288O8.1 with ImmuneScore, tumor-infiltrating immune cells (TICs), and immune inhibitory checkpoint molecules, illustrating that CTD-2288O8.1 was strongly associated with the TIME and has the potential to predict the effect of OC immunotherapy. In addition, basic experiments demonstrated that the expression of CTD-2288O8.1 impacted the EGFR/AKT signal pathway activity of OC tumor cells. Of greater significance, it promoted the M2 polarization of macrophage, which is a type of the most important components of the TIME in solid tumor. Taking together, our study revealed cisplatin resistance-related lncRNAs closely linked with tumor immunity in OC, underscoring the potential mechanism of the TIME in conferring cisplatin resistance, which provided the research basis for further clinical treatment. CTD-2288O8.1 was identified to mediate cisplatin resistance and affect the response of immunotherapy, which could serve as a promising biomarker for guiding clinical treatment and improving prognosis in OC.
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Affiliation(s)
- Tingwei Liu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jiacheng Shen
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qizhi He
- Department of Pathology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Qizhi He, ; Shaohua Xu,
| | - Shaohua Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Qizhi He, ; Shaohua Xu,
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9
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Kim Y, Zharkinbekov Z, Sarsenova M, Yeltay G, Saparov A. Recent Advances in Gene Therapy for Cardiac Tissue Regeneration. Int J Mol Sci 2021; 22:9206. [PMID: 34502115 PMCID: PMC8431496 DOI: 10.3390/ijms22179206] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/16/2021] [Accepted: 08/16/2021] [Indexed: 12/12/2022] Open
Abstract
Cardiovascular diseases (CVDs) are responsible for enormous socio-economic impact and the highest mortality globally. The standard of care for CVDs, which includes medications and surgical interventions, in most cases, can delay but not prevent the progression of disease. Gene therapy has been considered as a potential therapy to improve the outcomes of CVDs as it targets the molecular mechanisms implicated in heart failure. Cardiac reprogramming, therapeutic angiogenesis using growth factors, antioxidant, and anti-apoptotic therapies are the modalities of cardiac gene therapy that have led to promising results in preclinical studies. Despite the benefits observed in animal studies, the attempts to translate them to humans have been inconsistent so far. Low concentration of the gene product at the target site, incomplete understanding of the molecular pathways of the disease, selected gene delivery method, difference between animal models and humans among others are probable causes of the inconsistent results in clinics. In this review, we discuss the most recent applications of the aforementioned gene therapy strategies to improve cardiac tissue regeneration in preclinical and clinical studies as well as the challenges associated with them. In addition, we consider ongoing gene therapy clinical trials focused on cardiac regeneration in CVDs.
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Affiliation(s)
| | | | | | | | - Arman Saparov
- Department of Medicine, School of Medicine, Nazarbayev University, Nur-Sultan 010000, Kazakhstan; (Y.K.); (Z.Z.); (M.S.); (G.Y.)
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10
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Qian L, TCW J. Human iPSC-Based Modeling of Central Nerve System Disorders for Drug Discovery. Int J Mol Sci 2021; 22:1203. [PMID: 33530458 PMCID: PMC7865494 DOI: 10.3390/ijms22031203] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
A high-throughput drug screen identifies potentially promising therapeutics for clinical trials. However, limitations that persist in current disease modeling with limited physiological relevancy of human patients skew drug responses, hamper translation of clinical efficacy, and contribute to high clinical attritions. The emergence of induced pluripotent stem cell (iPSC) technology revolutionizes the paradigm of drug discovery. In particular, iPSC-based three-dimensional (3D) tissue engineering that appears as a promising vehicle of in vitro disease modeling provides more sophisticated tissue architectures and micro-environmental cues than a traditional two-dimensional (2D) culture. Here we discuss 3D based organoids/spheroids that construct the advanced modeling with evolved structural complexity, which propels drug discovery by exhibiting more human specific and diverse pathologies that are not perceived in 2D or animal models. We will then focus on various central nerve system (CNS) disease modeling using human iPSCs, leading to uncovering disease pathogenesis that guides the development of therapeutic strategies. Finally, we will address new opportunities of iPSC-assisted drug discovery with multi-disciplinary approaches from bioengineering to Omics technology. Despite technological challenges, iPSC-derived cytoarchitectures through interactions of diverse cell types mimic patients' CNS and serve as a platform for therapeutic development and personalized precision medicine.
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Affiliation(s)
- Lu Qian
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Ronald Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Julia TCW
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Ronald Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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11
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Kim JY, Lee DH, Kim JK, Choi HS, Dwivedi B, Rupji M, Kowalski J, Green SJ, Song H, Park WJ, Chang JY, Kim TM, Park C. ETV2/ER71 regulates the generation of FLK1 + cells from mouse embryonic stem cells through miR-126-MAPK signaling. Stem Cell Res Ther 2019; 10:328. [PMID: 31744543 PMCID: PMC6862833 DOI: 10.1186/s13287-019-1466-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/28/2019] [Accepted: 10/22/2019] [Indexed: 11/10/2022] Open
Abstract
Previous studies including ours have demonstrated a critical function of the transcription factor ETV2 (ets variant 2; also known as ER71) in determining the fate of cardiovascular lineage development. However, the underlying mechanisms of ETV2 function remain largely unknown. In this study, we demonstrated the novel function of the miR (micro RNA)-126-MAPK (mitogen-activated protein kinase) pathway in ETV2-mediated FLK1 (fetal liver kinase 1; also known as VEGFR2)+ cell generation from the mouse embryonic stem cells (mESCs). By performing a series of experiments including miRNA sequencing and ChIP (chromatin immunoprecipitation)-PCR, we found that miR-126 is directly induced by ETV2. Further, we identified that miR-126 can positively regulate the generation of FLK1+ cells by activating the MAPK pathway through targeting SPRED1 (sprouty-related EVH1 domain containing 1). Further, we showed evidence that JUN/FOS activate the enhancer region of FLK1 through AP1 (activator protein 1) binding sequences. Our findings provide insight into the novel molecular mechanisms of ETV2 function in regulating cardiovascular lineage development from mESCs.
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Affiliation(s)
- Ju Young Kim
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Dr. Atlanta, Atlanta, GA, 30322, USA.,Children's Heart Research & Outcomes (HeRO) Center, Children's Healthcare of Atlanta & Emory University, Atlanta, GA, USA.,Molecular and Systems Pharmacology Program, Emory University, Atlanta, GA, USA
| | - Dong Hun Lee
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Dr. Atlanta, Atlanta, GA, 30322, USA.,Children's Heart Research & Outcomes (HeRO) Center, Children's Healthcare of Atlanta & Emory University, Atlanta, GA, USA
| | - Joo Kyung Kim
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Dr. Atlanta, Atlanta, GA, 30322, USA.,Children's Heart Research & Outcomes (HeRO) Center, Children's Healthcare of Atlanta & Emory University, Atlanta, GA, USA
| | - Hong Seo Choi
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Dr. Atlanta, Atlanta, GA, 30322, USA
| | - Bhakti Dwivedi
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Manali Rupji
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Jeanne Kowalski
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.,Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA.,Present Address: Department of Oncology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Stefan J Green
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Heesang Song
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Dr. Atlanta, Atlanta, GA, 30322, USA.,Department of Biochemistry and Molecular Biology, Chosun University School of Medicine, Gwangju, IL, Republic of Korea
| | - Won Jong Park
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Dr. Atlanta, Atlanta, GA, 30322, USA
| | - Ji Young Chang
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Dr. Atlanta, Atlanta, GA, 30322, USA
| | - Tae Min Kim
- Graduate School of International Agricultural Technology and Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang, Gangwon-do, Republic of Korea
| | - Changwon Park
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Dr. Atlanta, Atlanta, GA, 30322, USA. .,Children's Heart Research & Outcomes (HeRO) Center, Children's Healthcare of Atlanta & Emory University, Atlanta, GA, USA. .,Molecular and Systems Pharmacology Program, Emory University, Atlanta, GA, USA. .,Biochemistry, Cell Biology and Developmental Biology Program, Emory University, Atlanta, GA, USA.
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