1
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Oliveira RHDM, Annex BH, Popel AS. Endothelial cells signaling and patterning under hypoxia: a mechanistic integrative computational model including the Notch-Dll4 pathway. Front Physiol 2024; 15:1351753. [PMID: 38455844 PMCID: PMC10917925 DOI: 10.3389/fphys.2024.1351753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/12/2024] [Indexed: 03/09/2024] Open
Abstract
Introduction: Several signaling pathways are activated during hypoxia to promote angiogenesis, leading to endothelial cell patterning, interaction, and downstream signaling. Understanding the mechanistic signaling differences between endothelial cells under normoxia and hypoxia and their response to different stimuli can guide therapies to modulate angiogenesis. We present a novel mechanistic model of interacting endothelial cells, including the main pathways involved in angiogenesis. Methods: We calibrate and fit the model parameters based on well-established modeling techniques that include structural and practical parameter identifiability, uncertainty quantification, and global sensitivity. Results: Our results indicate that the main pathways involved in patterning tip and stalk endothelial cells under hypoxia differ, and the time under hypoxia interferes with how different stimuli affect patterning. Additionally, our simulations indicate that Notch signaling might regulate vascular permeability and establish different Nitric Oxide release patterns for tip/stalk cells. Following simulations with various stimuli, our model suggests that factors such as time under hypoxia and oxygen availability must be considered for EC pattern control. Discussion: This project provides insights into the signaling and patterning of endothelial cells under various oxygen levels and stimulation by VEGFA and is our first integrative approach toward achieving EC control as a method for improving angiogenesis. Overall, our model provides a computational framework that can be built on to test angiogenesis-related therapies by modulation of different pathways, such as the Notch pathway.
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Affiliation(s)
| | - Brian H. Annex
- Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Aleksander S. Popel
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
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2
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Zhang X, Yassouf Y, Huang K, Xu Y, Huang ZS, Zhai D, Sekiya R, Liu KX, Li TS. Ex Vivo Hydrostatic Pressure Loading of Atrial Tissues Activates Profibrotic Transcription via TGF-β Signal Pathway. Int Heart J 2022; 63:367-374. [PMID: 35296614 DOI: 10.1536/ihj.21-481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Excessive mechanical stress causes fibrosis-related atrial arrhythmia. Herein, we tried to investigate the mechanism of atrial fibrogenesis in response to mechanical stress by ex vivo approach. We collected atrial tissues from mice and then cultured them as "explants" under atmospheric pressure (AP group) or 50 mmHg hydrostatic pressure loading (HP group) conditions. Pathway-specific PCR array analysis on the expression of fibrosis-related genes indicated that the loading of atrial tissues to 50 mmHg for 24 hours extensively upregulated a series of profibrotic genes. qRT-PCR data also showed that loading atrial tissues to 50 mmHg enhanced Rhoa, Rock2, and Thbs1 expression at different time points. Interestingly, the enhanced expression of Thbs1 at 1 hour declined at 6-24 hours and then increased again at 72 hours. In contrast, an enhanced expression of Tgfb1 was observed at 72 hours. In contrast, daily loading to 50 mmHg for 3 hours significantly accelerated the outgrowth of mesenchymal stem-like stromal cells from atrial tissues; however, we did not observe significant phenotypic changes in these outgrowing cells. Our ex vivo experimental data clearly show the induction of profibrotic transcription of atrial tissues by HP loading, which confirms the common pathological feature of atrial fibrosis following pressure overload.
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Affiliation(s)
- Xu Zhang
- Department of Stem Cell Biology, Nagasaki University Graduate School of Biomedical Sciences.,Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University
| | - Yousuf Yassouf
- Department of Stem Cell Biology, Nagasaki University Graduate School of Biomedical Sciences.,Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University
| | - Kai Huang
- Department of Stem Cell Biology, Nagasaki University Graduate School of Biomedical Sciences.,Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University
| | - Yong Xu
- Department of Stem Cell Biology, Nagasaki University Graduate School of Biomedical Sciences.,Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University
| | - Zi-Sheng Huang
- Department of Stem Cell Biology, Nagasaki University Graduate School of Biomedical Sciences.,Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University
| | - Da Zhai
- Department of Stem Cell Biology, Nagasaki University Graduate School of Biomedical Sciences.,Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University
| | - Reiko Sekiya
- Department of Stem Cell Biology, Nagasaki University Graduate School of Biomedical Sciences.,Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University
| | - Ke-Xiang Liu
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University
| | - Tao-Sheng Li
- Department of Stem Cell Biology, Nagasaki University Graduate School of Biomedical Sciences.,Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University
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3
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Zhang Y, Wang H, Oliveira RHM, Zhao C, Popel AS. Systems biology of angiogenesis signaling: Computational models and omics. WIREs Mech Dis 2021; 14:e1550. [PMID: 34970866 PMCID: PMC9243197 DOI: 10.1002/wsbm.1550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 01/10/2023]
Abstract
Angiogenesis is a highly regulated multiscale process that involves a plethora of cells, their cellular signal transduction, activation, proliferation, differentiation, as well as their intercellular communication. The coordinated execution and integration of such complex signaling programs is critical for physiological angiogenesis to take place in normal growth, development, exercise, and wound healing, while its dysregulation is critically linked to many major human diseases such as cancer, cardiovascular diseases, and ocular disorders; it is also crucial in regenerative medicine. Although huge efforts have been devoted to drug development for these diseases by investigation of angiogenesis‐targeted therapies, only a few therapeutics and targets have proved effective in humans due to the innate multiscale complexity and nonlinearity in the process of angiogenic signaling. As a promising approach that can help better address this challenge, systems biology modeling allows the integration of knowledge across studies and scales and provides a powerful means to mechanistically elucidate and connect the individual molecular and cellular signaling components that function in concert to regulate angiogenesis. In this review, we summarize and discuss how systems biology modeling studies, at the pathway‐, cell‐, tissue‐, and whole body‐levels, have advanced our understanding of signaling in angiogenesis and thereby delivered new translational insights for human diseases. This article is categorized under:Cardiovascular Diseases > Computational Models Cancer > Computational Models
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Affiliation(s)
- Yu Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hanwen Wang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rebeca Hannah M Oliveira
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chen Zhao
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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4
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Hisaoka-Nakashima K, Yokoe T, Watanabe S, Nakamura Y, Kajitani N, Okada-Tsuchioka M, Takebayashi M, Nakata Y, Morioka N. Lysophosphatidic acid induces thrombospondin-1 production in primary cultured rat cortical astrocytes. J Neurochem 2020; 158:849-864. [PMID: 33118159 DOI: 10.1111/jnc.15227] [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: 07/07/2020] [Revised: 10/09/2020] [Accepted: 10/25/2020] [Indexed: 11/25/2022]
Abstract
Lysophosphatidic acid (LPA), a brain membrane-derived lipid mediator, plays important roles including neural development, function, and behavior. In the present study, the effects of LPA on astrocyte-derived synaptogenesis factor thrombospondins (TSPs) production were examined by real-time PCR and western blotting, and the mechanism underlying this event was examined by pharmacological approaches in primary cultured rat cortical astrocytes. Treatment of astrocytes with LPA increased TSP-1 mRNA, and TSP-2 mRNA, but not TSP-4 mRNA expression. TSP-1 protein expression and release were also increased by LPA. LPA-induced TSP-1 production were inhibited by AM966 a LPA1 receptor antagonist, and Ki16425, LPA1/3 receptors antagonist, but not by H2L5146303, LPA2 receptor antagonist. Pertussis toxin, Gi/o inhibitor, but not YM-254890, Gq inhibitor, and NF499, Gs inhibitor, inhibited LPA-induced TSP-1 production, indicating that LPA increases TSP-1 production through Gi/o-coupled LPA1 and LPA3 receptors. LPA treatment increased phosphorylation of extracellular signal-regulated kinase (ERK), p38 mitogen-activated protein kinase (MAPK), and c-Jun N-terminal kinase (JNK). LPA-induced TSP-1 mRNA expression was inhibited by U0126, MAPK/ERK kinase (MEK) inhibitor, but not SB202190, p38 MAPK inhibitor, or SP600125, JNK inhibitor. However, LPA-induced TSP-1 protein expression was diminished with inhibition of all three MAPKs, indicating that these signaling molecules are involved in TSP-1 protein production. Treatment with antidepressants, which bind to astrocytic LPA1 receptors, increased TSP-1 mRNA and protein production. The current findings show that LPA/LPA1/3 receptors signaling increases TSP-1 production in astrocytes, which could be important in the pathogenesis of affective disorders and could potentially be a target for the treatment of affective disorders.
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Affiliation(s)
- Kazue Hisaoka-Nakashima
- Department of Pharmacology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Toshiki Yokoe
- Department of Pharmacology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Shintaro Watanabe
- Department of Pharmacology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yoki Nakamura
- Department of Pharmacology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Naoto Kajitani
- Department of Neuropsychiatry, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.,Division of Psychiatry and Neuroscience, Institute for Clinical Research, National Hospital Organization Kure Medical Center and Chugoku Cancer Center, Kure, Japan
| | - Mami Okada-Tsuchioka
- Division of Psychiatry and Neuroscience, Institute for Clinical Research, National Hospital Organization Kure Medical Center and Chugoku Cancer Center, Kure, Japan
| | - Minoru Takebayashi
- Department of Neuropsychiatry, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.,Division of Psychiatry and Neuroscience, Institute for Clinical Research, National Hospital Organization Kure Medical Center and Chugoku Cancer Center, Kure, Japan
| | - Yoshihiro Nakata
- Department of Pharmacology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Norimitsu Morioka
- Department of Pharmacology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
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5
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Wu J, Chu Y, Jiang Z, Yu Q. Losartan protects against intermittent hypoxia-induced peritubular capillary loss by modulating the renal renin-angiotensin system and angiogenesis factors. Acta Biochim Biophys Sin (Shanghai) 2020; 52:38-48. [PMID: 31836883 DOI: 10.1093/abbs/gmz136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 10/14/2019] [Indexed: 12/21/2022] Open
Abstract
Obstructive sleep apnea is characterized by chronic intermittent hypoxia (CIH), which is a risk factor for renal peritubular capillary (PTC) loss, and angiotensin II receptor blockers can alleviate PTC loss. However, the mechanism by which losartan (an angiotensin II receptor blocker) reduces CIH-induced PTC loss and attenuates kidney damage is still unknown. Thus, in this study, we examined the protective effects of losartan against CIH-induced PTC loss and explored the underlying mechanisms in rat CIH model. The immunohistochemical staining of CD34 and morphological examination showed that CIH reduced PTC density and damaged tubular epithelial cells. Immunohistochemistry, enzyme-linked immunosorbent assay (ELISA), real-time quantitative PCR, and western blot analysis results revealed that CIH increased the expression of hypoxia inducible factor-1α (HIF-1α), angiotensin II (Ang II), angiotensin II type 1 receptor (AT1R), pro-angiogenesis factor vascular endothelial growth factor (VEGF), and anti-angiogenesis factor thrombospondin-1 (TSP-1) in the renal cortex of rats. CIH may up-regulate VEGF expression and simultaneously increase TSP-1 production. By histopathological, immunohistochemistry, ELISA, RT-qPCR, and western blot analysis, we found that the expressions of renal renin-angiotensin system (RAS), HIF-1α, VEGF, and TSP-1 were decreased, and PTC loss and tubular epithelial cell injury were attenuated with losartan treatment. Losartan ameliorated CIH-induced PTC loss by modulating renal RAS to improve the crosstalk between endothelial cells and tubular epithelial cells and subsequently regulate the balance of angiogenesis factors. Our study provided novel insights into the mechanisms of CIH-induced kidney damage and indicated that losartan could be a potential therapeutic agent for renal protection by alleviating CIH-induced PTC loss.
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Affiliation(s)
- Jiqiang Wu
- Department of Respiratory Medicine, the First School of Clinical Medicine, Lanzhou University, Lanzhou 730000, China
| | - Yao Chu
- Department of Respiratory Medicine, the First School of Clinical Medicine, Lanzhou University, Lanzhou 730000, China
| | - Zhenxiu Jiang
- Department of Respiratory Medicine, the First School of Clinical Medicine, Lanzhou University, Lanzhou 730000, China
| | - Qin Yu
- Department of Respiratory Medicine, the First Hospital of Lanzhou University, Lanzhou 730000, China
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6
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Pillman KA, Scheer KG, Hackett-Jones E, Saunders K, Bert AG, Toubia J, Whitfield HJ, Sapkota S, Sourdin L, Pham H, Le TD, Cursons J, Davis MJ, Gregory PA, Goodall GJ, Bracken CP. Extensive transcriptional responses are co-ordinated by microRNAs as revealed by Exon-Intron Split Analysis (EISA). Nucleic Acids Res 2019; 47:8606-8619. [PMID: 31372646 PMCID: PMC6895270 DOI: 10.1093/nar/gkz664] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 07/16/2019] [Accepted: 07/30/2019] [Indexed: 12/29/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) has been a subject of intense scrutiny as it facilitates metastasis and alters drug sensitivity. Although EMT-regulatory roles for numerous miRNAs and transcription factors are known, their functions can be difficult to disentangle, in part due to the difficulty in identifying direct miRNA targets from complex datasets and in deciding how to incorporate 'indirect' miRNA effects that may, or may not, represent biologically relevant information. To better understand how miRNAs exert effects throughout the transcriptome during EMT, we employed Exon-Intron Split Analysis (EISA), a bioinformatic technique that separates transcriptional and post-transcriptional effects through the separate analysis of RNA-Seq reads mapping to exons and introns. We find that in response to the manipulation of miRNAs, a major effect on gene expression is transcriptional. We also find extensive co-ordination of transcriptional and post-transcriptional regulatory mechanisms during both EMT and mesenchymal to epithelial transition (MET) in response to TGF-β or miR-200c respectively. The prominent transcriptional influence of miRNAs was also observed in other datasets where miRNA levels were perturbed. This work cautions against a narrow approach that is limited to the analysis of direct targets, and demonstrates the utility of EISA to examine complex regulatory networks involving both transcriptional and post-transcriptional mechanisms.
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Affiliation(s)
- Katherine A Pillman
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Kaitlin G Scheer
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Emily Hackett-Jones
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Klay Saunders
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Andrew G Bert
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - John Toubia
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Holly J Whitfield
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Sunil Sapkota
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Laura Sourdin
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Hoang Pham
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia
| | - Thuc D Le
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia
| | - Joseph Cursons
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Melissa J Davis
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia.,Department of Biochemistry, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Philip A Gregory
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.,School of Medicine, Discipline of Medicine, University of Adelaide, SA, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.,School of Medicine, Discipline of Medicine, University of Adelaide, SA, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.,School of Medicine, Discipline of Medicine, University of Adelaide, SA, Australia
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7
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Zhao C, Mirando AC, Sové RJ, Medeiros TX, Annex BH, Popel AS. A mechanistic integrative computational model of macrophage polarization: Implications in human pathophysiology. PLoS Comput Biol 2019; 15:e1007468. [PMID: 31738746 PMCID: PMC6860420 DOI: 10.1371/journal.pcbi.1007468] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/08/2019] [Indexed: 12/24/2022] Open
Abstract
Macrophages respond to signals in the microenvironment by changing their functional phenotypes, a process known as polarization. Depending on the context, they acquire different patterns of transcriptional activation, cytokine expression and cellular metabolism which collectively constitute a continuous spectrum of phenotypes, of which the two extremes are denoted as classical (M1) and alternative (M2) activation. To quantitatively decode the underlying principles governing macrophage phenotypic polarization and thereby harness its therapeutic potential in human diseases, a systems-level approach is needed given the multitude of signaling pathways and intracellular regulation involved. Here we develop the first mechanism-based, multi-pathway computational model that describes the integrated signal transduction and macrophage programming under M1 (IFN-γ), M2 (IL-4) and cell stress (hypoxia) stimulation. Our model was calibrated extensively against experimental data, and we mechanistically elucidated several signature feedbacks behind the M1-M2 antagonism and investigated the dynamical shaping of macrophage phenotypes within the M1-M2 spectrum. Model sensitivity analysis also revealed key molecular nodes and interactions as targets with potential therapeutic values for the pathophysiology of peripheral arterial disease and cancer. Through simulations that dynamically capture the signal integration and phenotypic marker expression in the differential macrophage polarization responses, our model provides an important computational basis toward a more quantitative and network-centric understanding of the complex physiology and versatile functions of macrophages in human diseases.
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Affiliation(s)
- Chen Zhao
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
| | - Adam C. Mirando
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Richard J. Sové
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Thalyta X. Medeiros
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, United States of America
- Divison of Cardiovascular Medicine, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Brian H. Annex
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, United States of America
- Divison of Cardiovascular Medicine, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Aleksander S. Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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8
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Discovery of Biomarker Panels for Neural Dysfunction in Inborn Errors of Amino Acid Metabolism. Sci Rep 2019; 9:9128. [PMID: 31235756 PMCID: PMC6591213 DOI: 10.1038/s41598-019-45674-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/07/2019] [Indexed: 12/11/2022] Open
Abstract
Patients with inborn errors of amino acid metabolism frequently show neuropsychiatric symptoms despite accurate metabolic control. This study aimed to gain insight into the underlying mechanisms of neural dysfunction. Here we analyzed the expression of brain-derived neurotrophic factor (BDNF) and 10 genes required for correct brain functioning in plasma and blood of patients with Urea Cycle Disorders (UCD), Maple Syrup Urine Disease (MSUD) and controls. Receiver-operating characteristic (ROC) analysis was used to evaluate sensitivity and specificity of potential biomarkers. CACNA2D2 (α2δ2 subunit of voltage-gated calcium channels) and MECP2 (methyl-CpG binding protein 2) mRNA and protein showed an excellent neural function biomarker signature (AUC ≥ 0,925) for recognition of MSUD. THBS3 (thrombospondin 3) mRNA and AABA gave a very good biomarker signature (AUC 0,911) for executive-attention deficits. THBS3, LIN28A mRNA, and alanine showed a perfect biomarker signature (AUC 1) for behavioral and mood disorders. Finally, a panel of BDNF protein and at least two large neural AAs showed a perfect biomarker signature (AUC 1) for recognition of psychomotor delay, pointing to excessive protein restriction as central causative of psychomotor delay. To conclude, our study has identified promising biomarker panels for neural function evaluation, providing a base for future studies with larger samples.
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9
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Abstract
Classically, phenotype is what is observed, and genotype is the genetic makeup. Statistical studies aim to project phenotypic likelihoods of genotypic patterns. The traditional genotype-to-phenotype theory embraces the view that the encoded protein shape together with gene expression level largely determines the resulting phenotypic trait. Here, we point out that the molecular biology revolution at the turn of the century explained that the gene encodes not one but ensembles of conformations, which in turn spell all possible gene-associated phenotypes. The significance of a dynamic ensemble view is in understanding the linkage between genetic change and the gained observable physical or biochemical characteristics. Thus, despite the transformative shift in our understanding of the basis of protein structure and function, the literature still commonly relates to the classical genotype–phenotype paradigm. This is important because an ensemble view clarifies how even seemingly small genetic alterations can lead to pleiotropic traits in adaptive evolution and in disease, why cellular pathways can be modified in monogenic and polygenic traits, and how the environment may tweak protein function.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
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10
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Ren J, Gu C, Yang Y, Xue J, Sun Y, Jian F, Chen D, Bian L, Sun Q. TSP-1 is downregulated and inversely correlates with miR-449c expression in Cushing's disease. J Cell Mol Med 2019; 23:4097-4110. [PMID: 31016850 PMCID: PMC6533510 DOI: 10.1111/jcmm.14297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/29/2019] [Accepted: 03/04/2019] [Indexed: 12/11/2022] Open
Abstract
The pathogenesis of Cushing's disease, which is caused by pituitary corticotroph adenoma, remains to be studied. Secreted angioinhibitory factor thrombospondin-1 (TSP-1) is an adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions and is associated with platelet aggregation, angiogenesis and tumorigenesis. We have found that the expression of TSP-1 is significantly lower in human pituitary corticotroph tumours compared with normal adenohypophysis. This study aims to elucidate the role of TSP-1 in regulating the tumour function of pituitary adenomas. Forced overexpression of TSP-1 in a murine AtT20 pituitary corticotroph tumour cell line decreased corticotroph precursor hormone proopiomelanocortin (POMC) transcription and adrenocorticotropic hormone (ACTH) secretion. Functional studies showed that TSP-1 overexpression in pituitary adenoma cells suppressed proliferation, migration and invasion. We have demonstrated that TSP-1 is a direct target of miR-449c. Further study showed that miR-449c activity enhanced tumorigenesis by directly inhibiting TSP-1 expression. Low expression of lncTHBS1, along with low expression of TSP-1, was associated with the high expression of miR-449c in Cushing's disease patients. Furthermore, RNA-immunoprecipitation associates miR-449c with lncTHBS1 suggesting that lncTHBS1 might be a negative regulator of miR-449c. Taken together, this study has demonstrated that lncTHBS1 might function as competing endogenous RNA for miR-449c, which could suppress the development of Cushing's disease.
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Affiliation(s)
- Jie Ren
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Changwei Gu
- Department of Neurosurgery, Ruijin Hospital, Luwan Branch, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Yong Yang
- Department of Neurosurgery, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jun Xue
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Yuhao Sun
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Fangfang Jian
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Dongjiang Chen
- Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida
| | - Liuguan Bian
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Qingfang Sun
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China.,Department of Neurosurgery, Ruijin Hospital, Luwan Branch, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
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11
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Daubon T, Léon C, Clarke K, Andrique L, Salabert L, Darbo E, Pineau R, Guérit S, Maitre M, Dedieu S, Jeanne A, Bailly S, Feige JJ, Miletic H, Rossi M, Bello L, Falciani F, Bjerkvig R, Bikfalvi A. Deciphering the complex role of thrombospondin-1 in glioblastoma development. Nat Commun 2019; 10:1146. [PMID: 30850588 PMCID: PMC6408502 DOI: 10.1038/s41467-019-08480-y] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 01/09/2019] [Indexed: 12/17/2022] Open
Abstract
We undertook a systematic study focused on the matricellular protein Thrombospondin-1 (THBS1) to uncover molecular mechanisms underlying the role of THBS1 in glioblastoma (GBM) development. THBS1 was found to be increased with glioma grades. Mechanistically, we show that the TGFβ canonical pathway transcriptionally regulates THBS1, through SMAD3 binding to the THBS1 gene promoter. THBS1 silencing inhibits tumour cell invasion and growth, alone and in combination with anti-angiogenic therapy. Specific inhibition of the THBS1/CD47 interaction using an antagonist peptide decreases cell invasion. This is confirmed by CD47 knock-down experiments. RNA sequencing of patient-derived xenograft tissue from laser capture micro-dissected peripheral and central tumour areas demonstrates that THBS1 is one of the gene with the highest connectivity at the tumour borders. All in all, these data show that TGFβ1 induces THBS1 expression via Smad3 which contributes to the invasive behaviour during GBM expansion. Furthermore, tumour cell-bound CD47 is implicated in this process. Thrombospondin-1 (THSB1) is a component of the ECM with a role in regulating cancer development and tumour vasculature. Here, the authors show that TGF-beta-induced THBS1 expression contributes to the invasive behaviour of GBM cells and promotes resistance to antiangiogenic therapy partially through interaction with CD47.
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Affiliation(s)
- Thomas Daubon
- INSERM U1029, Institut Nationale de la Santé et de la Recherche Médicale, 33615, Pessac, France. .,University Bordeaux, 33615, Pessac, France. .,KG Jebsen Brain Tumor Research Center, University of Bergen, 5020, Bergen, Norway. .,Norlux Beuro-Oncology, Department of Biomedicine, University of Bergen, 5020, Bergen, Norway.
| | - Céline Léon
- INSERM U1029, Institut Nationale de la Santé et de la Recherche Médicale, 33615, Pessac, France.,University Bordeaux, 33615, Pessac, France
| | - Kim Clarke
- Computational Biology Facility, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Laetitia Andrique
- INSERM U1029, Institut Nationale de la Santé et de la Recherche Médicale, 33615, Pessac, France.,University Bordeaux, 33615, Pessac, France
| | - Laura Salabert
- INSERM U1029, Institut Nationale de la Santé et de la Recherche Médicale, 33615, Pessac, France.,University Bordeaux, 33615, Pessac, France
| | - Elodie Darbo
- UMR1218 ACTION, Bioinformatic Center CBiB, University of Bordeaux, 33076, Bordeaux, France
| | - Raphael Pineau
- Animal Facility, University Bordeaux, 33615, Pessac, France
| | - Sylvaine Guérit
- INSERM U1029, Institut Nationale de la Santé et de la Recherche Médicale, 33615, Pessac, France.,University Bordeaux, 33615, Pessac, France
| | - Marlène Maitre
- INSERM U1215, Neurocenter Magendie, Pathophysiology of Addiction Group, 33076, Bordeaux, France
| | | | - Albin Jeanne
- CNRS UMR 7369, MEDyC, 51687, Reims, France.,SATT Nord, 59800, Lille, France
| | | | | | - Hrvoje Miletic
- KG Jebsen Brain Tumor Research Center, University of Bergen, 5020, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, 5020, Bergen, Norway
| | - Marco Rossi
- Neurosurgical Oncology Unit, Department of Oncology and Hemato-Oncology, Humanitas Research Hospital, Universita Degli Studi di Milano, 20089, Rozzano, Milan, Italy
| | - Lorenzo Bello
- Neurosurgical Oncology Unit, Department of Oncology and Hemato-Oncology, Humanitas Research Hospital, Universita Degli Studi di Milano, 20089, Rozzano, Milan, Italy
| | - Francesco Falciani
- Computational Biology Facility, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Rolf Bjerkvig
- KG Jebsen Brain Tumor Research Center, University of Bergen, 5020, Bergen, Norway.,Norlux Beuro-Oncology, Department of Biomedicine, University of Bergen, 5020, Bergen, Norway.,Oncology Department, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg
| | - Andréas Bikfalvi
- INSERM U1029, Institut Nationale de la Santé et de la Recherche Médicale, 33615, Pessac, France. .,University Bordeaux, 33615, Pessac, France.
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Zhao C, Zhang Y, Popel AS. Mechanistic Computational Models of MicroRNA-Mediated Signaling Networks in Human Diseases. Int J Mol Sci 2019; 20:ijms20020421. [PMID: 30669429 PMCID: PMC6358731 DOI: 10.3390/ijms20020421] [Citation(s) in RCA: 15] [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: 12/29/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRs) are endogenous non-coding RNA molecules that play important roles in human health and disease by regulating gene expression and cellular processes. In recent years, with the increasing scientific knowledge and new discovery of miRs and their gene targets, as well as the plentiful experimental evidence that shows dysregulation of miRs in a wide variety of human diseases, the computational modeling approach has emerged as an effective tool to help researchers identify novel functional associations between differential miR expression and diseases, dissect the phenotypic expression patterns of miRs in gene regulatory networks, and elucidate the critical roles of miRs in the modulation of disease pathways from mechanistic and quantitative perspectives. Here we will review the recent systems biology studies that employed different kinetic modeling techniques to provide mechanistic insights relating to the regulatory function and therapeutic potential of miRs in human diseases. Some of the key computational aspects to be discussed in detail in this review include (i) models of miR-mediated network motifs in the regulation of gene expression, (ii) models of miR biogenesis and miR–target interactions, and (iii) the incorporation of such models into complex disease pathways in order to generate mechanistic, molecular- and systems-level understanding of pathophysiology. Other related bioinformatics tools such as computational platforms that predict miR-disease associations will also be discussed, and we will provide perspectives on the challenges and opportunities in the future development and translational application of data-driven systems biology models that involve miRs and their regulatory pathways in human diseases.
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Affiliation(s)
- Chen Zhao
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Yu Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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13
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Bazzazi H, Zhang Y, Jafarnejad M, Isenberg JS, Annex BH, Popel AS. Computer Simulation of TSP1 Inhibition of VEGF-Akt-eNOS: An Angiogenesis Triple Threat. Front Physiol 2018; 9:644. [PMID: 29899706 PMCID: PMC5988849 DOI: 10.3389/fphys.2018.00644] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/11/2018] [Indexed: 01/08/2023] Open
Abstract
The matricellular protein thrombospondin-1 (TSP1) is a potent inhibitor of angiogenesis. Specifically, TSP1 has been experimentally shown to inhibit signaling downstream of vascular endothelial growth factor (VEGF). The molecular mechanism of this inhibition is not entirely clear. We developed a detailed computational model of VEGF signaling to Akt-endothelial nitric oxide synthase (eNOS) to investigate the quantitative molecular mechanism of TSP1 inhibition. The model demonstrated that TSP1 acceleration of VEGFR2 degradation is sufficient to explain the inhibition of VEGFR2 and eNOS phosphorylation. However, Akt inhibition requires TSP1-induced phosphatase recruitment to VEGFR2. The model was then utilized to test various strategies for the rescue of VEGF signaling to Akt and eNOS. Inhibiting TSP1 was predicted to be not as effective as CD47 depletion in rescuing signaling to Akt. The model further predicts that combination strategy involving depletion of CD47 and inhibition of TSP1 binding to CD47 is necessary for effective recovery of signaling to eNOS. In all, computational modeling offers insight to molecular mechanisms involving TSP1 interaction with VEGF signaling and provides strategies for rescuing angiogenesis by targeting TSP1-CD47 axis.
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Affiliation(s)
- Hojjat Bazzazi
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Yu Zhang
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Mohammad Jafarnejad
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Jeffrey S Isenberg
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, United States.,Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Brian H Annex
- Division of Cardiovascular Medicine, Department of Medicine, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Aleksander S Popel
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
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14
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Zhao C, Isenberg JS, Popel AS. Human expression patterns: qualitative and quantitative analysis of thrombospondin-1 under physiological and pathological conditions. J Cell Mol Med 2018; 22:2086-2097. [PMID: 29441713 PMCID: PMC5867078 DOI: 10.1111/jcmm.13565] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/07/2018] [Indexed: 12/12/2022] Open
Abstract
Thrombospondin-1 (TSP-1), a matricellular protein and one of the first endogenous anti-angiogenic molecules identified, has long been considered a potent modulator of human diseases. While the therapeutic effect of TSP-1 to suppress cancer was investigated in both research and clinical settings, the mechanisms of how TSP-1 is regulated in cancer remain elusive, and the scientific answers to the question of whether TSP-1 expressions can be utilized as diagnostic or prognostic marker for patients with cancer are largely inconsistent. Moreover, TSP-1 plays crucial functions in angiogenesis, inflammation and tissue remodelling, which are essential biological processes in the progression of many cardiovascular diseases, and therefore, its dysregulated expressions in such conditions may have therapeutic significance. Herein, we critically analysed the literature pertaining to TSP-1 expression in circulating blood and pathological tissues in various types of cancer as well as cardiovascular and inflammation-related diseases in humans. We compare the secretion rates of TSP-1 by different cancer and non-cancer cells and discuss the potential connection between the expression changes of TSP-1 and vascular endothelial growth factor (VEGF) observed in patients with cancer. Moreover, the pattern and emerging significance of TSP-1 profiles in cardiovascular disease, such as peripheral arterial disease, diabetes and other related non-cancer disorders, are highlighted. The analysis of published TSP-1 data presented in this review may have implications for the future exploration of novel TSP-1-based treatment strategies for cancer and cardiovascular-related diseases.
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Affiliation(s)
- Chen Zhao
- Department of Biomedical EngineeringSchool of MedicineJohns Hopkins UniversityBaltimoreMDUSA
| | - Jeffrey S. Isenberg
- Division of Pulmonary, Allergy and Critical CareDepartment of MedicineHeart, Lung, Blood and Vascular Medicine InstituteUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Aleksander S. Popel
- Department of Biomedical EngineeringSchool of MedicineJohns Hopkins UniversityBaltimoreMDUSA
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