1
|
Hu H, Cai J, Qi D, Li B, Yu L, Wang C, Bajpai AK, Huang X, Zhang X, Lu L, Liu J, Zheng F. Identification of Potential Biomarkers for Group I Pulmonary Hypertension Based on Machine Learning and Bioinformatics Analysis. Int J Mol Sci 2023; 24:ijms24098050. [PMID: 37175757 PMCID: PMC10178909 DOI: 10.3390/ijms24098050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/20/2023] [Accepted: 03/31/2023] [Indexed: 05/15/2023] Open
Abstract
A number of processes and pathways have been reported in the development of Group I pulmonary hypertension (Group I PAH); however, novel biomarkers need to be identified for a better diagnosis and management. We employed a robust rank aggregation (RRA) algorithm to shortlist the key differentially expressed genes (DEGs) between Group I PAH patients and controls. An optimal diagnostic model was obtained by comparing seven machine learning algorithms and was verified in an independent dataset. The functional roles of key DEGs and biomarkers were analyzed using various in silico methods. Finally, the biomarkers and a set of key candidates were experimentally validated using patient samples and a cell line model. A total of 48 key DEGs with preferable diagnostic value were identified. A gradient boosting decision tree algorithm was utilized to build a diagnostic model with three biomarkers, PBRM1, CA1, and TXLNG. An immune-cell infiltration analysis revealed significant differences in the relative abundances of seven immune cells between controls and PAH patients and a correlation with the biomarkers. Experimental validation confirmed the upregulation of the three biomarkers in Group I PAH patients. In conclusion, machine learning and a bioinformatics analysis along with experimental techniques identified PBRM1, CA1, and TXLNG as potential biomarkers for Group I PAH.
Collapse
Affiliation(s)
- Hui Hu
- Center for Gene Diagnosis, Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jie Cai
- Department of Cardial Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430060, China
| | - Daoxi Qi
- Center for Gene Diagnosis, Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Boyu Li
- Center for Gene Diagnosis, Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Li Yu
- Center for Gene Diagnosis, Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Chen Wang
- Center for Gene Diagnosis, Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Akhilesh K Bajpai
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Sciences Center, Memphis, TN 38163, USA
| | - Xiaoqin Huang
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Xiaokang Zhang
- Center for Gene Diagnosis, Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Sciences Center, Memphis, TN 38163, USA
| | - Jinping Liu
- Department of Cardial Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430060, China
| | - Fang Zheng
- Center for Gene Diagnosis, Department of Clinical Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| |
Collapse
|
2
|
Ivnitsky JJ, Schäfer TV, Rejniuk VL, Golovko AI. Endogenous humoral determinants of vascular endothelial dysfunction as triggers of acute poisoning complications. J Appl Toxicol 2023; 43:47-65. [PMID: 35258106 DOI: 10.1002/jat.4312] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/13/2022] [Accepted: 02/26/2022] [Indexed: 12/16/2022]
Abstract
The vascular endothelium is not only the semipermeable membrane that separates tissue from blood but also an organ that regulates inflammation, vascular tone, blood clotting, angiogenesis and synthesis of connective tissue proteins. It is susceptible to the direct cytotoxic action of numerous xenobiotics and to the acute hypoxia that accompanies acute poisoning. This damage is superimposed on the preformed state of the vascular endothelium, which, in turn, depends on many humoral factors. The probability that an exogenous toxicant will cause life-threatening dysfunction of the vascular endothelium, thereby complicating the course of acute poisoning, increases with an increase in the content of endogenous substances in the blood that disrupt endothelial function. These include ammonia, bacterial endotoxin, indoxyl sulfate, para-cresyl sulfate, trimethylamine N-oxide, asymmetric dimethylarginine, glucose, homocysteine, low-density and very-low-density lipoproteins, free fatty acids and products of intravascular haemolysis. Some other endogenous substances (albumin, haptoglobin, haemopexin, biliverdin, bilirubin, tetrahydrobiopterin) or food-derived compounds (ascorbic acid, rutin, omega-3 polyunsaturated fatty acids, etc.) reduce the risk of lethal vascular endothelial dysfunction. The individual variability of the content of these substances in the blood contributes to the stochasticity of the complications of acute poisoning and is a promising target for the risk reduction measures. Another feasible option may be the repositioning of drugs that affect the function of the vascular endothelium while being currently used for other indications.
Collapse
Affiliation(s)
- Jury Ju Ivnitsky
- Golikov Research Clinical Center of Toxicology under the Federal Medical Biological Agency, Saint Petersburg, Russia
| | - Timur V Schäfer
- State Scientific Research Test Institute of the Military Medicine of Defense Ministry of the Russian Federation, Saint Petersburg, Russia
| | - Vladimir L Rejniuk
- Golikov Research Clinical Center of Toxicology under the Federal Medical Biological Agency, Saint Petersburg, Russia
| | - Alexandr I Golovko
- Golikov Research Clinical Center of Toxicology under the Federal Medical Biological Agency, Saint Petersburg, Russia
| |
Collapse
|
3
|
Li S, Zhang H, Chang J, Li D, Cao P. Iron overload and mitochondrial dysfunction orchestrate pulmonary fibrosis. Eur J Pharmacol 2021; 912:174613. [PMID: 34740581 DOI: 10.1016/j.ejphar.2021.174613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 09/06/2021] [Accepted: 09/11/2021] [Indexed: 12/26/2022]
Abstract
Pulmonary fibrosis (PF) is a chronic, progressive heterogeneous disease of lung tissues with poor lung function caused by scar tissue. Due to our limited understanding of its mechanism, there is currently no treatment strategy that can prevent the development of PF. In recent years, iron accumulation and mitochondrial damage have been reported to participate in PF, and drugs that reduce iron content and improve mitochondrial function have shown significant efficacy in animal experimental models. Excessive iron leads to mitochondrial impairment, which may be the key cause that results in the dysfunction of various kinds of pulmonary cells and further promotes PF. As an emerging research hotspot, there are few targeted effective therapeutic strategies at present due to limited mechanistic understanding. In this review, the roles of iron homeostasis imbalance and mitochondrial damage in PF are summarized and discussed, highlighting a promising direction for finding truly effective therapeutics for PF.
Collapse
Affiliation(s)
- Shuxin Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China
| | - Hongmin Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China
| | - Jing Chang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China
| | - Dongming Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China.
| | - Pengxiu Cao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China.
| |
Collapse
|
4
|
Ramakrishnan L, Pedersen SL, Toe QK, West LE, Mumby S, Casbolt H, Issitt T, Garfield B, Lawrie A, Wort SJ, Quinlan GJ. The Hepcidin/Ferroportin axis modulates proliferation of pulmonary artery smooth muscle cells. Sci Rep 2018; 8:12972. [PMID: 30154413 PMCID: PMC6113242 DOI: 10.1038/s41598-018-31095-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 08/10/2018] [Indexed: 12/22/2022] Open
Abstract
Studies were undertaken to examine any role for the hepcidin/ferroportin axis in proliferative responses of human pulmonary artery smooth muscle cells (hPASMCs). Entirely novel findings have demonstrated the presence of ferroportin in hPASMCs. Hepcidin treatment caused increased proliferation of these cells most likely by binding ferroportin resulting in internalisation and cellular iron retention. Cellular iron content increased with hepcidin treatment. Stabilisation of ferroportin expression and activity via intervention with the therapeutic monoclonal antibody LY2928057 reversed proliferation and cellular iron accumulation. Additionally, IL-6 treatment was found to enhance proliferation and iron accumulation in hPASMCs; intervention with LY2928057 prevented this response. IL-6 was also found to increase hepcidin transcription and release from hPASMCs suggesting a potential autocrine response. Hepcidin or IL-6 mediated iron accumulation contributes to proliferation in hPASMCs; ferroportin mediated cellular iron excretion limits proliferation. Haemoglobin also caused proliferation of hPASMCs; in other novel findings, CD163, the haemoglobin/haptoglobin receptor, was found on these cells and offers a means for cellular uptake of iron via haemoglobin. Il-6 was also found to modulate CD163 on these cells. These data contribute to a better understanding of how disrupted iron homeostasis may induce vascular remodelling, such as in pulmonary arterial hypertension.
Collapse
MESH Headings
- Antibodies, Monoclonal/pharmacology
- Antigens, CD/metabolism
- Antigens, Differentiation, Myelomonocytic/metabolism
- Autocrine Communication/drug effects
- Autocrine Communication/physiology
- Cation Transport Proteins/biosynthesis
- Cell Proliferation
- Cells, Cultured
- Gene Expression Regulation/drug effects
- Gene Expression Regulation/physiology
- Hepcidins/biosynthesis
- Humans
- Interleukin-6/metabolism
- Iron/metabolism
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/metabolism
- Myocytes, Smooth Muscle/cytology
- Myocytes, Smooth Muscle/metabolism
- Pulmonary Artery/cytology
- Pulmonary Artery/metabolism
- Receptors, Cell Surface/metabolism
- Transcription, Genetic/drug effects
- Transcription, Genetic/physiology
Collapse
Affiliation(s)
- Latha Ramakrishnan
- Vascular Biology Group, National Heart and Lung Institute, Imperial College London, Faculty of Medicine, Guy Scadding Building, London, SW3 6LY, UK
| | - Sofia L Pedersen
- Vascular Biology Group, National Heart and Lung Institute, Imperial College London, Faculty of Medicine, Guy Scadding Building, London, SW3 6LY, UK
| | - Quezia K Toe
- Vascular Biology Group, National Heart and Lung Institute, Imperial College London, Faculty of Medicine, Guy Scadding Building, London, SW3 6LY, UK
| | - Laura E West
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, S10 2RX, Sheffield, UK
| | - Sharon Mumby
- Vascular Biology Group, National Heart and Lung Institute, Imperial College London, Faculty of Medicine, Guy Scadding Building, London, SW3 6LY, UK
| | - Helen Casbolt
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, S10 2RX, Sheffield, UK
| | - Theo Issitt
- Vascular Biology Group, National Heart and Lung Institute, Imperial College London, Faculty of Medicine, Guy Scadding Building, London, SW3 6LY, UK
| | - Benjamin Garfield
- Vascular Biology Group, National Heart and Lung Institute, Imperial College London, Faculty of Medicine, Guy Scadding Building, London, SW3 6LY, UK
| | - Allan Lawrie
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, S10 2RX, Sheffield, UK
| | - S John Wort
- Vascular Biology Group, National Heart and Lung Institute, Imperial College London, Faculty of Medicine, Guy Scadding Building, London, SW3 6LY, UK
| | - Gregory J Quinlan
- Vascular Biology Group, National Heart and Lung Institute, Imperial College London, Faculty of Medicine, Guy Scadding Building, London, SW3 6LY, UK.
| |
Collapse
|
5
|
Ramakrishnan L, Pedersen SL, Toe QK, Quinlan GJ, Wort SJ. Pulmonary Arterial Hypertension: Iron Matters. Front Physiol 2018; 9:641. [PMID: 29904352 PMCID: PMC5990599 DOI: 10.3389/fphys.2018.00641] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/11/2018] [Indexed: 12/16/2022] Open
Abstract
The interplay between iron and oxygen is longstanding and central to all aerobic life. Tight regulation of these interactions including homeostatic regulation of iron utilization ensures safe usage of this limited resource. However, when control is lost adverse events can ensue, which are known to contribute to an array of disease processes. Recently, associations between disrupted iron homeostasis and pulmonary artery hypertension (PAH) have been described with the suggestion that there is a contributory link with disease. This review provides a background for iron regulation in humans, describes PAH classifications, and discusses emerging literature, which suggests a role for disrupted iron homeostatic control in various sub-types of PAH, including a role for decompartmentalization of hemoglobin. Finally, the potential for therapeutic options to restore iron homeostatic balance in PAH are discussed.
Collapse
|
6
|
A new fluorescent dye accumulation assay for parallel measurements of the ABCG2, ABCB1 and ABCC1 multidrug transporter functions. PLoS One 2018; 13:e0190629. [PMID: 29342177 PMCID: PMC5771559 DOI: 10.1371/journal.pone.0190629] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/18/2017] [Indexed: 01/01/2023] Open
Abstract
ABC multidrug transporters are key players in cancer multidrug resistance and in general xenobiotic elimination, thus their functional assays provide important tools for research and diagnostic applications. In this study we have examined the potential interactions of three key human ABC multidrug transporters with PhenGreen diacetate (PGD), a cell permeable fluorescent metal ion indicator. The non-fluorescent, hydrophobic PGD rapidly enters the cells and, after cleavage by cellular esterases, in the absence of quenching metal ions, PhenGreen (PG) becomes highly fluorescent. We found that in cells expressing functional ABCG2, ABCB1, or ABCC1 transporters, cellular PG fluorescence is strongly reduced. This fluorescence signal in the presence of specific transporter inhibitors is increased to the fluorescence levels in the control cells. Thus the PG accumulation assay is a new, unique tool for the parallel determination of the function of the ABCG2, ABCB1, and ABCC1 multidrug transporters. Since PG has very low cellular toxicity, the PG accumulation assay also allows the selection, separation and culturing of selected cell populations expressing either of these transporters.
Collapse
|
7
|
Peluso I, Cavaliere A, Palmery M. Plasma total antioxidant capacity and peroxidation biomarkers in psoriasis. J Biomed Sci 2016; 23:52. [PMID: 27377373 PMCID: PMC4932672 DOI: 10.1186/s12929-016-0268-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 06/28/2016] [Indexed: 01/05/2023] Open
Abstract
Systemic biomarkers of oxidative stress can be relevant for assessment of psoriasis severity, for prediction of the outcome of therapy and of the development of comorbidities. In this review we aimed to evaluate the relationship between plasma total antioxidant capacity (TAC) and peroxidation biomarkers, as well as their association with dyslipidemia and systemic inflammation in psoriasis. The review of 59 case–control comparisons (from 41 studies) and 17 interventions (from 13 studies) suggests that peroxidation markers are more sensitive than TAC in the evaluation of oxidative stress in psoriasis. Although few studies investigated the effect of treatment on oxidative stress, it seems that biological drugs could be the better choice in the treatment of psoriasis. However, considering the limitations of TAC and plasma peroxidation markers, this review suggests that new methods should be developed in order to evaluate systemic oxidative stress in psoriasis.
Collapse
Affiliation(s)
- Ilaria Peluso
- Center of Nutrition, Council for Agricultural Research and Economics (CREA-NUT), Via Ardeatina 546, Rome, 00178, Italy.
| | - Arturo Cavaliere
- Dermopathic Institute of the Immaculate IDI-IRCCS, Via dei Monti di Creta, 104, Rome, 00167, Italy
| | - Maura Palmery
- Department of Physiology and Pharmacology "V. Erspamer", "Sapienza" University of Rome, P.le Aldo Moro 5, Rome, 00185, Italy
| |
Collapse
|
8
|
Duluc L, Wojciak-Stothard B. Rho GTPases in the regulation of pulmonary vascular barrier function. Cell Tissue Res 2014; 355:675-85. [PMID: 24599334 DOI: 10.1007/s00441-014-1805-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 01/10/2014] [Indexed: 12/12/2022]
Abstract
Pulmonary endothelial permeability is an important determinant of vascular adaptation to changes in oxygen tension, blood pressure, levels of growth factors or inflammatory cytokines. The Ras homologous (Rho) family of guanosine triphosphate phosphatases (Rho GTPases), key regulators of the actin cytoskeleton, regulate endothelial barrier function in response to a variety of environmental factors and signalling agents via the reorganization of the actin cytoskeleton, changes in receptor trafficking or the phosphorylation of junctional proteins. This review provides a brief summary of recent knowledge on Rho-GTPase-mediated effects on pulmonary endothelial barrier function and focuses in particular on their role in pulmonary vascular disorders, including pulmonary hypertension, chronic obstructive pulmonary disease, acute lung injury and acute respiratory distress syndrome.
Collapse
Affiliation(s)
- Lucie Duluc
- Centre for Pharmacology & Therapeutics, Imperial College London, London, UK
| | | |
Collapse
|
9
|
Storck EM, Wojciak-Stothard B. Rho GTPases in pulmonary vascular dysfunction. Vascul Pharmacol 2013; 58:202-10. [DOI: 10.1016/j.vph.2012.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 09/05/2012] [Accepted: 09/09/2012] [Indexed: 12/19/2022]
|
10
|
Sun J, Zhang D, Zheng Y, Zhao Q, Zheng M, Kovacevic Z, Richardson DR. Targeting the metastasis suppressor, NDRG1, using novel iron chelators: regulation of stress fiber-mediated tumor cell migration via modulation of the ROCK1/pMLC2 signaling pathway. Mol Pharmacol 2012. [PMID: 23188716 DOI: 10.1124/mol.112.083097] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The iron-regulated metastasis suppressor, N-myc downstream-regulated gene 1 (NDRG1), is up-regulated by cellular iron depletion mediated by iron chelators and can inhibit cancer cell migration. However, the mechanism of how NDRG1 achieves this effect remains unclear. In this study, we implemented established and newly constructed NDRG1 overexpression and knockdown models using the DU145, HT29, and HCT116 cancer cell lines to investigate the molecular basis by which NDRG1 exerts its inhibitory effect on cell migration. Using these models, we demonstrated that NDRG1 overexpression inhibits cell migration by preventing actin-filament polymerization, stress fiber assembly and formation. In contrast, NDRG1 knockdown had the opposite effect. Moreover, we identified that NDRG1 inhibited an important regulatory pathway mediated by the Rho-associated, coiled-coil containing protein kinase 1 (ROCK1)/phosphorylated myosin light chain 2 (pMLC2) pathway that modulates stress fiber assembly. The phosphorylation of MLC2 is a key process in inducing stress fiber contraction, and this was shown to be markedly decreased or increased by NDRG1 overexpression or knockdown, respectively. The mechanism involved in the inhibition of MLC2 phosphorylation by NDRG1 was mediated by a significant (P < 0.001) decrease in ROCK1 expression that is a key kinase involved in MLC2 phosphorylation. Considering that NDRG1 is up-regulated after cellular iron depletion, novel thiosemicarbazone iron chelators (e.g., di-2-pyridylketone 4,4-dimethyl-3-thiosemicarbazone) were demonstrated to inhibit ROCK1/pMLC2-modulated actin-filament polymerization, stress fiber assembly, and formation via a mechanism involving NDRG1. These results highlight the role of the ROCK1/pMLC2 pathway in the NDRG1-mediated antimetastatic signaling network and the therapeutic potential of iron chelators at inhibiting metastasis.
Collapse
Affiliation(s)
- Jing Sun
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | | | | | | | | | | | | |
Collapse
|