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Yang Z, Chen L, Huang Y, Dong J, Yan Q, Li Y, Qiu J, Li H, Zhao D, Liu F, Tang D, Dai Y. Proteomic profiling of laser capture microdissection kidneys from diabetic nephropathy patients. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1243:124231. [PMID: 38996754 DOI: 10.1016/j.jchromb.2024.124231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/23/2024] [Accepted: 07/01/2024] [Indexed: 07/14/2024]
Abstract
Diabetic nephropathy (DN) remains the primary cause of end-stage renal disease (ESRD), warranting equal attention and separate analysis of glomerular, tubular, and interstitial lesions in its diagnosis and intervention. This study aims to identify the specific proteomics characteristics of DN, and assess changes in the biological processes associated with DN. 5 patients with DN and 5 healthy kidney transplant donor control individuals were selected for analysis. The proteomic characteristics of glomeruli, renal tubules, and renal interstitial tissue obtained through laser capture microscopy (LCM) were studied using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). Significantly, the expression of multiple heat shock proteins (HSPs), tubulins, and heterogeneous nuclear ribonucleoproteins (hnRNPs) in glomeruli and tubules was significantly reduced. Differentially expressed proteins (DEPs) in the glomerulus showed significant enrichment in pathways related to cell junctions and cell movement, including the regulation of actin cytoskeleton and tight junction. DEPs in renal tubules were significantly enriched in glucose metabolism-related pathways, such as glucose metabolism, glycolysis/gluconeogenesis, and the citric acid cycle. Moreover, the glycolysis/gluconeogenesis pathway was a co-enrichment pathway in both DN glomeruli and tubules. Notably, ACTB emerged as the most crucial protein in the protein-protein interaction (PPI) analysis of DEPs in both glomeruli and renal tubules. In this study, we delve into the unique proteomic characteristics of each sub-region of renal tissue. This enhances our understanding of the potential pathophysiological changes in DN, particularly the potential involvement of glycolysis metabolic disorder, glomerular cytoskeleton and cell junctions. These insights are crucial for further research into the identification of disease biomarkers and the pathogenesis of DN.
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Affiliation(s)
- Zhiqian Yang
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China; Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Liangmei Chen
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Yingxin Huang
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China; Department of Nephrology, Xiaolan People's Hospital of Zhongshan, 528400, China
| | - Jingjing Dong
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China; Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Qiang Yan
- Department of Organ Transplantation, 924 Hospital, Guilin 541002, China
| | - Ya Li
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China
| | - Jing Qiu
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China
| | - Haitao Li
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China
| | - Da Zhao
- The First Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan 232001, Anhui, China
| | - Fanna Liu
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China.
| | - Donge Tang
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China.
| | - Yong Dai
- Comprehensive Health Industry Research Center, Taizhou Research Institute, Southern University of Science and Technology, Taizhou 317000, China; The First Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan 232001, Anhui, China.
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Mitrovic K, Zivotic I, Kolic I, Zakula J, Zivkovic M, Stankovic A, Jovanovic I. A preliminary study of the miRNA restitution effect on CNV-induced miRNA downregulation in CAKUT. BMC Genomics 2024; 25:218. [PMID: 38413914 PMCID: PMC10900603 DOI: 10.1186/s12864-024-10121-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/14/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND The majority of CAKUT-associated CNVs overlap at least one miRNA gene, thus affecting the cellular levels of the corresponding miRNA. We aimed to investigate the potency of restitution of CNV-affected miRNA levels to remediate the dysregulated expression of target genes involved in kidney physiology and development in vitro. METHODS Heterozygous MIR484 knockout HEK293 and homozygous MIR185 knockout HEK293 cell lines were used as models depicting the deletion of the frequently affected miRNA genes by CAKUT-associated CNVs. After treatment with the corresponding miRNA mimics, the levels of the target genes have been compared to the non-targeting control treatment. For both investigated miRNAs, MDM2 and PKD1 were evaluated as common targets, while additional 3 genes were investigated as targets of each individual miRNA (NOTCH3, FIS1 and APAF1 as hsa-miR-484 targets and RHOA, ATF6 and CDC42 as hsa-miR-185-5p targets). RESULTS Restitution of the corresponding miRNA levels in both knockout cell lines has induced a change in the mRNA levels of certain candidate target genes, thus confirming the potential to alleviate the CNV effect on miRNA expression. Intriguingly, HEK293 WT treatment with investigated miRNA mimics has triggered a more pronounced effect, thus suggesting the importance of miRNA interplay in different genomic contexts. CONCLUSIONS Dysregulation of multiple mRNA targets mediated by CNV-affected miRNAs could represent the underlying mechanism behind the unresolved CAKUT occurrence and phenotypic variability observed in CAKUT patients. Characterizing miRNAs located in CNVs and their potential to become molecular targets could eventually help in understanding and improving the management of CAKUT.
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Affiliation(s)
- Kristina Mitrovic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Ivan Zivotic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Ivana Kolic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Jelena Zakula
- Department of Molecular Biology and Endocrinology, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Maja Zivkovic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Aleksandra Stankovic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Ivan Jovanovic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia.
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Abstract
Rho family GTPases are molecular switches best known for their pivotal role in dynamic regulation of the actin cytoskeleton, but also of cellular morphology, motility, adhesion and proliferation. The prototypic members of this family (RhoA, Rac1 and Cdc42) also contribute to the normal kidney function and play important roles in the structure and function of various kidney cells including tubular epithelial cells, mesangial cells and podocytes. The kidney's vital filtration function depends on the structural integrity of the glomerulus, the proximal portion of the nephron. Within the glomerulus, the architecturally actin-based cytoskeleton podocyte forms the final cellular barrier to filtration. The glomerulus appears as a highly dynamic signalling hub that is capable of integrating intracellular cues from its individual structural components. Dynamic regulation of the podocyte cytoskeleton is required for efficient barrier function of the kidney. As master regulators of actin cytoskeletal dynamics, Rho GTPases are therefore of critical importance for sustained kidney barrier function. Dysregulated activities of the Rho GTPases and of their effectors are implicated in the pathogenesis of both hereditary and idiopathic forms of kidney diseases. Diabetic nephropathy is a progressive kidney disease that is caused by injury to kidney glomeruli. High glucose activates RhoA/Rho-kinase in mesangial cells, leading to excessive extracellular matrix production (glomerulosclerosis). This RhoA/Rho-kinase pathway also seems involved in the post-transplant hypertension frequently observed during treatment with calcineurin inhibitors, whereas Rac1 activation was observed in post-transplant ischaemic acute kidney injury.
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Affiliation(s)
- Clara Steichen
- Inserm UMR-1082 Irtomit, Poitiers, France,Faculté De Médecine Et De Pharmacie, Université De Poitiers, Poitiers, France
| | - Claude Hervé
- Inserm UMR-1082 Irtomit, Poitiers, France,CONTACT Claude HervéInserm UMR-1082 Irtomit, Poitiers, France
| | - Thierry Hauet
- Inserm UMR-1082 Irtomit, Poitiers, France,Faculté De Médecine Et De Pharmacie, Université De Poitiers, Poitiers, France,Department of Medical Biology, Service De Biochimie, CHU De Poitiers, Poitiers, France
| | - Nicolas Bourmeyster
- Faculté De Médecine Et De Pharmacie, Université De Poitiers, Poitiers, France,Department of Medical Biology, Service De Biochimie, CHU De Poitiers, Poitiers, France,Laboratoire STIM CNRS ERL 7003, Université de Poitiers, Poitiers Cédex, France
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Wu SZ, Peng FF, Li JL, Ye F, Lei SQ, Zhang BF. Akt and RhoA activation in response to high glucose require caveolin-1 phosphorylation in mesangial cells. Am J Physiol Renal Physiol 2014; 306:F1308-17. [PMID: 24694591 DOI: 10.1152/ajprenal.00447.2013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Glomerular matrix accumulation is a hallmark of diabetic renal disease. Serine/threonine kinase PKC-β1 mediates glucose-induced Akt S473 phosphorylation, RhoA activation, and transforming growth factor (TGF)-β1 upregulation and finally leads to matrix upregulation in mesangial cells (MCs). It has been reported that glucose-induced PKC-β1 activation is dependent on caveolin-1 and the presence of intact caveolae in MCs; however, whether activated PKC-β1 regulates caveolin-1 expression and phosphorylation are unknown. Here, we showed that, although the caveolin-1 protein level had no significant change, the PKC-β-specific inhibitor LY-333531 blocked caveolin-1 Y14 phosphorylation in high glucose (HG)-treated MCs and in the renal cortex of diabetic rats. The Src-specific inhibitor SU-6656 prevented the HG-induced association between PKC-β1 and caveolin-1 and PKC-β1 membrane translocation, whereas PKC-β1 small interfering RNA failed to block Src activation, indicating that Src kinase is upstream of PKC-β1 activation. Although LY-333531 blocked PKC-β1 membrane translocation, it had no effect on the PKC-β1/caveolin-1 association, suggesting that PKC-β1 activation requires the interaction of caveolin-1 and PKC-β1. PKC-β1-mediated Akt S473 phosphorylation, RhoA activation, and fibronectin upregulation in response to HG were prevented by SU-6656 and nonphosphorylatable mutant caveolin-1 Y14A. In conclusion, Src activation by HG mediates the PKC-β1/caveolin-1 association and PKC-β1 activation, which assists in caveolin-1 Y14 phosphorylation by Src kinase. The downstream effects, including Akt S473 phosphorylation, RhoA activation, and fibronectin upregulation, require caveolin-1 Y14 phosphorylation. Caveolin-1 is thus an important mediator of the profibrogenic process in diabetic renal disease.
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Affiliation(s)
- Su-Zhen Wu
- Department of Biochemistry, Wuhan University School of Basic Medical Sciences, Wuhan, People's Republic of China; and
| | - Fang-Fang Peng
- Department of Biochemistry, Wuhan University School of Basic Medical Sciences, Wuhan, People's Republic of China; and
| | - Jia-Lin Li
- Gannan Medical University, Ganzhou, People's Republic of China; and
| | - Feng Ye
- Department of Biochemistry, Wuhan University School of Basic Medical Sciences, Wuhan, People's Republic of China; and
| | - Shao-Qing Lei
- Department of Biochemistry, Wuhan University School of Basic Medical Sciences, Wuhan, People's Republic of China; and
| | - Bai-Fang Zhang
- Department of Biochemistry, Wuhan University School of Basic Medical Sciences, Wuhan, People's Republic of China; and Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, People's Republic of China
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Korostylev A, Worzfeld T, Deng S, Friedel RH, Swiercz JM, Vodrazka P, Maier V, Hirschberg A, Ohoka Y, Inagaki S, Offermanns S, Kuner R. A functional role for semaphorin 4D/plexin B1 interactions in epithelial branching morphogenesis during organogenesis. Development 2008; 135:3333-43. [PMID: 18799546 DOI: 10.1242/dev.019760] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Semaphorins and their receptors, plexins, carry out important functions during development and disease. In contrast to the well-characterized plexin A family, however, very little is known about the functional relevance of B-type plexins in organogenesis, particularly outside the nervous system. Here, we demonstrate that plexin B1 and its ligand Sema4d are selectively expressed in epithelial and mesenchymal compartments during key steps in the genesis of some organs. This selective expression suggests a role in epithelial-mesenchymal interactions. Importantly, using the developing metanephros as a model system, we have observed that endogenously expressed and exogenously supplemented Sema4d inhibits branching morphogenesis during early stages of development of the ureteric collecting duct system. Our results further suggest that the RhoA-ROCK pathway, which is activated downstream of plexin B1, mediates these inhibitory morphogenetic effects of Sema4d and suppresses branch-promoting signalling effectors of the plexin B1 signalling complex. Finally, mice that lack plexin B1 show early anomalies in kidney development in vivo. These results identify a novel function for plexin B1 as a negative regulator of branching morphogenesis during kidney development, and suggest that the Sema4d-plexin B1 ligand-receptor pair contributes to epithelial-mesenchymal interactions during organogenesis via modulation of RhoA signalling.
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Affiliation(s)
- Alexander Korostylev
- Pharmacology Institute, Im Neuenheimer Feld 366, University of Heidelberg, 69120 Heidelberg, Germany
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Zhu S, Liu L, Korzh V, Gong Z, Low BC. RhoA acts downstream of Wnt5 and Wnt11 to regulate convergence and extension movements by involving effectors Rho Kinase and Diaphanous: Use of zebrafish as an in vivo model for GTPase signaling. Cell Signal 2006; 18:359-72. [PMID: 16019189 DOI: 10.1016/j.cellsig.2005.05.019] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2005] [Accepted: 05/06/2005] [Indexed: 01/09/2023]
Abstract
Gastrulation shapes the early embryos by forming three germ layers, ectoderm, mesoderm and endoderm. In vertebrates, this process requires massive cell rearrangement including convergence and extension (CE) movements that involve narrowing and lengthening of embryonic tissues as well as cell elongation. Such polarization and movements require precise reorganization and regulation of the cytoskeleton network and cell adhesion. Rho small GTPases are key regulators for dynamic actin cytoskeleton. However, the signaling mechanisms underlying their functions in CE remain to be further elucidated. We have cloned the zebrafish Danio rerio rhoA and by capitalizing on the specific functional knockdown using morpholinos against rhoA and the availability of CE mutants defective in Wnt signaling, we showed that rhoA morphants were reminiscent to noncanonical wnt mutants with serious disruption in CE movements. Injection of rhoA mRNA effectively rescued such defects in wnt5 and wnt11 mutants. Furthermore, CE defects in rhoA knockdown or wnt mutants can be suppressed through functional bypass after ectopic expression of the two mammalian Rho effectors, the Rho kinase and Diaphanous (mDia). These results provide the first evidence that the RhoA in vivo acts downstream of Wnt5 and Wnt11 to effect, without affecting cell fates, on the CE movements in zebrafish embryos. Significantly, it elicits such effect via both effectors, Rho kinase and Dia. These findings also support the versatility of the zebrafish as a model to further investigate the roles of various classes of small GTPases in regulating cell dynamics in vivo.
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Affiliation(s)
- Shizhen Zhu
- Cell Signaling and Developmental Biology Laboratory, National University of Singapore, 14 Science Drive 4, Singapore 117543, The Republic of Singapore
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Moore KA, Polte T, Huang S, Shi B, Alsberg E, Sunday ME, Ingber DE. Control of basement membrane remodeling and epithelial branching morphogenesis in embryonic lung by Rho and cytoskeletal tension. Dev Dyn 2005; 232:268-81. [PMID: 15614768 DOI: 10.1002/dvdy.20237] [Citation(s) in RCA: 187] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Local alterations in the mechanical compliance of the basement membrane that alter the level of isometric tension in the cell have been postulated to influence tissue morphogenesis. To explore whether cell tension contributes to tissue pattern formation in vivo, we modulated cytoskeletal force generation in embryonic mouse lung (embryonic days 12-14) rudiments using inhibitors of Rho-associated kinase (ROCK), myosin light chain kinase, myosin ATPase, and microfilament integrity, or a Rho stimulator (cytotoxic necrotizing factor-1). Tension inhibition resulted in loss of normal differentials in basement membrane thickness, inhibition of new terminal bud formation, and disorganization of epithelial growth patterns as well as disruption of capillary blood vessels. In contrast, increasing cell tension through Rho activation, as confirmed by quantitation of myosin light chain phosphorylation and immunohistocytochemical analysis of actin organization, accelerated lung branching and increase capillary elongation. These data suggest that changes in cytoskeletal tension mediated by Rho signaling through ROCK may play an important role in the establishment of the spatial differentials in cell growth and extracellular matrix remodeling that drive embryonic lung development.
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Affiliation(s)
- Kimberly A Moore
- Vascular Biology Program, Department of Surgery, Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
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Collier FM, Gregorio-King CC, Gough TJ, Talbot CD, Walder K, Kirkland MA. Identification and characterization of a lymphocytic Rho-GTPase effector: rhotekin-2. Biochem Biophys Res Commun 2005; 324:1360-9. [PMID: 15504364 DOI: 10.1016/j.bbrc.2004.09.205] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2004] [Indexed: 01/19/2023]
Abstract
Rhotekin belongs to the group of proteins containing a Rho-binding domain that are target peptides (effectors) for the Rho-GTPases. We previously identified a novel cDNA with homology to human rhotekin and in this study we cloned and characterized the coding region of this novel 12-exon gene. The ORF encodes a 609 amino-acid protein comprising a Class I Rho-binding domain and pleckstrin homology (PH) domain. Cellular cDNA expression of this new protein, designated Rhotekin-2 (RTKN2), was shown in the cytosol and nucleus of CHO cells. Using bioinformatics and RTPCR we identified three major splice variants, which vary in both the Rho-binding and PH domains. Real-time PCR studies showed exclusive RTKN2 expression in pooled lymphocytes and further purification indicated sole expression in CD4(pos) T-cells and bone marrow-derived B-cells. Gene expression was increased in quiescent T-cells but negligible in activated proliferating cells. In malignant samples expression was absent in myeloid leukaemias, low in most B-cell malignancies and CD8(pos) T-cell malignancies, but very high in CD4(pos)/CD8(pos) T-lymphoblastic lymphoma. As the Rho family is critical in lymphocyte development and function, RTKN2 may play an important role in lymphopoiesis.
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Affiliation(s)
- F M Collier
- Douglas Hocking Research Institute, Barwon Health, The Geelong Hospital, Geelong, Victoria 3220, Australia.
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