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Di Camillo B, Puricelli L, Iori E, Toffolo GM, Tessari P, Arrigoni G. Modeling SILAC Data to Assess Protein Turnover in a Cellular Model of Diabetic Nephropathy. Int J Mol Sci 2023; 24:ijms24032811. [PMID: 36769128 PMCID: PMC9917874 DOI: 10.3390/ijms24032811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Protein turnover rate is finely regulated through intracellular mechanisms and signals that are still incompletely understood but that are essential for the correct function of cellular processes. Indeed, a dysfunctional proteostasis often impacts the cell's ability to remove unfolded, misfolded, degraded, non-functional, or damaged proteins. Thus, altered cellular mechanisms controlling protein turnover impinge on the pathophysiology of many diseases, making the study of protein synthesis and degradation rates an important step for a more comprehensive understanding of these pathologies. In this manuscript, we describe the application of a dynamic-SILAC approach to study the turnover rate and the abundance of proteins in a cellular model of diabetic nephropathy. We estimated protein half-lives and relative abundance for thousands of proteins, several of which are characterized by either an altered turnover rate or altered abundance between diabetic nephropathic subjects and diabetic controls. Many of these proteins were previously shown to be related to diabetic complications and represent therefore, possible biomarkers or therapeutic targets. Beside the aspects strictly related to the pathological condition, our data also represent a consistent compendium of protein half-lives in human fibroblasts and a rich source of important information related to basic cell biology.
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Affiliation(s)
- Barbara Di Camillo
- Department of Information Engineering, University of Padova, 35131 Padova, Italy
- Correspondence: (B.D.C.); (G.A.)
| | - Lucia Puricelli
- Department of Medicine, University of Padova, 35128 Padova, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, 35128 Padova, Italy
| | - Elisabetta Iori
- Department of Medicine, University of Padova, 35128 Padova, Italy
| | - Gianna Maria Toffolo
- Department of Information Engineering, University of Padova, 35131 Padova, Italy
| | - Paolo Tessari
- Department of Medicine, University of Padova, 35128 Padova, Italy
| | - Giorgio Arrigoni
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, 35128 Padova, Italy
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Correspondence: (B.D.C.); (G.A.)
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Hor CHH, Goh ELK. Rab23 Regulates Radial Migration of Projection Neurons via N-cadherin. Cereb Cortex 2019; 28:1516-1531. [PMID: 29420702 PMCID: PMC6093454 DOI: 10.1093/cercor/bhy018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Indexed: 01/12/2023] Open
Abstract
Radial migration of cortical projection neurons is a prerequisite for shaping a distinct multilayered cerebral cortex during mammalian corticogenesis. Members of Rab GTPases family were reported to regulate radial migration. Here, in vivo conditional knockout or in utero knockdown (KD) of Rab23 in mice neocortex causes aberrant polarity and halted migration of cortical projection neurons. Further investigation of the underlying mechanism reveals down-regulation of N-cadherin in the Rab23-deficient neurons, which is a cell adhesion protein previously known to modulate radial migration. (Shikanai M, Nakajima K, Kawauchi T. 2011. N-cadherin regulates radial glial fiber-dependent migration of cortical locomoting neurons. Commun Integr Biol. 4:326–330.) Interestingly, pharmacological inhibition of extracellular signal-regulated kinases (ERK1/2) also decreases the expression of N-cadherin, implicating an upstream effect of ERK1/2 on N-cadherin and also suggesting a link between Rab23 and ERK1/2. Further biochemical studies show that silencing of Rab23 impedes activation of ERK1/2 via perturbed platelet-derived growth factor-alpha (PDGFRα) signaling. Restoration of the expression of Rab23 or N-cadherin in Rab23-KD neurons could reverse neuron migration defects, indicating that Rab23 modulates migration through N-cadherin. These studies suggest that cortical neuron migration is mediated by a molecular hierarchy downstream of Rab23 via N-cadherin.
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Affiliation(s)
- Catherine H H Hor
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, Singapore 169857, Singapore.,Department of Research, National Neuroscience Institute, Singapore 308433, Singapore
| | - Eyleen L K Goh
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, Singapore 169857, Singapore.,Department of Research, National Neuroscience Institute, Singapore 308433, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore.,KK Research Center, KK Women's and Children's Hospital, Singapore 229899, Singapore
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Hor CH, Tang BL, Goh EL. Rab23 and developmental disorders. Rev Neurosci 2018; 29:849-860. [DOI: 10.1515/revneuro-2017-0110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/03/2018] [Indexed: 02/07/2023]
Abstract
Abstract
Rab23 is a conserved member of the Rab family of small GTPases that regulates membrane trafficking in eukaryotes. It is unique amongst the Rabs in terms of its implicated role in mammalian development, as originally illustrated by the embryonic lethality and open neural tube phenotype of a spontaneous mouse mutant that carries homozygous mutation of open brain, a gene encoding Rab23. Rab23 was initially identified to act as an antagonist of Sonic hedgehog (Shh) signaling, and has since been implicated in a number of physiological and pathological roles, including oncogenesis. Interestingly, RAB23 null allele homozygosity in humans is not lethal, but instead causes the developmental disorder Carpenter’s syndrome (CS), which is characterized by craniofacial malformations, polysyndactyly, obesity and intellectual disability. CS bears some phenotypic resemblance to a spectrum of hereditary defects associated with the primary cilium, or the ciliopathies. Recent findings have in fact implicated Rab23 in protein traffic to the primary cilium, thus linking it with the primary cellular locale of Shh signaling. Rab23 also has Shh and cilia-independent functions. It is known to mediate the expression of Nodal at the mouse left lateral plate mesoderm and Kupffer’s vesicle, the zebrafish equivalent of the mouse node. It is thus important for the left-right patterning of vertebrate embryos. In this review, we discuss the developmental disorders associated with Rab23 and attempt to relate its cellular activities to its roles in development.
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Affiliation(s)
- Catherine H.H. Hor
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School , 8 College Road , Singapore 169857 , Singapore
- Department of Research , National Neuroscience Institute , Singapore 308433 , Singapore
| | - Bor Luen Tang
- Department of Biochemistry , Yong Loo Lin School of Medicine , National University of Singapore , Singapore 117597 , Singapore
- NUS Graduate School for Integrative Sciences and Engineering , National University of Singapore, Medical Drive , Singapore 117456 , Singapore
| | - Eyleen L.K. Goh
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School , 8 College Road , Singapore 169857 , Singapore
- Department of Research , National Neuroscience Institute , Singapore 308433 , Singapore
- Department of Physiology , Yong Loo Lin School of Medicine , National University of Singapore , 8 Medical Drive , Singapore 117597 , Singapore
- KK Research Center, KK Women’s and Children’s Hospital , Singapore 229899 , Singapore
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Zheng LQ, Chi SM, Li CX. Rab23's genetic structure, function and related diseases: a review. Biosci Rep 2017; 37:BSR20160410. [PMID: 28104793 PMCID: PMC5333778 DOI: 10.1042/bsr20160410] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 12/15/2016] [Accepted: 01/18/2017] [Indexed: 12/31/2022] Open
Abstract
Rab23 has been proven to play a role in membrane trafficking and protein transport in eukaryotic cells. Rab23 is also a negative regulator of the Sonic hedgehog (Shh) signaling pathway in an indirect way. The nonsense mutation and loss of protein of Rab23 has been associated with neural tube defect in mice and aberrant expression in various diseases in human such as neural system, breast, visceral, and cutaneous tumor. In addition, Rab23 may play joint roles in autophagosome formation during anti-infection process against Group A streptococcus. In this review, we give a brief review on the functions of Rab23, summarize the involvement of Rab23 in genetic research, membrane trafficking, and potential autophagy pathway, especially focus on tumor promotion, disease pathogenesis, and discuss the possible underlying mechanisms that are regulated by Rab23.
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Affiliation(s)
- Li-Qiang Zheng
- Department of Dermatology, Chinese PLA General Hospital, Beijing, China
- Department of Dermatology, the 251st Hospital of Chinese PLA, No.13.Jian'guo Road, Zhangjiakou City, Hebei Province, 075100, China
| | - Su-Min Chi
- Department of Physiology, Fourth Military Medical University, Xi'an, China
| | - Cheng-Xin Li
- Department of Dermatology, Chinese PLA General Hospital, Beijing, China
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Rab23 activities and human cancer—emerging connections and mechanisms. Tumour Biol 2016; 37:12959-12967. [DOI: 10.1007/s13277-016-5207-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 07/13/2016] [Indexed: 12/19/2022] Open
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Rinschen MM, Benzing T, Limbutara K, Pisitkun T. Proteomic analysis of the kidney filtration barrier--Problems and perspectives. Proteomics Clin Appl 2015; 9:1053-68. [PMID: 25907645 DOI: 10.1002/prca.201400201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/21/2015] [Accepted: 04/20/2015] [Indexed: 12/12/2022]
Abstract
Diseases of the glomerular filter of the kidney are a leading cause of end-stage renal failure. The kidney filter is localized within the renal glomeruli, small microvascular units that are responsible for ultrafiltration of about 180 liters of primary urine every day. The renal filter consists of three layers, fenestrated endothelial cells, glomerular basement membrane, and the podocytes, terminally differentiated, arborized epithelial cells. This review demonstrates the use of proteomics to generate insights into the regulation of the renal filtration barrier at a molecular level. The advantages and disadvantages of different glomerular purification methods are examined, and the technical limitations that have been significantly improved by in silico or biochemical approaches are presented. We also comment on phosphoproteomic studies that have generated considerable molecular-level understanding of the physiological regulation of the kidney filter. Lastly, we conclude with an analysis of urinary exosomes as a potential filter-derived resource for the noninvasive discovery of glomerular disease mechanisms.
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Affiliation(s)
- Markus M Rinschen
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Kavee Limbutara
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Trairak Pisitkun
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Proteomics and bioinformatics analysis of lovastatin-induced differentiation in ARO cells. J Proteomics 2011; 75:1170-80. [PMID: 22086082 DOI: 10.1016/j.jprot.2011.10.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 10/22/2011] [Accepted: 10/28/2011] [Indexed: 01/05/2023]
Abstract
Lovastatin (lova), a 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitor, can induce differentiation in cancer cells at low concentration, thus having potential to be used as an auxiliary agent in cancer therapy. However, biological networks associated with the differentiation effect of lova have not been elucidated. To investigate molecular mechanisms of lova, the present study was aimed at proteomics and bioinformatics analyses on anaplastic thyroid cancer cell line ARO differentiated with low concentration of lova. Thyroid differentiation was induced by treating ARO cells with 25 μM of lova and confirmed by checking upregulation of some thyroid differentiation markers. Gel-based proteomics analysis was then performed to identify proteins differentially expressed between undifferentiated and lova-differentiated ARO cells. Bioinformatics analysis was finally performed to estimate biological networks regulated by lova. Our results showed that lova impacted on proteins involved in protein folding, biomolecule metabolism, signal transduction, protein expression and protein degradation. Specifically, transfecting ARO cells with plasmid DNA encoding flotillin 1 (FLOT1) up-regulated the thyroid differentiation markers, indicating that FLOT1 might at least partially mediate the lova-induced thyroid differentiation. These data may shed light on the mechanism underlying lova-induced re-differentiation of thyroid cancer, and give a rationale for clinical use of lova as an auxiliary agent in cancer therapy.
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Chen PH, Wang CY, Hsia CW, Ho MY, Chen A, Tseng MJ, Wu YF, Chen HM, Huang TH, Liu HT, Shui HA. Impact of taxol on dermal papilla cells — A proteomics and bioinformatics analysis. J Proteomics 2011; 74:2760-73. [DOI: 10.1016/j.jprot.2011.09.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 09/16/2011] [Accepted: 09/25/2011] [Indexed: 12/23/2022]
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