Generic placeholder image

Protein & Peptide Letters


ISSN (Print): 0929-8665
ISSN (Online): 1875-5305

Research Article

A Knock-Down Cell-Based Study for the Functional Analysis of Chloride Intracellular Channel 1 (CLIC1): Integrated Proteomics and Microarray Study

Author(s): Shang-Jun Yin, Jae-Rin Lee, Bit-Na Lee, Jun-Mo Yang, Guo-Ying Qian, Yong-Doo Park* and Myong-Joon Hahn*

Volume 28, Issue 1, 2021

Published on: 25 June, 2020

Page: [84 - 100] Pages: 17

DOI: 10.2174/0929866527666200625204650

Price: $65


Background: Previously, we detected that chloride intracellular channel 1 (CLIC1) was involved in the pathogenesis of atopic dermatitis (AD).

Objective: In this study, we aimed to use high-throughput screening (HTS) approaches to identify critical factors associated with the function of CLIC1 in knock-down cells.

Methods: We down-regulated CLIC1 in human A549 cells via siRNA and then conducted serial HTS studies, including proteomics integrated with a microarray and the implementation of bioinformatics algorithms.

Results: Together, these approaches identified several important proteins and genes associated with the function of CLIC1. These proteins and genes included tumor rejection antigen (gp96) 1, nucleophosmin, annexin I, keratin 1 and 10, FLNA protein, enolase 1, and metalloprotease 1, which were found using two-dimensional electrophoresis (2-DE) proteomics. Separately, NTNG1, SEMA5A, CLEC3A, GRPR, GNGT2, GRM5, GRM7, DNMT3B, CXCR5, CCL11, CD86, IL2, MNDA, TLR5, IL23R, DPP6, DLGAP1, CAT, GSTA1, GSTA2, GSTA5, CYP2E1, ADH1A, ESR1, ARRDC3, A1F1, CCL5, CASP8, DNTT, SQSTM1, PCYT1A, and SLCO4C1 were found using a DNA microarray integrated with PPI mapping.

Conclusion: CCL11 is thought to be a particularly critical gene among the candidate genes detected in this study. By integrating the datasets and utilizing the strengths of HTS, we obtained new insights into the functional role of CLIC1, including the use of CLIC1-associated applications in the treatment of human diseases such as AD.

Keywords: CLIC1, knock-down, proteomics, microarray, bioinformatics, PPI mappings.

Graphical Abstract
Valenzuela, S.M.; Martin, D.K.; Por, S.B.; Robbins, J.M.; Warton, K.; Bootcov, M.R.; Schofield, P.R.; Campbell, T.J.; Breit, S.N. Molecular cloning and expression of a chloride ion channel of cell nuclei. J. Biol. Chem., 1997, 272(19), 12575-12582.
[] [PMID: 9139710]
Harrop, S.J.; DeMaere, M.Z.; Fairlie, W.D.; Reztsova, T.; Valenzuela, S.M.; Mazzanti, M.; Tonini, R.; Qiu, M.R.; Jankova, L.; Warton, K.; Bauskin, A.R.; Wu, W.M.; Pankhurst, S.; Campbell, T.J.; Breit, S.N.; Curmi, P.M. Crystal structure of a soluble form of the intracellular chloride ion channel CLIC1 (NCC27) at 1.4-A resolution. J. Biol. Chem., 2001, 276(48), 44993-45000.
[] [PMID: 11551966]
Heiss, N.S.; Poustka, A. Genomic structure of a novel chloride channel gene, CLIC2, in Xq28. Genomics, 1997, 45(1), 224-228.
[] [PMID: 9339381]
Tulk, B.M.; Edwards, J.C. NCC27, a homolog of intracellular Cl- channel p64, is expressed in brush border of renal proximal tubule. Am. J. Physiol., 1998, 274(6), F1140-F1149.
[] [PMID: 9841507]
Suárez-Fariñas, M.; Shah, K.R.; Haider, A.S.; Krueger, J.G.; Lowes, M.A. Personalized medicine in psoriasis: developing a genomic classifier to predict histological response to Alefacept. BMC Dermatol., 2010, 10, 1.
[] [PMID: 20152045]
Park, Y.D.; Kim, S.Y.; Jang, H.S.; Seo, E.Y.; Namkung, J.H.; Park, H.S.; Cho, S.Y.; Paik, Y.K.; Yang, J.M. Towards a proteomic analysis of atopic dermatitis: a two-dimensional-polyacrylamide gel electrophoresis/mass spectrometric analysis of cultured patient-derived fibroblasts. Proteomics, 2004, 4(11), 3446-3455.
[] [PMID: 15468290]
Park, Y.D.; Jang, H.S.; Kim, S.Y.; Ko, S.K.; Lyou, Y.J.; Lee, D.Y.; Paik, Y.K.; Yang, J.M. Two-dimensional electrophoretic profiling of atopic dermatitis in primary cultured keratinocytes from patients. Proteomics, 2006, 6(4), 1362-1370.
[] [PMID: 16402356]
Tonini, R.; Ferroni, A.; Valenzuela, S.M.; Warton, K.; Campbell, T.J.; Breit, S.N.; Mazzanti, M. Functional characterization of the NCC27 nuclear protein in stable transfected CHO-K1 cells. FASEB J., 2000, 14(9), 1171-1178.
[] [PMID: 10834939]
Valenzuela, S.M.; Mazzanti, M.; Tonini, R.; Qiu, M.R.; Warton, K.; Musgrove, E.A.; Campbell, T.J.; Breit, S.N. The nuclear chloride ion channel NCC27 is involved in regulation of the cell cycle. J. Physiol., 2000, 529(Pt 3), 541-552.
[] [PMID: 11195932]
Wang, Z.J.; Zheng, L.; Yang, J.M.; Kang, Y.; Park, Y.D. Proteomic analyses for profiling regulated proteins/enzymes by Fucus vesiculosus fucoidan in B16 melanoma cells: A combination of enzyme kinetics functional study. Int. J. Biol. Macromol., 2018, 112, 667-674.
[] [PMID: 29408614]
Yin, S.J.; Cho, I.H.; Yang, H.S.; Park, Y.D.; Yang, J.M. Analysis of the peptides detected in atopic dermatitis and various inflammatory diseases patients-derived sera. Int. J. Biol. Macromol., 2018, 106, 1052-1061.
[] [PMID: 28842203]
Ahmadi, Z.; Hassanshahi, G.; Khorramdelazad, H.; Zainodini, N.; Koochakzadeh, L. An overlook to the characteristics and roles played by eotaxin network in the pathophysiology of food allergies: Allergic asthma and atopic dermatitis. Inflammation, 2016, 39(3), 1253-1267.
[] [PMID: 26861136]
Brunner, P.M.; Suárez-Fariñas, M.; He, H.; Malik, K.; Wen, H.C.; Gonzalez, J.; Chan, T.C.; Estrada, Y.; Zheng, X.; Khattri, S.; Dattola, A.; Krueger, J.G.; Guttman-Yassky, E. The atopic dermatitis blood signature is characterized by increases in inflammatory and cardiovascular risk proteins. Sci. Rep., 2017, 7(1), 8707.
[] [PMID: 28821884]
Imai, Y.; Yasuda, K.; Sakaguchi, Y.; Haneda, T.; Mizutani, H.; Yoshimoto, T.; Nakanishi, K.; Yamanishi, K. Skin-specific expression of IL-33 activates group 2 innate lymphoid cells and elicits atopic dermatitis-like inflammation in mice. Proc. Natl. Acad. Sci. USA, 2013, 110(34), 13921-13926.
[] [PMID: 23918359]
Warton, K.; Tonini, R.; Fairlie, W.D.; Matthews, J.M.; Valenzuela, S.M.; Qiu, M.R.; Wu, W.M.; Pankhurst, S.; Bauskin, A.R.; Harrop, S.J.; Campbell, T.J.; Curmi, P.M.; Breit, S.N.; Mazzanti, M. Recombinant CLIC1 (NCC27) assembles in lipid bilayers via a pH-dependent two-state process to form chloride ion channels with identical characteristics to those observed in Chinese hamster ovary cells expressing CLIC1. J. Biol. Chem., 2002, 277(29), 26003-26011.
[] [PMID: 11978800]
Park, Y.D.; Lyou, Y.J.; Lee, K.J.; Lee, D.Y.; Yang, J.M. Towards profiling the gene expression of fibroblasts from atopic dermatitis patients: human 8K complementary DNA microarray. Clin. Exp. Allergy, 2006, 36(5), 649-657.
[] [PMID: 16650051]
Park, Y.D.; Lyou, Y.J.; Yang, J.M. Detection of down-regulated acetaldehyde dehydrogenase 1 in atopic dermatitis patients by two-dimensional electrophoresis. Exp. Dermatol., 2007, 16(2), 130-134.
[] [PMID: 17222227]
Park, Y.D.; Lyou, Y.J.; Yang, J.M. Two-dimensional electrophoresis analyses of atopic dermatitis and the chances to detect new candidate proteins by the variations in immobilized pH gradient strips. J. Dermatol. Sci., 2007, 47(1), 9-17.
[] [PMID: 17353112]
Lü, Z.R.; Park, T.H.; Lee, E.S.; Kim, K.J.; Park, D.; Kim, B.C.; Cho, S.W.; Bhak, J.; Park, Y.D.; Zou, F.; Yang, J.M. Dysregulated genes of extrinsic type of atopic dermatitis: 34K microarray and interactomic analyses. J. Dermatol. Sci., 2009, 53(2), 146-150.
[] [PMID: 18824329]
Lü, Z.R.; Park, D.; Lee, K.A.; Ryu, J.W.; Bhak, J.; Shi, L.; Lee, D.Y.; Park, Y.D.; Zou, F.; Yang, J.M. Profiling the dysregulated genes of keratinocytes in atopic dermatitis patients: cDNA microarray and interactomic analyses. J. Dermatol. Sci., 2009, 54(2), 126-129.
[] [PMID: 19157793]
Lü, Z.R.; Kim, W.S.; Cho, I.H.; Park, D.; Bhak, J.; Shi, L.; Zhou, H.W.; Lee, D.Y.; Park, Y.D.; Yang, J.M.; Zou, F. DNA microarray analyses and interactomic predictions for atopic dermatitis. J. Dermatol. Sci., 2009, 55(2), 123-125.
[] [PMID: 19443183]
Yang, H.S.; Cho, I.H.; Wang, Q.; Park, Y.D.; Yang, J.M. Serum proteomic analyses for probing C3 fragment protein. Process Biochem., 2016, 51, 981-988.
Yin, S.J.; Si, Y.X.; Zhang, M.; Qian, G.Y.; Zhang, F.; Yan, L.; Lü, Z.R.; Zhou, H.M.; Yang, H.S.; Park, Y.D.; Yang, J.M. Combination of free-flow electrophoresis and interactomics to analyze the dysregulated proteins of fibroblasts from atopic dermatitis patients. J. Dermatol. Sci., 2011, 61(2), 148-150.
[] [PMID: 21242061]
Yin, S.J.; Yang, H.S.; Cho, I.H.; Wang, Q.; Park, Y.D.; Yang, J.M. An integrated method for the detection of basic proteins in serum-derived proteomes. Process Biochem., 2016, 51, 973-980.
Park, Y.D.; Park, D.; Bhak, J.; Yang, J.M. Proteomic approaches to the analysis of atopic dermatitis and new insights from interactomics. Proteomics Clin. Appl., 2008, 2(3), 290-300.
[] [PMID: 21136834]
Hung, H.C.; Feng, C.W.; Lin, Y.Y.; Chen, C.H.; Tsui, K.H.; Chen, W.F.; Pan, C.Y.; Sheu, J.H.; Sung, C.S.; Wen, Z.H. Nucleophosmin modulates the alleviation of atopic dermatitis caused by the marine-derived compound dihydroaustrasulfone alcohol. Exp. Mol. Med., 2018, 50(2), e446.
[] [PMID: 29504608]
Parisi, J.D.S.; Corrêa, M.P.; Gil, C.D. Lack of Endogenous annexin A1 increases mast cell activation and exacerbates experimental atopic dermatitis. Cells, 2019, 8(1), E51.
[] [PMID: 30650525]
Totsuka, A.; Omori-Miyake, M.; Kawashima, M.; Yagi, J.; Tsunemi, Y. Expression of keratin 1, keratin 10, desmoglein 1 and desmocollin 1 in the epidermis: possible downregulation by interleukin-4 and interleukin-13 in atopic dermatitis. Eur. J. Dermatol., 2017, 27(3), 247-253.
[] [PMID: 28524044]
Kim, W.K.; Cho, H.J.; Ryu, S.I.; Hwang, H.R.; Kim, D.H.; Ryu, H.Y.; Chung, J.W.; Kim, T.Y.; Park, B.C.; Bae, K.H.; Ko, Y.; Lee, S.C. Comparative proteomic analysis of peripheral blood mononuclear cells from atopic dermatitis patients and healthy donors. BMB Rep., 2008, 41(8), 597-603.
[] [PMID: 18755076]
Tohgasaki, T.; Ozawa, N.; Yoshino, T.; Ishiwatari, S.; Matsukuma, S.; Yanagi, S.; Fukuda, H. Enolase-1 expression in the stratum corneum is elevated with parakeratosis of atopic dermatitis and disrupts the cellular tight junction barrier in keratinocytes. Int. J. Cosmet. Sci., 2018, 40(2), 178-186.
[] [PMID: 29430682]
Correa da Rosa, J.; Malajian, D.; Shemer, A.; Rozenblit, M.; Dhingra, N.; Czarnowicki, T.; Khattri, S.; Ungar, B.; Finney, R.; Xu, H.; Zheng, X.; Estrada, Y.D.; Peng, X.; Suárez-Fariñas, M.; Krueger, J.G.; Guttman-Yassky, E. Patients with atopic dermatitis have attenuated and distinct contact hypersensitivity responses to common allergens in skin. J. Allergy Clin. Immunol., 2015, 135(3), 712-720.
[] [PMID: 25583101]
Foster, P.S.; Maltby, S.; Rosenberg, H.F.; Tay, H.L.; Hogan, S.P.; Collison, A.M.; Yang, M.; Kaiko, G.E.; Hansbro, P.M.; Kumar, R.K.; Mattes, J. Modeling TH 2 responses and airway inflammation to understand fundamental mechanisms regulating the pathogenesis of asthma. Immunol. Rev., 2017, 278(1), 20-40.
[] [PMID: 28658543]
Gahr, N.; Fölster-Holst, R.; Weichenthal, M.; Christophers, E.; Schröder, J.M.; Bartels, J. Dermal fibroblasts from acute inflamed atopic dermatitis lesions display increased eotaxin/CCL11 responsiveness to interleukin-4 stimulation. Br. J. Dermatol., 2011, 164(3), 586-592.
[] [PMID: 21039413]
Parajuli, B.; Horiuchi, H.; Mizuno, T.; Takeuchi, H.; Suzumura, A. CCL11 enhances excitotoxic neuronal death by producing reactive oxygen species in microglia. Glia, 2015, 63(12), 2274-2284.
[] [PMID: 26184677]
Guttman-Yassky, E.; Pavel, A.B.; Zhou, L.; Estrada, Y.D.; Zhang, N.; Xu, H.; Peng, X.; Wen, H.C.; Govas, P.; Gudi, G.; Ca, V.; Fang, H.; Salhi, Y.; Back, J.; Reddy, V.; Bissonnette, R.; Maari, C.; Grossman, F.; Wolff, G. GBR 830, an anti-OX40, improves skin gene signatures and clinical scores in patients with atopic dermatitis. J. Allergy Clin. Immunol., 2019, 144(2), 482-493.e7.
[] [PMID: 30738171]
Radman, M.; Hassanshahi, G.; Vazirinejad, R.; Arababadi, M.K.; Karimabad, M.N.; Khorramdelazad, H.; Rafatpanah, H.; Iranmanesh, F.; Hakimizadeh, E.; Ahmadi, Z. Serum levels of the CC chemokines CCL2, CCL5, and CCL11 in food allergic children with different clinical manifestations. Inflammation, 2013, 36(3), 561-566.
[] [PMID: 23180368]
Szabó, K.; Gáspár, K.; Dajnoki, Z.; Papp, G.; Fábos, B.; Szegedi, A.; Zeher, M. Expansion of circulating follicular T helper cells associates with disease severity in childhood atopic dermatitis. Immunol. Lett., 2017, 189, 101-108.
[] [PMID: 28431963]
Nedoszytko, B.; Sokołowska-Wojdyło, M.; Ruckemann-Dziurdzińska, K.; Roszkiewicz, J.; Nowicki, R.J. Chemokines and cytokines network in the pathogenesis of the inflammatory skin diseases: atopic dermatitis, psoriasis and skin mastocytosis. Postepy Dermatol. Alergol., 2014, 31(2), 84-91.
[] [PMID: 25097473]
Hershko, A.Y.; Suzuki, R.; Charles, N.; Alvarez-Errico, D.; Sargent, J.L.; Laurence, A.; Rivera, J. Mast cell interleukin-2 production contributes to suppression of chronic allergic dermatitis. Immunity, 2011, 35(4), 562-571.
[] [PMID: 21982597]
Antúnez, C.; Torres, M.J.; Mayorga, C.; Corzo, J.L.; Jurado, A.; Santamaría-Babi, L.F.; Vera, A.; Blanca, M. Cytokine production, activation marker, and skin homing receptor in children with atopic dermatitis and bronchial asthma. Pediatr. Allergy Immunol., 2006, 17(3), 166-174.
[] [PMID: 16672002]

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy