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Groza Y, Lacina L, Kuchař M, Rašková Kafková L, Zachová K, Janoušková O, Osička R, Černý J, Petroková H, Mierzwicka JM, Panova N, Kosztyu P, Sloupenská K, Malý J, Škarda J, Raška M, Smetana K, Malý P. Small protein blockers of human IL-6 receptor alpha inhibit proliferation and migration of cancer cells. Cell Commun Signal 2024; 22:261. [PMID: 38715108 PMCID: PMC11075285 DOI: 10.1186/s12964-024-01630-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Interleukin-6 (IL-6) is a multifunctional cytokine that controls the immune response, and its role has been described in the development of autoimmune diseases. Signaling via its cognate IL-6 receptor (IL-6R) complex is critical in tumor progression and, therefore, IL-6R represents an important therapeutic target. METHODS An albumin-binding domain-derived highly complex combinatorial library was used to select IL-6R alpha (IL-6Rα)-targeted small protein binders using ribosome display. Large-scale screening of bacterial lysates of individual clones was performed using ELISA, and their IL-6Rα blocking potential was verified by competition ELISA. The binding of proteins to cells was monitored by flow cytometry and confocal microscopy on HEK293T-transfected cells, and inhibition of signaling function was examined using HEK-Blue IL-6 reporter cells. Protein binding kinetics to living cells was measured by LigandTracer, cell proliferation and toxicity by iCELLigence and Incucyte, cell migration by the scratch wound healing assay, and prediction of binding poses using molecular modeling by docking. RESULTS We demonstrated a collection of protein variants called NEF ligands, selected from an albumin-binding domain scaffold-derived combinatorial library, and showed their binding specificity to human IL-6Rα and antagonistic effect in HEK-Blue IL-6 reporter cells. The three most promising NEF108, NEF163, and NEF172 variants inhibited cell proliferation of malignant melanoma (G361 and A2058) and pancreatic (PaTu and MiaPaCa) cancer cells, and suppressed migration of malignant melanoma (A2058), pancreatic carcinoma (PaTu), and glioblastoma (GAMG) cells in vitro. The NEF binders also recognized maturation-induced IL-6Rα expression and interfered with IL-6-induced differentiation in primary human B cells. CONCLUSION We report on the generation of small protein blockers of human IL-6Rα using directed evolution. NEF proteins represent a promising class of non-toxic anti-tumor agents with migrastatic potential.
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Affiliation(s)
- Yaroslava Groza
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Lukáš Lacina
- Institute of Anatomy, 1st Faculty of Medicine, Charles University, U Nemocnice 3, Prague 2, 12800, Czech Republic.
- Department of Dermatovenerology, 1st Faculty of Medicine, Charles University, U Nemocnice 2, Prague 2, 12000, Czech Republic.
| | - Milan Kuchař
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Leona Rašková Kafková
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hněvotínská 3, Olomouc, 779 00, Czech Republic
| | - Kateřina Zachová
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hněvotínská 3, Olomouc, 779 00, Czech Republic
| | - Olga Janoušková
- Centre of Nanomaterials and Biotechnologies, University of J. E. Purkyně in Ústí nad Labem, Pasteurova 3632/15, Ústí nad Labem, 400 96, Czech Republic
| | - Radim Osička
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague, 14220, Czech Republic
| | - Jiří Černý
- Laboratory of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Hana Petroková
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Joanna Maria Mierzwicka
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Natalya Panova
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Petr Kosztyu
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hněvotínská 3, Olomouc, 779 00, Czech Republic
| | - Kristýna Sloupenská
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hněvotínská 3, Olomouc, 779 00, Czech Republic
| | - Jan Malý
- Centre of Nanomaterials and Biotechnologies, University of J. E. Purkyně in Ústí nad Labem, Pasteurova 3632/15, Ústí nad Labem, 400 96, Czech Republic
| | - Jozef Škarda
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hněvotínská 3, Olomouc, 779 00, Czech Republic
| | - Milan Raška
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hněvotínská 3, Olomouc, 779 00, Czech Republic
| | - Karel Smetana
- Institute of Anatomy, 1st Faculty of Medicine, Charles University, U Nemocnice 3, Prague 2, 12800, Czech Republic
| | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova 595, Vestec, 252 50, Czech Republic.
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Sommer KM, Lee Y, Donovan SM, Dilger RN. Purification methods to reduce interference by dextran sodium sulfate with quantification of gene expression in intestinal tissue samples from a piglet model of colitis. J Anim Sci 2023; 101:skad202. [PMID: 37330677 PMCID: PMC10317179 DOI: 10.1093/jas/skad202] [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: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
Dextran sodium sulfate (DSS) is commonly used to induce intestinal (i.e., colonic) inflammation in a variety of animal models. However, DSS is known to cause interference when using quantitative-real time polymerase chain reaction (qRT-PCR) methods, thereby invalidating accurate and precise measurement of tissue gene expression. Therefore, the goal of this study was to determine whether different mRNA purification methods would reduce DSS-interference. Colonic tissue samples were collected at postnatal days (PND) 27 or 28 from pigs that had not been administered DSS (Control), and two independent groups of pigs that received 1.25 g of DSS/kg of BW/d (DSS-1 and DSS-2) from PND 14 to 18. Tissue samples collected were subsequently stratified into three purification methods (i.e., 9 total treatment × method combinations), including: 1) no purification, 2) purification with lithium chloride (LiCl), or 3) purification using spin column filtration. All data were analyzed using a one-way ANOVA in the Mixed procedure of SAS. The average RNA concentrations across all treatments were between 1,300 and 1,800 μg/μL for all three in vivo groups. Although there were statistical differences among purification methods, the 260/280 and 260/230 ratios fell between acceptable limits of 2.0 to 2.1 and 2.0 to 2.2, respectively, for all treatment groups. This confirms the RNA quality was adequate and not influenced by purification method in addition to suggesting the absence of phenol, salts, and carbohydrate contamination. For pigs in the Control group that did not receive DSS, qRT-PCR Ct values of four cytokines were achieved, though these values were not altered by purification method. For pigs that had undergone DSS dosing, those tissues subjected to either no purification or purification using LiCl did not generate applicable Ct values. However, when tissues derive from DSS-treated pigs underwent spin column purification, half of the samples from DSS-1 and DSS-2 groups generated appropriate Ct estimates. Therefore, spin column purification appeared to be more effective than LiCl purification, but no method was 100% effective, so caution should be exercised when interpreting gene expression results from studies where animals are exposed to DSS-induced colitis.
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Affiliation(s)
- Kaitlyn M Sommer
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA
| | - Youngsoo Lee
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, Illinois, USA
| | - Sharon M Donovan
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, Illinois, USA
| | - Ryan N Dilger
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA
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Luo T, Wang D, Zhao Y, Li X, Yang G, Jin Y. Polystyrene microplastics exacerbate experimental colitis in mice tightly associated with the occurrence of hepatic inflammation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:156884. [PMID: 35752249 DOI: 10.1016/j.scitotenv.2022.156884] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/14/2022] [Accepted: 06/18/2022] [Indexed: 05/27/2023]
Abstract
The potential health effects of microplastics (MPs) have become a public concern due to their ubiquitousness in the environment and life. Numerous studies have demonstrated that a high dose of MPs can adversely affect gastrointestinal health. However, few studies have focused on the impact of microplastics on patients' health with respect to gastrointestinal diseases. Inflammatory bowel disease (IBD) has emerged as a global disease with a rapidly increasing incidence. IBD, a specific gastrointestinal illness characterized by acute, chronic inflammation and intestinal barrier dysfunction, might increase sensitivity to MPs exposure. Herein, we investigated the impact and mechanism of PS-MPs on dextran sodium sulfate (DSS)-induced colitis. The results demonstrated that gavage with PS-MPs alone caused minimal effects on the intestinal barrier and liver status of mice. For mice with colitis, additional PS-MPs exposure caused a shorter colon length, aggravated histopathological damage and inflammation, reduced mucus secretion, and increased the colon permeability. Furthermore, PS-MPs exposure also increased the risk of secondary liver injury associated with inflammatory cell infiltration. These findings provide more histopathological evidence and suggest a need for more research on the health risk of MPs for sensitive individuals.
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Affiliation(s)
- Ting Luo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Laboratory (Hangzhou) for Risk Assessment of Agricultural Products of Ministry of Agriculture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China; College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Dou Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Laboratory (Hangzhou) for Risk Assessment of Agricultural Products of Ministry of Agriculture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Yao Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Laboratory (Hangzhou) for Risk Assessment of Agricultural Products of Ministry of Agriculture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Xinfang Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Laboratory (Hangzhou) for Risk Assessment of Agricultural Products of Ministry of Agriculture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Guiling Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Laboratory (Hangzhou) for Risk Assessment of Agricultural Products of Ministry of Agriculture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China.
| | - Yuanxiang Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
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Desideri F, D’Ambra E, Laneve P, Ballarino M. Advances in endogenous RNA pull-down: A straightforward dextran sulfate-based method enhancing RNA recovery. Front Mol Biosci 2022; 9:1004746. [PMID: 36339717 PMCID: PMC9629853 DOI: 10.3389/fmolb.2022.1004746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Detecting RNA/RNA interactions in the context of a given cellular system is crucial to gain insights into the molecular mechanisms that stand beneath each specific RNA molecule. When it comes to non-protein coding RNA (ncRNAs), and especially to long noncoding RNAs (lncRNAs), the reliability of the RNA purification is dramatically dependent on their abundance. Exogenous methods, in which lncRNAs are in vitro transcribed and incubated with protein extracts or overexpressed by cell transfection, have been extensively used to overcome the problem of abundance. However, although useful to study the contribution of single RNA sub-modules to RNA/protein interactions, these exogenous practices might fail in revealing biologically meaningful contacts occurring in vivo and risk to generate non-physiological artifacts. Therefore, endogenous methods must be preferred, especially for the initial identification of partners specifically interacting with elected RNAs. Here, we apply an endogenous RNA pull-down to lncMN2-203, a neuron-specific lncRNA contributing to the robustness of motor neurons specification, through the interaction with miRNA-466i-5p. We show that both the yield of lncMN2-203 recovery and the specificity of its interaction with the miRNA dramatically increase in the presence of Dextran Sulfate Sodium (DSS) salt. This new set-up may represent a powerful means for improving the study of RNA-RNA interactions of biological significance, especially for those lncRNAs whose role as microRNA (miRNA) sponges or regulators of mRNA stability was demonstrated.
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Affiliation(s)
- Fabio Desideri
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Eleonora D’Ambra
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Pietro Laneve
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Monica Ballarino
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Rome, Italy
- *Correspondence: Monica Ballarino,
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