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Luz IS, Takaya R, Ribeiro DG, Castro MS, Fontes W. Proteomics: Unraveling the Cross Talk Between Innate Immunity and Disease Pathophysiology, Diagnostics, and Treatment Options. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1443:221-242. [PMID: 38409424 DOI: 10.1007/978-3-031-50624-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Inflammation is crucial in diseases, and proteins play a key role in the interplay between innate immunity and pathology. This review explores how proteomics helps understanding this relationship, focusing on diagnosis and treatment. We explore the dynamic innate response and the significance of proteomic techniques in deciphering the complex network of proteins involved in prevalent diseases, including infections, cancer, autoimmune and neurodegenerative disorders. Proteomics identifies key proteins in host-pathogen interactions, shedding light on infection mechanisms and inflammation. These discoveries hold promise for diagnostic tools, therapies, and vaccines. In cancer research, proteomics reveals innate signatures associated with tumor development, immune evasion, and therapeutic response. Additionally, proteomic analysis has unveiled autoantigens and dysregulation of the innate immune system in autoimmunity, offering opportunities for early diagnosis, disease monitoring, and new therapeutic targets. Moreover, proteomic analysis has identified altered protein expression patterns in neurodegenerative diseases like Alzheimer's and Parkinson's, providing insights into potential therapeutic strategies. Proteomics of the innate immune system provides a comprehensive understanding of disease mechanisms, identifies biomarkers, and enables effective interventions in various diseases. Despite still in its early stages, this approach holds great promise to revolutionize innate immunity research and significantly improve patient outcomes across a wide range of diseases.
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Affiliation(s)
- Isabelle Souza Luz
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Raquel Takaya
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Daiane Gonzaga Ribeiro
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Mariana S Castro
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasília, Federal District, Brazil.
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Chase Huizar C, Raphael I, Forsthuber TG. Genomic, proteomic, and systems biology approaches in biomarker discovery for multiple sclerosis. Cell Immunol 2020; 358:104219. [PMID: 33039896 PMCID: PMC7927152 DOI: 10.1016/j.cellimm.2020.104219] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/13/2020] [Accepted: 09/16/2020] [Indexed: 12/12/2022]
Abstract
Multiple sclerosis (MS) is a neuroinflammatory disorder characterized by autoimmune-mediated inflammatory lesions in CNS leading to myelin damage and axonal loss. MS is a heterogenous disease with variable and unpredictable disease course. Due to its complex nature, MS is difficult to diagnose and responses to specific treatments may vary between individuals. Therefore, there is an indisputable need for biomarkers for early diagnosis, prediction of disease exacerbations, monitoring the progression of disease, and for measuring responses to therapy. Genomic and proteomic studies have sought to understand the molecular basis of MS and find biomarker candidates. Advances in next-generation sequencing and mass-spectrometry techniques have yielded an unprecedented amount of genomic and proteomic data; yet, translation of the results into the clinic has been underwhelming. This has prompted the development of novel data science techniques for exploring these large datasets to identify biologically relevant relationships and ultimately point towards useful biomarkers. Herein we discuss optimization of omics study designs, advances in the generation of omics data, and systems biology approaches aimed at improving biomarker discovery and translation to the clinic for MS.
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Affiliation(s)
- Carol Chase Huizar
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Itay Raphael
- Department of Neurological Surgery, University of Pittsburgh, UPMC Children's Hospital, Pittsburgh, PA, USA.
| | - Thomas G Forsthuber
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA.
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He S, Liu X, Lin Z, Liu Y, Gu L, Zhou H, Tang W, Zuo J. Reversible SAHH inhibitor protects against glomerulonephritis in lupus-prone mice by downregulating renal α-actinin-4 expression and stabilizing integrin-cytoskeleton linkage. Arthritis Res Ther 2019; 21:40. [PMID: 30696480 PMCID: PMC6352376 DOI: 10.1186/s13075-019-1820-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/11/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Glomerulonephritis is one of the major complications and causes of death in systemic lupus erythematosus (SLE) and is characterized by glomerulosclerosis, interstitial fibrosis, and tubular atrophy, along with severe persistent proteinuria. DZ2002 is a reversible S-adenosyl-L-homocysteine hydrolase (SAHH) inhibitor with potent therapeutic activity against lupus nephritis in mice. However, the molecular events underlying the renal protective effects of DZ2002 remained unclear. This study is designed to uncover the molecular mechanisms of DZ2002 on glomerulonephritis of lupus-prone mice. METHODS We conducted a twice-daily treatment of DZ2002 on the lupus-prone NZB/WF1 mice, and the progression of lupus nephritis and alteration of renal function were monitored. The LC-MS-based label-free quantitative (LFQ) proteomic approach was applied to analyze the kidney tissue samples from the normal C57BL/6 mice and the NZB/WF1 mice treated with DZ2002 or vehicle. KEGG pathway enrichment and direct protein-protein interaction (PPI) network analyses were used to map the pathways in which the significantly changed proteins (SCPs) are involved. The selected proteins from proteomic analysis were validated by Western blot analysis and immunohistochemistry in the kidney tissues. RESULTS The twice-daily regimen of DZ2002 administration significantly ameliorated the lupus nephritis and improved the renal function in NZB/WF1 mice. A total of 3275 proteins were quantified, of which 253 proteins were significantly changed across normal C57BL/6 mice and the NZB/WF1 mice treated with DZ2002 or vehicle. Pathway analysis revealed that 13 SCPs were involved in tight junction and focal adhesion process. Further protein expression validation demonstrated that DZ2002-treated NZB/WF1 mice exhibited downregulation of α-actinin-4 and integrin-linked kinase (ILK), as well as the restoration of β1-integrin activation in the kidney tissues compared with the vehicle-treated ones. CONCLUSIONS Our study demonstrated the first evidence for the molecular mechanism of SAHH inhibitor on glomerulonephritis in SLE via the modulation of α-actinin-4 expression and focal adhesion-associated signaling proteins in the kidney.
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Affiliation(s)
- Shijun He
- Laboratory of Immunopharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Xing Liu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Zemin Lin
- Laboratory of Immunopharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yuting Liu
- Laboratory of Immunopharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Lei Gu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hu Zhou
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China. .,Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Wei Tang
- Laboratory of Immunopharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China.
| | - Jianping Zuo
- Laboratory of Immunopharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China.
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