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Fucito M, Spedicato M, Felletti S, Yu AC, Busin M, Pasti L, Franchina FA, Cavazzini A, De Luca C, Catani M. A Look into Ocular Diseases: The Pivotal Role of Omics Sciences in Ophthalmology Research. ACS MEASUREMENT SCIENCE AU 2024; 4:247-259. [PMID: 38910860 PMCID: PMC11191728 DOI: 10.1021/acsmeasuresciau.3c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 06/25/2024]
Abstract
Precision medicine is a new medical approach which considers both population characteristics and individual variability to provide customized healthcare. The transition from traditional reactive medicine to personalized medicine is based on a biomarker-driven process and a deep knowledge of biological mechanisms according to which the development of diseases occurs. In this context, the advancements in high-throughput omics technologies represent a unique opportunity to discover novel biomarkers and to provide an unbiased picture of the biological system. One of the medical fields in which omics science has started to be recently applied is that of ophthalmology. Ocular diseases are very common, and some of them could be highly disabling, thus leading to vision loss and blindness. The pathogenic mechanism of most ocular diseases may be dependent on various genetic and environmental factors, whose effect has not been yet completely understood. In this context, large-scale omics approaches are fundamental to have a comprehensive evaluation of the whole system and represent an essential tool for the development of novel therapies. This Review summarizes the recent advancements in omics science applied to ophthalmology in the last ten years, in particular by focusing on proteomics, metabolomics and lipidomics applications from an analytical perspective. The role of high-efficiency separation techniques coupled to (high-resolution) mass spectrometry ((HR)MS) is also discussed, as well as the impact of sampling, sample preparation and data analysis as integrating parts of the analytical workflow.
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Affiliation(s)
- Maurine Fucito
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy
| | - Matteo Spedicato
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy
| | - Simona Felletti
- Department
of Environmental and Prevention Sciences, University of Ferrara, via L. Borsari 46, Ferrara 44121, Italy
| | - Angeli Christy Yu
- Department
of Translational Medicine and for Romagna, University of Ferrara, via Aldo Moro 8, 44124 Ferrara, Italy
| | - Massimo Busin
- Department
of Translational Medicine and for Romagna, University of Ferrara, via Aldo Moro 8, 44124 Ferrara, Italy
| | - Luisa Pasti
- Department
of Environmental and Prevention Sciences, University of Ferrara, via L. Borsari 46, Ferrara 44121, Italy
| | - Flavio A. Franchina
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy
| | - Alberto Cavazzini
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy
- Council
for Agricultural Research and Economics, via della Navicella 2/4, Rome 00184, Italy
| | - Chiara De Luca
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy
| | - Martina Catani
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy
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Wolf J, Franco JA, Yip R, Dabaja MZ, Velez G, Liu F, Bassuk AG, Mruthyunjaya P, Dufour A, Mahajan VB. Liquid Biopsy Proteomics in Ophthalmology. J Proteome Res 2024; 23:511-522. [PMID: 38171013 PMCID: PMC10845144 DOI: 10.1021/acs.jproteome.3c00756] [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: 11/11/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024]
Abstract
Minimally invasive liquid biopsies from the eye capture locally enriched fluids that contain thousands of proteins from highly specialized ocular cell types, presenting a promising alternative to solid tissue biopsies. The advantages of liquid biopsies include sampling the eye without causing irreversible functional damage, potentially better reflecting tissue heterogeneity, collecting samples in an outpatient setting, monitoring therapeutic response with sequential sampling, and even allowing examination of disease mechanisms at the cell level in living humans, an approach that we refer to as TEMPO (Tracing Expression of Multiple Protein Origins). Liquid biopsy proteomics has the potential to transform molecular diagnostics and prognostics and to assess disease mechanisms and personalized therapeutic strategies in individual patients. This review addresses opportunities, challenges, and future directions of high-resolution liquid biopsy proteomics in ophthalmology, with particular emphasis on the large-scale collection of high-quality samples, cutting edge proteomics technology, and artificial intelligence-supported data analysis.
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Affiliation(s)
- Julian Wolf
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Joel A. Franco
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Rui Yip
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Mohamed Ziad Dabaja
- Departments
of Physiology and Pharmacology & Biochemistry and Molecular Biology,
Cumming School of Medicine, University of
Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Gabriel Velez
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Fei Liu
- Department
of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Alexander G. Bassuk
- Department
of Pediatrics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Prithvi Mruthyunjaya
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Antoine Dufour
- Departments
of Physiology and Pharmacology & Biochemistry and Molecular Biology,
Cumming School of Medicine, University of
Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Vinit B. Mahajan
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
- Veterans
Affairs Palo Alto Health Care System, Palo Alto, California 94304, United States
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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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Mishra K, Velez G, Chemudupati T, Tang PH, Mruthyunjaya P, Sanislo SR, Mahajan VB. Intraoperative Complications With Vitreous Biopsy for Molecular Proteomics. Ophthalmic Surg Lasers Imaging Retina 2023; 54:32-36. [PMID: 36626208 PMCID: PMC10790578 DOI: 10.3928/23258160-20221214-02] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
OBJECTIVE To study the incidence of intraoperative complications while collecting a vitreous sample for proteomic biomarker analyses during small-gauge pars plana vitrectomy (PPV). METHODS A retrospective case series was assembled from the surgical logs and charts of patients who underwent 23-, 25-, and 27-gauge PPV along with an undiluted vitreous biopsy. Primary surgical indication and detailed operative reports were reviewed. Complications specific to vitreous biopsy were assessed while complications related to vitrectomy in general without biopsy were not tabulated. RESULTS In 1190 eyes that underwent vitreous biopsy, the most common indications for PPV were rhegmatogenous retinal detachment (24.2%), epiretinal membrane (ERM) (21.7%), vitreous hemorrhage (11.0%), uveitis (8.3%), and macular hole (7.5%). An adequate sample of 0.5 cc to 1.0 cc was obtained in all cases. There was one sclerotomy break associated with biopsy, but no instances of lens touch, retinal contusion, retinal detachment, or intraocular hemorrhage. CONCLUSIONS Undiluted vitreous biopsy obtained at the time of small-gauge vitrectomy is a generally safe procedure and may be considered for collection of samples for proteomic analysis. [Ophthalmic Surg Lasers Imaging Retina 2023;54:32-36.].
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