1
|
Paz-González R, Lourido L, Calamia V, Fernández-Puente P, Quaranta P, Picchi F, Blanco FJ, Ruiz-Romero C. An Atlas of the Knee Joint Proteins and Their Role in Osteoarthritis Defined by Literature Mining. Mol Cell Proteomics 2023; 22:100606. [PMID: 37356495 PMCID: PMC10393810 DOI: 10.1016/j.mcpro.2023.100606] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/14/2023] [Accepted: 06/18/2023] [Indexed: 06/27/2023] Open
Abstract
Osteoarthritis (OA) is the most prevalent rheumatic pathology. However, OA is not simply a process of wear and tear affecting articular cartilage but rather a disease of the entire joint. One of the most common locations of OA is the knee. Knee tissues have been studied using molecular strategies, generating a large amount of complex data. As one of the goals of the Rheumatic and Autoimmune Diseases initiative of the Human Proteome Project, we applied a text-mining strategy to publicly available literature to collect relevant information and generate a systematically organized overview of the proteins most closely related to the different knee components. To this end, the PubPular literature-mining software was employed to identify protein-topic relationships and extract the most frequently cited proteins associated with the different knee joint components and OA. The text-mining approach searched over eight million articles in PubMed up to November 2022. Proteins associated with the six most representative knee components (articular cartilage, subchondral bone, synovial membrane, synovial fluid, meniscus, and cruciate ligament) were retrieved and ranked by their relevance to the tissue and OA. Gene ontology analyses showed the biological functions of these proteins. This study provided a systematic and prioritized description of knee-component proteins most frequently cited as associated with OA. The study also explored the relationship of these proteins to OA and identified the processes most relevant to proper knee function and OA pathophysiology.
Collapse
Affiliation(s)
- Rocío Paz-González
- Grupo de Investigación de Reumatología (GIR) - Unidad de Proteómica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Sergas, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain
| | - Lucía Lourido
- Grupo de Investigación de Reumatología (GIR) - Unidad de Proteómica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Sergas, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain
| | - Valentina Calamia
- Grupo de Investigación de Reumatología (GIR) - Unidad de Proteómica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Sergas, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain
| | - Patricia Fernández-Puente
- Departamento de Fisioterapia, Medicina y Ciencias Biomédicas, Grupo de Investigación de Reumatología y Salud (GIR-S), Centro Interdisciplinar de Química e Bioloxía (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Patricia Quaranta
- Grupo de Investigación de Reumatología (GIR) - Unidad de Proteómica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Sergas, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain
| | - Florencia Picchi
- Grupo de Investigación de Reumatología (GIR) - Unidad de Proteómica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Sergas, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain
| | - Francisco J Blanco
- Grupo de Investigación de Reumatología (GIR) - Unidad de Proteómica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Sergas, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain; Departamento de Fisioterapia, Medicina y Ciencias Biomédicas, Grupo de Investigación de Reumatología y Salud (GIR-S), Centro Interdisciplinar de Química e Bioloxía (CICA), Universidade da Coruña (UDC), A Coruña, Spain.
| | - Cristina Ruiz-Romero
- Grupo de Investigación de Reumatología (GIR) - Unidad de Proteómica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Sergas, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain; Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.
| |
Collapse
|
2
|
Sîrbe C, Badii M, Crişan TO, Bența G, Grama A, Joosten LAB, Rednic S, Pop TL. Detection of Novel Biomarkers in Pediatric Autoimmune Hepatitis by Proteomic Profiling. Int J Mol Sci 2023; 24:ijms24087479. [PMID: 37108648 PMCID: PMC10141667 DOI: 10.3390/ijms24087479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/14/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Autoimmune hepatitis (AIH) is characterized by immune-mediated hepatocyte injury resulting in the destruction of liver cells, causing inflammation, liver failure, and fibrosis. Pediatric (AIH) is an autoimmune inflammatory disease that usually requires immunosuppression for an extended period. Frequent relapses after treatment discontinuation demonstrate that current therapies do not control intrahepatic immune processes. This study describes targeted proteomic profiling data in patients with AIH and controls. A total of 92 inflammatory and 92 cardiometabolic plasma markers were assessed for (i) pediatric AIH versus controls, (ii) AIH type 1 versus type 2, (iii) AIH and AIH-autoimmune sclerosing cholangitis overlapping syndrome and (iv) correlations with circulating vitamin D levels in AIH. A total of 16 proteins showed a nominally significant differential abundance in pediatric patients with AIH compared to controls. No clustering of AIH subphenotypes based on all protein data was observed, and no significant correlation of vitamin D levels was observed for the identified proteins. The proteins that showed variable expression include CA1, CA3, GAS6, FCGR2A, 4E-BP1 and CCL19, which may serve as potential biomarkers for patients with AIH. CX3CL1, CXCL10, CCL23, CSF1 and CCL19 showed homology to one another and may be coexpressed in AIH. CXCL10 seems to be the central intermediary link for the listed proteins. These proteins were involved in relevant mechanistic pathways for liver diseases and immune processes in AIH pathogenesis. This is the first report on the proteomic profile of pediatric AIH. The identified markers could potentially lead to new diagnostic and therapeutic tools. Nevertheless, considering the complex pathogenesis of AIH, more extensive studies are warranted to replicate and validate the present study's findings.
Collapse
Affiliation(s)
- Claudia Sîrbe
- 2nd Pediatric Discipline, Department of Mother and Child, "Iuliu Hațieganu" University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- 2nd Pediatric Clinic, Center of Expertise in Pediatric Liver Rare Disorders, Emergency Clinical Hospital for Children, 400177 Cluj-Napoca, Romania
| | - Medeea Badii
- Department of Medical Genetics, "Iuliu Hațieganu" University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Department of Internal Medicine, Radboud University Medical Centre, 6525 XZ Nijmegen, The Netherlands
| | - Tania O Crişan
- Department of Medical Genetics, "Iuliu Hațieganu" University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Department of Internal Medicine, Radboud University Medical Centre, 6525 XZ Nijmegen, The Netherlands
| | - Gabriel Bența
- 2nd Pediatric Discipline, Department of Mother and Child, "Iuliu Hațieganu" University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- 2nd Pediatric Clinic, Center of Expertise in Pediatric Liver Rare Disorders, Emergency Clinical Hospital for Children, 400177 Cluj-Napoca, Romania
| | - Alina Grama
- 2nd Pediatric Discipline, Department of Mother and Child, "Iuliu Hațieganu" University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- 2nd Pediatric Clinic, Center of Expertise in Pediatric Liver Rare Disorders, Emergency Clinical Hospital for Children, 400177 Cluj-Napoca, Romania
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Centre, 6525 XZ Nijmegen, The Netherlands
| | - Simona Rednic
- Rheumatology Department, Emergency County Hospital Cluj, 400347 Cluj-Napoca, Romania
- Rheumatology Discipline, "Iuliu Hațieganu" University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Tudor Lucian Pop
- 2nd Pediatric Discipline, Department of Mother and Child, "Iuliu Hațieganu" University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- 2nd Pediatric Clinic, Center of Expertise in Pediatric Liver Rare Disorders, Emergency Clinical Hospital for Children, 400177 Cluj-Napoca, Romania
| |
Collapse
|
3
|
Fuentes M, Ruiz-Romero C, Misiego S, Juanes-Velasco P, Landeira-Viñuela A, Torres-Roda A, Lorenzo-Gil H, González-González M, Hernández ÁP, Lourido L, Sjöberg R, Pin E, de Las Rivas J, Sánchez-Santos JM, Nilsson P, Blanco FJ. Exploring High-Throughput Immunoassays for Biomarker Validation in Rheumatic Diseases in the Context of the Human Proteome Project. J Proteome Res 2022; 22:1105-1115. [PMID: 36475733 DOI: 10.1021/acs.jproteome.2c00387] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rheumatic diseases are high prevalence pathologies with different etiology and evolution and low sensitivity in clinical diagnosis. Therefore, it is necessary to develop an early diagnosis method which allows personalized treatment, depending on the specific pathology. The biology/disease initiative, at Human Proteome Project, is an integrative approach to identify relevant proteins in the human proteome associated with pathologies. A previously reported literature data mining analysis, which identified proteins related to osteoarthritis (OA), rheumatoid arthritis (RA), and psoriatic arthritis (PSA) was used to establish a systematic prioritization of potential biomarkers candidates for further evaluation by functional proteomics studies. The aim was to study the protein profile of serum samples from patients with rheumatic diseases such as OA, RA, and PSA. To achieve this goal, customized antibody microarrays (containing 151 antibodies targeting 121 specific proteins) were used to identify biomarkers related to early and specific diagnosis in a screening of 960 serum samples (nondepleted) (OA, n = 480; RA, n = 192; PSA, n = 288). This functional proteomics screening has allowed the determination of a panel (30 serum proteins) as potential biomarkers for these rheumatic diseases, displaying receiver operating characteristics curves with area under the curve values of 80-90%.
Collapse
Affiliation(s)
- Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007Salamanca, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007Salamanca, Spain
| | - Cristina Ruiz-Romero
- Unidad de Proteómica, Grupo de Investigación de Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas. C/As Xubias de Arriba 84, 15006A Coruña, Spain.,Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Av. Monforte de Lemos, 3-5. Pabellón 11, 28029Madrid, Spain
| | - Sara Misiego
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007Salamanca, Spain
| | - Pablo Juanes-Velasco
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007Salamanca, Spain
| | - Alicia Landeira-Viñuela
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007Salamanca, Spain
| | - Adrián Torres-Roda
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007Salamanca, Spain
| | - Héctor Lorenzo-Gil
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007Salamanca, Spain
| | - María González-González
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007Salamanca, Spain
| | - Ángela P Hernández
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007Salamanca, Spain.,Department of Pharmaceutical Sciences: Organic Chemistry, Faculty of Pharmacy, University of Salamanca, CIETUS, IBSAL, 37007Salamanca, Spain
| | - Lucía Lourido
- Unidad de Proteómica, Grupo de Investigación de Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas. C/As Xubias de Arriba 84, 15006A Coruña, Spain
| | - Ronald Sjöberg
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, 114 28Stockholm, Sweden
| | - Elisa Pin
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, 114 28Stockholm, Sweden
| | - Javier de Las Rivas
- Bioinformatics and Functional Genomics Research Group, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007Salamanca, Spain
| | - José Manuel Sánchez-Santos
- Bioinformatics and Functional Genomics Research Group, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007Salamanca, Spain
| | - Peter Nilsson
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, 114 28Stockholm, Sweden
| | - Francisco J Blanco
- Unidad de Proteómica, Grupo de Investigación de Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas. C/As Xubias de Arriba 84, 15006A Coruña, Spain.,Grupo de Investigación de Reumatología y Salud (GIR-S), Departamento de Fisioterapia, Medicina y Ciencias Biomédicas, Centro de investigaciones Avanzadas (CICA), Universidade da Coruaña (UDC), 15008A Coruña, Spain
| |
Collapse
|
4
|
Martini MC, Vacca C, Torres Tejerizo GA, Draghi WO, Pistorio M, Lozano MJ, Lagares A, Del Papa MF. ubiF is involved in acid stress tolerance and symbiotic competitiveness in Rhizobium favelukesii LPU83. Braz J Microbiol 2022; 53:1633-1643. [PMID: 35704174 DOI: 10.1007/s42770-022-00780-8] [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: 03/05/2022] [Accepted: 06/06/2022] [Indexed: 11/26/2022] Open
Abstract
The acidity of soils significantly reduces the productivity of legumes mainly because of the detrimental effects of hydrogen ions on the legume plants, leading to the establishment of an inefficient symbiosis and poor biological nitrogen fixation. We recently reported the analysis of the fully sequenced genome of Rhizobium favelukesii LPU83, an alfalfa-nodulating rhizobium with a remarkable ability to grow, nodulate and compete in acidic conditions. To gain more insight into the genetic mechanisms leading to acid tolerance in R. favelukesii LPU83, we constructed a transposon mutant library and screened for mutants displaying a more acid-sensitive phenotype than the parental strain. We identified mutant Tn833 carrying a single-transposon insertion within LPU83_2531, an uncharacterized short ORF located immediately upstream from ubiF homolog. This gene encodes a protein with an enzymatic activity involved in the biosynthesis of ubiquinone. As the transposon was inserted near the 3' end of LPU83_2531 and these genes are cotranscribed as a part of the same operon, we hypothesized that the phenotype in Tn833 is most likely due to a polar effect on ubiF transcription.We found that a mutant in ubiF was impaired to grow at low pH and other abiotic stresses including 5 mM ascorbate and 0.500 mM Zn2+. Although the ubiF mutant retained the ability to nodulate alfalfa and Phaseolus vulgaris, it was unable to compete with the R. favelukesii LPU83 wild-type strain for nodulation in Medicago sativa and P. vulgaris, suggesting that ubiF is important for competitiveness. Here, we report for the first time an ubiF homolog being essential for nodulation competitiveness and tolerance to specific stresses in rhizobia.
Collapse
Affiliation(s)
- María Carla Martini
- Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 115 49 y 50 (1900), Buenos Aires, La Plata, Argentina
| | - Carolina Vacca
- Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 115 49 y 50 (1900), Buenos Aires, La Plata, Argentina
| | - Gonzalo A Torres Tejerizo
- Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 115 49 y 50 (1900), Buenos Aires, La Plata, Argentina
| | - Walter O Draghi
- Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 115 49 y 50 (1900), Buenos Aires, La Plata, Argentina
| | - Mariano Pistorio
- Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 115 49 y 50 (1900), Buenos Aires, La Plata, Argentina
| | - Mauricio J Lozano
- Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 115 49 y 50 (1900), Buenos Aires, La Plata, Argentina
| | - Antonio Lagares
- Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 115 49 y 50 (1900), Buenos Aires, La Plata, Argentina
| | - María Florencia Del Papa
- Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 115 49 y 50 (1900), Buenos Aires, La Plata, Argentina.
| |
Collapse
|
5
|
Nony E, Moingeon P. Proteomics in support of immunotherapy: contribution to model-based precision medicine. Expert Rev Proteomics 2021; 19:33-42. [PMID: 34937491 DOI: 10.1080/14789450.2021.2020653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Proteomics encompasses a wide and expanding range of methods to identify, characterize, and quantify thousands of proteins from a variety of biological samples, including blood samples, tumors, and tissues. Such methods are supportive of various forms of immunotherapy applied to chronic conditions such as allergies, autoimmune diseases, cancers, and infectious diseases. AREAS COVERED In support of immunotherapy, proteomics based on mass spectrometry has multiple specific applications related to (i) disease modeling and patient stratification, (ii) antigen/ autoantigen/neoantigen/ allergen identification, (iii) characterization of proteins and monoclonal antibodies used for immunotherapeutic or diagnostic purposes, (iv) identification of biomarkers and companion diagnostics and (v) monitoring by immunoproteomics of immune responses elicited in the course of the disease or following immunotherapy. EXPERT OPINION Proteomics contributes as an enabling technology to an evolution of immunotherapy toward a precision medicine approach aiming to better tailor treatments to patients' specificities in multiple disease areas. This trend is favored by a better understanding through multi-omics profiling of both the patient's characteristics, his/her immune status as well as of the features of the immunotherapeutic drug.
Collapse
Affiliation(s)
- Emmanuel Nony
- Protein Sciences Department, Institut de Recherches Servier, Croissy Sur Seine, France
| | - Philippe Moingeon
- Center for Therapeutic Innovation, Immuno-inflammatory Disease, Institut de Recherches Servier, Croissy Sur Seine, France
| |
Collapse
|
6
|
McArdle A, Washington KE, Chazarin Orgel B, Binek A, Manalo DM, Rivas A, Ayres M, Pandey R, Phebus C, Raedschelders K, Fert-Bober J, Van Eyk JE. Discovery Proteomics for COVID-19: Where We Are Now. J Proteome Res 2021; 20:4627-4639. [PMID: 34550702 PMCID: PMC8482317 DOI: 10.1021/acs.jproteome.1c00475] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible coronavirus responsible for the pandemic coronavirus disease 2019 (COVID-19), which has had a devastating impact on society. Here, we summarize proteomic research that has helped elucidate hallmark proteins associated with the disease with respect to both short- and long-term diagnosis and prognosis. Additionally, we review the highly variable humoral response associated with COVID-19 and the increased risk of autoimmunity.
Collapse
Affiliation(s)
- Angela McArdle
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Kirstin E. Washington
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Blandine Chazarin Orgel
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Aleksandra Binek
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Danica-Mae Manalo
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Alejandro Rivas
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Matthew Ayres
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Rakhi Pandey
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Connor Phebus
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Koen Raedschelders
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Justyna Fert-Bober
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
- Department
of Cardiology, Smidt Heart Institute, Cedars-Sinai
Medical Center, Los Angeles, California 90048, United States
| | - Jennifer E. Van Eyk
- Advanced
Clinical Biosystems Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
- Department
of Cardiology, Smidt Heart Institute, Cedars-Sinai
Medical Center, Los Angeles, California 90048, United States
| |
Collapse
|
7
|
Zhang L, Xing R, Huang Z, Ding L, Zhang L, Li M, Li X, Wang P, Mao J. Synovial Fibrosis Involvement in Osteoarthritis. Front Med (Lausanne) 2021; 8:684389. [PMID: 34124114 PMCID: PMC8187615 DOI: 10.3389/fmed.2021.684389] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/03/2021] [Indexed: 12/14/2022] Open
Abstract
Bone changes have always been the focus of research on osteoarthritis, but the number of studies on synovitis has increased only over the last 10 years. Our current understanding is that the mechanism of osteoarthritis involves all the tissues that make up the joints, including nerve sprouting, pannus formation, and extracellular matrix environmental changes in the synovium. These factors together determine synovial fibrosis and may be closely associated with the clinical symptoms of pain, hyperalgesia, and stiffness in osteoarthritis. In this review, we summarize the consensus of clinical work, the potential pathological mechanisms, the possible therapeutic targets, and the available therapeutic strategies for synovial fibrosis in osteoarthritis to gain insight and provide a foundation for further study.
Collapse
Affiliation(s)
- Li Zhang
- Departments of Orthopedics, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Runlin Xing
- Departments of Orthopedics, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Zhengquan Huang
- Departments of Orthopedics, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Liang Ding
- Departments of Orthopedics, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Li Zhang
- Departments of Orthopedics, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Mingchao Li
- Departments of Orthopedics, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaochen Li
- Departments of Orthopedics, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Peimin Wang
- Departments of Orthopedics, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Jun Mao
- Departments of Orthopedics, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| |
Collapse
|
8
|
Padern G, Duflos C, Ferreira R, Assou S, Guilpain P, Maria ATJ, Goulabchand R, Galea P, Jurtela M, Jorgensen C, Pers YM. Identification of a Novel Serum Proteomic Signature for Primary Sjögren's Syndrome. Front Immunol 2021; 12:631539. [PMID: 33708222 PMCID: PMC7942395 DOI: 10.3389/fimmu.2021.631539] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022] Open
Abstract
Context Primary Sjögren's syndrome (pSS) is a complex heterogeneous autoimmune disease (AID) which can mimic rheumatoid arthritis (RA) or systemic lupus erythematosus (SLE). Our exploratory study investigated serum biomarkers that may discriminate pSS from RA and SLE. Methods Serum concentrations of 63 biomarkers involved in immune cell trafficking, inflammatory response, cellular movement, and cell-to-cell signaling were measured in AID patients, included prospectively into the study at the Montpellier University Hospital. A multivariate analysis by multiple logistic regression was performed, and discriminative power assessed using logistic regression adjusted on significant demographic factors. Results Among the 95 patients enrolled, 42 suffered from pSS, 28 from RA, and 25 from SLE. Statistical analysis showed that concentrations of BDNF (OR = 0.493 with 95% CI [0.273-0.891]; p = 0.0193) and I-TAC/CXCL11 (OR = 1.344 with 95% CI [1.027-1.76]; p = 0.0314) can significantly discriminate pSS from RA. Similarly, greater concentrations of sCD163 (OR = 0.803 with 95% CI [0.649-0.994]; p = 0.0436), Fractalkine/CX3CL1 (OR = 0.534 with 95% CI [0.287-0. 991]; p = 0.0466), MCP-1/CCL2 (OR = 0.839 with 95% CI [0.732-0.962]; p = 0.0121), and TNFa (OR = 0.479 with 95% CI [0.247-0.928]; p = 0.0292) were associated with SLE diagnosis compared to pSS. In addition, the combination of low concentrations of BDNF and Fractalkine/CX3CL1 was highly specific for pSS (specificity 96.2%; positive predictive value 80%) compared to RA and SLE, as well as the combination of high concentrations of I-TAC/CXCL11 and low concentrations of sCD163 (specificity 98.1%; positive predictive value 75%). Conclusion Our study highlights biomarkers potentially involved in pSS, RA, and SLE pathophysiology that could be useful for developing a pSS-specific diagnostic tool.
Collapse
Affiliation(s)
- Guillaume Padern
- IRMB, University of Montpellier, INSERM, CHU Montpellier, Montpellier, France
| | - Claire Duflos
- Clinical Research and Epidemiology Unit, CHU Montpellier, Montpellier University, Montpellier, France
| | - Rosanna Ferreira
- IRMB, University of Montpellier, INSERM, CHU Montpellier, Montpellier, France
| | - Said Assou
- IRMB, University of Montpellier, INSERM, CHU Montpellier, Montpellier, France
| | - Philippe Guilpain
- IRMB, University of Montpellier, INSERM, CHU Montpellier, Montpellier, France
- Internal Medicine and Multi-Organic Diseases Department, Hôpital Saint Éloi, CHU Montpellier, Montpellier, France
| | - Alexandre Thibault Jacques Maria
- IRMB, University of Montpellier, INSERM, CHU Montpellier, Montpellier, France
- Internal Medicine and Multi-Organic Diseases Department, Hôpital Saint Éloi, CHU Montpellier, Montpellier, France
| | - Radjiv Goulabchand
- Internal Medicine Department, Caremeau University Hospital, Nîmes, France
| | - Pascale Galea
- BioRad Laboratory, Research and Development Department, Montpellier, France
| | - Maja Jurtela
- Clinical Research and Epidemiology Unit, CHU Montpellier, Montpellier University, Montpellier, France
| | - Christian Jorgensen
- IRMB, University of Montpellier, INSERM, CHU Montpellier, Montpellier, France
| | - Yves-Marie Pers
- IRMB, University of Montpellier, INSERM, CHU Montpellier, Montpellier, France
| |
Collapse
|
9
|
Bowden TJ, Kraev I, Lange S. Extracellular vesicles and post-translational protein deimination signatures in haemolymph of the American lobster (Homarus americanus). FISH & SHELLFISH IMMUNOLOGY 2020; 106:79-102. [PMID: 32731012 DOI: 10.1016/j.fsi.2020.06.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/21/2020] [Accepted: 06/27/2020] [Indexed: 06/11/2023]
Abstract
The American lobster (Homarus americanus) is a commercially important crustacean with an unusual long life span up to 100 years and a comparative animal model of longevity. Therefore, research into its immune system and physiology is of considerable importance both for industry and comparative immunology studies. Peptidylarginine deiminases (PADs) are a phylogenetically conserved enzyme family that catalyses post-translational protein deimination via the conversion of arginine to citrulline. This can lead to structural and functional protein changes, sometimes contributing to protein moonlighting, in health and disease. PADs also regulate the cellular release of extracellular vesicles (EVs), which is an important part of cellular communication, both in normal physiology and in immune responses. Hitherto, studies on EVs in Crustacea are limited and neither PADs nor associated protein deimination have been studied in a Crustacean species. The current study assessed EV and deimination signatures in haemolymph of the American lobster. Lobster EVs were found to be a poly-dispersed population in the 10-500 nm size range, with the majority of smaller EVs, which fell within 22-115 nm. In lobster haemolymph, 9 key immune and metabolic proteins were identified to be post-translationally deiminated, while further 41 deiminated protein hits were identified when searching against a Crustacean database. KEGG (Kyoto encyclopedia of genes and genomes) and GO (gene ontology) enrichment analysis of these deiminated proteins revealed KEGG and GO pathways relating to a number of immune, including anti-pathogenic (viral, bacterial, fungal) and host-pathogen interactions, as well as metabolic pathways, regulation of vesicle and exosome release, mitochondrial function, ATP generation, gene regulation, telomerase homeostasis and developmental processes. The characterisation of EVs, and post-translational deimination signatures, reported in lobster in the current study, and the first time in Crustacea, provides insights into protein moonlighting functions of both species-specific and phylogenetically conserved proteins and EV-mediated communication in this long-lived crustacean. The current study furthermore lays foundation for novel biomarker discovery for lobster aquaculture.
Collapse
Affiliation(s)
- Timothy J Bowden
- Aquaculture Research Institute, School of Food & Agriculture, University of Maine, Orono, ME, USA.
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science,Technology, Engineering and Mathematics, Open University, Milton Keynes, MK7 6AA, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London, W1W 6UW, UK.
| |
Collapse
|
10
|
Omenn GS, Lane L, Overall CM, Cristea IM, Corrales FJ, Lindskog C, Paik YK, Van Eyk JE, Liu S, Pennington SR, Snyder MP, Baker MS, Bandeira N, Aebersold R, Moritz RL, Deutsch EW. Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. J Proteome Res 2020; 19:4735-4746. [PMID: 32931287 DOI: 10.1021/acs.jproteome.0c00485] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
According to the 2020 Metrics of the HUPO Human Proteome Project (HPP), expression has now been detected at the protein level for >90% of the 19 773 predicted proteins coded in the human genome. The HPP annually reports on progress made throughout the world toward credibly identifying and characterizing the complete human protein parts list and promoting proteomics as an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2020-01 classified 17 874 proteins as PE1, having strong protein-level evidence, up 180 from 17 694 one year earlier. These represent 90.4% of the 19 773 predicted coding genes (all PE1,2,3,4 proteins in neXtProt). Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), was reduced by 230 from 2129 to 1899 since the neXtProt 2019-01 release. PeptideAtlas is the primary source of uniform reanalysis of raw mass spectrometry data for neXtProt, supplemented this year with extensive data from MassIVE. PeptideAtlas 2020-01 added 362 canonical proteins between 2019 and 2020 and MassIVE contributed 84 more, many of which converted PE1 entries based on non-MS evidence to the MS-based subgroup. The 19 Biology and Disease-driven B/D-HPP teams continue to pursue the identification of driver proteins that underlie disease states, the characterization of regulatory mechanisms controlling the functions of these proteins, their proteoforms, and their interactions, and the progression of transitions from correlation to coexpression to causal networks after system perturbations. And the Human Protein Atlas published Blood, Brain, and Metabolic Atlases.
Collapse
Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States.,Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | | | - Ileana M Cristea
- Princeton University, Princeton, New Jersey 08544, United States
| | | | | | | | | | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | | | | | - Mark S Baker
- Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California 92093, United States
| | - Ruedi Aebersold
- ETH-Zurich and University of Zurich, 8092 Zurich, Switzerland
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| |
Collapse
|
11
|
Bowden TJ, Kraev I, Lange S. Post-translational protein deimination signatures and extracellular vesicles (EVs) in the Atlantic horseshoe crab (Limulus polyphemus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 110:103714. [PMID: 32335073 DOI: 10.1016/j.dci.2020.103714] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
The horseshoe crab is a living fossil and a species of marine arthropod with unusual immune system properties which are also exploited commercially. Given its ancient status dating to the Ordovician period (450 million years ago), its standing in phylogeny and unusual immunological characteristics, the horseshoe crab may hold valuable information for comparative immunology studies. Peptidylarginine deiminases (PADs) are calcium dependent enzymes that are phylogenetically conserved and cause protein deimination via conversion of arginine to citrulline. This post-translational modification can lead to structural and functional protein changes contributing to protein moonlighting in health and disease. PAD-mediated regulation of extracellular vesicle (EV) release, a critical component of cellular communication, has furthermore been identified to be a phylogenetically conserved mechanism. PADs, protein deimination and EVs have hitherto not been studied in the horseshoe crab and were assessed in the current study. Horseshoe crab haemolymph serum-EVs were found to be a poly-dispersed population in the 20-400 nm size range, with the majority of EVs falling within 40-123 nm. Key immune proteins were identified to be post-translationally deiminated in horseshoe crab haemolymph serum, providing insights into protein moonlighting function of Limulus and phylogenetically conserved immune proteins. KEGG (Kyoto encyclopaedia of genes and genomes) and GO (gene ontology) enrichment analysis of deiminated proteins identified in Limulus revealed KEGG pathways relating to complement and coagulation pathways, Staphylococcus aureus infection, glycolysis/gluconeogenesis and carbon metabolism, while GO pathways of biological and molecular pathways related to a range of immune and metabolic functions, as well as developmental processes. The characterisation of EVs, and post-translational deimination signatures, revealed here in horseshoe crab, contributes to current understanding of protein moonlighting functions and EV-mediated communication in this ancient arthropod and throughout phylogeny.
Collapse
Affiliation(s)
- Timothy J Bowden
- Aquaculture Research Institute, School of Food & Agriculture, University of Maine, University of Maine, Orono, ME, USA.
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science Technology, Engineering and Mathematics Open University, Milton Keynes, MK7 6AA, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London, W1W 6UW, UK.
| |
Collapse
|