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Bazin T, Nozeret K, Julié C, Lamarque D, Touati E. Protein Biomarkers of Gastric Preneoplasia and Cancer Lesions in Blood: A Comprehensive Review. Cancers (Basel) 2024; 16:3019. [PMID: 39272877 PMCID: PMC11394471 DOI: 10.3390/cancers16173019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 08/20/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
Gastric cancer (GC) is a major cause of cancer-related mortality worldwide. It is often associated with a bad prognosis because of its asymptomatic phenotype until advanced stages, highlighting the need for its prevention and early detection. GC development is preceded by the emergence of gastric preneoplasia lesions (GPNLs), namely atrophic gastritis (AG), intestinal metaplasia (IM), and dysplasia (DYS). GC is currently diagnosed by endoscopy, which is invasive and costly and has limited effectiveness for the detection of GPNLs. Therefore, the discovery of non-invasive biomarkers in liquid biopsies, such as blood samples, in order to identify the presence of gastric preneoplasia and/or cancer lesions at asymptomatic stages is of paramount interest. This comprehensive review provides an overview of recently identified plasma/serum proteins and their diagnostic performance for the prediction of GPNLs and early cancer lesions. Autoantibodies appear to be promising biomarkers for AG, IM and early gastric cancer detection, along with inflammation and immunity-related proteins and antibodies against H. pylori virulence factors. There is a lack of specific protein biomarkers with which to detect DYS. Despite the need for further investigation and validation, some emerging candidates could pave the way for the development of reliable, non-invasive diagnostic tests for the detection and prevention of GC.
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Affiliation(s)
- Thomas Bazin
- Department of Gastroenterology and Nutritional Support, Center for Intestinal Failure, Reference Centre of Rare Disease MarDI, Assistance Publique-Hôpitaux de Paris (AP-HP) Beaujon Hospital, University Paris Cité, F-92110 Clichy, France
- Infection & Inflammation, Unité Mixte de Recherche (UMR) 1173, Inserm, Université de Versailles-Saint-Quentin-en-Yvelines (UVSQ)/Université Paris Saclay, F-78180 Montigny-le-Bretonneux, France
| | - Karine Nozeret
- Équipe DMic01-Infection, Génotoxicité et Cancer, Département de Microbiologie, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6047, Institut Pasteur, Université Paris Cité, F-75015 Paris, France
| | - Catherine Julié
- Department of Anatomical Pathology, Université Paris Saclay/Université de Versailles-Saint-Quentin-en-Yvelines (UVSQ), Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Ambroise Paré, F-92100 Boulogne-Billancourt, France
| | - Dominique Lamarque
- Infection & Inflammation, Unité Mixte de Recherche (UMR) 1173, Inserm, Université de Versailles-Saint-Quentin-en-Yvelines (UVSQ)/Université Paris Saclay, F-78180 Montigny-le-Bretonneux, France
- Department of Gastroenterology, Université Paris Saclay/Université de Versailles-Saint-Quentin-en-Yvelines (UVSQ), Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Ambroise Paré, F-92100 Boulogne Billancourt, France
| | - Eliette Touati
- Équipe DMic01-Infection, Génotoxicité et Cancer, Département de Microbiologie, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6047, Institut Pasteur, Université Paris Cité, F-75015 Paris, France
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2
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Farrell LA, O’Rourke MB, Padula MP, Souza-Fonseca-Guimaraes F, Caramori G, Wark PAB, Dharmage SC, Hansbro PM. The Current Molecular and Cellular Landscape of Chronic Obstructive Pulmonary Disease (COPD): A Review of Therapies and Efforts towards Personalized Treatment. Proteomes 2024; 12:23. [PMID: 39189263 PMCID: PMC11348234 DOI: 10.3390/proteomes12030023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) ranks as the third leading cause of global illness and mortality. It is commonly triggered by exposure to respiratory irritants like cigarette smoke or biofuel pollutants. This multifaceted condition manifests through an array of symptoms and lung irregularities, characterized by chronic inflammation and reduced lung function. Present therapies primarily rely on maintenance medications to alleviate symptoms, but fall short in impeding disease advancement. COPD's diverse nature, influenced by various phenotypes, complicates diagnosis, necessitating precise molecular characterization. Omics-driven methodologies, including biomarker identification and therapeutic target exploration, offer a promising avenue for addressing COPD's complexity. This analysis underscores the critical necessity of improving molecular profiling to deepen our comprehension of COPD and identify potential therapeutic targets. Moreover, it advocates for tailoring treatment strategies to individual phenotypes. Through comprehensive exploration-based molecular characterization and the adoption of personalized methodologies, innovative treatments may emerge that are capable of altering the trajectory of COPD, instilling optimism for efficacious disease-modifying interventions.
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Affiliation(s)
- Luke A. Farrell
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Centre for Inflammation, Ultimo, NSW 2007, Australia;
| | - Matthew B. O’Rourke
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Centre for Inflammation, Ultimo, NSW 2007, Australia;
| | - Matthew P. Padula
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia;
| | | | - Gaetano Caramori
- Pulmonology, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy;
| | - Peter A. B. Wark
- School of Translational Medicine, Monash University, Melbourne, VIC 3000, Australia;
| | - Shymali C. Dharmage
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Phillip M. Hansbro
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Centre for Inflammation, Ultimo, NSW 2007, Australia;
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3
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Ciordia S, Santos FM, Dias JML, Lamas JR, Paradela A, Alvarez-Sola G, Ávila MA, Corrales F. Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network. Talanta 2024; 274:125988. [PMID: 38569368 DOI: 10.1016/j.talanta.2024.125988] [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: 01/25/2024] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Despite technological advances in the proteomics field, sample preparation still represents the main bottleneck in mass spectrometry (MS) analysis. Bead-based protein aggregation techniques have recently emerged as an efficient, reproducible, and high-throughput alternative for protein extraction and digestion. Here, a refined paramagnetic bead-based digestion protocol is described for Opentrons® OT-2 platform (OT-2) as a versatile, reproducible, and affordable alternative for the automatic sample preparation for MS analysis. For this purpose, an artificial neural network (ANN) was applied to maximize the number of peptides without missed cleavages identified in HeLa extract by combining factors such as the quantity (μg) of trypsin/Lys-C and beads (MagReSyn® Amine), % (w/v) SDS, % (v/v) acetonitrile, and time of digestion (h). ANN model predicted the optimal conditions for the digestion of 50 μg of HeLa extract, pointing to the use of 2.5% (w/v) SDS and 300 μg of beads for sample preparation and long-term digestion (16h) with 0.15 μg Lys-C and 2.5 μg trypsin (≈1:17 ratio). Based on the results of the ANN model, the manual protocol was automated in OT-2. The performance of the automatic protocol was evaluated with different sample types, including human plasma, Arabidopsis thaliana leaves, Escherichia coli cells, and mouse tissue cortex, showing great reproducibility and low sample-to-sample variability in all cases. In addition, we tested the performance of this method in the preparation of a challenging biological fluid such as rat bile, a proximal fluid that is rich in bile salts, bilirubin, cholesterol, and fatty acids, among other MS interferents. Compared to other protocols described in the literature for the extraction and digestion of bile proteins, the method described here allowed identify 385 unique proteins, thus contributing to improving the coverage of the bile proteome.
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Affiliation(s)
- Sergio Ciordia
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Fátima Milhano Santos
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - João M L Dias
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom; Early Cancer Institute, University of Cambridge, Cambridge, United Kingdom
| | - José Ramón Lamas
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Alberto Paradela
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Gloria Alvarez-Sola
- Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029, Madrid, Spain; IdiSNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Matías A Ávila
- Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029, Madrid, Spain; IdiSNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain.
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4
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Zhong Z, Sun MM, He M, Huang HP, Hu GY, Ma SQ, Zheng HZ, Li MY, Yao L, Cong DY, Wang HF. Proteomics and its application in the research of acupuncture: An updated review. Heliyon 2024; 10:e33233. [PMID: 39022010 PMCID: PMC11253069 DOI: 10.1016/j.heliyon.2024.e33233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/06/2023] [Accepted: 06/17/2024] [Indexed: 07/20/2024] Open
Abstract
As a complementary and alternative therapy, acupuncture is widely used in the prevention and treatment of various diseases. However, the understanding of the mechanism of acupuncture effects is still limited due to the lack of systematic biological validation. Notably, proteomics technologies in the field of acupuncture are rapidly evolving, and these advances are greatly contributing to the research of acupuncture. In this study, we review the progress of proteomics research in analyzing the molecular mechanisms of acupuncture for neurological disorders, pain, circulatory disorders, digestive disorders, and other diseases, with an in-depth discussion around acupoint prescription and acupuncture manipulation modalities. The study found that proteomics has great potential in understanding the mechanisms of acupuncture. This study will help explore the mechanisms of acupuncture from a proteomic perspective and provide information to support future clinical decisions.
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Affiliation(s)
- Zhen Zhong
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Meng-Meng Sun
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Min He
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Hai-Peng Huang
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Guan-Yu Hu
- The Third Affiliated Hospital of Southern Medical University, No.183, West of Zhongshan Avenue, Tianhe District, Guangzhou, 510630, Guangdong Province, China
| | - Shi-Qi Ma
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Hai-Zhu Zheng
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Meng-Yuan Li
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Lin Yao
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - De-Yu Cong
- Department of Tuina, Traditional Chinese Medicine Hospital of Jilin Province, 130000, Changchun, China
| | - Hong-Feng Wang
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
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5
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Kernohan KD, Boycott KM. The expanding diagnostic toolbox for rare genetic diseases. Nat Rev Genet 2024; 25:401-415. [PMID: 38238519 DOI: 10.1038/s41576-023-00683-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 05/23/2024]
Abstract
Genomic technologies, such as targeted, exome and short-read genome sequencing approaches, have revolutionized the care of patients with rare genetic diseases. However, more than half of patients remain without a diagnosis. Emerging approaches from research-based settings such as long-read genome sequencing and optical genome mapping hold promise for improving the identification of disease-causal genetic variants. In addition, new omic technologies that measure the transcriptome, epigenome, proteome or metabolome are showing great potential for variant interpretation. As genetic testing options rapidly expand, the clinical community needs to be mindful of their individual strengths and limitations, as well as remaining challenges, to select the appropriate diagnostic test, correctly interpret results and drive innovation to address insufficiencies. If used effectively - through truly integrative multi-omics approaches and data sharing - the resulting large quantities of data from these established and emerging technologies will greatly improve the interpretative power of genetic and genomic diagnostics for rare diseases.
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Affiliation(s)
- Kristin D Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
- Newborn Screening Ontario, CHEO, Ottawa, ON, Canada
| | - Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada.
- Department of Genetics, CHEO, Ottawa, ON, Canada.
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6
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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7
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Topitsch A, Halstenbach T, Rothweiler R, Fretwurst T, Nelson K, Schilling O. Mass Spectrometry-Based Proteomics of Poly(methylmethacrylate)-Embedded Bone. J Proteome Res 2024; 23:1810-1820. [PMID: 38634750 DOI: 10.1021/acs.jproteome.4c00046] [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] [Indexed: 04/19/2024]
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely employed technique in proteomics research for studying the proteome biology of various clinical samples. Hard tissues, such as bone and teeth, are routinely preserved using synthetic poly(methyl methacrylate) (PMMA) embedding resins that enable histological, immunohistochemical, and morphological examination. However, the suitability of PMMA-embedded hard tissues for large-scale proteomic analysis remained unexplored. This study is the first to report on the feasibility of PMMA-embedded bone samples for LC-MS/MS analysis. Conventional workflows yielded merely limited coverage of the bone proteome. Using advanced strategies of prefractionation by high-pH reversed-phase liquid chromatography in combination with isobaric tandem mass tag labeling resulted in proteome coverage exceeding 1000 protein identifications. The quantitative comparison with cryopreserved samples revealed that each sample preparation workflow had a distinct impact on the proteomic profile. However, workflow replicates exhibited a high reproducibility for PMMA-embedded samples. Our findings further demonstrate that decalcification prior to protein extraction, along with the analysis of solubilization fractions, is not preferred for PMMA-embedded bone. The biological applicability of the proposed workflow was demonstrated using samples of human PMMA-embedded alveolar bone and the iliac crest, which revealed anatomical site-specific proteomic profiles. Overall, these results establish a crucial foundation for large-scale proteomics studies contributing to our knowledge of bone biology.
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Affiliation(s)
- Annika Topitsch
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tim Halstenbach
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - René Rothweiler
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tobias Fretwurst
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Katja Nelson
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
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8
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Ha A, Khoo A, Ignatchenko V, Khan S, Waas M, Vesprini D, Liu SK, Nyalwidhe JO, Semmes OJ, Boutros PC, Kislinger T. Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine. J Proteome Res 2024; 23:1768-1778. [PMID: 38580319 PMCID: PMC11077481 DOI: 10.1021/acs.jproteome.4c00009] [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: 01/04/2024] [Revised: 03/02/2024] [Accepted: 03/06/2024] [Indexed: 04/07/2024]
Abstract
Biofluids contain molecules in circulation and from nearby organs that can be indicative of disease states. Characterizing the proteome of biofluids with DIA-MS is an emerging area of interest for biomarker discovery; yet, there is limited consensus on DIA-MS data analysis approaches for analyzing large numbers of biofluids. To evaluate various DIA-MS workflows, we collected urine from a clinically heterogeneous cohort of prostate cancer patients and acquired data in DDA and DIA scan modes. We then searched the DIA data against urine spectral libraries generated using common library generation approaches or a library-free method. We show that DIA-MS doubles the sample throughput compared to standard DDA-MS with minimal losses to peptide detection. We further demonstrate that using a sample-specific spectral library generated from individual urines maximizes peptide detection compared to a library-free approach, a pan-human library, or libraries generated from pooled, fractionated urines. Adding urine subproteomes, such as the urinary extracellular vesicular proteome, to the urine spectral library further improves the detection of prostate proteins in unfractionated urine. Altogether, we present an optimized DIA-MS workflow and provide several high-quality, comprehensive prostate cancer urine spectral libraries that can streamline future biomarker discovery studies of prostate cancer using DIA-MS.
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Affiliation(s)
- Annie Ha
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Amanda Khoo
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Vladimir Ignatchenko
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Shahbaz Khan
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Matthew Waas
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Danny Vesprini
- Department
of Radiation Oncology, University of Toronto, Toronto, Ontario M5T 1P5, Canada
- Odette
Cancer Research Program, Sunnybrook Research
Institute, Toronto, Ontario M4N 3M5, Canada
| | - Stanley K. Liu
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department
of Radiation Oncology, University of Toronto, Toronto, Ontario M5T 1P5, Canada
- Odette
Cancer Research Program, Sunnybrook Research
Institute, Toronto, Ontario M4N 3M5, Canada
| | - Julius O. Nyalwidhe
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23501, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23501, United States
| | - Oliver John Semmes
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23501, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23501, United States
| | - Paul C. Boutros
- Department
of Human Genetics, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Urology, University of California, Los
Angeles, Los Angeles, California 90095, United States
- Institute
for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Eli
and Edythe Broad Stem Cell Research Center, University of California, Los
Angeles, California 90095, United States
- Broad
Stem Cell Research Center, University of
California, Los Angeles, California 90095, United States
- Jonsson
Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90024, United States
- Department
of Human Genetics, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Thomas Kislinger
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
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9
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Yang J, Zhou Y, Wang T, Li N, Chao Y, Gao S, Zhang Q, Wu S, Zhao L, Dong X. A multi-omics study to monitor senescence-associated secretory phenotypes of Alzheimer's disease. Ann Clin Transl Neurol 2024; 11:1310-1324. [PMID: 38605603 DOI: 10.1002/acn3.52047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/04/2024] [Accepted: 03/10/2024] [Indexed: 04/13/2024] Open
Abstract
OBJECTIVE Alzheimer's disease (AD) is characterized by the progressive degeneration and damage of neurons in the brain. However, developing an accurate diagnostic assay using blood samples remains a challenge in clinic practice. The aim of this study was to explore senescence-associated secretory phenotypes (SASPs) in peripheral blood using mass spectrometry based multi-omics approach and to establish diagnostic assays for AD. METHODS This retrospective study included 88 participants, consisting of 29 AD patients and 59 cognitively normal (CN) individuals. Plasma and serum samples were examined using high-resolution mass spectrometry to identify proteomic and metabolomic profiles. Receiver operating characteristic (ROC) analysis was employed to screen biomarkers with diagnostic potential. K-nearest neighbors (KNN) algorithm was utilized to construct a multi-dimensional model for distinguishing AD from CN. RESULTS Proteomics analysis revealed upregulation of five plasma proteins in AD, including RNA helicase aquarius (AQR), zinc finger protein 587B (ZNF587B), C-reactive protein (CRP), fibronectin (FN1), and serum amyloid A-1 protein (SAA1), indicating their potential for AD classification. Interestingly, KNN-based three-dimensional model, comprising AQR, ZNF587B, and CRP, demonstrated its high accuracy in AD recognition, with evaluation possibilities of 0.941, 1.000, and 1.000 for the training, testing, and validation datasets, respectively. Besides, metabolomics analysis suggested elevated levels of serum phenylacetylglutamine (PAGIn) in AD. INTERPRETATION The multi-omics outcomes highlighted the significance of the SASPs, specifically AQR, ZNF587B, CRP, and PAGIn, in terms of their potential for diagnosing AD and suggested neuronal aging-associated pathophysiology.
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Affiliation(s)
- Jingzhi Yang
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
| | - Yinge Zhou
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Tianjiao Wang
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Na Li
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Yufan Chao
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Songyan Gao
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
| | - Qun Zhang
- Department of Internal Medicine, Shanghai Baoshan Elderly Nursing Hospital, Shanghai, 200435, China
| | - Shuo Wu
- Neurology Department, Shanghai Baoshan Luodian Hospital, Shanghai, 201908, China
| | - Liang Zhao
- Department of Pharmacy, Shanghai Baoshan Luodian Hospital, Shanghai, 201908, China
| | - Xin Dong
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- School of Medicine, Shanghai University, Shanghai, 200444, China
- Suzhou Innovation Center of Shanghai University, Suzhou, 215000, Jiangsu, China
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10
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Kimura Y, Nakai Y, Ino Y, Akiyama T, Moriyama K, Aiba T, Ohira T, Egashira K, Yamamoto Y, Takeda Y, Inaba Y, Ryo A, Saito T, Kumagai K, Hirano H. Changes in the astronaut serum proteome during prolonged spaceflight. Proteomics 2024; 24:e2300328. [PMID: 38185763 DOI: 10.1002/pmic.202300328] [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: 09/01/2023] [Revised: 09/01/2023] [Accepted: 12/20/2023] [Indexed: 01/09/2024]
Abstract
The molecular mechanisms associated with spaceflight-induced biological adaptations that may affect many healthy tissue functions remain poorly understood. In this study, we analyzed temporal changes in the serum proteome of six astronauts during prolonged spaceflight missions using quantitative comprehensive proteome analysis performed with the data-independent acquisition method of mass spectrometry (DIA-MS). All six astronauts participated in a spaceflight mission for approximately 6 months and showed a decreasing trend in T-scores at almost all sites where dual-energy X-ray absorptiometry scans were performed. DIA-MS successfully identified 624 nonredundant proteins in sera and further quantitative analysis for each sampling point provided information on serum protein profiles closely related to several time points before (pre-), during (in-), and after (post-) spaceflight. Changes in serum protein levels between spaceflight and on the ground suggest that abnormalities in bone metabolism are induced in astronauts during spaceflight. Furthermore, changes in the proteomic profile occurring during spaceflight suggest that serum levels of bone metabolism-related proteins, namely ALPL, COL1A1, SPP1, and POSTN, could serve as highly responsive indicators of bone metabolism status in spaceflight missions. This study will allow us to accelerate research to improve our understanding of the molecular mechanisms of biological adaptations associated with prolonged spaceflight.
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Affiliation(s)
- Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Yusuke Nakai
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Yoko Ino
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Tomoko Akiyama
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Kayano Moriyama
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Tatsuya Aiba
- Japan Aerospace Exploration Agency, Tsukuba, Japan
| | - Takashi Ohira
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
- Department of Physiology and Regenerative Medicine, Kindai University Faculty of Medicine, Osaka, Japan
| | - Kenji Egashira
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
- R&D Headquarters, LION Corporation, Tokyo, Japan
| | - Yu Yamamoto
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
- R&D Headquarters, LION Corporation, Tokyo, Japan
| | - Yuriko Takeda
- Department of Biostatistics, Yokohama City University School of Medicine, Yokohama, Japan
| | - Yutaka Inaba
- Department of Orthopaedic Surgery, Yokohama City University School of Medicine, Yokohama, Japan
| | - Akihide Ryo
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | | | - Ken Kumagai
- Department of Orthopaedic Surgery, Yokohama City University School of Medicine, Yokohama, Japan
| | - Hisashi Hirano
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
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11
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Duda HC, von Toerne C, Korbonits L, Didier A, Scholz AM, Märtlbauer E, Hauck SM, Deeg CA. Cathepsin S Is More Abundant in Serum of Mycobacterium avium subsp. paratuberculosis-Infected Dairy Cows. Metabolites 2024; 14:215. [PMID: 38668343 PMCID: PMC11051907 DOI: 10.3390/metabo14040215] [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: 03/09/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of bovine paratuberculosis, a chronic granulomatous enteritis leading to economic losses and posing a risk to human health due to its zoonotic potential. The pathogen cannot reliably be detected by standard methods, and immunological procedures during the infection are not well understood. Therefore, the aim of our study was to explore host-pathogen interactions in MAP-infected dairy cows and to improve diagnostic tests. Serum proteomics analysis using quantitative label-free LC-MS/MS revealed 60 differentially abundant proteins in MAP-infected dairy cows compared to healthy controls from the same infected herd and 90 differentially abundant proteins in comparison to another control group from an uninfected herd. Pathway enrichment analysis provided new insights into the immune response to MAP and susceptibility to the infection. Furthermore, we found a higher abundance of Cathepsin S (CTSS) in the serum of MAP-infected dairy cows, which is involved in multiple enriched pathways associated with the immune system. Confirmed with Western blotting, we identified CTSS as a potential biomarker for bovine paratuberculosis. This study enabled a better understanding of procedures in the host-pathogen response to MAP and improved detection of paratuberculosis-diseased cattle.
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Affiliation(s)
- Heidi C. Duda
- Chair of Physiology, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-82152 Martinsried, Germany
| | - Christine von Toerne
- Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health, D-85763 Neuherberg, Germany (S.M.H.)
| | - Lucia Korbonits
- Chair of Physiology, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-82152 Martinsried, Germany
| | - Andrea Didier
- Chair of Hygiene and Technology of Milk, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-85764 Oberschleißheim, Germany; (A.D.)
| | - Armin M. Scholz
- Livestock Center of the Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, D-85764 Oberschleißheim, Germany;
| | - Erwin Märtlbauer
- Chair of Hygiene and Technology of Milk, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-85764 Oberschleißheim, Germany; (A.D.)
| | - Stefanie M. Hauck
- Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health, D-85763 Neuherberg, Germany (S.M.H.)
| | - Cornelia A. Deeg
- Chair of Physiology, Department of Veterinary Sciences, Ludwig Maximilian University of Munich, D-82152 Martinsried, Germany
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12
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Gao R, Chen Y, Liu H, Ye M, Chu L, Wang T. CD109 identified in circulating proteomics mitigates postoperative recurrence in chronic rhinosinusitis with nasal polyps by suppressing TGF-β1-induced epithelial-mesenchymal transition. Int Immunopharmacol 2024; 130:111793. [PMID: 38442581 DOI: 10.1016/j.intimp.2024.111793] [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: 12/07/2023] [Revised: 02/17/2024] [Accepted: 02/29/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Chronic rhinosinusitis with nasal polyps (CRSwNP) is a common inflammatory disorder with a high rate of recurrence. This study aimed to explore biomarkers for identifying patients with recurrent CRSwNP (rCRSwNP). METHODS We recruited two independent cohorts. In the discovery cohort, rCRSwNP patients and non-recurrent CRSwNP (non-rCRSwNP) patients were recruited, and the serum proteomic profile was characterized. The top 5 upregulated and downregulated proteins were confirmed in the validation cohort by ELISA, WB, and qRT-PCR, and their predictive values for postoperative recurrence were assessed. In vitro, human nasal epithelial cells (HNEpCs) were employed to assess the ability of candidate proteins to induce epithelial-mesenchymal transition (EMT). RESULTS Serum proteomics identified 53 different proteins, including 30 increased and 23 decreased, between the rCRSwNP and non-rCRSwNP groups. ELISA results revealed that serum levels of CD163 and TGF-β1 were elevated, CD109 and PRDX2 were decreased in the rCRSwNP group compared to the non-rCRSwNP group, and serum CD163, TGF-β1, and CD109 levels were proved to be associated with the risk of postoperative recurrence. In addition, qRT-PCR and WB revealed that tissue CD163, TGF-β1, and CD109 expressions in rCRSwNP patients were enhanced compared to those non-rCRSwNP patients. Kaplan-Meier analysis showed that increased CD163 and TGF-β1 expression and decreased CD109 expression are associated with the risk of recurrence in CRSwNP patients. Receiver operating characteristic curves showed that TGF-β1 and CD109 had superior diagnostic performances for rCRSwNP. In vitro experiments showed that TGF-β1 promoted EMT in HNEpCs, and overexpression of CD109 reversed this effect. Functional recovery experiments confirmed that CD109 could attenuate EMT in HNEpCs by inhibiting the TGF-β1/Smad signaling pathway, attenuating EMT in epithelial cells. CONCLUSION Our data suggested that TGF-β1 and CD109 might serve as promising predictors of rCRSwNP. The TGF-β1/Smad pathway was implicated in fostering EMT in epithelial cells, particularly those exhibiting low expression of CD109. Consequently, the absence of CD109 expression in epithelial cells could be a potential mechanism underlying rCRSwNP.
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Affiliation(s)
- Ru Gao
- Department of Otolaryngology-Head and Neck Surgery, the Third Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Yu Chen
- Department of Otolaryngology-Head and Neck Surgery, the Third Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Huihong Liu
- Department of Otolaryngology-Head and Neck Surgery, the Third Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Maoyu Ye
- Department of Otolaryngology-Head and Neck Surgery, the Third Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Ling Chu
- Department of Pathology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Tiansheng Wang
- Department of Otolaryngology-Head and Neck Surgery, the Third Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.
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13
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Smith H, Giulivi C. Starch treatment improves the salivary proteome for subject identification purposes. Forensic Sci Med Pathol 2024; 20:117-128. [PMID: 37084127 PMCID: PMC10944386 DOI: 10.1007/s12024-023-00629-y] [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] [Accepted: 04/04/2023] [Indexed: 04/22/2023]
Abstract
Identification of subjects, including perpetrators, is one of the most crucial goals of forensic science. Saliva is among the most common biological fluids found at crime scenes, containing identifiable components. DNA has been the most prominent identifier to date, but its analysis can be complex due to low DNA yields and issues preserving its integrity at the crime scene. Proteins are emerging as viable candidates for subject identification. Previous work has shown that the salivary proteome of the least-abundant proteins may be helpful for subject identification, but more optimized techniques are needed. Among them is removing the most abundant proteins, such as salivary α-amylase. Starch treatment of saliva samples elicited the removal of this enzyme and that of glycosylated, low-molecular-weight proteins, proteases, and immunoglobulins, resulting in a saliva proteome profile enriched with a subset of proteins, allowing a more reliable and nuanced subject identification.
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Affiliation(s)
- Hannah Smith
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Cecilia Giulivi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA.
- MIND Institute, University of California at Davis Medical Center, Sacramento, CA, USA.
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14
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Zhang D, Jia N, Hu Z, Keqing Z, Chenxi S, Chunying S, Chen C, Chen W, Hu Y, Ruan Z. Bioinformatics identification of potential biomarkers and therapeutic targets for ischemic stroke and vascular dementia. Exp Gerontol 2024; 187:112374. [PMID: 38320734 DOI: 10.1016/j.exger.2024.112374] [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: 11/26/2023] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Ischemic stroke and vascular dementia, as common cerebrovascular diseases, with the former causing irreversible neurological damage and the latter causing cognitive and memory impairment, are closely related and have long received widespread attention. Currently, the potential causative genes of these two diseases have yet to be investigated, and effective early diagnostic tools for the diseases have not yet emerged. In this study, we screened new potential biomarkers and analyzed new therapeutic targets for both diseases from the perspective of immune infiltration. Two gene expression profiles on ischemic stroke and vascular dementia were obtained from the NCBI GEO database, and key genes were identified by LASSO regression and SVM-RFE algorithms, and key genes were analyzed by GO and KEGG enrichment. The CIBERSORT algorithm was applied to the gene expression profile species of the two diseases to quantify the 24 subpopulations of immune cells. Moreover, logistic regression modeling analysis was applied to illustrate the stability of the key genes in the diagnosis. Finally, the key genes were validated using RT-PCR assay. A total of 105 intersecting DEGs genes were obtained in the 2 sets of GEO datasets, and bioinformatics functional analysis of the intersecting DEGs genes showed that GO was mainly involved in the purine ribonucleoside triphosphate metabolic process,respiratory chain complex,DNA-binding transcription factor binding and active transmembrane transporter activity. KEGG is mainly involved in the Oxidative phosphorylation, cAMP signaling pathway. The LASSO regression algorithm and SVM-RFE algorithm finally obtained three genes, GAS2L1, ARHGEF40 and PFKFB3, and the logistic regression prediction model determined that the three genes, GAS2L1 (AUC: 0.882), ARHGEF40 (AUC: 0.867) and PFKFB3 (AUC: 0.869), had good diagnostic performance. Meanwhile, the two disease core genes and immune infiltration were closely related, GAS2L1 and PFKFB3 had the highest positive correlation with macrophage M1 (p < 0.001) and the highest negative correlation with mast cell activation (p = 0.0017); ARHGEF40 had the highest positive correlation with macrophage M1 and B cells naive (p < 0.001), the highest negative correlation with B cell memory highest correlation (p = 0.0047). RT-PCR results showed that the relative mRNA expression levels of GAS2L1, ARHGEF40, and PFKFB3 were significantly elevated in the populations of both disease groups (p < 0.05). Immune infiltration-based models can be used to predict the diagnosis of patients with ischemic stroke and vascular dementia and provide a new perspective on the early diagnosis and treatment of both diseases.
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Affiliation(s)
- Ding Zhang
- Guangxi university of chinese medicine Nanning, China
| | - Ni Jia
- Shaanxi University of Traditional Chinese Medicine Xianyang, China
| | - Zhihan Hu
- Shanghai University of Traditional Chinese Medicine Shanghai, China
| | - Zhou Keqing
- Guangxi university of chinese medicine Nanning, China
| | - Song Chenxi
- Guangxi university of chinese medicine Nanning, China
| | - Sun Chunying
- Guangxi university of chinese medicine Nanning, China
| | - Canrong Chen
- Guangxi university of chinese medicine Nanning, China
| | - Wei Chen
- Guangxi university of chinese medicine First Affiliated Hospital Nanning, China
| | - Yueqiang Hu
- Guangxi university of chinese medicine First Affiliated Hospital Nanning, China.
| | - Ziyun Ruan
- Guangxi university of chinese medicine Nanning, China
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15
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Iacobescu M, Pop C, Uifălean A, Mogoşan C, Cenariu D, Zdrenghea M, Tănase A, Bergthorsson JT, Greiff V, Cenariu M, Iuga CA, Tomuleasa C, Tătaru D. Unlocking protein-based biomarker potential for graft-versus-host disease following allogenic hematopoietic stem cell transplants. Front Immunol 2024; 15:1327035. [PMID: 38433830 PMCID: PMC10904603 DOI: 10.3389/fimmu.2024.1327035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/01/2024] [Indexed: 03/05/2024] Open
Abstract
Despite the numerous advantages of allogeneic hematopoietic stem cell transplants (allo-HSCT), there exists a notable association with risks, particularly during the preconditioning period and predominantly post-intervention, exemplified by the occurrence of graft-versus-host disease (GVHD). Risk stratification prior to symptom manifestation, along with precise diagnosis and prognosis, relies heavily on clinical features. A critical imperative is the development of tools capable of early identification and effective management of patients undergoing allo-HSCT. A promising avenue in this pursuit is the utilization of proteomics-based biomarkers obtained from non-invasive biospecimens. This review comprehensively outlines the application of proteomics and proteomics-based biomarkers in GVHD patients. It delves into both single protein markers and protein panels, offering insights into their relevance in acute and chronic GVHD. Furthermore, the review provides a detailed examination of the site-specific involvement of GVHD. In summary, this article explores the potential of proteomics as a tool for timely and accurate intervention in the context of GVHD following allo-HSCT.
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Affiliation(s)
- Maria Iacobescu
- Department of Proteomics and Metabolomics, MEDFUTURE Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristina Pop
- Department of Pharmacology, Physiology and Pathophysiology, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alina Uifălean
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristina Mogoşan
- Department of Pharmacology, Physiology and Pathophysiology, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Diana Cenariu
- Department of Translational Medicine, MEDFUTURE Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihnea Zdrenghea
- Department of Hematology, Faculty of Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alina Tănase
- Department of Stem Cell Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Jon Thor Bergthorsson
- Department of Laboratory Hematology, Stem Cell Research Unit, Biomedical Center, School of Health Sciences, University Iceland, Reykjavik, Iceland
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Mihai Cenariu
- Department of Animal Reproduction, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Cristina Adela Iuga
- Department of Proteomics and Metabolomics, MEDFUTURE Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ciprian Tomuleasa
- Department of Translational Medicine, MEDFUTURE Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Hematology, Faculty of Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Dan Tătaru
- Department of Internal Medicine, Faculty of Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
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Shi Y, Chen J, Cai L, Zhang X, Chen Z, Yang J, Jiang Y, Lu Y. Uncovering the Hidden World of Aqueous Humor Proteins for Discovery of Biomarkers for Marfan Syndrome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303161. [PMID: 38088571 PMCID: PMC10853735 DOI: 10.1002/advs.202303161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/23/2023] [Indexed: 12/19/2023]
Abstract
Ectopia lentis is a hallmark of Marfan syndrome (MFS), a genetic connective tissue disorder affecting 1/5000 to 1/10 000 individuals worldwide. Early detection in ophthalmology clinics and timely intervention of cardiovascular complications can be lifesaving. In this study, a modified proteomics workflow with liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based data-independent acquisition (DIA) and field asymmetric ion mobility spectrometry (FAIMS) to profile the proteomes of aqueous humor (AH) and lens tissue from MFS children with ectopia lentis is utilized. Over 2300 and 2938 comparable proteins are identified in AH and the lens capsule, respectively. Functional enrichment analyses uncovered dysregulation of complement and coagulation-related pathways, collagen binding, and cell adhesion in MFS. Through weighted correlation network analysis (WGCNA) and machine learning, distinct modules associated with clinical traits are constructed and a unique biomarker panel (Q14376, Q99972, P02760, Q07507; gene names: GALE, MYOC, AMBP, DPT) is defined. These biomarkers are further validated using advanced parallel reaction monitoring (PRM) in an independent patient cohort. The results provide novel insights into the proteome characterization of ectopia lentis and offer a promising approach for developing a valuable biomarker panel to aid in the early diagnosis of Marfan syndrome via AH proteome.
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Affiliation(s)
- Yumeng Shi
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Jiahui Chen
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Lei Cai
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Xueling Zhang
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Zexu Chen
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Jin Yang
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Yongxiang Jiang
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Yi Lu
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
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17
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Cartas-Cejudo P, Cortés A, Lachén-Montes M, Anaya-Cubero E, Peral E, Ausín K, Díaz-Peña R, Fernández-Irigoyen J, Santamaría E. Mapping the human brain proteome: opportunities, challenges, and clinical potential. Expert Rev Proteomics 2024; 21:55-63. [PMID: 38299555 DOI: 10.1080/14789450.2024.2313073] [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: 09/25/2023] [Accepted: 01/24/2024] [Indexed: 02/02/2024]
Abstract
INTRODUCTION Due to the segmented functions and complexity of the human brain, the characterization of molecular profiles within specific areas such as brain structures and biofluids is essential to unveil the molecular basis for structure specialization as well as the molecular imbalance associated with neurodegenerative and psychiatric diseases. AREAS COVERED Much of our knowledge about brain functionality derives from neurophysiological, anatomical, and transcriptomic approaches. More recently, laser capture and imaging proteomics, technological and computational developments in LC-MS/MS, as well as antibody/aptamer-based platforms have allowed the generation of novel cellular, spatial, and posttranslational dimensions as well as innovative facets in biomarker validation and druggable target identification. EXPERT OPINION Proteomics is a powerful toolbox to functionally characterize, quantify, and localize the extensive protein catalog of the human brain across physiological and pathological states. Brain function depends on multi-dimensional protein homeostasis, and its elucidation will help us to characterize biological pathways that are essential to properly maintain cognitive functions. In addition, comprehensive human brain pathological proteomes may be the basis in computational drug-repositioning methods as a strategy for unveiling potential new therapies in neurodegenerative and psychiatric disorders.
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Affiliation(s)
- Paz Cartas-Cejudo
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Adriana Cortés
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Elena Anaya-Cubero
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Erika Peral
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Karina Ausín
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Ramón Díaz-Peña
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
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18
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Repetto O, Vettori R, Steffan A, Cannizzaro R, De Re V. Circulating Proteins as Diagnostic Markers in Gastric Cancer. Int J Mol Sci 2023; 24:16931. [PMID: 38069253 PMCID: PMC10706891 DOI: 10.3390/ijms242316931] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Gastric cancer (GC) is a highly malignant disease affecting humans worldwide and has a poor prognosis. Most GC cases are detected at advanced stages due to the cancer lacking early detectable symptoms. Therefore, there is great interest in improving early diagnosis by implementing targeted prevention strategies. Markers are necessary for early detection and to guide clinicians to the best personalized treatment. The current semi-invasive endoscopic methods to detect GC are invasive, costly, and time-consuming. Recent advances in proteomics technologies have enabled the screening of many samples and the detection of novel biomarkers and disease-related signature signaling networks. These biomarkers include circulating proteins from different fluids (e.g., plasma, serum, urine, and saliva) and extracellular vesicles. We review relevant published studies on circulating protein biomarkers in GC and detail their application as potential biomarkers for GC diagnosis. Identifying highly sensitive and highly specific diagnostic markers for GC may improve patient survival rates and contribute to advancing precision/personalized medicine.
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Affiliation(s)
- Ombretta Repetto
- Facility of Bio-Proteomics, Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy
| | - Roberto Vettori
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy; (R.V.); (A.S.)
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy; (R.V.); (A.S.)
| | - Renato Cannizzaro
- Oncological Gastroenterology, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy;
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy
| | - Valli De Re
- Facility of Bio-Proteomics, Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy
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19
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Rogers ML, Schultz DW, Karnaros V, Shepheard SR. Urinary biomarkers for amyotrophic lateral sclerosis: candidates, opportunities and considerations. Brain Commun 2023; 5:fcad287. [PMID: 37946793 PMCID: PMC10631861 DOI: 10.1093/braincomms/fcad287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/23/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
Amyotrophic lateral sclerosis is a relentless neurodegenerative disease that is mostly fatal within 3-5 years and is diagnosed on evidence of progressive upper and lower motor neuron degeneration. Around 15% of those with amyotrophic lateral sclerosis also have frontotemporal degeneration, and gene mutations account for ∼10%. Amyotrophic lateral sclerosis is a variable heterogeneous disease, and it is becoming increasingly clear that numerous different disease processes culminate in the final degeneration of motor neurons. There is a profound need to clearly articulate and measure pathological process that occurs. Such information is needed to tailor treatments to individuals with amyotrophic lateral sclerosis according to an individual's pathological fingerprint. For new candidate therapies, there is also a need for methods to select patients according to expected treatment outcomes and measure the success, or not, of treatments. Biomarkers are essential tools to fulfil these needs, and urine is a rich source for candidate biofluid biomarkers. This review will describe promising candidate urinary biomarkers of amyotrophic lateral sclerosis and other possible urinary candidates in future areas of investigation as well as the limitations of urinary biomarkers.
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Affiliation(s)
- Mary-Louise Rogers
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide 5042, South Australia, Australia
| | - David W Schultz
- Neurology Department and MND Clinic, Flinders Medical Centre, Adelaide 5042, South Australia, Australia
| | - Vassilios Karnaros
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide 5042, South Australia, Australia
| | - Stephanie R Shepheard
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide 5042, South Australia, Australia
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20
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Diaz PM, Leehans A, Ravishankar P, Daily A. Multiomic Approaches for Cancer Biomarker Discovery in Liquid Biopsies: Advances and Challenges. Biomark Insights 2023; 18:11772719231204508. [PMID: 37846373 PMCID: PMC10576933 DOI: 10.1177/11772719231204508] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023] Open
Abstract
Cancer is a complex and heterogeneous disease that poses a significant threat to global health. Early diagnosis and treatment are critical for improving patient outcomes, and the use of liquid biopsies has emerged as a promising approach for cancer detection and monitoring. Traditionally, cancer diagnosis has relied on invasive tissue biopsies, the collection of which can prove challenging for patients and the results of which may not always provide accurate results due to tumor heterogeneity. Liquid biopsies have gained increasing attention as they provide a non-invasive and accessible source of cancer biomarkers, which can be used to diagnose cancer, monitor treatment response, and detect relapse. The integration of -omics technologies, such as proteomics, genomics, and metabolomics, has further enhanced the capabilities of liquid biopsies by introducing precision oncology and enabling the tailoring of treatment for individual patients based on their unique tumor biology. In this review, we will discuss the challenges and advances in the field of cancer liquid biopsies and the integration of -omics technologies for different types of liquid biopsies, including blood, tear, urine, sweat, saliva, and cerebrospinal fluid.
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Affiliation(s)
- Paola Monterroso Diaz
- Namida Lab Inc., Fayetteville, AR, USA
- University of Arkansas, Department of Biomedical Engineering, Fayetteville, AR, USA
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21
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Kussmann M. Mass spectrometry as a lens into molecular human nutrition and health. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2023; 29:370-379. [PMID: 37587732 DOI: 10.1177/14690667231193555] [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: 08/18/2023]
Abstract
Mass spectrometry (MS) has developed over the last decades into the most informative and versatile analytical technology in molecular and structural biology (). The platform enables discovery, identification, and characterisation of non-volatile biomolecules, such as proteins, peptides, DNA, RNA, nutrients, metabolites, and lipids at both speed and scale and can elucidate their interactions and effects. The versatility, robustness, and throughput have rendered MS a major research and development platform in molecular human health and biomedical science. More recently, MS has also been established as the central tool for 'Molecular Nutrition', enabling comprehensive and rapid identification and characterisation of macro- and micronutrients, bioactives, and other food compounds. 'Molecular Nutrition' thereby helps understand bioaccessibility, bioavailability, and bioefficacy of macro- and micronutrients and related health effects. Hence, MS provides a lens through which the fate of nutrients can be monitored along digestion via absorption to metabolism. This in turn provides the bioanalytical foundation for 'Personalised Nutrition' or 'Precision Nutrition' in which design and development of diets and nutritional products is tailored towards consumer and patient groups sharing similar genetic and environmental predisposition, health/disease conditions and lifestyles, and/or objectives of performance and wellbeing. The next level of integrated nutrition science is now being built as 'Systems Nutrition' where public and personal health data are correlated with life condition and lifestyle factors, to establish directional relationships between nutrition, lifestyle, environment, and health, eventually translating into science-based public and personal heath recommendations and actions. This account provides a condensed summary of the contributions of MS to a precise, quantitative, and comprehensive nutrition and health science and sketches an outlook on its future role in this fascinating and relevant field.
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Affiliation(s)
- Martin Kussmann
- Abteilung Wissenschaft, Kompetenzzentrum für Ernährung (KErn), Germany
- Kussmann Biotech GmbH, Germany
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22
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Schumann G, Andreassen OA, Banaschewski T, Calhoun VD, Clinton N, Desrivieres S, Brandlistuen RE, Feng J, Hese S, Hitchen E, Hoffmann P, Jia T, Jirsa V, Marquand AF, Nees F, Nöthen MM, Novarino G, Polemiti E, Ralser M, Rapp M, Schepanski K, Schikowski T, Slater M, Sommer P, Stahl BC, Thompson PM, Twardziok S, van der Meer D, Walter H, Westlye L. Addressing Global Environmental Challenges to Mental Health Using Population Neuroscience: A Review. JAMA Psychiatry 2023; 80:1066-1074. [PMID: 37610741 DOI: 10.1001/jamapsychiatry.2023.2996] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Importance Climate change, pollution, urbanization, socioeconomic inequality, and psychosocial effects of the COVID-19 pandemic have caused massive changes in environmental conditions that affect brain health during the life span, both on a population level as well as on the level of the individual. How these environmental factors influence the brain, behavior, and mental illness is not well known. Observations A research strategy enabling population neuroscience to contribute to identify brain mechanisms underlying environment-related mental illness by leveraging innovative enrichment tools for data federation, geospatial observation, climate and pollution measures, digital health, and novel data integration techniques is described. This strategy can inform innovative treatments that target causal cognitive and molecular mechanisms of mental illness related to the environment. An example is presented of the environMENTAL Project that is leveraging federated cohort data of over 1.5 million European citizens and patients enriched with deep phenotyping data from large-scale behavioral neuroimaging cohorts to identify brain mechanisms related to environmental adversity underlying symptoms of depression, anxiety, stress, and substance misuse. Conclusions and Relevance This research will lead to the development of objective biomarkers and evidence-based interventions that will significantly improve outcomes of environment-related mental illness.
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Affiliation(s)
- Gunter Schumann
- Centre for Population Neuroscience and Stratified Medicine (PONS), Department of Psychiatry and Clinical Neuroscience, Charité Universitätsmedizin Berlin, Berlin, Germany
- Centre for Population Neuroscience and Precision Medicine (PONS), Institute for Science and Technology of Brain-inspired Intelligence (ISTBI), Fudan University, Shanghai, China
| | - Ole A Andreassen
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tobias Banaschewski
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Vince D Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State, Georgia Tech, Emory, Atlanta, Georgia
| | | | - Sylvane Desrivieres
- Institute of Psychiatry, Psychology & Neuroscience, SGDP Centre, King's College London, London, United Kingdom
| | | | - Jianfeng Feng
- Institute for Science and Technology of Brain-inspired Intelligence (ISTBI), Fudan University, Shanghai, China
| | - Soeren Hese
- Institute of Geography, Friedrich Schiller University Jena, Jena, Germany
| | - Esther Hitchen
- Centre for Population Neuroscience and Stratified Medicine (PONS), Department of Psychiatry and Clinical Neuroscience, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University Hospital of Bonn, Bonn, Germany
| | - Tianye Jia
- Centre for Population Neuroscience and Precision Medicine (PONS), Institute for Science and Technology of Brain-inspired Intelligence (ISTBI), Fudan University, Shanghai, China
| | - Viktor Jirsa
- Institut National de la Santé et de la Recherche Médicale (Inserm), Institut de Neurosciences des Systèmes (INS) UMR1106, Aix Marseille Université, Marseille, France
| | | | - Frauke Nees
- Institute of Medical Psychology and Medical Sociology, University Medical Center Schleswig-Holstein, Kiel University, Kiel, Germany
- Institute of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University Hospital of Bonn, Bonn, Germany
| | - Gaia Novarino
- Institute of Science and Technology, Klosterneuburg, Austria
| | - Elli Polemiti
- Centre for Population Neuroscience and Stratified Medicine (PONS), Department of Psychiatry and Clinical Neuroscience, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Ralser
- Institute of Biochemistry Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Rapp
- Department for Social and Preventive Medicine, University of Potsdam, Potsdam, Germany
| | | | - Tamara Schikowski
- NAKO, Leibniz Institute for Environmental Medicine, Duesseldorf, Germany
| | - Mel Slater
- Campus de Mundet, ICREA-University of Barcelona, Barcelona, Spain
- Department of Computer Science, University College London, London, United Kingdom
| | | | - Bernd Carsten Stahl
- School of Computer Science, University of Nottingham, Nottingham, United Kingdom
| | - Paul M Thompson
- Imaging Genetics Center, Mark & Mary Stevens Institute for Neuroimaging & Informatics, Los Angeles, California
| | - Sven Twardziok
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Dennis van der Meer
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Henrik Walter
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Psychiatry and Psychotherapy CCM, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lars Westlye
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
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23
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Waury K, de Wit R, Verberk IMW, Teunissen CE, Abeln S. Deciphering Protein Secretion from the Brain to Cerebrospinal Fluid for Biomarker Discovery. J Proteome Res 2023; 22:3068-3080. [PMID: 37606934 PMCID: PMC10476268 DOI: 10.1021/acs.jproteome.3c00366] [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: 06/19/2023] [Indexed: 08/23/2023]
Abstract
Cerebrospinal fluid (CSF) is an essential matrix for the discovery of neurological disease biomarkers. However, the high dynamic range of protein concentrations in CSF hinders the detection of the least abundant protein biomarkers by untargeted mass spectrometry. It is thus beneficial to gain a deeper understanding of the secretion processes within the brain. Here, we aim to explore if and how the secretion of brain proteins to the CSF can be predicted. By combining a curated CSF proteome and the brain elevated proteome of the Human Protein Atlas, brain proteins were classified as CSF or non-CSF secreted. A machine learning model was trained on a range of sequence-based features to differentiate between CSF and non-CSF groups and effectively predict the brain origin of proteins. The classification model achieves an area under the curve of 0.89 if using high confidence CSF proteins. The most important prediction features include the subcellular localization, signal peptides, and transmembrane regions. The classifier generalized well to the larger brain detected proteome and is able to correctly predict novel CSF proteins identified by affinity proteomics. In addition to elucidating the underlying mechanisms of protein secretion, the trained classification model can support biomarker candidate selection.
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Affiliation(s)
- Katharina Waury
- Department
of Computer Science, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Renske de Wit
- Department
of Computer Science, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Inge M. W. Verberk
- Neurochemistry
Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - Charlotte E. Teunissen
- Neurochemistry
Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - Sanne Abeln
- Department
of Computer Science, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, The Netherlands
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24
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Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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25
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Liu N, Wang J, Wang X, Zhang M. Analysis of urine differential proteins in patients with allergic rhinitis. Heliyon 2023; 9:e17323. [PMID: 37426793 PMCID: PMC10329111 DOI: 10.1016/j.heliyon.2023.e17323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/04/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023] Open
Abstract
Background Allergic rhinitis (AR) is one of the most common clinical allergic diseases. Early diagnosis and medical intervention will benefit patients with allergic rhinitis. In this study, we focused on changes in urine proteomics in AR patients to investigate their potential clinical utility in AR diagnosis and evaluation. Material and methods TMT-labeled mass spectrometry-based proteomics was carried out to identify differentially expressed proteins (DEPs) in urine between allergic rhinitis patients and normal control groups. The molecular biological role of DEPs was investigated by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and protein-protein interaction (PPI) network analysis. Results Enrichment analysis showed that the differentially expressed proteins were mainly related to cell-cell adhesion, complement and coagulation cascades, peptidase activity regulation, MAP kinase activity, etc. Compared with the NC group, HLA-DRB1, WFDC12, and DEFA4, among the top ten up-regulated proteins in the urine of the AR group, were related to the biological process of the humoral immune response. Among the top 10 down-regulated proteins, GUSB, SQSTM1, and KIT are related to protein domain-specific binding in terms of molecular function. Conclusions We found differential protein changes between AR patients and normal subjects may be related to the pathophysiological changes of AR, which provides the possibility for further exploration of urinary proteomics biomarkers in the future.
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Affiliation(s)
- Na Liu
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Peking University Ninth School of Clinical Medicine, Beijing, China
- Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China
| | - Jitu Wang
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Peking University Ninth School of Clinical Medicine, Beijing, China
- Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China
| | - Xueyan Wang
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Man Zhang
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Peking University Ninth School of Clinical Medicine, Beijing, China
- Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China
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26
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Bader JM, Albrecht V, Mann M. MS-based proteomics of body fluids: The end of the beginning. Mol Cell Proteomics 2023:100577. [PMID: 37209816 PMCID: PMC10388585 DOI: 10.1016/j.mcpro.2023.100577] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023] Open
Abstract
Accurate biomarkers are a crucial and necessary precondition for precision medicine, yet existing ones are often unspecific and new ones have been very slow to enter the clinic. Mass spectrometry (MS)-based proteomics excels by its untargeted nature, specificity of identification and quantification making it an ideal technology for biomarker discovery and routine measurement. It has unique attributes compared to affinity binder technologies, such as OLINK Proximity Extension Assay and SOMAscan. In a previous review we described technological and conceptual limitations that had held back success (Geyer et al., 2017). We proposed a 'rectangular strategy' to better separate true biomarkers by minimizing cohort-specific effects. Today, this has converged with advances in MS-based proteomics technology, such as increased sample throughput, depth of identification and quantification. As a result, biomarker discovery studies have become more successful, producing biomarker candidates that withstand independent verification and, in some cases, already outperform state-of-the-art clinical assays. We summarize developments over the last years, including the benefits of large and independent cohorts, which are necessary for clinical acceptance. They are also required for machine learning or deep learning. Shorter gradients, new scan modes and multiplexing are about to drastically increase throughput, cross-study integration, and quantification, including proxies for absolute levels. We have found that multi-protein panels are inherently more robust than current single analyte tests and better capture the complexity of human phenotypes. Routine MS measurement in the clinic is fast becoming a viable option. The full set of proteins in a body fluid (global proteome) is the most important reference and the best process control. Additionally, it increasingly has all the information that could be obtained from targeted analysis although the latter may be the most straightforward way to enter into regular use. Many challenges remain, not least of a regulatory and ethical nature, but the outlook for MS-based clinical applications has never been brighter.
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Affiliation(s)
- Jakob M Bader
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Vincent Albrecht
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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27
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Safari F, Kehelpannala C, Safarchi A, Batarseh AM, Vafaee F. Biomarker Reproducibility Challenge: A Review of Non-Nucleotide Biomarker Discovery Protocols from Body Fluids in Breast Cancer Diagnosis. Cancers (Basel) 2023; 15:2780. [PMID: 37345117 DOI: 10.3390/cancers15102780] [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: 02/24/2023] [Revised: 05/02/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023] Open
Abstract
Breast cancer has now become the most commonly diagnosed cancer, accounting for one in eight cancer diagnoses worldwide. Non-invasive diagnostic biomarkers and associated tests are superlative candidates to complement or improve current approaches for screening, early diagnosis, or prognosis of breast cancer. Biomarkers detected from body fluids such as blood (serum/plasma), urine, saliva, nipple aspiration fluid, and tears can detect breast cancer at its early stages in a minimally invasive way. The advancements in high-throughput molecular profiling (omics) technologies have opened an unprecedented opportunity for unbiased biomarker detection. However, the irreproducibility of biomarkers and discrepancies of reported markers have remained a major roadblock to clinical implementation, demanding the investigation of contributing factors and the development of standardised biomarker discovery pipelines. A typical biomarker discovery workflow includes pre-analytical, analytical, and post-analytical phases, from sample collection to model development. Variations introduced during these steps impact the data quality and the reproducibility of the findings. Here, we present a comprehensive review of methodological variations in biomarker discovery studies in breast cancer, with a focus on non-nucleotide biomarkers (i.e., proteins, lipids, and metabolites), highlighting the pre-analytical to post-analytical variables, which may affect the accurate identification of biomarkers from body fluids.
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Affiliation(s)
- Fatemeh Safari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
| | - Cheka Kehelpannala
- BCAL Diagnostics Ltd., Suite 506, 50 Clarence St, Sydney, NSW 2000, Australia
- BCAL Dx, The University of Sydney, Sydney Knowledge Hub, Merewether Building, Sydney, NSW 2006, Australia
| | - Azadeh Safarchi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- Microbiomes for One Systems Health, Health and Biosecurity, CSIRO, Westmead, NSW 2145, Australia
| | - Amani M Batarseh
- BCAL Diagnostics Ltd., Suite 506, 50 Clarence St, Sydney, NSW 2000, Australia
- BCAL Dx, The University of Sydney, Sydney Knowledge Hub, Merewether Building, Sydney, NSW 2006, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- UNSW Data Science Hub (uDASH), University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- OmniOmics.ai Pty Ltd., Sydney, NSW 2035, Australia
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28
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Zhang Q, Song J, Cao L, Sun M, Xu T, Yang S, Li S, Wang H, Fu X. RNF113A targeted by miR-197 promotes proliferation and inhibits autophagy via CXCR4/CXCL12/AKT/ERK/Beclin1 axis in cervical cancer. Exp Cell Res 2023; 428:113632. [PMID: 37164050 DOI: 10.1016/j.yexcr.2023.113632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 05/03/2023] [Accepted: 05/07/2023] [Indexed: 05/12/2023]
Abstract
Ring Finger Protein 113 (RNF113A), an ubiquitin E3 ligase, is genetically associated with many biological processes, including proliferation, differentiation, cell death, and neurogenesis. Recently, RNF113A has been found to be an abnormal expression in many diseases, such as X-linked trichothiodystrophy syndrome and esophageal cancer. Here, we explore the potential mechanism of RNF113A in the progression of cervical cancer (CC). In this study, we evaluated the expression level and biological function of RNF113A in CC both in vitro and in vivo by bioinformatic prediction, DIA proteomic analysis, compensation experiment, Co-IP, dual-luciferase reporter assay and nude mouse xenograft to identify the RNF113A-associated autophagy pathways involved with tumorigenesis. Consistent with the prediction from biological information analysis, we found that RNF113A was highly expressed in human CC tissues and cells. In addition, this study illustrated that the high expression of RNF113A dramatically promoted proliferation and suppressed autophagy both in vitro and in vivo. In contrast, low expression of RNF113A enhanced autophagy activities and inhibited tumor growth in CC. We also found that miRNA-197, the level of which (negative correlation with RNF113A) declined in human CC, directly restrained the expression of RNF113A. Mechanistically, proteomic and mechanistic assays uncovered that RNF113A confirmed as the direct downstream target of miR-197, promoted proliferation and restrained autophagy in CC not through direct ubiquitination degradation of autophagy marker Beclin1 but via CXCR4/CXCL12/AKT/ERK/Beclin1 signal transduction axis. In summary, we found a new miR-197/RNF113 A/CXCR4/CXCL12/AKT/ERK/Beclin1 regulation pathway that plays an important part in the survival and progression of CC.
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Affiliation(s)
- Qingwei Zhang
- Department of Obstetrics and Gynaecology, Luohe Central Hospital, Luohe, 462000, Henan, China; Henan Key Laboratory of Fertility Protection and Aristogenesis, Luohe, 462000, China
| | - Jiayu Song
- Department of Pharmacology, Luohe Medical College, Luohe, 462000, Henan, China; School of Pharmaceutical Science, Shanxi Medical University, Taiyuan, 030001, China.
| | - Liejia Cao
- Department of Obstetrics and Gynaecology, Luohe Central Hospital, Luohe, 462000, Henan, China; Henan Key Laboratory of Fertility Protection and Aristogenesis, Luohe, 462000, China
| | - Mingzheng Sun
- Department of Pharmacology, Luohe Medical College, Luohe, 462000, Henan, China
| | - Tenghan Xu
- Department of Obstetrics and Gynaecology, Luohe Central Hospital, Luohe, 462000, Henan, China; Henan Key Laboratory of Fertility Protection and Aristogenesis, Luohe, 462000, China
| | - Shaozhe Yang
- Department of Obstetrics and Gynaecology, Luohe Central Hospital, Luohe, 462000, Henan, China; Henan Key Laboratory of Fertility Protection and Aristogenesis, Luohe, 462000, China
| | - Suhong Li
- Department of Obstetrics and Gynaecology, Luohe Central Hospital, Luohe, 462000, Henan, China; Henan Key Laboratory of Fertility Protection and Aristogenesis, Luohe, 462000, China
| | - Huifen Wang
- Department of Obstetrics and Gynaecology, Luohe Central Hospital, Luohe, 462000, Henan, China; Henan Key Laboratory of Fertility Protection and Aristogenesis, Luohe, 462000, China
| | - Xiuhong Fu
- Department of Obstetrics and Gynaecology, Luohe Central Hospital, Luohe, 462000, Henan, China; Henan Key Laboratory of Fertility Protection and Aristogenesis, Luohe, 462000, China.
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29
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Blatt S, Kämmerer PW, Krüger M, Surabattula R, Thiem DGE, Dillon ST, Al-Nawas B, Libermann TA, Schuppan D. High-Multiplex Aptamer-Based Serum Proteomics to Identify Candidate Serum Biomarkers of Oral Squamous Cell Carcinoma. Cancers (Basel) 2023; 15:cancers15072071. [PMID: 37046731 PMCID: PMC10093013 DOI: 10.3390/cancers15072071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/17/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Improved serological biomarkers are needed for the early detection, risk stratification and treatment surveillance of patients with oral squamous cell carcinoma (OSCC). We performed an exploratory study using advanced, highly specific, DNA-aptamer-based serum proteomics (SOMAscan, 1305-plex) to identify distinct proteomic changes in patients with OSCC pre- vs. post-resection and compared to healthy controls. A total of 63 significantly differentially expressed serum proteins (each p < 0.05) were found that could discriminate between OSCC and healthy controls with 100% accuracy. Furthermore, 121 proteins were detected that were significantly altered between pre- and post-resection sera, and 12 OSCC-associated proteins reversed to levels equivalent to healthy controls after resection. Of these, 6 were increased and 6 were decreased relative to healthy controls, highlighting the potential relevance of these proteins as OSCC tumor markers. Pathway analyses revealed potential pathophysiological mechanisms associated with OSCC. Hence, quantitative proteome analysis using SOMAscan technology is promising and may aid in the development of defined serum marker assays to predict tumor occurrence, progression and recurrence in OSCC, and to guide personalized therapies.
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30
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Vergouwen DPC, Schotting AJ, Endermann T, van de Werken HJG, Grashof DGB, Arumugam S, Nuijts RMMA, Ten Berge JC, Rothova A, Schreurs MWJ, Gijs M. Evaluation of pre-processing methods for tear fluid proteomics using proximity extension assays. Sci Rep 2023; 13:4433. [PMID: 36932139 PMCID: PMC10023677 DOI: 10.1038/s41598-023-31227-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/08/2023] [Indexed: 03/19/2023] Open
Abstract
Tear fluid forms a potential source for biomarker identification, and can be minimal invasively collected via Schirmer strips. The lack of knowledge on the processing of Schirmer strips however complicates the analysis and between-study comparisons. We studied two different pre-processing methods, specifically the use of punches of the strip versus elution of the strip in a buffer. Tear fluid filled Schirmer strips were collected from 5 healthy participants, and divided into two halves over the length of the strip. In either part, punches or eluates were obtained from 4 different locations, from the first part touching the eye (head) to the end, to assess the protein distribution along the strips. The levels of 92 inflammatory proteins were measured in the punches/eluates using proximity extension assays. The punch method yielded higher protein detectability compared to the elution method (76% vs 66%; p ≤ 0.001). Protein expression level was found to be slightly higher in the head of the strip, however, 3 out of 5 punches from the head failed quality control. Protein expression levels over the remaining parts of the strips were similar. Our study showed beneficial use of punches of any part of the strip except the head in future biomarker research.
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Affiliation(s)
- Daphne P C Vergouwen
- Department of Ophthalmology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Amber J Schotting
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Harmen J G van de Werken
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Dwin G B Grashof
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Sinthuja Arumugam
- University Eye Clinic Maastricht, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Rudy M M A Nuijts
- University Eye Clinic Maastricht, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Josianne C Ten Berge
- Department of Ophthalmology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Aniki Rothova
- Department of Ophthalmology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marco W J Schreurs
- Department of Ophthalmology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marlies Gijs
- University Eye Clinic Maastricht, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
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31
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Dunphy K, Bazou D, Dowling P. Analysis of Cancer Cell Line Secretomes: A Complementary Source of Disease-Specific Protein Biomarkers. Methods Mol Biol 2023; 2645:277-287. [PMID: 37202627 DOI: 10.1007/978-1-0716-3056-3_18] [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: 05/20/2023]
Abstract
Various types of cancer cells enrich or condition the medium that they are cultured in by secreting or shedding proteins and small molecules. These secreted or shed factors are involved in key biological processes, including cellular communication, proliferation, and migration, and are represented by protein families, including cytokines, growth factors, and enzymes. The rapid development of high-resolution mass spectrometry and shotgun strategies for proteome analysis facilitates the identification of these factors in biological models and elucidation of their potential roles in pathophysiology. Hence, the following protocol provides details on how to prepare proteins present in conditioned media for mass spectrometry analysis.
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Affiliation(s)
- Katie Dunphy
- Department of Biology, Maynooth University, National University of Ireland, Kildare, Ireland
| | - Despina Bazou
- Department of Haematology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Kildare, Ireland.
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32
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Rabl M, Clark C, Dayon L, Bowman GL, Popp J. Blood plasma protein profiles of neuropsychiatric symptoms and related cognitive decline in older people. J Neurochem 2023; 164:242-254. [PMID: 36281546 DOI: 10.1111/jnc.15715] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/20/2022] [Accepted: 10/20/2022] [Indexed: 01/31/2023]
Abstract
Neuropsychiatric symptoms (NPS) severely affect patients and their caregivers, and are associated with worse long-term outcomes. This study tested the hypothesis that altered protein levels in blood plasma could serve as biomarkers of NPS; and that altered protein levels are associated with persisting NPS and cognitive decline over time. We performed a cross-sectional and longitudinal study in older subjects with cognitive impairment and cognitively unimpaired in a memory clinic setting. NPS were recorded through the Neuropsychiatric Inventory Questionnaire (NPI-Q) while cognitive and functional impairment was assessed using the clinical dementia rating sum of boxes (CDR-SoB) score at baseline and follow-up visits. Shotgun proteomic analysis based on liquid chromatography-mass spectrometry was conducted in blood plasma samples, identifying 420 proteins. The presence of Alzheimer's Disease (AD) pathology was determined by cerebrospinal fluid biomarkers. Eighty-five subjects with a mean age of 70 (±7.4) years, 62% female and 54% with mild cognitive impairment or mild dementia were included. We found 15 plasma proteins with altered baseline levels in participants with NPS (NPI-Q score > 0). Adding those 15 proteins to a reference model based on clinical data (age, CDR-SoB) significantly improved the prediction of NPS (from receiver operating characteristic area under the curve [AUC] 0.75 to AUC 0.91, p = 0.004) with a specificity of 89% and a sensitivity of 74%. The identified proteins additionally predicted both persisting NPS and cognitive decline at follow-up visits. The observed associations were independent of the presence of AD pathology. Using proteomics, we identified a panel of specific blood proteins associated with current and future NPS, and related cognitive decline in older people. These findings show the potential of untargeted proteomics to identify blood-based biomarkers of pathological alterations relevant for NPS and related clinical disease progression.
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Affiliation(s)
- Miriam Rabl
- Department of Geriatric Psychiatry, University Hospital of Psychiatry Zurich, Zurich, Switzerland.,University of Lausanne, Lausanne, Switzerland
| | - Christopher Clark
- Department of Psychiatry, Psychotherapy and Psychosomatics, University of Zurich, Zurich, Switzerland
| | - Loïc Dayon
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Lausanne, Switzerland.,Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gene L Bowman
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Julius Popp
- Department of Geriatric Psychiatry, University Hospital of Psychiatry Zurich, Zurich, Switzerland.,Department of Psychiatry, Psychotherapy and Psychosomatics, University of Zurich, Zurich, Switzerland.,Old Age Psychiatry, Department of Psychiatry, Lausanne University Hospital, Lausanne, Switzerland
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33
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Ahmed S, van Zalm P, Rudmann EA, Leone M, Keller K, Branda JA, Steen J, Mukerji SS, Steen H. Using CSF Proteomics to Investigate Herpesvirus Infections of the Central Nervous System. Viruses 2022; 14:2757. [PMID: 36560759 PMCID: PMC9780940 DOI: 10.3390/v14122757] [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: 11/08/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022] Open
Abstract
Herpesviruses have complex mechanisms enabling infection of the human CNS and evasion of the immune system, allowing for indefinite latency in the host. Herpesvirus infections can cause severe complications of the central nervous system (CNS). Here, we provide a novel characterization of cerebrospinal fluid (CSF) proteomes from patients with meningitis or encephalitis caused by human herpes simplex virus 1 (HSV-1), which is the most prevalent human herpesvirus associated with the most severe morbidity. The CSF proteome was compared with those from patients with meningitis or encephalitis due to human herpes simplex virus 2 (HSV-2) or varicella-zoster virus (VZV, also known as human herpesvirus 3) infections. Virus-specific differences in CSF proteomes, most notably elevated 14-3-3 family proteins and calprotectin (i.e., S100-A8 and S100-A9), were observed in HSV-1 compared to HSV-2 and VZV samples, while metabolic pathways related to cellular and small molecule metabolism were downregulated in HSV-1 infection. Our analyses show the feasibility of developing CNS proteomic signatures of the host response in alpha herpes infections, which is paramount for targeted studies investigating the pathophysiology driving virus-associated neurological disorders, developing biomarkers of morbidity, and generating personalized therapeutic strategies.
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Affiliation(s)
- Saima Ahmed
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Patrick van Zalm
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Emily A. Rudmann
- Neuroimmunology and Neuro-Infectious Diseases Division, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Leone
- Neuroimmunology and Neuro-Infectious Diseases Division, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kiana Keller
- Neuroimmunology and Neuro-Infectious Diseases Division, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - John A. Branda
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Judith Steen
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shibani S. Mukerji
- Neuroimmunology and Neuro-Infectious Diseases Division, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hanno Steen
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Precision Vaccines Program and Neurobiology Program, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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34
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Chantada-Vázquez MDP, Bravo SB, Barbosa-Gouveia S, Alvarez JV, Couce ML. Proteomics in Inherited Metabolic Disorders. Int J Mol Sci 2022; 23:14744. [PMID: 36499071 PMCID: PMC9740208 DOI: 10.3390/ijms232314744] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Inherited metabolic disorders (IMD) are rare medical conditions caused by genetic defects that interfere with the body's metabolism. The clinical phenotype is highly variable and can present at any age, although it more often manifests in childhood. The number of treatable IMDs has increased in recent years, making early diagnosis and a better understanding of the natural history of the disease more important than ever. In this review, we discuss the main challenges faced in applying proteomics to the study of IMDs, and the key advances achieved in this field using tandem mass spectrometry (MS/MS). This technology enables the analysis of large numbers of proteins in different body fluids (serum, plasma, urine, saliva, tears) with a single analysis of each sample, and can even be applied to dried samples. MS/MS has thus emerged as the tool of choice for proteome characterization and has provided new insights into many diseases and biological systems. In the last 10 years, sequential window acquisition of all theoretical fragmentation spectra mass spectrometry (SWATH-MS) has emerged as an accurate, high-resolution technique for the identification and quantification of proteins differentially expressed between healthy controls and IMD patients. Proteomics is a particularly promising approach to help obtain more information on rare genetic diseases, including identification of biomarkers to aid early diagnosis and better understanding of the underlying pathophysiology to guide the development of new therapies. Here, we summarize new and emerging proteomic technologies and discuss current uses and limitations of this approach to identify and quantify proteins. Moreover, we describe the use of proteomics to identify the mechanisms regulating complex IMD phenotypes; an area of research essential to better understand these rare disorders and many other human diseases.
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Affiliation(s)
- Maria del Pilar Chantada-Vázquez
- Proteomic Platform, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Susana B. Bravo
- Proteomic Platform, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Sofía Barbosa-Gouveia
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain
| | - José V. Alvarez
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain
| | - María L. Couce
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain
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