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Kumar R, Zemaitis KJ, Fulcher JM, Paša-Tolić L. Advances in mass spectrometry-enabled multiomics at single-cell resolution. Curr Opin Biotechnol 2024; 87:103096. [PMID: 38432187 DOI: 10.1016/j.copbio.2024.103096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Biological organisms are multifaceted, intricate systems where slight perturbations can result in extensive changes in gene expression, protein abundance and/or activity, and metabolic flux. These changes occur at different timescales, spatially across cells of heterogeneous origins, and within single-cells. Hence, multimodal measurements at the smallest biological scales are necessary to capture dynamic changes in heterogeneous biological systems. Of the analytical techniques used to measure biomolecules, mass spectrometry (MS) has proven to be a powerful option due to its sensitivity, robustness, and flexibility with regard to the breadth of biomolecules that can be analyzed. Recently, many studies have coupled MS to other analytical techniques with the goal of measuring multiple modalities from the same single-cell. It is with these concepts in mind that we focus this review on MS-enabled multiomic measurements at single-cell or near-single- cell resolution.
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Affiliation(s)
- Rashmi Kumar
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kevin J Zemaitis
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - James M Fulcher
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
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Li R, Koh JH, Park WJ, Choi Y, Kim WU. Serum and urine lipidomic profiles identify biomarkers diagnostic for seropositive and seronegative rheumatoid arthritis. Front Immunol 2024; 15:1410365. [PMID: 38765010 PMCID: PMC11099275 DOI: 10.3389/fimmu.2024.1410365] [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: 04/01/2024] [Accepted: 04/22/2024] [Indexed: 05/21/2024] Open
Abstract
Objective Seronegative rheumatoid arthritis (RA) is defined as RA without circulating autoantibodies such as rheumatoid factor and anti-citrullinated protein antibodies; thus, early diagnosis of seronegative RA can be challenging. Here, we aimed to identify diagnostic biomarkers for seronegative RA by performing lipidomic analyses of sera and urine samples from patients with RA. Methods We performed untargeted lipidomic analysis of sera and urine samples from 111 RA patients, 45 osteoarthritis (OA) patients, and 25 healthy controls (HC). These samples were divided into a discovery cohort (n = 97) and a validation cohort (n = 84). Serum samples from 20 patients with systemic lupus erythematosus (SLE) were also used for validation. Results The serum lipidome profile of RA was distinguishable from that of OA and HC. We identified a panel of ten serum lipids and three urine lipids in the discovery cohort that showed the most significant differences. These were deemed potential lipid biomarker candidates for RA. The serum lipid panel was tested using a validation cohort; the results revealed an accuracy of 79%, a sensitivity of 71%, and a specificity of 86%. Both seropositive and seronegative RA patients were differentiated from patients with OA, SLE, and HC. Three urinary lipids showing differential expression between RA from HC were identified with an accuracy of 84%, but they failed to differentiate RA from OA. There were five lipid pathways that differed between seronegative and seropositive RA. Conclusion Here, we identified a panel of ten serum lipids as potential biomarkers that can differentiate RA from OA and SLE, regardless of seropositivity. In addition, three urinary lipids had diagnostic utility for differentiating RA from HC.
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Affiliation(s)
- Rong Li
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
- Department of Marine Bio Food Science, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Jung Hee Koh
- Division of Rheumatology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Woo Jung Park
- Department of Marine Bio Food Science, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Yongsoo Choi
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
- Division of National Product Applied Science, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
| | - Wan-Uk Kim
- Division of Rheumatology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Fu Y, Wang Z, Qin H. Examining the Pathogenesis of MAFLD and the Medicinal Properties of Natural Products from a Metabolic Perspective. Metabolites 2024; 14:218. [PMID: 38668346 PMCID: PMC11052500 DOI: 10.3390/metabo14040218] [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: 03/17/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Metabolic-associated fatty liver disease (MAFLD), characterized primarily by hepatic steatosis, has become the most prevalent liver disease worldwide, affecting approximately two-fifths of the global population. The pathogenesis of MAFLD is extremely complex, and to date, there are no approved therapeutic drugs for clinical use. Considerable evidence indicates that various metabolic disorders play a pivotal role in the progression of MAFLD, including lipids, carbohydrates, amino acids, and micronutrients. In recent years, the medicinal properties of natural products have attracted widespread attention, and numerous studies have reported their efficacy in ameliorating metabolic disorders and subsequently alleviating MAFLD. This review aims to summarize the metabolic-associated pathological mechanisms of MAFLD, as well as the natural products that regulate metabolic pathways to alleviate MAFLD.
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Affiliation(s)
| | | | - Hong Qin
- Department of Nutrition and Food Hygiene, Xiangya School of Public Health, Central South University, Changsha 410006, China; (Y.F.); (Z.W.)
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Perramón M, Navalón-López M, Fernández-Varo G, Moreno-Lanceta A, García-Pérez R, Faneca J, López-Moya M, Fornaguera C, García-Villoria J, Morales-Ruiz M, Melgar-Lesmes P, Borrós S, Jiménez W. Liver-targeted nanoparticles delivering nitric oxide reduce portal hypertension in cirrhotic rats. Biomed Pharmacother 2024; 171:116143. [PMID: 38219387 DOI: 10.1016/j.biopha.2024.116143] [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: 12/21/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/16/2024] Open
Abstract
Nitric oxide (NO) is a small vasodilator playing a key role in the pathogenesis of portal hypertension. Here, we assessed the potential therapeutic effect of a NO donor targeted to the liver by poly(beta-amino ester) nanoparticles (pBAE NPs) in experimental cirrhosis. Retinol-functionalized NO donor pBAE NPs (Ret pBAE NPs) were synthetized with the aim of actively targeting the liver. Administration of Ret pBAE NPs resulted in uptake and transfection by the liver and spleen. NPs were not found in other organs or the systemic circulation. Treatment with NO donor Ret pBAE NPs (30 mg/ kg body weight) significantly decreased aspartate aminotransferase, lactate dehydrogenase and portal pressure (9.75 ± 0.64 mmHg) compared to control NPs (13.4 ± 0.53 mmHg) in cirrhotic rats. There were no effects on mean arterial pressure and cardiac output. Liver-targeted NO donor NPs reduced collagen fibers and steatosis, activation of hepatic stellate cells and mRNA expression of profibrogenic and proinflammatory genes. Finally, Ret pBAE NPs displayed efficient transfection in human liver slices. Overall, liver-specific NO donor NPs effectively target the liver and mitigated inflammation and portal hypertension in cirrhotic rats. The use of Ret pBAE may prove to be an effective therapeutic strategy to treat advanced liver disease.
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Affiliation(s)
- Meritxell Perramón
- Biochemistry and Molecular Genetics Service, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain.
| | - María Navalón-López
- Grup d'Enginyeria de Materials (Gemat), Institut Químic de Sarrià (IQS), Universitat Ramon Llull (URL), Barcelona, Spain
| | - Guillermo Fernández-Varo
- Biochemistry and Molecular Genetics Service, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Alazne Moreno-Lanceta
- Biochemistry and Molecular Genetics Service, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Department of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Rocío García-Pérez
- Hepatopancreatobiliary Surgery & Transplantation, General & Digestive Surgery Service, Digestive & Metabolic Disease Institute (ICMDM) of Hospital Clínic of Barcelona, Barcelona, Spain. Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Joana Faneca
- Biochemistry and Molecular Genetics Service, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Mario López-Moya
- Grup d'Enginyeria de Materials (Gemat), Institut Químic de Sarrià (IQS), Universitat Ramon Llull (URL), Barcelona, Spain
| | - Cristina Fornaguera
- Grup d'Enginyeria de Materials (Gemat), Institut Químic de Sarrià (IQS), Universitat Ramon Llull (URL), Barcelona, Spain
| | - Judith García-Villoria
- Biochemistry and Molecular Genetics Service, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Manuel Morales-Ruiz
- Biochemistry and Molecular Genetics Service, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Department of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Pedro Melgar-Lesmes
- Biochemistry and Molecular Genetics Service, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Department of Biomedicine, University of Barcelona, Barcelona, Spain; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, USA
| | - Salvador Borrós
- Grup d'Enginyeria de Materials (Gemat), Institut Químic de Sarrià (IQS), Universitat Ramon Llull (URL), Barcelona, Spain
| | - Wladimiro Jiménez
- Biochemistry and Molecular Genetics Service, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Department of Biomedicine, University of Barcelona, Barcelona, Spain
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Wang Z, Yang Y, Xing Y, Si D, Wang S, Lin J, Li C, Zhang J, Yin D. Combined metabolomic and lipidomic analysis uncovers metabolic profile and biomarkers for papillary thyroid carcinoma. Sci Rep 2023; 13:17666. [PMID: 37848492 PMCID: PMC10582036 DOI: 10.1038/s41598-023-41176-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/23/2023] [Indexed: 10/19/2023] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most common endocrine malignancy with a rapidly increasing incidence. The pathogenesis of PTC is unclear, but metabolic and lipidomic reprogramming may play a role in tumor growth. We applied ultra-performance liquid chromatography-tandem mass spectrometry to perform widely targeted metabolomics and lipidomics on plasma samples from 94 patients with PTC and 100 healthy controls. We identified 113 differential metabolites and 236 differential lipids, mainly involved in branched-chain amino acid metabolism, glutamate and glutamine metabolism, tricarboxylic acid cycle, and lipid metabolism. We also screened three potential metabolite biomarkers: sebacic acid, L-glutamine, and indole-3-carboxaldehyde. These biomarkers showed excellent diagnostic performance for PTC in both discovery and validation cohorts, with areas under the receiver operating characteristic curves of 0.994 and 0.925, respectively. Our findings reveal distinct metabolic and lipidomic features of PTC and provide novel targets for diagnosis and treatment.
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Affiliation(s)
- Zipeng Wang
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Engineering Research Center of Multidisciplinary Diagnosis and Treatment of Thyroid Cancer of Henan Province, Zhengzhou, 450052, China
- Key Medicine Laboratory of Thyroid Cancer of Henan Province, Zhengzhou, 450052, China
| | - Yiqin Yang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Yurong Xing
- Physical Examination Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | | | - Suhua Wang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Jiashuo Lin
- School of Medicine, Zhengzhou University, Zhengzhou, 450052, China
| | - Cai Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China.
| | - Ji Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China.
| | - Detao Yin
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Engineering Research Center of Multidisciplinary Diagnosis and Treatment of Thyroid Cancer of Henan Province, Zhengzhou, 450052, China.
- Key Medicine Laboratory of Thyroid Cancer of Henan Province, Zhengzhou, 450052, China.
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