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Schlosser P, Surapaneni AL, Borisov O, Schmidt IM, Zhou L, Anderson A, Deo R, Dubin R, Ganz P, He J, Kimmel PL, Li H, Nelson RG, Porter AC, Rahman M, Rincon-Choles H, Shah V, Unruh ML, Vasan RS, Zheng Z, Feldman HI, Waikar SS, Köttgen A, Rhee EP, Coresh J, Grams ME. Association of Integrated Proteomic and Metabolomic Modules with Risk of Kidney Disease Progression. J Am Soc Nephrol 2024; 35:923-935. [PMID: 38640019 PMCID: PMC11230725 DOI: 10.1681/asn.0000000000000343] [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: 12/06/2023] [Accepted: 04/01/2024] [Indexed: 04/21/2024] Open
Abstract
Key Points Integrated analysis of proteome and metabolome identifies modules associated with CKD progression and kidney failure. Ephrin transmembrane proteins and podocyte-expressed CRIM1 and NPNT emerged as central components and warrant experimental and clinical investigation. Background Proteins and metabolites play crucial roles in various biological functions and are frequently interconnected through enzymatic or transport processes. Methods We present an integrated analysis of 4091 proteins and 630 metabolites in the Chronic Renal Insufficiency Cohort study (N =1708; average follow-up for kidney failure, 9.5 years, with 537 events). Proteins and metabolites were integrated using an unsupervised clustering method, and we assessed associations between clusters and CKD progression and kidney failure using Cox proportional hazards models. Analyses were adjusted for demographics and risk factors, including the eGFR and urine protein–creatinine ratio. Associations were identified in a discovery sample (random two thirds, n =1139) and then evaluated in a replication sample (one third, n =569). Results We identified 139 modules of correlated proteins and metabolites, which were represented by their principal components. Modules and principal component loadings were projected onto the replication sample, which demonstrated a consistent network structure. Two modules, representing a total of 236 proteins and 82 metabolites, were robustly associated with both CKD progression and kidney failure in both discovery and validation samples. Using gene set enrichment, several transmembrane-related terms were identified as overrepresented in these modules. Transmembrane–ephrin receptor activity displayed the largest odds (odds ratio=13.2, P value = 5.5×10−5). A module containing CRIM1 and NPNT expressed in podocytes demonstrated particularly strong associations with kidney failure (P value = 2.6×10−5). Conclusions This study demonstrates that integration of the proteome and metabolome can identify functions of pathophysiologic importance in kidney disease.
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Affiliation(s)
- Pascal Schlosser
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Institute of Genetic Epidemiology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Aditya L. Surapaneni
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Division of Precision Medicine, Department of Medicine, NYU Langone Health, New York, New York
| | - Oleg Borisov
- Institute of Genetic Epidemiology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Insa M. Schmidt
- Section of Nephrology, Department of Medicine, Boston Medical Center and Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - Linda Zhou
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Amanda Anderson
- Department of Epidemiology, Tulane University, New Orleans, Louisiana
| | - Rajat Deo
- Division of Cardiovascular Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ruth Dubin
- Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Peter Ganz
- Division of Cardiology, University of California, San Francisco, San Francisco, California
| | - Jiang He
- Department of Epidemiology, Tulane University, New Orleans, Louisiana
| | - Paul L. Kimmel
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robert G. Nelson
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona
- Research Division, Joslin Diabetes Center, Boston, Massachusetts
| | - Anna C. Porter
- Renal Service, Wellington Regional Hospital, Wellington, New Zealand
| | - Mahboob Rahman
- Department of Kidney Medicine, Cleveland Clinic Foundation, Cleveland, Ohio
| | | | - Vallabh Shah
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Mark L. Unruh
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Ramachandran S. Vasan
- University of Texas Health Sciences Center, San Antonio, Texas
- Section of Preventive Medicine and Epidemiology, Department of Medicine, Boston Medical Center and Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - Zihe Zheng
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Harold I. Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sushrut S. Waikar
- Section of Nephrology, Department of Medicine, Boston Medical Center and Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Institute of Genetic Epidemiology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eugene P. Rhee
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Optimal Aging Institute, Departments of Population Health and Medicine, NYU Grossman School of Medicine, New York, New York
| | - Morgan E. Grams
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Division of Precision Medicine, Department of Medicine, NYU Langone Health, New York, New York
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Ibrahim Z, Khan NA, Qaisar R, Saleh MA, Siddiqui R, Al-Hroub HM, Giddey AD, Semreen MH, Soares NC, Elmoselhi AB. Serum multi-omics analysis in hindlimb unloading mice model: Insights into systemic molecular changes and potential diagnostic and therapeutic biomarkers. Heliyon 2024; 10:e23592. [PMID: 38187258 PMCID: PMC10770503 DOI: 10.1016/j.heliyon.2023.e23592] [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: 08/06/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
Microgravity, in space travel and prolonged bed rest conditions, induces cardiovascular deconditioning along with skeletal muscle mass loss and weakness. The findings of microgravity research may also aid in the understanding and treatment of human health conditions on Earth such as muscle atrophy, and cardiovascular diseases. Due to the paucity of biomarkers and the unknown underlying mechanisms of cardiovascular and skeletal muscle deconditioning in these environments, there are insufficient diagnostic and preventative measures. In this study, we employed hindlimb unloading (HU) mouse model, which mimics astronauts in space and bedridden patients, to first evaluate cardiovascular and skeletal muscle function, followed by proteomics and metabolomics LC-MS/MS-based analysis using serum samples. Three weeks of unloading caused changes in the function of the cardiovascular system in c57/Bl6 mice, as seen by a decrease in mean arterial pressure and heart weight. Unloading for three weeks also changed skeletal muscle function, causing a loss in grip strength in HU mice and atrophy of skeletal muscle indicated by a reduction in muscle mass. These modifications were partially reversed by a two-week recovery period of reloading condition, emphasizing the significance of the recovery process. Proteomics analysis revealed 12 dysregulated proteins among the groups, such as phospholipid transfer protein, Carbonic anhydrase 3, Parvalbumin alpha, Major urinary protein 20 (Mup20), Thrombospondin-1, and Apolipoprotein C-IV. On the other hand, metabolomics analysis showed altered metabolites among the groups such as inosine, hypoxanthine, xanthosine, sphinganine, l-valine, 3,4-Dihydroxyphenylglycol, and l-Glutamic acid. The joint data analysis revealed that HU conditions mainly impacted pathways such as ABC transporters, complement and coagulation cascades, nitrogen metabolism, and purine metabolism. Overall, our results indicate that microgravity environment induces significant alterations in the function, proteins, and metabolites of these mice. These observations suggest the potential utilization of these proteins and metabolites as novel biomarkers for assessing and mitigating cardiovascular and skeletal muscle deconditioning associated with such conditions.
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Affiliation(s)
- Zeinab Ibrahim
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Basic Medical Sciences Department, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Naveed A. Khan
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Microbiota Research Center, Istinye University, Istanbul, 34010, Turkey
| | - Rizwan Qaisar
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Basic Medical Sciences Department, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohamed A. Saleh
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Ruqaiyyah Siddiqui
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University Edinburgh, EH14 4AS UK
- Microbiota Research Center, Istinye University, Istanbul, 34010, Turkey
| | - Hamza M. Al-Hroub
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Alexander D. Giddey
- Center for Applied and Translational Genomics, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Mohammad Harb Semreen
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Nelson C. Soares
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Laboratory of Proteomics, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Av. Padre Cruz, Lisbon, 1649-016, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), NOVA School/ Faculdade de Lisboa, Lisbon, Portugal
| | - Adel B. Elmoselhi
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Basic Medical Sciences Department, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
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Chen Q, Dwaraka VB, Carreras-Gallo N, Mendez K, Chen Y, Begum S, Kachroo P, Prince N, Went H, Mendez T, Lin A, Turner L, Moqri M, Chu SH, Kelly RS, Weiss ST, Rattray NJ, Gladyshev VN, Karlson E, Wheelock C, Mathé EA, Dahlin A, McGeachie MJ, Smith R, Lasky-Su JA. OMICmAge: An integrative multi-omics approach to quantify biological age with electronic medical records. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562114. [PMID: 37904959 PMCID: PMC10614756 DOI: 10.1101/2023.10.16.562114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Biological aging is a multifactorial process involving complex interactions of cellular and biochemical processes that is reflected in omic profiles. Using common clinical laboratory measures in ~30,000 individuals from the MGB-Biobank, we developed a robust, predictive biological aging phenotype, EMRAge, that balances clinical biomarkers with overall mortality risk and can be broadly recapitulated across EMRs. We then applied elastic-net regression to model EMRAge with DNA-methylation (DNAm) and multiple omics, generating DNAmEMRAge and OMICmAge, respectively. Both biomarkers demonstrated strong associations with chronic diseases and mortality that outperform current biomarkers across our discovery (MGB-ABC, n=3,451) and validation (TruDiagnostic, n=12,666) cohorts. Through the use of epigenetic biomarker proxies, OMICmAge has the unique advantage of expanding the predictive search space to include epigenomic, proteomic, metabolomic, and clinical data while distilling this in a measure with DNAm alone, providing opportunities to identify clinically-relevant interconnections central to the aging process.
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Affiliation(s)
- Qingwen Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Kevin Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Yulu Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Sofina Begum
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Nicole Prince
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Aaron Lin
- TruDiagnostic, Inc., Lexington, KY USA
| | | | - Mahdi Moqri
- Division of Genetics, Dept. of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Su H. Chu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Rachel S. Kelly
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Nicholas J.W Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde, Glasgow, UK
| | - Vadim N. Gladyshev
- Division of Genetics, Dept. of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Karlson
- Department of Personalized Medicine, Mass General Brigham and Harvard Medical School, Boston, MA, USA
| | - Craig Wheelock
- Division of Physiological Chemistry 2, Dept of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Ewy A. Mathé
- Division of Preclinical Innovation, National Center for Advancing Translational Science, National Institutes of Health, Rockville, MD, USA
| | - Amber Dahlin
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Michae J. McGeachie
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Jessica A. Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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Teng D, Chen H, Jia W, Ren Q, Ding X, Zhang L, Gong L, Wang H, Zhong L, Yang J. Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics. PeerJ 2023; 11:e16122. [PMID: 37810795 PMCID: PMC10557941 DOI: 10.7717/peerj.16122] [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: 06/08/2023] [Accepted: 08/27/2023] [Indexed: 10/10/2023] Open
Abstract
Background Foam cells play crucial roles in all phases of atherosclerosis. However, until now, the specific mechanisms by which these foam cells contribute to atherosclerosis remain unclear. We aimed to identify novel foam cell biomarkers and interventional targets for atherosclerosis, characterizing their potential mechanisms in the progression of atherosclerosis. Methods Microarray data of atherosclerosis and foam cells were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expression genes (DEGs) were screened using the "LIMMA" package in R software. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Ontology (GO) annotation were both carried out. Hub genes were found in Cytoscape after a protein-protein interaction (PPI) enrichment analysis was carried out. Validation of important genes in the GSE41571 dataset, cellular assays, and tissue samples. Results A total of 407 DEGs in atherosclerosis and 219 DEGs in foam cells were identified, and the DEGs in atherosclerosis were mainly involved in cell proliferation and differentiation. CSF1R and PLAUR were identified as common hub genes and validated in GSE41571. In addition, we also found that the expression of CSF1R and PLAUR gradually increased with the accumulation of lipids and disease progression in cell and tissue experiments. Conclusion CSF1R and PLAUR are key hub genes of foam cells and may play an important role in the biological process of atherosclerosis. These results advance our understanding of the mechanism behind atherosclerosis and potential therapeutic targets for future development.
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Affiliation(s)
- Da Teng
- Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, China
- Qingdao University, Qingdao, China
| | - Hongping Chen
- Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Wenjuan Jia
- Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, China
- Qingdao University, Qingdao, China
| | - Qingmiao Ren
- The Precision Medicine Laboratory, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xiaoning Ding
- Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, China
| | - Lihui Zhang
- Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, China
- Qingdao University, Qingdao, China
| | - Lei Gong
- Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, China
| | - Hua Wang
- Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, China
| | - Lin Zhong
- Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, China
| | - Jun Yang
- Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, China
- Qingdao University, Qingdao, China
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Srialluri N, Surapaneni A, Schlosser P, Chen TK, Schmidt IM, Rhee EP, Coresh J, Grams ME. Circulating Proteins and Mortality in CKD: A Proteomics Study of the AASK and ARIC Cohorts. Kidney Med 2023; 5:100714. [PMID: 37711886 PMCID: PMC10498294 DOI: 10.1016/j.xkme.2023.100714] [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] [Indexed: 09/16/2023] Open
Abstract
Rationale & Objective Proteomics could provide pathophysiologic insight into the increased risk of mortality in patients with chronic kidney disease (CKD). This study aimed to investigate associations between the circulating proteome and all-cause mortality among patients with CKD. Study Design Observational cohort study. Setting & Participants Primary analysis in 703 participants in the African American Study of Kidney Disease and Hypertension (AASK) and validation in 1,628 participants with CKD in the Atherosclerosis Risk in Communities (ARIC) study who attended visit 5. Exposure Circulating proteins. Outcome All-cause mortality. Analytical Approach Among AASK participants, we evaluated the associations of 6,790 circulating proteins with all-cause mortality using multivariable Cox proportional hazards models. Proteins with significant associations were further studied in ARIC Visit 5 participants with CKD. Results In the AASK cohort, the mean age was 54.5 years, 271 (38.5%) were women, and the mean measured glomerular filtration rate (GFR) was 46 mL/min/1.73 m2. The median follow-up was 9.6 years, and 7 distinct proteins were associated with all-cause mortality at the Bonferroni-level threshold (P < 0.05 of the 6,790) after adjustment for demographics and clinical factors, including baseline measured estimated GFR and proteinuria. In the ARIC visit 5 cohort, the mean age was 77.2 years, 903 (55.5%) were women, the mean estimated GFR was 54 mL/min/1.73 m2 and median follow-up was 6.9 years. Of the 7 proteins found in AASK, 3 (β2-microglobulin, spondin-1, and N-terminal pro-brain natriuretic peptide) were available in the ARIC data, with all 3 significantly associated with death in ARIC. Limitations Possibility of unmeasured confounding. Cause of death was not known. Conclusions Using large-scale proteomic analysis, proteins were reproducibly associated with mortality in 2 cohorts of participants with CKD. Plain-Language Summary Patients with chronic kidney disease (CKD) have a high risk of premature death, with various pathophysiological processes contributing to this increased risk of mortality. This observational cohort study aimed to investigate the associations between circulating proteins and all-cause mortality in patients with CKD using large-scale proteomic analysis. The study analyzed data from the African American Study of Kidney Disease and Hypertension (AASK) study and validated the findings in the Atherosclerosis Risk in Communities (ARIC) Study. A total of 6,790 circulating proteins were evaluated in AASK, and 7 proteins were significantly associated with all-cause mortality. Three of these proteins (β2-microglobulin, spondin-1, and N-terminal pro-brain natriuretic peptide (BNP)) were also measured in ARIC and were significantly associated with death. Additional studies assessing biomarkers associated with mortality among patients with CKD are needed to evaluate their use in clinical practice.
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Affiliation(s)
- Nityasree Srialluri
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
- Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, Maryland
| | - Aditya Surapaneni
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
- Division of Precision Medicine, Department of Medicine, New York University, New York, New York
| | - Pascal Schlosser
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Teresa K. Chen
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
- Kidney Health Research Collaborative; Division of Nephrology, Department of Medicine, University of California San Francisco and San Francisco VA Health Care System, San Francisco, California
| | - Insa M. Schmidt
- Department of Medicine, Boston University School of Medicine, Boston Medical Center, Boston, Massachusetts
| | - Eugene P. Rhee
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Josef Coresh
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
- Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, Maryland
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Morgan E. Grams
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
- Division of Precision Medicine, Department of Medicine, New York University, New York, New York
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Wu Z, Lohmöller J, Kuhl C, Wehrle K, Jankowski J. Use of Computation Ecosystems to Analyze the Kidney-Heart Crosstalk. Circ Res 2023; 132:1084-1100. [PMID: 37053282 DOI: 10.1161/circresaha.123.321765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
The identification of mediators for physiologic processes, correlation of molecular processes, or even pathophysiological processes within a single organ such as the kidney or heart has been extensively studied to answer specific research questions using organ-centered approaches in the past 50 years. However, it has become evident that these approaches do not adequately complement each other and display a distorted single-disease progression, lacking holistic multilevel/multidimensional correlations. Holistic approaches have become increasingly significant in understanding and uncovering high dimensional interactions and molecular overlaps between different organ systems in the pathophysiology of multimorbid and systemic diseases like cardiorenal syndrome because of pathological heart-kidney crosstalk. Holistic approaches to unraveling multimorbid diseases are based on the integration, merging, and correlation of extensive, heterogeneous, and multidimensional data from different data sources, both -omics and nonomics databases. These approaches aimed at generating viable and translatable disease models using mathematical, statistical, and computational tools, thereby creating first computational ecosystems. As part of these computational ecosystems, systems medicine solutions focus on the analysis of -omics data in single-organ diseases. However, the data-scientific requirements to address the complexity of multimodality and multimorbidity reach far beyond what is currently available and require multiphased and cross-sectional approaches. These approaches break down complexity into small and comprehensible challenges. Such holistic computational ecosystems encompass data, methods, processes, and interdisciplinary knowledge to manage the complexity of multiorgan crosstalk. Therefore, this review summarizes the current knowledge of kidney-heart crosstalk, along with methods and opportunities that arise from the novel application of computational ecosystems providing a holistic analysis on the example of kidney-heart crosstalk.
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Affiliation(s)
- Zhuojun Wu
- Institute of Molecular Cardiovascular Research (Z.W., J.J.), Rheinisch-Westfälische Technische Hochschule Aachen University, Germany
- Department of Radiology (C.K.), Rheinisch-Westfälische Technische Hochschule Aachen University, Germany
| | - Johannes Lohmöller
- Medical Faculty, and Department of Computer Science, Communication and Distributed Systems (COMSYS) (J.L., K.W.), Rheinisch-Westfälische Technische Hochschule Aachen University, Germany
| | - Christiane Kuhl
- Department of Radiology (C.K.), Rheinisch-Westfälische Technische Hochschule Aachen University, Germany
| | - Klaus Wehrle
- Institute of Molecular Cardiovascular Research (Z.W., J.J.), Rheinisch-Westfälische Technische Hochschule Aachen University, Germany
- Medical Faculty, and Department of Computer Science, Communication and Distributed Systems (COMSYS) (J.L., K.W.), Rheinisch-Westfälische Technische Hochschule Aachen University, Germany
| | - Joachim Jankowski
- Institute of Molecular Cardiovascular Research (Z.W., J.J.), Rheinisch-Westfälische Technische Hochschule Aachen University, Germany
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), University of Maastricht, The Netherlands (J.J.)
- Aachen-Maastricht Institute for Cardiorenal Disease (AMICARE), University Hospital Rheinisch-Westfälische Technische Hochschule Aachen, Germany (J.J.)
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