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Sun Y, Zheng H, Wang M, Gu R, Wu X, Yang Q, Zhao H, Bi Y, Zheng J. The effect of histo-blood group ABO system transferase (BGAT) on pregnancy related outcomes:A Mendelian randomization study. Comput Struct Biotechnol J 2024; 23:2067-2075. [PMID: 38800635 PMCID: PMC11126538 DOI: 10.1016/j.csbj.2024.04.040] [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: 10/28/2023] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 05/29/2024] Open
Abstract
Protein level of Histo-Blood Group ABO System Transferase (BGAT) has been reported to be associated with cardiometabolic diseases. But its effect on pregnancy related outcomes still remains unclear. Here we conducted a two-sample Mendelian randomization (MR) study to ascertain the putative causal roles of protein levels of BGAT in pregnancy related outcomes. Cis-acting protein quantitative trait loci (pQTLs) robustly associated with protein level of BGAT (P < 5 ×10-8) were used as instruments to proxy the BGAT protein level (N = 35,559, data from deCODE), with two additional pQTL datasets from Fenland (N = 10,708) and INTERVAL (N = 3301) used as validation exposures. Ten pregnancy related diseases and complications were selected as outcomes. We observed that a higher protein level of BGAT showed a putative causal effect on venous complications and haemorrhoids in pregnancy (VH) (odds ratio [OR]=1.19, 95% confidence interval [95% CI]=1.12-1.27, colocalization probability=91%), which was validated by using pQTLs from Fenland and INTERVAL. The Mendelian randomization results further showed effects of the BGAT protein on gestational hypertension (GH) (OR=0.97, 95% CI=0.96-0.99), despite little colocalization evidence to support it. Sensitivity analyses, including proteome-wide Mendelian randomization of the cis-acting BGAT pQTLs, showed little evidence of horizontal pleiotropy. Correctively, our study prioritised BGAT as a putative causal protein for venous complications and haemorrhoids in pregnancy. Future epidemiology and clinical studies are needed to investigate whether BGAT can be considered as a drug target to prevent adverse pregnancy outcomes.
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Affiliation(s)
- Yuqi Sun
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Science and Technology,Shanghai Jiao Tong University School of Medicine, China
- Shanghai National Clinical Research Center for metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Shanghai Digital Medicine Innovation Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haonan Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Shanghai Digital Medicine Innovation Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Basic Medical Science,Shanghai Jiao Tong University School of Medicine, China
| | - Manqing Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Science and Technology,Shanghai Jiao Tong University School of Medicine, China
| | - Rongrong Gu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Science and Technology,Shanghai Jiao Tong University School of Medicine, China
| | - Xueyan Wu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Shanghai Digital Medicine Innovation Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qian Yang
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
| | - Huiling Zhao
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
| | - Yufang Bi
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Shanghai Digital Medicine Innovation Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Shanghai Digital Medicine Innovation Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
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Pleshakova TO, Ershova MO, Valueva AA, Ivanova IA, Ivanov YD, Archakov AI. AFM-fishing technology for protein detection in solutions. BIOMEDITSINSKAIA KHIMIIA 2024; 70:273-286. [PMID: 39324193 DOI: 10.18097/pbmc20247005273] [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: 09/27/2024]
Abstract
The review considers the possibility of using atomic force microscopy (AFM) as a basic method for protein detection in solutions with low protein concentrations. The demand for new bioanalytical approaches is determined by the problem of insufficient sensitivity of systems used in routine practice for protein detection. Special attention is paid to demonstration of the use in bioanalysis of a combination of AFM and fishing methods as an approach of concentrating biomolecules from a large volume of the analyzed solution on a small surface area.
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Affiliation(s)
| | - M O Ershova
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A A Valueva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - I A Ivanova
- Institute of Biomedical Chemistry, Moscow, Russia
| | - Yu D Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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Greenland P, Segal MR, McNeil RB, Parker CB, Pemberton VL, Grobman WA, Silver RM, Simhan HN, Saade GR, Ganz P, Mehta P, Catov JM, Bairey Merz CN, Varagic J, Khan SS, Parry S, Reddy UM, Mercer BM, Wapner RJ, Haas DM. Large-Scale Proteomics in Early Pregnancy and Hypertensive Disorders of Pregnancy. JAMA Cardiol 2024; 9:791-799. [PMID: 38958943 PMCID: PMC11223045 DOI: 10.1001/jamacardio.2024.1621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/29/2024] [Indexed: 07/04/2024]
Abstract
Importance There is no consensus regarding the best method for prediction of hypertensive disorders of pregnancy (HDP), including gestational hypertension and preeclampsia. Objective To determine predictive ability in early pregnancy of large-scale proteomics for prediction of HDP. Design, Setting, and Participants This was a nested case-control study, conducted in 2022 to 2023, using clinical data and plasma samples collected between 2010 and 2013 during the first trimester, with follow-up until pregnancy outcome. This multicenter observational study took place at 8 academic medical centers in the US. Nulliparous individuals during first-trimester clinical visits were included. Participants with HDP were selected as cases; controls were selected from those who delivered at or after 37 weeks without any HDP, preterm birth, or small-for-gestational-age infant. Age, self-reported race and ethnicity, body mass index, diabetes, health insurance, and fetal sex were available covariates. Exposures Proteomics using an aptamer-based assay that included 6481 unique human proteins was performed on stored plasma. Covariates were used in predictive models. Main Outcomes and Measures Prediction models were developed using the elastic net, and analyses were performed on a randomly partitioned training dataset comprising 80% of study participants, with the remaining 20% used as an independent testing dataset. Primary measure of predictive performance was area under the receiver operating characteristic curve (AUC). Results This study included 753 HDP cases and 1097 controls with a mean (SD) age of 26.9 (5.5) years. Maternal race and ethnicity were 51 Asian (2.8%), 275 non-Hispanic Black (14.9%), 275 Hispanic (14.9%), 1161 non-Hispanic White (62.8% ), and 88 recorded as other (4.8%), which included those who did not identify according to these designations. The elastic net model, allowing for forced inclusion of prespecified covariates, was used to adjust protein-based models for clinical and demographic variables. Under this approach, no proteins were selected to augment the clinical and demographic covariates. The predictive performance of the resulting model was modest, with a training set AUC of 0.64 (95% CI, 0.61-0.67) and a test set AUC of 0.62 (95% CI, 0.56-0.68). Further adjustment for study site yielded only minimal changes in AUCs. Conclusions and Relevance In this case-control study with detailed clinical data and stored plasma samples available in the first trimester, an aptamer-based proteomics panel did not meaningfully add to predictive utility over and above clinical and demographic factors that are routinely available.
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Affiliation(s)
- Philip Greenland
- Departments of Medicine and Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Mark R. Segal
- Department of Epidemiology and Biostatistics, University of California, San Francisco
| | | | | | - Victoria L. Pemberton
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - William A. Grobman
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Now with Department of Obstetrics and Gynecology, The Ohio State University, Columbus
| | - Robert M. Silver
- Department of Obstetrics and Gynecology, University of Utah Health, Salt Lake City
| | - Hyagriv N. Simhan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - George R. Saade
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology at UTMB Health, Galveston, Texas
- Now with Department of Obstetrics and Gynecology, Eastern Virginia Medical School, Norfolk
| | - Peter Ganz
- Department of Medicine, Zuckerberg San Francisco General Hospital and University of California, San Francisco
| | - Priya Mehta
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Janet M. Catov
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh and Magee-Women’s Research Institute, Pittsburgh, Pennsylvania
| | - C. Noel Bairey Merz
- Barbra Streisand Women’s Heart Center, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jasmina Varagic
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Sadiya S. Khan
- Division of Cardiology, Department of Medicine and Department of Preventive Medicine, Northwestern University, Chicago, Illinois
| | - Samuel Parry
- Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Uma M. Reddy
- Maternal & Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York
| | - Brian M. Mercer
- Department of Obstetrics & Gynecology, Case Western Reserve University—The MetroHealth System, Cleveland, Ohio
| | - Ronald J. Wapner
- Clinical Genetics and Genomics, Maternal & Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York
| | - David M. Haas
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis
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Rajagopalan S, Dobre M, Dazard JE, Vergara-Martel A, Connelly K, Farkouh ME, Gaztanaga J, Conger H, Dever A, Razavi-Nematollahi L, Fares A, Pereira G, Edwards-Glenn J, Cameron M, Cameron C, Al-Kindi S, Brook RD, Pitt B, Weir M. Mineralocorticoid Receptor Antagonism Prevents Aortic Plaque Progression and Reduces Left Ventricular Mass and Fibrosis in Patients With Type 2 Diabetes and Chronic Kidney Disease: The MAGMA Trial. Circulation 2024; 150:663-676. [PMID: 39129649 DOI: 10.1161/circulationaha.123.067620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 06/12/2024] [Indexed: 08/13/2024]
Abstract
BACKGROUND Persistent mineralocorticoid receptor activation is a pathologic response in type 2 diabetes and chronic kidney disease. Whereas mineralocorticoid receptor antagonists are beneficial in reducing cardiovascular complications, direct mechanistic pathways for these effects in humans are lacking. METHODS The MAGMA trial (Mineralocorticoid Receptor Antagonism Clinical Evaluation in Atherosclerosis) was a randomized, double-blind, placebo-controlled trial in patients with high-risk type 2 diabetes with chronic kidney disease (not receiving dialysis) on maximum tolerated renin-angiotensin system blockade. The primary end point was change in thoracic aortic wall volume, expressed as absolute or percent value (ΔTWV or ΔPWV), using 3T magnetic resonance imaging at 12 months. Secondary end points were changes in left ventricle (LV) mass; LV fibrosis, measured as a change in myocardial native T1; and 24-hour ambulatory and central aortic blood pressures. Tertiary end points included plasma proteomic changes in 7596 plasma proteins using an aptamer-based assay. RESULTS A total of 79 patients were randomized to placebo (n=42) or 25 mg of spironolactone daily (n=37). After a modified intent-to-treat, including available baseline data of study end points, patients who completed the trial protocol were included in the final analyses. At the 12-month follow-up, the average change in PWV was 7.1±10.7% in the placebo group and 0.87±10.0% in the spironolactone group (P=0.028), and ΔTWV was 1.2±1.7 cm3 in the placebo group and 0.037±1.9 cm3 in the spironolactone group (P=0.022). Change in LV mass was 3.1±8.4 g in the placebo group and -5.8±8.4 g in the spironolactone group (P=0.001). Changes in LV T1 values were significantly different between the placebo and spironolactone groups (26.0±41.9 ms in the placebo group versus a decrease of -10.1±36.3 ms in the spironolactone group; P=6.33×10-4). Mediation analysis revealed that the spironolactone effect on thoracic aortic wall volume and myocardial mass remained significant after adjustment for ambulatory and central blood pressures. Proteomic analysis revealed a dominant effect of spironolactone on pathways involving oxidative stress, inflammation, and leukocyte activation. CONCLUSIONS Among patients with diabetes with moderate to severe chronic kidney disease at elevated cardiovascular risk, treatment with spironolactone prevented progression of aortic wall volume and resulted in regression of LV mass and favorable alterations in native T1, suggesting amelioration of left-ventricular fibrosis. REGISTRATION URL: https://www.clinicaltrials.gov; Unique identifier: NCT02169089.
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Affiliation(s)
- Sanjay Rajagopalan
- University Hospitals (S.R., M.D., J.-E.D., A.V.-M., H.C., A.D., L.R.-N., A.F., G.P.), Cleveland, OH
- Case Western Reserve University (S.R., M.D., J.-E.D., A.V.-M., L.R.-N., J.E.-G., M.C., C.C.), Cleveland, OH
| | - Mirela Dobre
- University Hospitals (S.R., M.D., J.-E.D., A.V.-M., H.C., A.D., L.R.-N., A.F., G.P.), Cleveland, OH
- Case Western Reserve University (S.R., M.D., J.-E.D., A.V.-M., L.R.-N., J.E.-G., M.C., C.C.), Cleveland, OH
| | - Jean-Eudes Dazard
- University Hospitals (S.R., M.D., J.-E.D., A.V.-M., H.C., A.D., L.R.-N., A.F., G.P.), Cleveland, OH
| | - Armando Vergara-Martel
- University Hospitals (S.R., M.D., J.-E.D., A.V.-M., H.C., A.D., L.R.-N., A.F., G.P.), Cleveland, OH
- Case Western Reserve University (S.R., M.D., J.-E.D., A.V.-M., L.R.-N., J.E.-G., M.C., C.C.), Cleveland, OH
| | - Kim Connelly
- St Michael's Hospital, University of Toronto, Canada (K.C.)
| | | | - Juan Gaztanaga
- New York University Langone Health School of Medicine, Winthrop, Mineola (J.G.)
| | - Heather Conger
- University Hospitals (S.R., M.D., J.-E.D., A.V.-M., H.C., A.D., L.R.-N., A.F., G.P.), Cleveland, OH
| | - Ann Dever
- University Hospitals (S.R., M.D., J.-E.D., A.V.-M., H.C., A.D., L.R.-N., A.F., G.P.), Cleveland, OH
| | - Laleh Razavi-Nematollahi
- University Hospitals (S.R., M.D., J.-E.D., A.V.-M., H.C., A.D., L.R.-N., A.F., G.P.), Cleveland, OH
- Case Western Reserve University (S.R., M.D., J.-E.D., A.V.-M., L.R.-N., J.E.-G., M.C., C.C.), Cleveland, OH
| | - Anas Fares
- University Hospitals (S.R., M.D., J.-E.D., A.V.-M., H.C., A.D., L.R.-N., A.F., G.P.), Cleveland, OH
| | - Gabriel Pereira
- University Hospitals (S.R., M.D., J.-E.D., A.V.-M., H.C., A.D., L.R.-N., A.F., G.P.), Cleveland, OH
| | - Jonnelle Edwards-Glenn
- Case Western Reserve University (S.R., M.D., J.-E.D., A.V.-M., L.R.-N., J.E.-G., M.C., C.C.), Cleveland, OH
| | - Mark Cameron
- Case Western Reserve University (S.R., M.D., J.-E.D., A.V.-M., L.R.-N., J.E.-G., M.C., C.C.), Cleveland, OH
| | - Cheryl Cameron
- Case Western Reserve University (S.R., M.D., J.-E.D., A.V.-M., L.R.-N., J.E.-G., M.C., C.C.), Cleveland, OH
| | - Sadeer Al-Kindi
- Debakey Heart and Vascular Center Houston Methodist Hospital, TX (S.A.-K.)
| | - Robert D Brook
- University of Michigan Frankel Cardiovascular Center, Ann Arbor (R.D.B.)
| | | | - Matthew Weir
- Division of Nephrology, University of Maryland Medical Center, Baltimore (M.W.)
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5
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Ardissino M, Truong B, Slob EAW, Schuermans A, Yoshiji S, Morley AP, Burgess S, Ng FS, de Marvao A, Natarajan P, Nicolaides K, Gaziano L, Butterworth A, Honigberg MC. Proteome- and Transcriptome-Wide Genetic Analysis Identifies Biological Pathways and Candidate Drug Targets for Preeclampsia. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024:e004755. [PMID: 39119725 PMCID: PMC7616531 DOI: 10.1161/circgen.124.004755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Preeclampsia is a leading cause of maternal and perinatal morbidity and mortality. However, the current understanding of its underlying biological pathways remains limited. METHODS In this study, we performed a cross-platform proteome- and transcriptome-wide genetic analysis aimed at evaluating the causal relevance of >2000 circulating proteins with preeclampsia, supported by data on the expression of over 15 000 genes across 36 tissues leveraging large-scale preeclampsia genetic association data from women of European ancestry. RESULTS We demonstrate genetic associations of 18 circulating proteins with preeclampsia (SULT1A1, SH2B3, SERPINE2, RGS18, PZP, NOTUM, METAP1, MANEA, jun-D, GDF15 [growth/differentiation factor 15], FGL1, FGF5, FES, APOBR, ANP, ALDH-E2, ADAMTS13, and 3MG), among which 11 were either directly or indirectly supported by gene expression data, 9 were supported by Bayesian colocalization analyses, and 5 (SERPINE2, PZP, FGF5, FES, and ANP) were supported by all lines of evidence examined. Protein interaction mapping identified potential shared biological pathways through natriuretic peptide signaling, blood pressure regulation, immune tolerance, and thrombin activity regulation. CONCLUSIONS This investigation identified multiple targetable proteins linked to cardiovascular, inflammatory, and coagulation pathways, with SERPINE2, PZP, FGF5, FES, and ANP identified as pivotal proteins with likely causal roles in the development of preeclampsia. The identification of these potential targets may guide the development of targeted therapies for preeclampsia.
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Affiliation(s)
- Maddalena Ardissino
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care (M.A., L.G., A.B.)
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, United Kingdom. (M.A, A.B.)
- National Heart and Lung Institute, Imperial College London, United Kingdom. (M.A, F.S.N.)
- Medical Research Council, London Institute of Medical Sciences, Imperial College London, United Kingdom. (M.A.)
| | - Buu Truong
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, United Kingdom. (B.T., A.S., P.N., M.C.H.)
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston (B.T., A.S., P.N., M.C.H.)
| | - Eric A W Slob
- MRC Biostatistics Unit, University of Cambridge, United Kingdom. (E.A.W.S., S.B.)
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, the Netherlands. (E.A.W.S.)
- Erasmus University Rotterdam Institute for Behavior and Biology, Erasmus University Rotterdam, the Netherlands. (E.A.W.S.)
- Department of Psychology, Education and Child Studies, Erasmus University Rotterdam, the Netherlands. (E.A.W.S.)
| | - Art Schuermans
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, United Kingdom. (B.T., A.S., P.N., M.C.H.)
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston (B.T., A.S., P.N., M.C.H.)
- Faculty of Medicine, KU Leuven, Belgium (A.S.)
| | - Satoshi Yoshiji
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, United Kingdom. (S.Y.)
| | - Alec P Morley
- Department of Medicine, School of Clinical Medicine, University of Cambridge, United Kingdom. (A.P.M.)
- Gonville and Caius College, University of Cambridge, United Kingdom. (A.P.M.)
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, United Kingdom. (E.A.W.S., S.B.)
| | - Fu Siong Ng
- National Heart and Lung Institute, Imperial College London, United Kingdom. (M.A, F.S.N.)
| | - Antonio de Marvao
- Department of Women and Children's Health, King's College Hospital, London, United Kingdom. (A.d.M., K.N.)
- British Heart Foundation Center of Research Excellence, School of Cardiovascular Medicine and Sciences, King's College Hospital, London, United Kingdom. (A.d.M.)
- Fetal Medicine Research Institute, King's College Hospital, London, United Kingdom. (A.d.M., K.N.)
| | - Pradeep Natarajan
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, United Kingdom. (B.T., A.S., P.N., M.C.H.)
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston (B.T., A.S., P.N., M.C.H.)
| | - Kypros Nicolaides
- Department of Women and Children's Health, King's College Hospital, London, United Kingdom. (A.d.M., K.N.)
- Fetal Medicine Research Institute, King's College Hospital, London, United Kingdom. (A.d.M., K.N.)
| | - Liam Gaziano
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care (M.A., L.G., A.B.)
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Harvard Medical School, Boston. (L.G.)
| | - Adam Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care (M.A., L.G., A.B.)
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, United Kingdom. (M.A, A.B.)
- British Heart Foundation Center of Research Excellence, University of Cambridge, United Kingdom. (A.B.)
- Health Data Research UK Cambridge, Wellcome Genome Campus, University of Cambridge, United Kingdom. (A.B.)
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, United Kingdom. (A.B.)
| | - Michael C Honigberg
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, United Kingdom. (B.T., A.S., P.N., M.C.H.)
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston (B.T., A.S., P.N., M.C.H.)
- Department of Medicine, Harvard Medical School, Boston. (M.C.H.)
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6
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Buthmann JL, Miller JG, Aghaeepour N, King LS, Stevenson DK, Shaw GM, Wong RJ, Gotlib IH. Large-scale proteomics in the first trimester of pregnancy predict psychopathology and temperament in preschool children: an exploratory study. J Child Psychol Psychiatry 2024; 65:1098-1107. [PMID: 38287782 PMCID: PMC11265978 DOI: 10.1111/jcpp.13948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/23/2023] [Indexed: 01/31/2024]
Abstract
BACKGROUND Understanding the prenatal origins of children's psychopathology is a fundamental goal in developmental and clinical science. Recent research suggests that inflammation during pregnancy can trigger a cascade of fetal programming changes that contribute to vulnerability for the emergence of psychopathology. Most studies, however, have focused on a handful of proinflammatory cytokines and have not explored a range of prenatal biological pathways that may be involved in increasing postnatal risk for emotional and behavioral difficulties. METHODS Using extreme gradient boosted machine learning models, we explored large-scale proteomics, considering over 1,000 proteins from first trimester blood samples, to predict behavior in early childhood. Mothers reported on their 3- to 5-year-old children's (N = 89, 51% female) temperament (Child Behavior Questionnaire) and psychopathology (Child Behavior Checklist). RESULTS We found that machine learning models of prenatal proteomics predict 5%-10% of the variance in children's sadness, perceptual sensitivity, attention problems, and emotional reactivity. Enrichment analyses identified immune function, nervous system development, and cell signaling pathways as being particularly important in predicting children's outcomes. CONCLUSIONS Our findings, though exploratory, suggest processes in early pregnancy that are related to functioning in early childhood. Predictive features included far more proteins than have been considered in prior work. Specifically, proteins implicated in inflammation, in the development of the central nervous system, and in key cell-signaling pathways were enriched in relation to child temperament and psychopathology measures.
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Affiliation(s)
- Jessica L. Buthmann
- Department of Psychology, Stanford University, 450 Serra Mall, Stanford CA 94305
| | - Jonas G. Miller
- Department of Psychological Sciences, University of Connecticut, 406 Babbidge Road, Unit 1020, Storrs, CT 06269-1020
| | - Nima Aghaeepour
- Department of Pediatrics, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305
- Department of Biomedical Data Science, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305
| | - Lucy S. King
- Department of Psychology, Stanford University, 450 Serra Mall, Stanford CA 94305
| | - David K. Stevenson
- Department of Pediatrics, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305
| | - Ronald J. Wong
- Department of Pediatrics, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305
| | - Ian H. Gotlib
- Department of Psychology, Stanford University, 450 Serra Mall, Stanford CA 94305
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7
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Kraemer S, Schneider DJ, Paterson C, Perry D, Westacott MJ, Hagar Y, Katilius E, Lynch S, Russell TM, Johnson T, Astling DP, DeLisle RK, Cleveland J, Gold L, Drolet DW, Janjic N. Crossing the Halfway Point: Aptamer-Based, Highly Multiplexed Assay for the Assessment of the Proteome. J Proteome Res 2024. [PMID: 39038188 DOI: 10.1021/acs.jproteome.4c00411] [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: 07/24/2024]
Abstract
Measuring responses in the proteome to various perturbations improves our understanding of biological systems. The value of information gained from such studies is directly proportional to the number of proteins measured. To overcome technical challenges associated with highly multiplexed measurements, we developed an affinity reagent-based method that uses aptamers with protein-like side chains along with an assay that takes advantage of their unique properties. As hybrid affinity reagents, modified aptamers are fully comparable to antibodies in terms of binding characteristics toward proteins, including epitope size, shape complementarity, affinity and specificity. Our assay combines these intrinsic binding properties with serial kinetic proofreading steps to allow highly effective partitioning of stable specific complexes from unstable nonspecific complexes. The use of these orthogonal methods to enhance specificity effectively overcomes the severe limitation to multiplexing inherent to the use of sandwich-based methods. Our assay currently measures half of the unique proteins encoded in the human genome with femtomolar sensitivity, broad dynamic range and exceptionally high reproducibility. Using machine learning to identify patterns of change, we have developed tests based on measurement of multiple proteins predictive of current health states and future disease risk to guide a holistic approach to precision medicine.
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Affiliation(s)
- Stephan Kraemer
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Daniel J Schneider
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Clare Paterson
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Darryl Perry
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Matthew J Westacott
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Yolanda Hagar
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Evaldas Katilius
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Sean Lynch
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Theresa M Russell
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Ted Johnson
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - David P Astling
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Robert Kirk DeLisle
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Jason Cleveland
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Larry Gold
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Daniel W Drolet
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Nebojsa Janjic
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
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Patel‐Murray NL, Zhang L, Claggett BL, Xu D, Serrano‐Fernandez P, Healey M, Wandel S, Chen C, Jacob J, Xu H, Turner GM, Chutkow W, Yates DP, O'Donnell CJ, Prescott MF, Lefkowitz M, Gimpelewicz CR, Beste MT, Zhao F, Gou L, Desai AS, Jhund PS, Packer M, Pfeffer MA, Redfield MM, Rouleau JL, Zannad F, Zile MR, McMurray JJV, Mendelson MM, Solomon SD, Cunningham JW. Aptamer Proteomics for Biomarker Discovery in Heart Failure With Preserved Ejection Fraction: The PARAGON-HF Proteomic Substudy. J Am Heart Assoc 2024; 13:e033544. [PMID: 38904251 PMCID: PMC11255700 DOI: 10.1161/jaha.123.033544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/15/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Prognostic markers and biological pathways linked to detrimental clinical outcomes in heart failure with preserved ejection fraction (HFpEF) remain incompletely defined. METHODS AND RESULTS We measured serum levels of 4123 unique proteins in 1117 patients with HFpEF enrolled in the PARAGON-HF (Efficacy and Safety of LCZ696 Compared to Valsartan, on Morbidity and Mortality in Heart Failure Patients With Preserved Ejection Fraction) trial using a modified aptamer proteomic assay. Baseline circulating protein concentrations significantly associated with the primary end point and the timing and occurrence of total heart failure hospitalization and cardiovascular death were identified by recurrent events regression, accounting for multiple testing, adjusted for age, sex, treatment, and anticoagulant use, and compared with published analyses in 2515 patients with heart failure with reduced ejection fraction from the PARADIGM-HF (Prospective Comparison of ARNI With ACEI to Determine Impact on Global Mortality and Morbidity in Heart Failure) and ATMOSPHERE (Efficacy and Safety of Aliskiren and Aliskiren/Enalapril Combination on Morbidity-Mortality in Patients With Chronic Heart Failure) clinical trials. We identified 288 proteins that were robustly associated with the risk of heart failure hospitalization and cardiovascular death in patients with HFpEF. The baseline proteins most strongly related to outcomes included B2M (β-2 microglobulin), TIMP1 (tissue inhibitor of matrix metalloproteinase 1), SERPINA4 (serpin family A member 4), and SVEP1 (sushi, von Willebrand factor type A, EGF, and pentraxin domain containing 1). Overall, the protein-outcome associations in patients with HFpEF did not markedly differ as compared with patients with heart failure with reduced ejection fraction. A proteomic risk score derived in patients with HFpEF was not superior to a previous proteomic score derived in heart failure with reduced ejection fraction nor to clinical risk factors, NT-proBNP (N-terminal pro-B-type natriuretic peptide), or high-sensitivity cardiac troponin. CONCLUSIONS Numerous serum proteins linked to metabolic, coagulation, and extracellular matrix regulatory pathways were associated with worse HFpEF prognosis in the PARAGON-HF proteomic substudy. Our results demonstrate substantial similarities among serum proteomic risk markers for heart failure hospitalization and cardiovascular death when comparing clinical trial participants with heart failure across the ejection fraction spectrum. REGISTRATION URL: https://www.clinicaltrials.gov; Unique Identifiers: NCT01920711, NCT01035255, NCT00853658.
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Affiliation(s)
| | - Luqing Zhang
- Novartis Institutes for Biomedical ResearchCambridgeMAUSA
| | - Brian L. Claggett
- Cardiovascular Division, Brigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
| | - Dongchu Xu
- Cardiovascular Division, Brigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
| | | | | | | | | | - Jaison Jacob
- Novartis Institutes for Biomedical ResearchCambridgeMAUSA
| | - Huilei Xu
- Novartis Institutes for Biomedical ResearchCambridgeMAUSA
| | | | | | | | | | | | | | | | | | - Faye Zhao
- Novartis Institutes for Biomedical ResearchCambridgeMAUSA
| | - Liangke Gou
- Novartis Pharmaceuticals CorporationEast HanoverNJUSA
| | - Akshay S. Desai
- Cardiovascular Division, Brigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
| | - Pardeep S. Jhund
- BHF Glasgow Cardiovascular Research Center, School of Cardiovascular and Metabolic HealthUniversity of GlasgowGlasgowUK
| | | | - Marc A. Pfeffer
- Cardiovascular Division, Brigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
| | | | - Jean L. Rouleau
- Institut de Cardiologie de MontréalUniversité de MontréalQBCanada
| | - Faiez Zannad
- Inserm, Centre d’Investigation Clinique Plurithématique 1433, U1116, CHRU de Nancy, F‐CRIN INI‐CRCTUniversité de LorraineNancyFrance
| | - Michael R. Zile
- Medical University of South Carolina and RHJ Department of Veterans Administration Medical CenterCharlestonSCUSA
| | - John J. V. McMurray
- BHF Glasgow Cardiovascular Research Center, School of Cardiovascular and Metabolic HealthUniversity of GlasgowGlasgowUK
| | | | - Scott D. Solomon
- Cardiovascular Division, Brigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
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9
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Zhai J, Voraphani N, Imboden M, Keidel D, Liu C, Stern DA, Venker C, Petersen H, Bosco A, Sherrill DL, Morgan WJ, Tesfaigzi Y, Probst-Hensch NM, Martinez FD, Halonen M, Guerra S. Circulating biomarkers of airflow limitation across the life span. J Allergy Clin Immunol 2024; 153:1692-1703. [PMID: 38253260 PMCID: PMC11162345 DOI: 10.1016/j.jaci.2023.12.026] [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: 05/08/2023] [Revised: 12/16/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024]
Abstract
BACKGROUND Airflow limitation is a hallmark of chronic obstructive pulmonary disease, which can develop through different lung function trajectories across the life span. There is a need for longitudinal studies aimed at identifying circulating biomarkers of airflow limitation across different stages of life. OBJECTIVES This study sought to identify a signature of serum proteins associated with airflow limitation and evaluate their relation to lung function longitudinally in adults and children. METHODS This study used data from 3 adult cohorts (TESAOD [Tucson Epidemiological Study of Airway Obstructive Disease], SAPALDIA [Swiss Cohort Study on Air Pollution and Lung and Heart Diseases in Adults], LSC [Lovelace Smoker Cohort]) and 1 birth cohort (TCRS [Tucson Children's Respiratory Study]) (N = 1940). In TESAOD, among 46 circulating proteins, we identified those associated with FEV1/forced vital capacity (FVC) percent (%) predicted levels and generated a score based on the sum of their z-scores. Cross-sectional analyses were used to test the score for association with concomitant lung function. Longitudinal analyses were used to test the score for association with subsequent lung function growth in childhood and decline in adult life. RESULTS After false discovery rate adjustment, serum levels of 5 proteins (HP, carcinoembryonic antigen, ICAM1, CRP, TIMP1) were associated with percent predicted levels of FEV1/FVC and FEV1 in TESAOD. In cross-sectional multivariate analyses the 5-biomarker score was associated with FEV1 % predicted in all adult cohorts (meta-analyzed FEV1 decrease for 1-SD score increase: -2.9%; 95% CI: -3.9%, -1.9%; P = 2.4 × 10-16). In multivariate longitudinal analyses, the biomarker score at 6 years of age was inversely associated with FEV1 and FEV1/FVC levels attained by young adult life (P = .02 and .005, respectively). In adults, persistently high levels of the biomarker score were associated with subsequent accelerated decline of FEV1 and FEV1/FVC (P = .01 and .001). CONCLUSIONS A signature of 5 circulating biomarkers of airflow limitation was associated with both impaired lung function growth in childhood and accelerated lung function decline in adult life, indicating that these proteins may be involved in multiple lung function trajectories leading to chronic obstructive pulmonary disease.
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Affiliation(s)
- Jing Zhai
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Ariz
| | - Nipasiri Voraphani
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Ariz
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Dirk Keidel
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Congjian Liu
- Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Debra A Stern
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Ariz
| | - Claire Venker
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Ariz
| | - Hans Petersen
- Lovelace Respiratory Research Institute, Albuquerque, NM
| | - Anthony Bosco
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Ariz
| | - Duane L Sherrill
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Ariz
| | - Wayne J Morgan
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Ariz
| | - Yohannes Tesfaigzi
- Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Lovelace Respiratory Research Institute, Albuquerque, NM
| | - Nicole M Probst-Hensch
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Fernando D Martinez
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Ariz
| | - Marilyn Halonen
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Ariz
| | - Stefano Guerra
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Ariz.
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10
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Sproull M, Fan Y, Chen Q, Meerzaman D, Camphausen K. Comparison of Novel Proteomic Expression Profiles for Radiation Exposure in Male and Female C57BL6 Mice. Radiat Res 2024; 201:558-566. [PMID: 38684463 PMCID: PMC11257380 DOI: 10.1667/rade-23-00180.1] [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: 04/30/2023] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
There is a need for point-of-care diagnostics for future mass casualty events involving radiation exposure. The development of radiation exposure and dose prediction algorithms for biodosimetry is needed for screening of large populations during these scenarios, and exploration of the potential effects which sex, age, genetic heterogeneity, and physiological comorbidities may have on the utility of biodosimetry diagnostics is needed. In the current study, proteomic profiling was used to examine sex-specific differences in age-matched C57BL6 mice on the blood proteome after radiation exposure, and the usefulness of development and application of biodosimetry algorithms using both male and female samples. Male and female mice between 9-11 weeks of age received a dose of total-body irradiation (TBI) of either 2, 4 or 8 Gy and plasma was collected at days 1, 3 and 7 postirradiation. Plasma was then screened using the SomaScan v4.1 assay for ∼7,000 protein analytes. A subset panel of protein biomarkers demonstrated significant (FDR < 0.05 and |logFC| > 0.2) changes in expression after radiation exposure. All proteins were used for feature selection to build predictive models of radiation exposure using different sample and sex-specific cohorts. Both binary (prediction of any radiation exposure) and multidose (prediction of specific radiation dose) model series were developed using either female and male samples combined or only female or only male samples. The binary series (models 1, 2 and 3) and multidose series (models 4, 5 and 6) included female/male combined, female only and male only respectively. Detectable values were obtained for all ∼7,000 proteins included in the SomaScan assay for all samples. Each model algorithm built using a unique sample cohort was validated with a training set of samples and tested with a separate new sample series. Overall predictive accuracies in the binary model series was ∼100% at the model training level, and when tested with fresh samples, 97.9% for model 1 (female and male) and 100% for model 2 (female only) and model 3 (male only). When sex-specific models 2 and 3 were tested with the opposite sex, the overall predictive accuracy rate dropped to 62.5% for model 2 and remained 100% for model 3. The overall predictive accuracy rate in the multidose model series was 100% for all models at the model training level and, when tested with fresh samples, 83.3%, 75% and 83.3% for Multidose models 4-6, respectively. When sex-specific model 5 (female only) and model 6 (male only) were tested with the opposite sex, the overall predictive accuracy rate dropped to 52.1% and 68.8%, respectively. These models represent novel predictive panels of radiation-responsive proteomic biomarkers and illustrate the utility and necessity of considering sex-specific differences in development of radiation biodosimetry prediction algorithms. As sex-specific differences were observed in this study, and as use of point-of-care radiation diagnostics in future mass casualty settings will necessarily include persons of both sexes, consideration of sex-specific variation is essential to ensure these diagnostic tools have practical utility in the field.
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Affiliation(s)
- M. Sproull
- Radiation Oncology Branch, National Cancer Institute, Bethesda, Maryland
| | - Y. Fan
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institute of Health, Rockville, Maryland
| | - Q. Chen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institute of Health, Rockville, Maryland
| | - D. Meerzaman
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institute of Health, Rockville, Maryland
| | - K. Camphausen
- Radiation Oncology Branch, National Cancer Institute, Bethesda, Maryland
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11
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Mahjoubin-Tehran M, Rezaei S, Santos RD, Jamialahmadi T, Almahmeed W, Sahebkar A. Targeting PCSK9 as a key player in lipid metabolism: exploiting the therapeutic and biosensing potential of aptamers. Lipids Health Dis 2024; 23:156. [PMID: 38796450 PMCID: PMC11128129 DOI: 10.1186/s12944-024-02151-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/17/2024] [Indexed: 05/28/2024] Open
Abstract
The degradation of low-density lipoprotein receptor (LDLR) is induced by proprotein convertase subtilisin/kexin type 9 (PCSK9), resulting in elevated plasma concentrations of LDL cholesterol. Therefore, inhibiting the interactions between PCSK9 and LDLR is a desirable therapeutic goal for managing hypercholesterolemia. Aptamers, which are RNA or single-stranded DNA sequences, can recognize their targets based on their secondary structure. Aptamers exhibit high selectivity and affinity for binding to target molecules. The systematic evolution of ligands by exponential enrichment (SELEX), a combination of biological approaches, is used to screen most aptamers in vitro. Due to their unique advantages, aptamers have garnered significant interest since their discovery and have found extensive applications in various fields. Aptamers have been increasingly utilized in the development of biosensors for sensitive detection of pathogens, analytes, toxins, drug residues, and malignant cells. Furthermore, similar to monoclonal antibodies, aptamers can serve as therapeutic tools. Unlike certain protein therapeutics, aptamers do not elicit antibody responses, and their modified sugars at the 2'-positions generally prevent toll-like receptor-mediated innate immune responses. The focus of this review is on aptamer-based targeting of PCSK9 and the application of aptamers both as biosensors and therapeutic agents.
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Affiliation(s)
- Maryam Mahjoubin-Tehran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Rezaei
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Raul D Santos
- Lipid Clinic Heart Institute (Incor), University of São Paulo, Medical School Hospital, São Paulo, Brazil
| | - Tannaz Jamialahmadi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Wael Almahmeed
- Heart and Vascular Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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12
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Riviere-Cazaux C, Graser CJ, Warrington AE, Hoplin MD, Andersen KM, Malik N, Palmer EA, Carlstrom LP, Dasari S, Munoz-Casabella A, Ikram S, Ghadimi K, Himes BT, Jusue-Torres I, Sarkaria JN, Meyer FB, Van Gompel JJ, Kizilbash SH, Sener U, Michor F, Campian JL, Parney IF, Burns TC. The dynamic impact of location and resection on the glioma CSF proteome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.15.24307463. [PMID: 38798641 PMCID: PMC11118641 DOI: 10.1101/2024.05.15.24307463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
While serial sampling of glioma tissue is rarely performed prior to recurrence, cerebrospinal fluid (CSF) is an underutilized longitudinal source of candidate glioma biomarkers for understanding therapeutic impacts. However, the impact of key variables to consider in longitudinal CSF samples, including anatomical location and post-surgical changes, remains unknown. To that end, pre- versus post-resection intracranial CSF samples were obtained at early (1-16 days; n=20) or delayed (86-153 days; n=11) timepoints for patients with glioma. Paired lumbar-versus-intracranial glioma CSF samples were also obtained (n=14). Using aptamer-based proteomics, we identify significant differences in the CSF proteome between lumbar, subarachnoid, and ventricular CSF. Our analysis of serial intracranial CSF samples suggests the early potential for disease monitoring and evaluation of pharmacodynamic impact of targeted therapies. Importantly, we found that resection had a significant, evolving longitudinal impact on the CSF proteome. Proteomic data are provided with individual clinical annotations as a resource for the field. One Sentence Summary Glioma cerebrospinal fluid (CSF) accessed intra-operatively and longitudinally via devices can reveal impacts of treatment and anatomical location.
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Liang W, Wei T, Hu L, Chen M, Tong L, Zhou W, Duan X, Zhao X, Zhou W, Jiang Q, Xiao G, Zou W, Chen D, Zou Z, Bai X. An integrated multi-omics analysis reveals osteokines involved in global regulation. Cell Metab 2024; 36:1144-1163.e7. [PMID: 38574738 DOI: 10.1016/j.cmet.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/22/2024] [Accepted: 03/10/2024] [Indexed: 04/06/2024]
Abstract
Bone secretory proteins, termed osteokines, regulate bone metabolism and whole-body homeostasis. However, fundamental questions as to what the bona fide osteokines and their cellular sources are and how they are regulated remain unclear. In this study, we analyzed bone and extraskeletal tissues, osteoblast (OB) conditioned media, bone marrow supernatant (BMS), and serum, for basal osteokines and those responsive to aging and mechanical loading/unloading. We identified 375 candidate osteokines and their changes in response to aging and mechanical dynamics by integrating data from RNA-seq, scRNA-seq, and proteomic approaches. Furthermore, we analyzed their cellular sources in the bone and inter-organ communication facilitated by them (bone-brain, liver, and aorta). Notably, we discovered that senescent OBs secrete fatty-acid-binding protein 3 to propagate senescence toward vascular smooth muscle cells (VSMCs). Taken together, we identified previously unknown candidate osteokines and established a dynamic regulatory network among them, thus providing valuable resources to further investigate their systemic roles.
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Affiliation(s)
- Wenquan Liang
- State Key Laboratory of Organ Failure Research, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tiantian Wei
- State Key Laboratory of Organ Failure Research, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Le Hu
- State Key Laboratory of Organ Failure Research, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Meijun Chen
- State Key Laboratory of Organ Failure Research, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Liping Tong
- Research Center for Computer-Aided Drug Discovery, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wu Zhou
- State Key Laboratory of Organ Failure Research, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xingwei Duan
- State Key Laboratory of Organ Failure Research, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiaoyang Zhao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Weijie Zhou
- Department of Pathology, Nanfang Hospital, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Qing Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Guozhi Xiao
- Department of Biochemistry, School of Medicine, Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China
| | - Weiguo Zou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Di Chen
- Research Center for Computer-Aided Drug Discovery, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology, Shenzhen, China.
| | - Zhipeng Zou
- State Key Laboratory of Organ Failure Research, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Xiaochun Bai
- State Key Laboratory of Organ Failure Research, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Academy of Orthopedics, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong Province 510630, China.
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14
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Kurgan N, Kjærgaard Larsen J, Deshmukh AS. Harnessing the power of proteomics in precision diabetes medicine. Diabetologia 2024; 67:783-797. [PMID: 38345659 DOI: 10.1007/s00125-024-06097-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/20/2023] [Indexed: 03/21/2024]
Abstract
Precision diabetes medicine (PDM) aims to reduce errors in prevention programmes, diagnosis thresholds, prognosis prediction and treatment strategies. However, its advancement and implementation are difficult due to the heterogeneity of complex molecular processes and environmental exposures that influence an individual's disease trajectory. To address this challenge, it is imperative to develop robust screening methods for all areas of PDM. Innovative proteomic technologies, alongside genomics, have proven effective in precision cancer medicine and are showing promise in diabetes research for potential translation. This narrative review highlights how proteomics is well-positioned to help improve PDM. Specifically, a critical assessment of widely adopted affinity-based proteomic technologies in large-scale clinical studies and evidence of the benefits and feasibility of using MS-based plasma proteomics is presented. We also present a case for the use of proteomics to identify predictive protein panels for type 2 diabetes subtyping and the development of clinical prediction models for prevention, diagnosis, prognosis and treatment strategies. Lastly, we discuss the importance of plasma and tissue proteomics and its integration with genomics (proteogenomics) for identifying unique type 2 diabetes intra- and inter-subtype aetiology. We conclude with a call for action formed on advancing proteomics technologies, benchmarking their performance and standardisation across sites, with an emphasis on data sharing and the inclusion of diverse ancestries in large cohort studies. These efforts should foster collaboration with key stakeholders and align with ongoing academic programmes such as the Precision Medicine in Diabetes Initiative consortium.
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Affiliation(s)
- Nigel Kurgan
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Kjærgaard Larsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Atul S Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
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15
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Yan X, Huang S, Li H, Feng Z, Kong J, Liu J. The causal effect of mTORC1-dependent circulating protein levels on nonalcoholic fatty liver disease: A Mendelian randomization study. Dig Liver Dis 2024; 56:559-564. [PMID: 37778897 DOI: 10.1016/j.dld.2023.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/24/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND The mechanistic target of rapamycin (mTOR) signal pathway plays a crucial role in the development of nonalcoholic fatty liver disease (NAFLD). However, the causal effect of mTOR downstream proteins on NAFLD remains unknown. AIMS We conducted a two-sample Mendelian randomization (MR) study to investigate whether the mTOR-dependent circulating proteins, including Eukaryotic Initiation Factor 4E Binding Proteins (eIF4EBPs), Ribosomal Protein S6K kinase 1 (RP-S6K), Eukaryotic Initiation Factor 4E (eIF4E), Eukaryotic Initiation Factor 4A (eIF4A) and Eukaryotic Initiation Factor 4 G (eIF4G), have causal effects on the risk of NAFLD. METHODS The causal estimate was evaluated with the inverse-variance weighted (IVW) method in discovery stage and validation stage. The single-nucleotide polymorphisms (SNPs) were selected to genetically predict exposures from Genome-Wide Association Studies (GWAS). Exposures with statistically significant effects in the discovery dataset would be further validated in the validation dataset. RESULTS MR study revealed that eIF4E had a causal effect on NAFLD in both discovery stage (OR = 1.339, P = 0.037) and validation stage (OR = 1.0007, P = 0.022). Sensitivity analyses confirmed robustness of the results. CONCLUSION The genetically predicted higher level of mTOR-dependent eIF4E in plasma might have a causal effect on the occurrence of NAFLD.
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Affiliation(s)
- Xiangyu Yan
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Songhan Huang
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Hongxin Li
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Zichen Feng
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Junjie Kong
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China; Department of hepatobiliary surgery, Shandong Provincial Hospital affiliated to Shandong first medical university, Jinan, Shandong 250021, China
| | - Jun Liu
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China; Department of hepatobiliary surgery, Shandong Provincial Hospital affiliated to Shandong first medical university, Jinan, Shandong 250021, China.
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16
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Saloner R, Staffaroni A, Dammer E, Johnson ECB, Paolillo E, Wise A, Heuer H, Forsberg L, Lago AL, Webb J, Vogel J, Santillo A, Hansson O, Kramer J, Miller B, Li J, Loureiro J, Sivasankaran R, Worringer K, Seyfried N, Yokoyama J, Seeley W, Spina S, Grinberg L, VandeVrede L, Ljubenkov P, Bayram E, Bozoki A, Brushaber D, Considine C, Day G, Dickerson B, Domoto-Reilly K, Faber K, Galasko D, Geschwind D, Ghoshal N, Graff-Radford N, Hales C, Honig L, Hsiung GY, Huey E, Kornak J, Kremers W, Lapid M, Lee S, Litvan I, McMillan C, Mendez M, Miyagawa T, Pantelyat A, Pascual B, Paulson H, Petrucelli L, Pressman P, Ramos E, Rascovsky K, Roberson E, Savica R, Snyder A, Sullivan AC, Tartaglia C, Vandebergh M, Boeve B, Rosen H, Rojas J, Boxer A, Casaletto K. Large-scale network analysis of the cerebrospinal fluid proteome identifies molecular signatures of frontotemporal lobar degeneration. RESEARCH SQUARE 2024:rs.3.rs-4103685. [PMID: 38585969 PMCID: PMC10996789 DOI: 10.21203/rs.3.rs-4103685/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The pathophysiological mechanisms driving disease progression of frontotemporal lobar degeneration (FTLD) and corresponding biomarkers are not fully understood. We leveraged aptamer-based proteomics (> 4,000 proteins) to identify dysregulated communities of co-expressed cerebrospinal fluid proteins in 116 adults carrying autosomal dominant FTLD mutations (C9orf72, GRN, MAPT) compared to 39 noncarrier controls. Network analysis identified 31 protein co-expression modules. Proteomic signatures of genetic FTLD clinical severity included increased abundance of RNA splicing (particularly in C9orf72 and GRN) and extracellular matrix (particularly in MAPT) modules, as well as decreased abundance of synaptic/neuronal and autophagy modules. The generalizability of genetic FTLD proteomic signatures was tested and confirmed in independent cohorts of 1) sporadic progressive supranuclear palsy-Richardson syndrome and 2) frontotemporal dementia spectrum syndromes. Network-based proteomics hold promise for identifying replicable molecular pathways in adults living with FTLD. 'Hub' proteins driving co-expression of affected modules warrant further attention as candidate biomarkers and therapeutic targets.
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Affiliation(s)
| | | | | | | | | | - Amy Wise
- University of California, San Francisco
| | | | | | | | | | | | | | | | | | | | - Jingyao Li
- Novartis Institutes for Biomedical Research, Inc
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Suzee Lee
- University of California, San Francisco
| | | | - Corey McMillan
- Department of Neurology, University of Pennsylvania, Philadelphia, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Adam Boxer
- Memory and Aging Center, Department of Neurology, University of California, San Francisco
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17
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Dorian D, Gustafson D, Quinn R, Bentley RF, Dorian P, Goodman JM, Fish JE, Connelly KA. Exercise-Dependent Modulation of Immunological Response Pathways in Endurance Athletes With and Without Atrial Fibrillation. J Am Heart Assoc 2024; 13:e033640. [PMID: 38497478 PMCID: PMC11009995 DOI: 10.1161/jaha.123.033640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/12/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Atrial fibrillation (AF) is a common arrhythmia characterized by uncoordinated atrial electrical activity. Lone AF occurs in the absence of traditional risk factors and is frequently observed in male endurance athletes, who face a 2- to 5-fold higher risk of AF compared with healthy, moderately active males. Our understanding of how endurance exercise contributes to the pathophysiology of lone AF remains limited. This study aimed to characterize the circulating protein fluctuations during high-intensity exercise as well as explore potential biomarkers of exercise-associated AF. METHODS AND RESULTS A prospective cohort of 12 male endurance cyclists between the ages of 40 and 65 years, 6 of whom had a history of exercise-associated AF, were recruited to participate using a convenience sampling method. The circulating proteome was subsequently analyzed using multiplex immunoassays and aptamer-based proteomics before, during, and after an acute high-intensity endurance exercise bout to assess temporality and identify potential markers of AF. The endurance exercise bout resulted in significant alterations to proteins involved in immune modulation (eg, growth/differentiation factor 15), skeletal muscle metabolism (eg, α-actinin-2), cell death (eg, histones), and inflammation (eg, interleukin-6). Subjects with AF differed from those without, displaying modulation of proteins previously known to have associations with incident AF (eg, C-reactive protein, insulin-like growth factor-1, and angiopoietin-2), and also with proteins having no previous association (eg, tapasin-related protein and α2-Heremans-Schmid glycoprotein). CONCLUSIONS These findings provide insights into the proteomic response to acute intense exercise, provide mechanistic insights into the pathophysiology behind AF in athletes, and identify targets for future study and validation.
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Affiliation(s)
- David Dorian
- Department of Medicine, Division of CardiologyUniversity of TorontoTorontoOntarioCanada
| | - Dakota Gustafson
- Department of Laboratory Medicine & PathobiologyUniversity of TorontoTorontoOntarioCanada
- Toronto General Hospital Research InstituteUniversity Health NetworkTorontoOntarioCanada
- Faculty of Health SciencesQueen’s UniversityKingstonOntarioCanada
| | - Ryan Quinn
- Division of CardiologyLi Ka Shing Knowledge Institute of St. Michael’s HospitalTorontoOntarioCanada
| | - Robert F. Bentley
- Faculty of Kinesiology and Physical EducationUniversity of TorontoTorontoOntarioCanada
| | - Paul Dorian
- Department of Medicine, Division of CardiologyUniversity of TorontoTorontoOntarioCanada
- Division of CardiologyLi Ka Shing Knowledge Institute of St. Michael’s HospitalTorontoOntarioCanada
- Department of MedicineUniversity of TorontoTorontoOntarioCanada
- Keenan Research Centre for Biomedical ScienceSt Michael’s Hospital, University of TorontoTorontoOntarioCanada
- Department of PhysiologyUniversity of TorontoTorontoOntarioCanada
- Heart and Stroke Richard Lewar Centre for Research ExcellenceUniversity of TorontoTorontoOntarioCanada
| | - Jack M. Goodman
- Faculty of Kinesiology and Physical EducationUniversity of TorontoTorontoOntarioCanada
- Heart and Stroke Richard Lewar Centre for Research ExcellenceUniversity of TorontoTorontoOntarioCanada
- Division of CardiologySinai Health/University Health NetworkTorontoOntarioCanada
| | - Jason E. Fish
- Department of Laboratory Medicine & PathobiologyUniversity of TorontoTorontoOntarioCanada
- Toronto General Hospital Research InstituteUniversity Health NetworkTorontoOntarioCanada
- Peter Munk Cardiac CentreUniversity Health NetworkTorontoOntarioCanada
| | - Kim A. Connelly
- Department of Medicine, Division of CardiologyUniversity of TorontoTorontoOntarioCanada
- Division of CardiologyLi Ka Shing Knowledge Institute of St. Michael’s HospitalTorontoOntarioCanada
- Department of MedicineUniversity of TorontoTorontoOntarioCanada
- Keenan Research Centre for Biomedical ScienceSt Michael’s Hospital, University of TorontoTorontoOntarioCanada
- Department of PhysiologyUniversity of TorontoTorontoOntarioCanada
- Heart and Stroke Richard Lewar Centre for Research ExcellenceUniversity of TorontoTorontoOntarioCanada
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18
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Wittich H, Ardlie K, Taylor KD, Durda P, Liu Y, Mikhaylova A, Gignoux CR, Cho MH, Rich SS, Rotter JI, Manichaikul A, Im HK, Wheeler HE. Transcriptome-wide association study of the plasma proteome reveals cis and trans regulatory mechanisms underlying complex traits. Am J Hum Genet 2024; 111:445-455. [PMID: 38320554 PMCID: PMC10940016 DOI: 10.1016/j.ajhg.2024.01.006] [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: 09/25/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
Regulation of transcription and translation are mechanisms through which genetic variants affect complex traits. Expression quantitative trait locus (eQTL) studies have been more successful at identifying cis-eQTL (within 1 Mb of the transcription start site) than trans-eQTL. Here, we tested the cis component of gene expression for association with observed plasma protein levels to identify cis- and trans-acting genes that regulate protein levels. We used transcriptome prediction models from 49 Genotype-Tissue Expression (GTEx) Project tissues to predict the cis component of gene expression and tested the predicted expression of every gene in every tissue for association with the observed abundance of 3,622 plasma proteins measured in 3,301 individuals from the INTERVAL study. We tested significant results for replication in 971 individuals from the Trans-omics for Precision Medicine (TOPMed) Multi-Ethnic Study of Atherosclerosis (MESA). We found 1,168 and 1,210 cis- and trans-acting associations that replicated in TOPMed (FDR < 0.05) with a median expected true positive rate (π1) across tissues of 0.806 and 0.390, respectively. The target proteins of trans-acting genes were enriched for transcription factor binding sites and autoimmune diseases in the GWAS catalog. Furthermore, we found a higher correlation between predicted expression and protein levels of the same underlying gene (R = 0.17) than observed expression (R = 0.10, p = 7.50 × 10-11). This indicates the cis-acting genetically regulated (heritable) component of gene expression is more consistent across tissues than total observed expression (genetics + environment) and is useful in uncovering the function of SNPs associated with complex traits.
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Affiliation(s)
- Henry Wittich
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA
| | - Kristin Ardlie
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Peter Durda
- Laboratory for Clinical Biochemistry Research, University of Vermont, Colchester, VT 05446, USA
| | - Yongmei Liu
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anna Mikhaylova
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Chris R Gignoux
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Heather E Wheeler
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA; Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA.
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19
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Yu G, Tam HCH, Huang C, Shi M, Lim CKP, Chan JCN, Ma RCW. Lessons and Applications of Omics Research in Diabetes Epidemiology. Curr Diab Rep 2024; 24:27-44. [PMID: 38294727 PMCID: PMC10874344 DOI: 10.1007/s11892-024-01533-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
PURPOSE OF REVIEW Recent advances in genomic technology and molecular techniques have greatly facilitated the identification of disease biomarkers, advanced understanding of pathogenesis of different common diseases, and heralded the dawn of precision medicine. Much of these advances in the area of diabetes have been made possible through deep phenotyping of epidemiological cohorts, and analysis of the different omics data in relation to detailed clinical information. In this review, we aim to provide an overview on how omics research could be incorporated into the design of current and future epidemiological studies. RECENT FINDINGS We provide an up-to-date review of the current understanding in the area of genetic, epigenetic, proteomic and metabolomic markers for diabetes and related outcomes, including polygenic risk scores. We have drawn on key examples from the literature, as well as our own experience of conducting omics research using the Hong Kong Diabetes Register and Hong Kong Diabetes Biobank, as well as other cohorts, to illustrate the potential of omics research in diabetes. Recent studies highlight the opportunity, as well as potential benefit, to incorporate molecular profiling in the design and set-up of diabetes epidemiology studies, which can also advance understanding on the heterogeneity of diabetes. Learnings from these examples should facilitate other researchers to consider incorporating research on omics technologies into their work to advance the field and our understanding of diabetes and its related co-morbidities. Insights from these studies would be important for future development of precision medicine in diabetes.
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Affiliation(s)
- Gechang Yu
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Henry C H Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Chuiguo Huang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Mai Shi
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Cadmon K P Lim
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Juliana C N Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, HKSAR, China.
- Chinese University of Hong Kong- Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, HKSAR, China.
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, HKSAR, China.
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20
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Manoli I, Sysol JR, Head PE, Epping MW, Gavrilova O, Crocker MK, Sloan JL, Koutsoukos SA, Wang C, Ktena YP, Mendelson S, Pass AR, Zerfas PM, Hoffmann V, Vernon HJ, Fletcher LA, Reynolds JC, Tsokos MG, Stratakis CA, Voss SD, Chen KY, Brown RJ, Hamosh A, Berry GT, Chen XS, Yanovski JA, Venditti CP. Lipodystrophy in methylmalonic acidemia associated with elevated FGF21 and abnormal methylmalonylation. JCI Insight 2024; 9:e174097. [PMID: 38271099 DOI: 10.1172/jci.insight.174097] [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: 07/24/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
A distinct adipose tissue distribution pattern was observed in patients with methylmalonyl-CoA mutase deficiency, an inborn error of branched-chain amino acid (BCAA) metabolism, characterized by centripetal obesity with proximal upper and lower extremity fat deposition and paucity of visceral fat, that resembles familial multiple lipomatosis syndrome. To explore brown and white fat physiology in methylmalonic acidemia (MMA), body composition, adipokines, and inflammatory markers were assessed in 46 patients with MMA and 99 matched controls. Fibroblast growth factor 21 levels were associated with acyl-CoA accretion, aberrant methylmalonylation in adipose tissue, and an attenuated inflammatory cytokine profile. In parallel, brown and white fat were examined in a liver-specific transgenic MMA mouse model (Mmut-/- TgINS-Alb-Mmut). The MMA mice exhibited abnormal nonshivering thermogenesis with whitened brown fat and had an ineffective transcriptional response to cold stress. Treatment of the MMA mice with bezafibrates led to clinical improvement with beiging of subcutaneous fat depots, which resembled the distribution seen in the patients. These studies defined what we believe to be a novel lipodystrophy phenotype in patients with defects in the terminal steps of BCAA oxidation and demonstrated that beiging of subcutaneous adipose tissue in MMA could readily be induced with small molecules.
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Affiliation(s)
- Irini Manoli
- Metabolic Medicine Branch, National Human Genome Research Institute
| | - Justin R Sysol
- Metabolic Medicine Branch, National Human Genome Research Institute
| | | | | | - Oksana Gavrilova
- Mouse Metabolism Core, National Institute of Diabetes and Digestive and Kidney Diseases
| | - Melissa K Crocker
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development; and
| | - Jennifer L Sloan
- Metabolic Medicine Branch, National Human Genome Research Institute
| | | | - Cindy Wang
- Metabolic Medicine Branch, National Human Genome Research Institute
| | - Yiouli P Ktena
- Metabolic Medicine Branch, National Human Genome Research Institute
| | - Sophia Mendelson
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development; and
| | - Alexandra R Pass
- Metabolic Medicine Branch, National Human Genome Research Institute
| | - Patricia M Zerfas
- Office of Research Services, Division of Veterinary Resources, NIH, Bethesda, Maryland, USA
| | - Victoria Hoffmann
- Office of Research Services, Division of Veterinary Resources, NIH, Bethesda, Maryland, USA
| | - Hilary J Vernon
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Laura A Fletcher
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases
| | | | - Maria G Tsokos
- Ultrastructural Pathology Section, Center for Cancer Research; and
| | - Constantine A Stratakis
- Section on Endocrinology & Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Stephan D Voss
- Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kong Y Chen
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases
| | - Rebecca J Brown
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gerard T Berry
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaoyuan Shawn Chen
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, Maryland, USA
| | - Jack A Yanovski
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development; and
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21
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Walitt B, Singh K, LaMunion SR, Hallett M, Jacobson S, Chen K, Enose-Akahata Y, Apps R, Barb JJ, Bedard P, Brychta RJ, Buckley AW, Burbelo PD, Calco B, Cathay B, Chen L, Chigurupati S, Chen J, Cheung F, Chin LMK, Coleman BW, Courville AB, Deming MS, Drinkard B, Feng LR, Ferrucci L, Gabel SA, Gavin A, Goldstein DS, Hassanzadeh S, Horan SC, Horovitz SG, Johnson KR, Govan AJ, Knutson KM, Kreskow JD, Levin M, Lyons JJ, Madian N, Malik N, Mammen AL, McCulloch JA, McGurrin PM, Milner JD, Moaddel R, Mueller GA, Mukherjee A, Muñoz-Braceras S, Norato G, Pak K, Pinal-Fernandez I, Popa T, Reoma LB, Sack MN, Safavi F, Saligan LN, Sellers BA, Sinclair S, Smith B, Snow J, Solin S, Stussman BJ, Trinchieri G, Turner SA, Vetter CS, Vial F, Vizioli C, Williams A, Yang SB, Nath A. Deep phenotyping of post-infectious myalgic encephalomyelitis/chronic fatigue syndrome. Nat Commun 2024; 15:907. [PMID: 38383456 PMCID: PMC10881493 DOI: 10.1038/s41467-024-45107-3] [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: 06/24/2023] [Accepted: 01/16/2024] [Indexed: 02/23/2024] Open
Abstract
Post-infectious myalgic encephalomyelitis/chronic fatigue syndrome (PI-ME/CFS) is a disabling disorder, yet the clinical phenotype is poorly defined, the pathophysiology is unknown, and no disease-modifying treatments are available. We used rigorous criteria to recruit PI-ME/CFS participants with matched controls to conduct deep phenotyping. Among the many physical and cognitive complaints, one defining feature of PI-ME/CFS was an alteration of effort preference, rather than physical or central fatigue, due to dysfunction of integrative brain regions potentially associated with central catechol pathway dysregulation, with consequences on autonomic functioning and physical conditioning. Immune profiling suggested chronic antigenic stimulation with increase in naïve and decrease in switched memory B-cells. Alterations in gene expression profiles of peripheral blood mononuclear cells and metabolic pathways were consistent with cellular phenotypic studies and demonstrated differences according to sex. Together these clinical abnormalities and biomarker differences provide unique insight into the underlying pathophysiology of PI-ME/CFS, which may guide future intervention.
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Affiliation(s)
- Brian Walitt
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Komudi Singh
- National Heart, Lung and Blood Institute (NHLBI), Bethesda, MD, USA
| | - Samuel R LaMunion
- National Institute of Diabetes, Digestion, and Kidney Disease (NIDDK), Bethesda, MD, USA
| | - Mark Hallett
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Steve Jacobson
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Kong Chen
- National Institute of Diabetes, Digestion, and Kidney Disease (NIDDK), Bethesda, MD, USA
| | | | - Richard Apps
- NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), Bethesda, MD, USA
| | | | - Patrick Bedard
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Robert J Brychta
- National Institute of Diabetes, Digestion, and Kidney Disease (NIDDK), Bethesda, MD, USA
| | | | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research (NIDCR), Bethesda, MD, USA
| | - Brice Calco
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Brianna Cathay
- Texas A&M School of Engineering Medicine, College Station, TX, USA
| | - Li Chen
- Affiliated Hospital of North Sichuan Medical College, Sichuan, China
| | - Snigdha Chigurupati
- George Washington University Hospital, District of Columbia, Washington, DC, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), Bethesda, MD, USA
| | - Foo Cheung
- NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), Bethesda, MD, USA
| | | | | | - Amber B Courville
- National Institute of Diabetes, Digestion, and Kidney Disease (NIDDK), Bethesda, MD, USA
| | | | | | | | | | - Scott A Gabel
- National Institute of Environmental Health Sciences (NIEHS), Chapel Hill, NC, USA
| | - Angelique Gavin
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - David S Goldstein
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | | | - Sean C Horan
- Sidney Kimmel Medical College, Philadelphia, PA, USA
| | - Silvina G Horovitz
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Kory R Johnson
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Anita Jones Govan
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Kristine M Knutson
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Joy D Kreskow
- National Institute of Nursing Research (NINR), Bethesda, MD, USA
| | - Mark Levin
- National Heart, Lung and Blood Institute (NHLBI), Bethesda, MD, USA
| | - Jonathan J Lyons
- National Institute of Allergy and Infectious Disease (NIAID), Bethesda, MD, USA
| | - Nicholas Madian
- National Center for Complementary and Integrative Health (NCCIH), Bethesda, MD, USA
| | - Nasir Malik
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Andrew L Mammen
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), Bethesda, MD, USA
| | | | - Patrick M McGurrin
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | | | - Ruin Moaddel
- National Institute of Aging (NIA), Baltimore, MD, USA
| | - Geoffrey A Mueller
- National Institute of Environmental Health Sciences (NIEHS), Chapel Hill, NC, USA
| | - Amrita Mukherjee
- NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), Bethesda, MD, USA
| | - Sandra Muñoz-Braceras
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), Bethesda, MD, USA
| | - Gina Norato
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Katherine Pak
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), Bethesda, MD, USA
| | - Iago Pinal-Fernandez
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), Bethesda, MD, USA
| | - Traian Popa
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Lauren B Reoma
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Michael N Sack
- National Heart, Lung and Blood Institute (NHLBI), Bethesda, MD, USA
| | - Farinaz Safavi
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
- National Institute of Allergy and Infectious Disease (NIAID), Bethesda, MD, USA
| | - Leorey N Saligan
- National Institute of Nursing Research (NINR), Bethesda, MD, USA
| | - Brian A Sellers
- NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), Bethesda, MD, USA
| | | | - Bryan Smith
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Joseph Snow
- National Institute of Mental Health (NIMH), Bethesda, MD, USA
| | | | - Barbara J Stussman
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
- National Center for Complementary and Integrative Health (NCCIH), Bethesda, MD, USA
| | | | | | | | - Felipe Vial
- Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Carlotta Vizioli
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Ashley Williams
- Oakland University William Beaumont School of Medicine, Rochester, NY, USA
| | | | - Avindra Nath
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA.
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22
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Fu L, Guldiken N, Remih K, Karl AS, Preisinger C, Strnad P. Serum/Plasma Proteome in Non-Malignant Liver Disease. Int J Mol Sci 2024; 25:2008. [PMID: 38396688 PMCID: PMC10889128 DOI: 10.3390/ijms25042008] [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: 12/22/2023] [Revised: 01/31/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
The liver is the central metabolic organ and produces 85-90% of the proteins found in plasma. Accordingly, the plasma proteome is an attractive source of liver disease biomarkers that reflects the different cell types present in this organ, as well as the processes such as responses to acute and chronic injury or the formation of an extracellular matrix. In the first part, we summarize the biomarkers routinely used in clinical evaluations and their biological relevance in the different stages of non-malignant liver disease. Later, we describe the current proteomic approaches, including mass spectrometry and affinity-based techniques, that allow a more comprehensive assessment of the liver function but also require complex data processing. The many approaches of analysis and interpretation and their potential caveats are delineated. While these advances hold the promise to transform our understanding of liver diseases and support the development and validation of new liver-related drugs, an interdisciplinary collaboration is needed.
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Affiliation(s)
- Lei Fu
- Department of Internal Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (L.F.); (N.G.); (K.R.); (A.S.K.)
| | - Nurdan Guldiken
- Department of Internal Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (L.F.); (N.G.); (K.R.); (A.S.K.)
| | - Katharina Remih
- Department of Internal Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (L.F.); (N.G.); (K.R.); (A.S.K.)
| | - Anna Sophie Karl
- Department of Internal Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (L.F.); (N.G.); (K.R.); (A.S.K.)
| | - Christian Preisinger
- Proteomics Facility, Interdisciplinary Centre for Clinical Research (IZKF), Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany;
| | - Pavel Strnad
- Department of Internal Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (L.F.); (N.G.); (K.R.); (A.S.K.)
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23
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Di Mauro V, Lauta FC, Modica J, Appleton SL, De Franciscis V, Catalucci D. Diagnostic and Therapeutic Aptamers: A Promising Pathway to Improved Cardiovascular Disease Management. JACC Basic Transl Sci 2024; 9:260-277. [PMID: 38510714 PMCID: PMC10950404 DOI: 10.1016/j.jacbts.2023.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/29/2023] [Indexed: 03/22/2024]
Abstract
Despite advances in care, cardiovascular diseases remain the leading cause of death worldwide. As a result, identifying suitable biomarkers for early diagnosis and improving therapeutic and diagnostic strategies is crucial. Because of their significant advantages over other therapeutic approaches, nucleic-based therapies, particularly aptamers, are gaining increased attention. Aptamers are innovative synthetic polymers or oligomers of single-stranded DNA (ssDNA) or RNA molecules that can form 3-dimensional structures and thus interact with their targets with high specificity and affinity. Furthermore, they outperform classical protein-based antibodies in terms of in vitro selection, production, ease of modification and conjugation, high stability, low immunogenicity, and suitability for nanoparticle functionalization for targeted drug delivery. This work aims to review the advances made in the aptamers' field in biomarker detection, diagnosis, imaging, and targeted therapy, which highlight their huge potential in the management of cardiovascular diseases.
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Affiliation(s)
- Vittoria Di Mauro
- Veneto Institute of Molecular Medicine, Padua, Italy
- Institute of Genetic and Biomedical Research, Milan, Milan Italy
- Humanitas Cardio Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | | | - Jessica Modica
- Institute of Genetic and Biomedical Research, Milan, Milan Italy
- Humanitas Cardio Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Silvia Lucia Appleton
- Institute of Genetic and Biomedical Research, Milan, Milan Italy
- Humanitas Cardio Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | | | - Daniele Catalucci
- Institute of Genetic and Biomedical Research, Milan, Milan Italy
- Humanitas Cardio Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
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24
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Radulova P, Boncheva M, Nachev G, Slancheva B, Dimitrova V. Plasma KL-6 as a Potential Biomarker for Bronchopulmonary Dysplasia in Preterm Infants. Crit Care Res Pract 2024; 2024:3623948. [PMID: 38328675 PMCID: PMC10846922 DOI: 10.1155/2024/3623948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/20/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
Background KL-6 is a biomarker of interstitial lung injury and increases during repair. Aim Our aim was to determine the predictive value of plasma KL-6 for the development of bronchopulmonary dysplasia (BPD) in preterm infants. Methods Ninety-five extremely preterm infants (EPIs), born at <28 gestational age (GA), were divided into two main BPD groups as follows: the moderate/severe and the no/mild group. KL-6 was analyzed on days 7 and 14. Binary logistic regression analyses and ROC curve analyses were performed. Results Infants <26 + 0 weeks' GA have higher mean KL-6 than infants >25 + 6 weeks' GA on 7 and 14 days (335 vs. 286 U/ml and 378 vs. 260 U/ml; p = 0.005 and 0.018, respectively). In the binary regression model at KL-6 day 7, three of the prognostic factors remained significant-mechanical ventilation OR: 10.38 (95% CI: 3.57-30.14), PDA OR: 6.39 (95% CI: 0.87-46.74), and KL-6 OR: 4.98 (95% CI: 1.54-16.08). The AUC was 0.86 with a sensitivity and specificity of 79% at a cutoff value ≥0.34. In the binary regression model at KL-6 day 14, six of the prognostic factors were significant-PDA OR: 23.34 (95% CI: 2.14-254.24), KL-6 OR: 13.59 (95% CI: 3.19-57.96), GA OR: 4.58 (95% CI: 1.16-18.06), mechanical ventilation OR: 4.45 (95% CI: 1.23-16.16), antenatal steroids OR: 0.19 (95% CI: 0.04-0.95), and gender (female OR: 0.30 (95% CI 0.08-1.12)). The AUC was 0.91, and the sensitivity and accuracy for a cutoff ≥0.37 were 89% and 85%, respectively. Conclusion KL-6 could be a useful screening biomarker for early detection of infants at increased risk for developing BPD.
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Affiliation(s)
- Petya Radulova
- Department of Obstetrics and Gynecology, Medical University of Sofia, Zdrave 2 Street, Sofia 1431, Bulgaria
- Neonatology Clinic, University Hospital of Obstetrics and Gynecology “Maichin Dom”, Sofia, Bulgaria
| | - Margaritka Boncheva
- University Hospital for Active Treatment “St. Ekaterina”, Pencho Slaveikov Street, 52A, Sofia 1431, Bulgaria
| | - Gencho Nachev
- University Hospital for Active Treatment “St. Ekaterina”, Pencho Slaveikov Street, 52A, Sofia 1431, Bulgaria
| | - Boriana Slancheva
- Department of Obstetrics and Gynecology, Medical University of Sofia, Zdrave 2 Street, Sofia 1431, Bulgaria
- Neonatology Clinic, University Hospital of Obstetrics and Gynecology “Maichin Dom”, Sofia, Bulgaria
| | - Violeta Dimitrova
- Department of Obstetrics and Gynecology, Medical University of Sofia, Zdrave 2 Street, Sofia 1431, Bulgaria
- Neonatology Clinic, University Hospital of Obstetrics and Gynecology “Maichin Dom”, Sofia, Bulgaria
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Ben Yellin, Lahav C, Sela I, Yahalom G, Shoval SR, Elon Y, Fuller J, Harel M. Analytical validation of the PROphet test for treatment decision-making guidance in metastatic non-small cell lung cancer. J Pharm Biomed Anal 2024; 238:115803. [PMID: 37871417 DOI: 10.1016/j.jpba.2023.115803] [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: 08/07/2023] [Revised: 09/22/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
The blood proteome, consisting of thousands of proteins engaged in various biological processes, acts as a valuable source of potential biomarkers for various medical applications. PROphet is a plasma proteomics-based test that serves as a decision-support tool for non-small cell lung cancer (NSCLC) patients, combining proteomic profiling using SomaScan technology and subsequent computational algorithm. PROphet was implemented as a laboratory developed test (LDT). Under the Clinical Laboratory Improvement Amendments (CLIA) and Commission on Office Laboratory Accreditation (COLA) regulations, prior to releasing patient test results, a clinical laboratory located in the United States employing an LDT must examine its performance characteristics with regard to analytical validity. This study describes the experimental and computational analytical validity of the PROphet test, as required by CLIA/COLA regulations. Experimental precision analysis displayed a median coefficient of variation (CV) of 3.9 % and 4.7 % for intra-plate and inter-plate examination, respectively, and the median accuracy rate between sites was 88 %. Computational precision exhibited a high accuracy rate, with 93 % of samples displaying complete concordance in results. A cross-platform comparison between SomaScan and other proteomics platforms yielded a median Spearman's rank correlation coefficient of 0.51, affirming the consistency and reliability of the SomaScan platform as used under the PROphet test. Our study presents a robust framework for evaluating the analytical validity of a platform that combines an experimental assay with subsequent computational algorithms. When applied to the PROphet test, strong analytical performance of the test was demonstrated.
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Affiliation(s)
- Ben Yellin
- OncoHost LTD, Hamelacha 17 Binyamina, 3057324, Israel
| | - Coren Lahav
- OncoHost LTD, Hamelacha 17 Binyamina, 3057324, Israel
| | - Itamar Sela
- OncoHost LTD, Hamelacha 17 Binyamina, 3057324, Israel
| | - Galit Yahalom
- OncoHost LTD, Hamelacha 17 Binyamina, 3057324, Israel
| | | | | | - James Fuller
- OncoHost Inc., 1110 SE Cary Parkway, Suite 205, Cary, NC 27518, USA
| | - Michal Harel
- OncoHost LTD, Hamelacha 17 Binyamina, 3057324, Israel.
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26
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Wang Y, Yi K, Chen B, Zhang B, Jidong G. Elucidating the susceptibility to breast cancer: an in-depth proteomic and transcriptomic investigation into novel potential plasma protein biomarkers. Front Mol Biosci 2024; 10:1340917. [PMID: 38304232 PMCID: PMC10833003 DOI: 10.3389/fmolb.2023.1340917] [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: 11/19/2023] [Accepted: 12/29/2023] [Indexed: 02/03/2024] Open
Abstract
Objectives: This study aimed to identify plasma proteins that are associated with and causative of breast cancer through Proteome and Transcriptome-wide association studies combining Mendelian Randomization. Methods: Utilizing high-throughput datasets, we designed a two-phase analytical framework aimed at identifying novel plasma proteins that are both associated with and causative of breast cancer. Initially, we conducted Proteome/Transcriptome-wide association studies (P/TWAS) to identify plasma proteins with significant associations. Subsequently, Mendelian Randomization was employed to ascertain the causation. The validity and robustness of our findings were further reinforced through external validation and various sensitivity analyses, including Bayesian colocalization, Steiger filtering, heterogeneity and pleiotropy. Additionally, we performed functional enrichment analysis of the identified proteins to better understand their roles in breast cancer and to assess their potential as druggable targets. Results: We identified 5 plasma proteins demonstrating strong associations and causative links with breast cancer. Specifically, PEX14 (OR = 1.201, p = 0.016) and CTSF (OR = 1.114, p < 0.001) both displayed positive and causal association with breast cancer. In contrast, SNUPN (OR = 0.905, p < 0.001), CSK (OR = 0.962, p = 0.038), and PARK7 (OR = 0.954, p < 0.001) were negatively associated with the disease. For the ER-positive subtype, 3 plasma proteins were identified, with CSK and CTSF exhibiting consistent trends, while GDI2 (OR = 0.920, p < 0.001) was distinct to this subtype. In ER-negative subtype, PEX14 (OR = 1.645, p < 0.001) stood out as the sole protein, even showing a stronger causal effect compared to breast cancer. These associations were robustly supported by colocalization and sensitivity analyses. Conclusion: Integrating multiple data dimensions, our study successfully pinpointed plasma proteins significantly associated with and causative of breast cancer, offering valuable insights for future research and potential new biomarkers and therapeutic targets.
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Affiliation(s)
- Yang Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kexin Yi
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Baoyue Chen
- Department of General Surgery, Beijing Puren Hospital, Beijing, China
| | - Bailin Zhang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Gao Jidong
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
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27
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Curtis BE, Abdo Z, Graham B, LaVoy A, Evans SJM, Santangelo K, Dean GA. An Aptamer-Based Proteomic Analysis of Plasma from Cats ( Felis catus) with Clinical Feline Infectious Peritonitis. Viruses 2024; 16:141. [PMID: 38257841 PMCID: PMC10819688 DOI: 10.3390/v16010141] [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: 10/17/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Feline infectious peritonitis (FIP) is a systemic disease manifestation of feline coronavirus (FCoV) and is the most important cause of infectious disease-related deaths in domestic cats. FIP has a variable clinical manifestation but is most often characterized by widespread vasculitis with visceral involvement and/or neurological disease that is typically fatal in the absence of antiviral therapy. Using an aptamer-based proteomics assay, we analyzed the plasma protein profiles of cats who were naturally infected with FIP (n = 19) in comparison to the plasma protein profiles of cats who were clinically healthy and negative for FCoV (n = 17) and cats who were positive for the enteric form of FCoV (n = 9). We identified 442 proteins that were significantly differentiable; in total, 219 increased and 223 decreased in FIP plasma versus clinically healthy cat plasma. Pathway enrichment and associated analyses showed that differentiable proteins were related to immune system processes, including the innate immune response, cytokine signaling, and antigen presentation, as well as apoptosis and vascular integrity. The relevance of these findings is discussed in the context of previous studies. While these results have the potential to inform diagnostic, therapeutic, and preventative investigations, they represent only a first step, and will require further validation.
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Affiliation(s)
| | | | | | | | | | | | - Gregg A. Dean
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA; (B.E.C.); (A.L.); (S.J.M.E.); (K.S.)
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28
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Boehler JF, Brown KJ, Ricotti V, Morris CA. N-terminal titin fragment: a non-invasive, pharmacodynamic biomarker for microdystrophin efficacy. Skelet Muscle 2024; 14:2. [PMID: 38229112 PMCID: PMC10790446 DOI: 10.1186/s13395-023-00334-y] [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: 11/13/2023] [Accepted: 12/29/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Multiple clinical trials to assess the efficacy of AAV-directed gene transfer in participants with Duchenne muscular dystrophy (DMD) are ongoing. The success of these trials currently relies on standard functional outcome measures that may exhibit variability within and between participants, rendering their use as sole measures of drug efficacy challenging. Given this, supportive objective biomarkers may be useful in enhancing observed clinical results. Creatine kinase (CK) is traditionally used as a diagnostic biomarker of DMD, but its potential as a robust pharmacodynamic (PD) biomarker is difficult due to the wide variability seen within the same participant over time. Thus, there is a need for the discovery and validation of novel PD biomarkers to further support and bolster traditional outcome measures of efficacy in DMD. METHOD Potential PD biomarkers in DMD participant urine were examined using a proteomic approach on the Somalogic platform. Findings were confirmed in both mdx mice and Golden Retriever muscular dystrophy (GRMD) dog plasma samples. RESULTS Changes in the N-terminal fragment of titin, a well-known, previously characterized biomarker of DMD, were correlated with the expression of microdystrophin protein in mice, dogs, and humans. Further, titin levels were sensitive to lower levels of expressed microdystrophin when compared to CK. CONCLUSION The measurement of objective PD biomarkers such as titin may provide additional confidence in the assessment of the mechanism of action and efficacy in gene therapy clinical trials of DMD. TRIAL REGISTRATION ClinicalTrials.gov NCT03368742.
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Affiliation(s)
- Jessica F Boehler
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA, 02129, USA.
| | - Kristy J Brown
- Rejuvenate Bio, 11425 Sorrento Valley Road, San Diego, CA, 92121, USA
| | - Valeria Ricotti
- National Institute for Health and Care Research Great Ormond Street Hospital Biomedical Research Centre/University College London Great Ormond Street Institute of Child Health, London, UK
| | - Carl A Morris
- PHDL Consulting LLC, 43 Sylvanus Wood Lane, Woburn, MA, 01801, USA
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29
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Martin DR, Mutombwera AT, Madiehe AM, Onani MO, Meyer M, Cloete R. Molecular modeling and simulation studies of SELEX-derived high-affinity DNA aptamers to the Ebola virus nucleoprotein. J Biomol Struct Dyn 2024:1-18. [PMID: 38217874 DOI: 10.1080/07391102.2024.2302922] [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: 04/19/2023] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
Ebola viral disease (EVD) is a highly infectious and potentially fatal illness with a case fatality rate ranging from 25% to 90%. To effectively control its spread, there is a need for rapid, reliable and lowcost point-of-care (P OC) diagnostic tests. While various EVD diagnostic tests exist, few are P OC tests, and many are not cost-effective. The use of antibodies in these tests has limitations, prompting the exploration of aptamers as potential alternatives. Various proteins from the Ebola virus (EBOV) proteome, including EBOV nucleoprotein (NP), are considered viable targets for diagnostic assays. A previous study identified three aptamers (Apt1. Apt2 and Apt3) with high affinity for EBOV NP using systemic evolution of ligands by exponential enrichment (SELEX). This study aimed to employ in silico methods, such as Phyre2, RNAfold, RNAComposer, HADDOCK and GROMACS, to model the structures of EBOV NP and the aptamers, and to investigate their binding. The in silico analysis revealed successful binding of all the three aptamers to EBOV NP, with a suggested ranking of Apt1 > Apt2 > Apt3 based on binding affinity. Microscale thermophoresis (MST) analysis confirmed the binding, providing dissociation constants of 25 ± 2.84, 56 ± 2.76 and 140 ±3.69 nM for Apt1, Apt2 and Apt3, respectively. The study shows that the findings of the in silico analysis was in agreement with the MST analysis. Inclusion of these in silico approaches in diagnostic assay development can expedite the selection of candidate aptamers, potentially overcoming challenges associated with aptamer application in diagnostics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- D R Martin
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute (SANBI), University of the Western Cape, Bellville, South Africa Cape Town, South Africa
| | - A T Mutombwera
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, South Africa
| | - A M Madiehe
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
- Nanobiotechnology Research Group, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - M O Onani
- Department of Chemistry, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - M Meyer
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - R Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute (SANBI), University of the Western Cape, Bellville, South Africa Cape Town, South Africa
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30
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Majumdar B, Sarma D, Yu Y, Lozoya-Colinas A, Chaput JC. Increasing the functional density of threose nucleic acid. RSC Chem Biol 2024; 5:41-48. [PMID: 38179195 PMCID: PMC10763562 DOI: 10.1039/d3cb00159h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/18/2023] [Indexed: 01/06/2024] Open
Abstract
Chemical strategies that augment genetic polymers with amino acid residues that are overrepresented on the paratope surface of an antibody offer a promising route for enhancing the binding properties of nucleic acid aptamers. Here, we describe the chemical synthesis of α-l-threofuranosyl cytidine nucleoside triphosphate (tCTP) carrying either a benzyl or phenylpropyl side chain at the pyrimidine C-5 position. Polymerase recognition studies indicate that both substrates are readily incorporated into a full-length α-l-threofuranosyl nucleic acid (TNA) product by extension of a DNA primer-template duplex with an engineered TNA polymerase. Similar primer extension reactions performed using nucleoside triphosphate mixtures containing both C-5 modified tCTP and C-5 modified tUTP substrates enable the production of doubly modified TNA strands for a panel of 20 chemotype combinations. Kinetic measurements reveal faster on-rates (kon) and tighter binding affinity constants (Kd) for engineered versions of TNA aptamers carrying chemotypes at both pyrimidine positions as compared to their singly modified counterparts. These findings expand the chemical space of evolvable non-natural genetic polymers by offering a path for improving the quality of biologically stable TNA aptamers for future clinical applications.
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Affiliation(s)
- Biju Majumdar
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - Daisy Sarma
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - Yutong Yu
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - Adriana Lozoya-Colinas
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
- Department of Chemistry, University of California Irvine CA 92697-3958 USA
- Department of Molecular Biology and Biochemistry, University of California Irvine CA 92697-3958 USA
- Department of Chemical and Biomolecular Engineering, University of California Irvine CA 92697-3958 USA
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Hédou J, Marić I, Bellan G, Einhaus J, Gaudillière DK, Ladant FX, Verdonk F, Stelzer IA, Feyaerts D, Tsai AS, Ganio EA, Sabayev M, Gillard J, Amar J, Cambriel A, Oskotsky TT, Roldan A, Golob JL, Sirota M, Bonham TA, Sato M, Diop M, Durand X, Angst MS, Stevenson DK, Aghaeepour N, Montanari A, Gaudillière B. Discovery of sparse, reliable omic biomarkers with Stabl. Nat Biotechnol 2024:10.1038/s41587-023-02033-x. [PMID: 38168992 PMCID: PMC11217152 DOI: 10.1038/s41587-023-02033-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 10/16/2023] [Indexed: 01/05/2024]
Abstract
Adoption of high-content omic technologies in clinical studies, coupled with computational methods, has yielded an abundance of candidate biomarkers. However, translating such findings into bona fide clinical biomarkers remains challenging. To facilitate this process, we introduce Stabl, a general machine learning method that identifies a sparse, reliable set of biomarkers by integrating noise injection and a data-driven signal-to-noise threshold into multivariable predictive modeling. Evaluation of Stabl on synthetic datasets and five independent clinical studies demonstrates improved biomarker sparsity and reliability compared to commonly used sparsity-promoting regularization methods while maintaining predictive performance; it distills datasets containing 1,400-35,000 features down to 4-34 candidate biomarkers. Stabl extends to multi-omic integration tasks, enabling biological interpretation of complex predictive models, as it hones in on a shortlist of proteomic, metabolomic and cytometric events predicting labor onset, microbial biomarkers of pre-term birth and a pre-operative immune signature of post-surgical infections. Stabl is available at https://github.com/gregbellan/Stabl .
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Affiliation(s)
- Julien Hédou
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Ivana Marić
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Grégoire Bellan
- Télécom Paris, Institut Polytechnique de Paris, Paris, France
| | - Jakob Einhaus
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Dyani K Gaudillière
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University, Stanford, CA, USA
| | | | - Franck Verdonk
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
- Sorbonne University, GRC 29, AP-HP, DMU DREAM, Department of Anesthesiology and Intensive Care, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Ina A Stelzer
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Amy S Tsai
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Maximilian Sabayev
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Joshua Gillard
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jonas Amar
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Amelie Cambriel
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Tomiko T Oskotsky
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Alennie Roldan
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan L Golob
- Department of Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Thomas A Bonham
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Masaki Sato
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Maïgane Diop
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | - Xavier Durand
- École Polytechnique, Institut Polytechnique de Paris, Paris, France
| | - Martin S Angst
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
| | | | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Andrea Montanari
- Department of Statistics, Stanford University, Stanford, CA, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Brice Gaudillière
- Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University, Stanford, CA, USA.
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
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32
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Ren Y, Ruan P, Segal M, Dobre M, Schelling JR, Banerjee U, Shafi T, Ganz P, Dubin RF. Evaluation of a large-scale aptamer proteomics platform among patients with kidney failure on dialysis. PLoS One 2023; 18:e0293945. [PMID: 38079395 PMCID: PMC10712847 DOI: 10.1371/journal.pone.0293945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/22/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Patients with kidney failure suffer high mortality, and we currently lack markers for risk stratification for these patients. We carried out a quality control study of a modified aptamer assay (SomaScan v.4.0) that measures ~ 5000 proteins, in preparation for a larger study using this platform in cohorts with kidney failure. METHODS Forty participants from the Cardiac, Endothelial Function and Arterial Stiffness in End-Stage Renal Disease (CERES study) were selected to analyze technical and short-term biological variability, orthogonal correlations and differential protein expression in plasma from patients who died during 2.5 year follow-up. Long-term (one year) variability was studied in 421 participants in the Chronic Renal Insufficiency Cohort. We evaluated 4849 aptamers (4607 unique proteins) using data formats including raw data and data formatted using Adaptive Normalization by Maximum Likelihood (ANML), an algorithm developed for SomaScan data in individuals with normal kidney function. RESULTS In ANML format, median[IQR] intra-assay coefficient of variation (CV) was 2.38%[1.76, 3.40] and inter-assay CV was 7.38%[4.61, 13.12]. Short-term within-subject CV was 5.76% [3.35, 9.72]; long-term CV was 8.71%[5.91, 13.37]. Spearman correlations between aptamer and traditional assays for PTH, NT-proBNP, FGF-23 and CRP were all > 0.7. Fold-change (FC) in protein levels among non-survivors, significant after Bonferroni correction, included SVEP1 (FC[95% CI] 2.14 [1.62, 2.82]), keratocan (1.74 [1.40, 2.15]) and LanC-like protein 1 (0.56 [0.45, 0.70]). Compared to raw aptamer data, technical and short-term biological variability in paired samples was lower in ANML-formatted data. ANML formatting had minimal impact on orthogonal correlations with traditional assays or the associations of proteins with the phenotype of mortality. CONCLUSIONS SomaScan had excellent technical variability and low within-subject short-term variability. ANML formatting could facilitate comparison of biomarker results with other studies that utilize this format. We expect SomaScan to provide novel and reproducible information in patients with kidney failure on dialysis.
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Affiliation(s)
- Yue Ren
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Peifeng Ruan
- Peter O’Donnell Jr School of Public Health, UT Southwestern, Dallas, Texas, United States of America
| | - Mark Segal
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, United States of America
| | - Mirela Dobre
- Division of Nephrology and Hypertension, University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States of America
| | - Jeffrey R. Schelling
- Department of Physiology & Biophysics, Case Western Reserve University of School of Medicine, Cleveland, Ohio, United States of America
| | - Upasana Banerjee
- Department of Internal Medicine, Hurley Medical Center/Michigan State University, Flint, Michigan, United States of America
| | - Tariq Shafi
- Division of Kidney Diseases, Hypertension and Transplantation, Houston Methodist Hospital, Houston, Texas, United States of America
| | - Peter Ganz
- Division of Cardiology, University of California, San Francisco, San Francisco, California, United States of America
| | - Ruth F. Dubin
- Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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Wickramasinghe LC, Tsantikos E, Kindt A, Raftery AL, Gottschalk TA, Borger JG, Malhotra A, Anderson GP, van Wijngaarden P, Hilgendorff A, Hibbs ML. Granulocyte Colony-Stimulating Factor is a Determinant of Severe Bronchopulmonary Dysplasia and Coincident Retinopathy. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:2001-2016. [PMID: 37673326 DOI: 10.1016/j.ajpath.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/05/2023] [Accepted: 07/25/2023] [Indexed: 09/08/2023]
Abstract
Bronchopulmonary dysplasia (BPD), also called chronic lung disease of immaturity, afflicts approximately one third of all extremely premature infants, causing lifelong lung damage. There is no effective treatment other than supportive care. Retinopathy of prematurity (ROP), which impairs vision irreversibly, is common in BPD, suggesting a related pathogenesis. However, specific mechanisms of BPD and ROP are not known. Herein, a neonatal mouse hyperoxic model of coincident BPD and retinopathy was used to screen for candidate mediators, which revealed that granulocyte colony-stimulating factor (G-CSF), also known as colony-stimulating factor 3, was up-regulated significantly in mouse lung lavage fluid and plasma at postnatal day 14 in response to hyperoxia. Preterm infants with more severe BPD had increased plasma G-CSF. G-CSF-deficient neonatal pups showed significantly reduced alveolar simplification, normalized alveolar and airway resistance, and normalized weight gain compared with wild-type pups after hyperoxic lung injury. This was associated with a marked reduction in the intensity, and activation state, of neutrophilic and monocytic inflammation and its attendant oxidative stress response, and protection of lung endothelial cells. G-CSF deficiency also provided partial protection against ROP. The findings in this study implicate G-CSF as a pathogenic mediator of BPD and ROP, and suggest the therapeutic utility of targeting G-CSF biology to treat these conditions.
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Affiliation(s)
- Lakshanie C Wickramasinghe
- Leukocyte Signalling Laboratory, Department of Immunology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Evelyn Tsantikos
- Leukocyte Signalling Laboratory, Department of Immunology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Alida Kindt
- Metabolomics and Analytics Centre, Leiden University, Leiden, the Netherlands
| | - April L Raftery
- Leukocyte Signalling Laboratory, Department of Immunology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Timothy A Gottschalk
- Leukocyte Signalling Laboratory, Department of Immunology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Jessica G Borger
- Leukocyte Signalling Laboratory, Department of Immunology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Atul Malhotra
- Early Neurodevelopment Clinic, Monash Children's Hospital, Clayton, Victoria, Australia; Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Gary P Anderson
- Lung Health Research Centre, Department of Biochemistry and Pharmacology, University of Melbourne, Victoria, Australia
| | - Peter van Wijngaarden
- Division of Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Anne Hilgendorff
- Institute for Lung Health and Immunity, Helmholtz Zentrum Muenchen, Munich, Germany; Center for Comprehensive Developmental Care, Ludwig-Maximilian Hospital, Ludwig-Maximilian University, Munich, Germany
| | - Margaret L Hibbs
- Leukocyte Signalling Laboratory, Department of Immunology, Central Clinical School, Monash University, Melbourne, Victoria, Australia.
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34
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Debbs J, Hannawi B, Peterson E, Gui H, Zeld N, Luzum JA, Sabbah HN, Snider J, Pinto YM, Williams LK, Lanfear DE. Evaluation of a New Aptamer-Based Array for Soluble Suppressor of Tumorgenicity (ST2) and N-terminal Pro-B-Type Natriuretic Peptide (NTproBNP) in Heart Failure Patients. J Cardiovasc Transl Res 2023; 16:1343-1348. [PMID: 37191882 PMCID: PMC10651796 DOI: 10.1007/s12265-023-10397-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/08/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND Recent advances in multi-marker platforms offer faster data generation, but the fidelity of these methods compared to the ELISA is not established. We tested the correlation and predictive performance of SOMAscan vs. ELISA methods for NTproBNP and ST2. METHODS Patients ≥ 18 years with heart failure and ejection fraction < 50% were enrolled. We tested the correlation between SOMA and ELISA for each biomarker and their association with outcomes. RESULTS There was good correlation of SOMA vs. ELISA for ST2 (ρ = 0.71) and excellent correlation for NTproBNP (ρ = 0.94). The two versions of both markers were not significantly different regarding survival association. The two ST2 assays and NTproBNP assays were similarly associated with all-cause mortality and cardiovascular mortality. These associations remained statistically significant when adjusted for MAGGIC risk score (all p < 0.05). CONCLUSION SOMAscan quantifications of ST2 and NTproBNP correlate to ELISA versions and carry similar prognosis.
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Affiliation(s)
- Joseph Debbs
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Hospital, Detroit, MI, USA
| | - Bashar Hannawi
- Heart and Vascular Institute, Henry Ford Hospital, Detroit, MI, USA
| | - Edward Peterson
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | - Hongsheng Gui
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Hospital, Detroit, MI, USA
| | - Nicole Zeld
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Hospital, Detroit, MI, USA
| | - Jasmine A Luzum
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Hospital, Detroit, MI, USA
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI, USA
| | - Hani N Sabbah
- Heart and Vascular Institute, Henry Ford Hospital, Detroit, MI, USA
| | | | - Yigal M Pinto
- Department of Cardiology, University of Amsterdam, Amsterdam, the Netherlands
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Hospital, Detroit, MI, USA
| | - David E Lanfear
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Hospital, Detroit, MI, USA.
- Heart and Vascular Institute, Henry Ford Hospital, Detroit, MI, USA.
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35
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Koch C, Reilly-O'Donnell B, Gutierrez R, Lucarelli C, Ng FS, Gorelik J, Ivanov AP, Edel JB. Nanopore sequencing of DNA-barcoded probes for highly multiplexed detection of microRNA, proteins and small biomarkers. NATURE NANOTECHNOLOGY 2023; 18:1483-1491. [PMID: 37749222 PMCID: PMC10716039 DOI: 10.1038/s41565-023-01479-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/28/2023] [Indexed: 09/27/2023]
Abstract
There is an unmet need to develop low-cost, rapid and highly multiplexed diagnostic technology platforms for quantitatively detecting blood biomarkers to advance clinical diagnostics beyond the single biomarker model. Here we perform nanopore sequencing of DNA-barcoded molecular probes engineered to recognize a panel of analytes. This allows for highly multiplexed and simultaneous quantitative detection of at least 40 targets, such as microRNAs, proteins and neurotransmitters, on the basis of the translocation dynamics of each probe as it passes through a nanopore. Our workflow is built around a commercially available MinION sequencing device, offering a one-hour turnaround time from sample preparation to results. We also demonstrate that the strategy can directly detect cardiovascular disease-associated microRNA from human serum without extraction or amplification. Due to the modularity of barcoded probes, the number and type of targets detected can be significantly expanded.
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Affiliation(s)
- Caroline Koch
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Benedict Reilly-O'Donnell
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | | | - Carla Lucarelli
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | - Fu Siong Ng
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | - Julia Gorelik
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | - Aleksandar P Ivanov
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK.
| | - Joshua B Edel
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK.
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36
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Banerjee A, Anand M, Kalita S, Ganji M. Single-molecule analysis of DNA base-stacking energetics using patterned DNA nanostructures. NATURE NANOTECHNOLOGY 2023; 18:1474-1482. [PMID: 37591937 PMCID: PMC10716042 DOI: 10.1038/s41565-023-01485-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/10/2023] [Indexed: 08/19/2023]
Abstract
The DNA double helix structure is stabilized by base-pairing and base-stacking interactions. However, a comprehensive understanding of dinucleotide base-stacking energetics is lacking. Here we combined multiplexed DNA-based point accumulation in nanoscale topography (DNA-PAINT) imaging with designer DNA nanostructures and measured the free energy of dinucleotide base stacking at the single-molecule level. Multiplexed imaging enabled us to extract the binding kinetics of an imager strand with and without additional dinucleotide stacking interactions. The DNA-PAINT data showed that a single additional dinucleotide base stacking results in up to 250-fold stabilization for the DNA duplex nanostructure. We found that the dinucleotide base-stacking energies vary from -0.95 ± 0.12 kcal mol-1 to -3.22 ± 0.04 kcal mol-1 for C|T and A|C base-stackings, respectively. We demonstrate the application of base-stacking energetics in designing DNA-PAINT probes for multiplexed super-resolution imaging, and efficient assembly of higher-order DNA nanostructures. Our results will aid in designing functional DNA nanostructures, and DNA and RNA aptamers, and facilitate better predictions of the local DNA structure.
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Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Simanta Kalita
- New Chemistry Unit and Chemistry and Physics of Materials Unit, The Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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37
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Goudswaard LJ, Smith ML, Hughes DA, Taylor R, Lean M, Sattar N, Welsh P, McConnachie A, Blazeby JM, Rogers CA, Suhre K, Zaghlool SB, Hers I, Timpson NJ, Corbin LJ. Using trials of caloric restriction and bariatric surgery to explore the effects of body mass index on the circulating proteome. Sci Rep 2023; 13:21077. [PMID: 38030643 PMCID: PMC10686974 DOI: 10.1038/s41598-023-47030-x] [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: 07/11/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023] Open
Abstract
Thousands of proteins circulate in the bloodstream; identifying those which associate with weight and intervention-induced weight loss may help explain mechanisms of diseases associated with adiposity. We aimed to identify consistent protein signatures of weight loss across independent studies capturing changes in body mass index (BMI). We analysed proteomic data from studies implementing caloric restriction (Diabetes Remission Clinical trial) and bariatric surgery (By-Band-Sleeve), using SomaLogic and Olink Explore1536 technologies, respectively. Linear mixed models were used to estimate the effect of the interventions on circulating proteins. Twenty-three proteins were altered in a consistent direction after both bariatric surgery and caloric restriction, suggesting that these proteins are modulated by weight change, independent of intervention type. We also integrated Mendelian randomisation (MR) estimates of the effect of BMI on proteins measured by SomaLogic from a UK blood donor cohort as a third line of causal evidence. These MR estimates provided further corroborative evidence for a role of BMI in regulating the levels of six proteins including alcohol dehydrogenase-4, nogo receptor and interleukin-1 receptor antagonist protein. These results indicate the importance of triangulation in interrogating causal relationships; further study into the role of proteins modulated by weight in disease is now warranted.
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Affiliation(s)
- Lucy J Goudswaard
- Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
- MRC Integrative Epidemiology Unit, Bristol, UK.
- Physiology, Pharmacology & Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK.
| | - Madeleine L Smith
- Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- MRC Integrative Epidemiology Unit, Bristol, UK
| | - David A Hughes
- Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- MRC Integrative Epidemiology Unit, Bristol, UK
| | - Roy Taylor
- Newcastle Magnetic Resonance Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, NE4 5PL, UK
| | - Michael Lean
- Human Nutrition, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G31 2ER, UK
| | - Naveed Sattar
- School of Cardiovascular and Medical Science, University of Glasgow, Glasgow, G12 8TA, UK
| | - Paul Welsh
- School of Cardiovascular and Medical Science, University of Glasgow, Glasgow, G12 8TA, UK
| | - Alex McConnachie
- Robertson Centre for Biostatistics, School of Health and Wellbeing, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Jane M Blazeby
- Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Chris A Rogers
- Bristol Medical School, Bristol Trials Centre, University of Bristol, Bristol, BS8 1NU, UK
| | - Karsten Suhre
- Department of Biophysics and Physiology, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Shaza B Zaghlool
- Department of Biophysics and Physiology, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Ingeborg Hers
- Physiology, Pharmacology & Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Nicholas J Timpson
- Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- MRC Integrative Epidemiology Unit, Bristol, UK
| | - Laura J Corbin
- Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- MRC Integrative Epidemiology Unit, Bristol, UK
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38
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Lozoya-Colinas A, Yu Y, Chaput JC. Functionally Enhanced XNA Aptamers Discovered by Parallelized Library Screening. J Am Chem Soc 2023; 145:25789-25796. [PMID: 37962593 PMCID: PMC10690791 DOI: 10.1021/jacs.3c09497] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
In vitro evolution strategies have been used for >30 years to generate nucleic acid aptamers against therapeutic targets of interest, including disease-associated proteins. However, this process requires many iterative cycles of selection and amplification, which severely restricts the number of target and library design combinations that can be explored in parallel. Here, we describe a single-round screening approach to aptamer discovery that relies on function-enhancing chemotypes to increase the distribution of high-affinity sequences in a random-sequence library. We demonstrate the success of de novo discovery by affinity selection of threomers against the receptor binding domain of the S1 protein from SARS-CoV-2. Detailed biochemical characterization of the enriched population identified threomers with binding affinity values that are comparable to aptamers produced by conventional SELEX. This work establishes a highly parallelizable path for querying diverse chemical repertoires and may offer a viable route for accelerating the discovery of therapeutic aptamers.
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Affiliation(s)
- Adriana Lozoya-Colinas
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697-3958, United States
| | - Yutong Yu
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697-3958, United States
| | - John C. Chaput
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697-3958, United States
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697-3958, United States
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, Irvine, California 92697-3958, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3958, United States
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39
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Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
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Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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40
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Hanson BA, Visvabharathy L, Orban ZS, Jimenez M, Batra A, Liotta EM, DeLisle RK, Klausner JD, Cohen P, Padhye AS, Tachas G, Koralnik IJ. Plasma proteomics show altered inflammatory and mitochondrial proteins in patients with neurologic symptoms of post-acute sequelae of SARS-CoV-2 infection. Brain Behav Immun 2023; 114:462-474. [PMID: 37704012 PMCID: PMC10718560 DOI: 10.1016/j.bbi.2023.08.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/17/2023] [Accepted: 08/26/2023] [Indexed: 09/15/2023] Open
Abstract
Persistent symptoms of COVID-19 survivors constitute long COVID syndrome, also called post-acute sequelae of SARS-CoV-2 infection (PASC). Neurologic manifestations of PASC (Neuro-PASC) are particularly debilitating, long lasting, and poorly understood. To gain insight into the pathogenesis of PASC, we leveraged a well-characterized group of Neuro-PASC (NP) patients seen at our Neuro-COVID-19 clinic who had mild acute COVID-19 and never required hospitalization to investigate their plasma proteome. Using the SomaLogic platform, SomaScan, the plasma concentration of >7000 proteins was measured from 92 unvaccinated individuals, including 48 NP patients, 20 COVID-19 convalescents (CC) without lingering symptoms, and 24 unexposed healthy controls (HC) to interrogate underlying pathobiology and potential biomarkers of PASC. We analyzed the plasma proteome based on post-COVID-19 status, neurologic and non-neurologic symptoms, as well as subjective and objective standardized tests for changes in quality-of-life (QoL) and cognition associated with Neuro-PASC. The plasma proteome of NP patients differed from CC and HC subjects more substantially than post-COVID-19 groups (NP and CC combined) differed from HC. Proteomic differences in NP patients 3-9 months following acute COVID-19 showed alterations in inflammatory proteins and pathways relative to CC and HC subjects. Proteomic associations with Neuro-PASC symptoms of brain fog and fatigue included changes in markers of DNA repair, oxidative stress, and neutrophil degranulation. Furthermore, we discovered a correlation between NP patients lower subjective impression of recovery to pre-COVID-19 baseline with an increase in the concentration of the oxidative phosphorylation protein COX7A1, which was also associated with neurologic symptoms and fatigue, as well as impairment in QoL and cognitive dysfunction. Finally, we identified other oxidative phosphorylation-associated proteins correlating with central nervous system symptoms. Our results suggest ongoing inflammatory changes and mitochondrial involvement in Neuro-PASC and pave the way for biomarker validation for use in monitoring and development of therapeutic intervention for this debilitating condition.
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Affiliation(s)
- Barbara A Hanson
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lavanya Visvabharathy
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Zachary S Orban
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Millenia Jimenez
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ayush Batra
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Eric M Liotta
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Jeffrey D Klausner
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Pinchas Cohen
- The Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | | | - George Tachas
- Antisense Therapeutics Limited, Toorak, Victoria, Australia
| | - Igor J Koralnik
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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Sattar N, Taheri S, Astling DP, Chadwick J, Hinterberg MA, Holmes MV, Troth EV, Welsh P, Zaghloul H, Chagoury O, Lean M, Taylor R, Williams S. Prediction of Cardiometabolic Health Through Changes in Plasma Proteins With Intentional Weight Loss in the DiRECT and DIADEM-I Randomized Clinical Trials of Type 2 Diabetes Remission. Diabetes Care 2023; 46:1949-1957. [PMID: 37756566 PMCID: PMC10628468 DOI: 10.2337/dc23-0602] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/04/2023] [Indexed: 09/29/2023]
Abstract
OBJECTIVE To determine the extent to which changes in plasma proteins, previously predictive of cardiometabolic outcomes, predict changes in two diabetes remission trials. RESEARCH DESIGN AND METHODS We applied SomaSignal predictive tests (each derived from ∼5,000 plasma protein measurements using aptamer-based proteomics assay) to baseline and 1-year samples of trial intervention (Diabetes Remission Clinical Trial [DiRECT], n = 118, and Diabetes Intervention Accentuating Diet and Enhancing Metabolism [DIADEM-I], n = 66) and control (DiRECT, n = 144, DIADEM-I, n = 76) group participants. RESULTS Mean (SD) weight loss in DiRECT (U.K.) and DIADEM-I (Qatar) was 10.2 (7.4) kg and 12.1 (9.5) kg, respectively, vs. 1.0 (3.7) kg and 4.0 (5.4) kg in control groups. Cardiometabolic SomaSignal test results showed significant improvement (Bonferroni-adjusted P < 0.05) in DiRECT and DIADEM-I (expressed as relative difference, intervention minus control) as follows, respectively: liver fat (-26.4%, -37.3%), glucose tolerance (-36.6%, -37.4%), body fat percentage (-8.6%, -8.7%), resting energy rate (-8.0%, -5.1%), visceral fat (-34.3%, -26.1%), and cardiorespiratory fitness (9.5%, 10.3%). Cardiovascular risk (measured with SomaSignal tests) also improved in intervention groups relative to control, but this was significant only in DiRECT (DiRECT, -44.2%, and DIADEM-I, -9.2%). However, weight loss >10 kg predicted significant reductions in cardiovascular risk, -19.1% (95% CI -33.4 to -4.91) in DiRECT and -33.4% (95% CI -57.3, -9.6) in DIADEM-I. DIADEM-I also demonstrated rapid emergence of metabolic improvements at 3 months. CONCLUSIONS Intentional weight loss in recent-onset type 2 diabetes rapidly induces changes in protein-based risk models consistent with widespread cardiometabolic improvements, including cardiorespiratory fitness. Protein changes with greater (>10 kg) weight loss also predicted lower cardiovascular risk, providing a positive outlook for relevant ongoing trials.
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Affiliation(s)
- Naveed Sattar
- School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, U.K
| | - Shahrad Taheri
- Qatar Metabolic Institute, Hamad Medical Corporation, Doha, Qatar
- Weill Cornell Medicine-Qatar, Doha, Qatar
- Weill Cornell Medicine, New York, NY
| | | | | | | | - Michael V. Holmes
- Medical Research Council, Integrative Epidemiology Unit, University of Bristol, Bristol, U.K
| | | | - Paul Welsh
- School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, U.K
| | - Hadeel Zaghloul
- Weill Cornell Medicine-Qatar, Doha, Qatar
- Weill Cornell Medicine, New York, NY
| | - Odette Chagoury
- Qatar Metabolic Institute, Hamad Medical Corporation, Doha, Qatar
- Weill Cornell Medicine-Qatar, Doha, Qatar
- Weill Cornell Medicine, New York, NY
| | - Mike Lean
- School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, U.K
| | - Roy Taylor
- Magnetic Resonance Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, U.K
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Jestřábová I, Poštová Slavětínská L, Hocek M. Arylethynyl- or Alkynyl-Linked Pyrimidine and 7-Deazapurine 2'-Deoxyribonucleoside 3'-Phosphoramidites for Chemical Synthesis of Hypermodified Hydrophobic Oligonucleotides. ACS OMEGA 2023; 8:39447-39453. [PMID: 37901526 PMCID: PMC10601081 DOI: 10.1021/acsomega.3c05202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/28/2023] [Indexed: 10/31/2023]
Abstract
We designed and synthesized a set of 2'-deoxyribonucleoside 3'-phosphoramidites derived from 5-phenylethynyluracil, 5-(pentyn-1-yl)cytosine, 7-(indol-3-yl)ethynyl-7-deazaadenine, and 7-isopropylethynyl-7-deazaguanine. These nucleoside phosphoramidites were successfully used for automated solid-phase synthesis of oligonucleotides containing one or several modifications, including fully modified sequences where every nucleobase was displaying a modification, and their hybridization was studied. The phosphoramidite building blocks have potential for synthesis of hypermodified aptamers and other functional nucleic acid-based polymers, which sequence-specifically display amino acid-like hydrophobic substituents.
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Affiliation(s)
- Ivana Jestřábová
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Michal Hocek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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43
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Yamin D, Uskoković V, Wakil AM, Goni MD, Shamsuddin SH, Mustafa FH, Alfouzan WA, Alissa M, Alshengeti A, Almaghrabi RH, Fares MAA, Garout M, Al Kaabi NA, Alshehri AA, Ali HM, Rabaan AA, Aldubisi FA, Yean CY, Yusof NY. Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria. Diagnostics (Basel) 2023; 13:3246. [PMID: 37892067 PMCID: PMC10606640 DOI: 10.3390/diagnostics13203246] [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: 09/30/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
Antibiotic resistance is a global public health concern, posing a significant threat to the effectiveness of antibiotics in treating bacterial infections. The accurate and timely detection of antibiotic-resistant bacteria is crucial for implementing appropriate treatment strategies and preventing the spread of resistant strains. This manuscript provides an overview of the current and emerging technologies used for the detection of antibiotic-resistant bacteria. We discuss traditional culture-based methods, molecular techniques, and innovative approaches, highlighting their advantages, limitations, and potential future applications. By understanding the strengths and limitations of these technologies, researchers and healthcare professionals can make informed decisions in combating antibiotic resistance and improving patient outcomes.
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Affiliation(s)
- Dina Yamin
- Al-Karak Public Hospital, Karak 61210, Jordan;
- Institute for Research in Molecular Medicine, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia;
| | - Vuk Uskoković
- TardigradeNano LLC., Irvine, CA 92604, USA;
- Department of Mechanical Engineering, San Diego State University, San Diego, CA 92182, USA
| | - Abubakar Muhammad Wakil
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia;
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, University of Maiduguri, Maiduguri 600104, Borno, Nigeria
| | - Mohammed Dauda Goni
- Public Health and Zoonoses Research Group, Faculty of Veterinary Medicine, University Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia;
| | - Shazana Hilda Shamsuddin
- Department of Pathology, School of Medical Sciences, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia;
| | - Fatin Hamimi Mustafa
- Department of Electronic & Computer Engineering, Faculty of Electrical Engineering, University Teknologi Malaysia, Johor Bharu 81310, Johor, Malaysia;
| | - Wadha A. Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait;
- Microbiology Unit, Department of Laboratories, Farwania Hospital, Farwania 85000, Kuwait
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia;
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah 41491, Saudi Arabia
| | - Rana H. Almaghrabi
- Pediatric Department, Prince Sultan Medical Military City, Riyadh 12233, Saudi Arabia;
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
| | - Mona A. Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia;
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Nawal A. Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates;
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi 51900, United Arab Emirates
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia;
| | - Hamza M. Ali
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah 41411, Saudi Arabia;
| | - Ali A. Rabaan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | | | - Chan Yean Yean
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, University Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
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Dubin RF, Deo R, Ren Y, Wang J, Zheng Z, Shou H, Go AS, Parsa A, Lash JP, Rahman M, Hsu CY, Weir MR, Chen J, Anderson A, Grams ME, Surapaneni A, Coresh J, Li H, Kimmel PL, Vasan RS, Feldman H, Segal MR, Ganz P. Proteomics of CKD progression in the chronic renal insufficiency cohort. Nat Commun 2023; 14:6340. [PMID: 37816758 PMCID: PMC10564759 DOI: 10.1038/s41467-023-41642-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/13/2023] [Indexed: 10/12/2023] Open
Abstract
Progression of chronic kidney disease (CKD) portends myriad complications, including kidney failure. In this study, we analyze associations of 4638 plasma proteins among 3235 participants of the Chronic Renal Insufficiency Cohort Study with the primary outcome of 50% decline in estimated glomerular filtration rate or kidney failure over 10 years. We validate key findings in the Atherosclerosis Risk in the Communities study. We identify 100 circulating proteins that are associated with the primary outcome after multivariable adjustment, using a Bonferroni statistical threshold of significance. Individual protein associations and biological pathway analyses highlight the roles of bone morphogenetic proteins, ephrin signaling, and prothrombin activation. A 65-protein risk model for the primary outcome has excellent discrimination (C-statistic[95%CI] 0.862 [0.835, 0.889]), and 14/65 proteins are druggable targets. Potentially causal associations for five proteins, to our knowledge not previously reported, are supported by Mendelian randomization: EGFL9, LRP-11, MXRA7, IL-1 sRII and ILT-2. Modifiable protein risk markers can guide therapeutic drug development aimed at slowing CKD progression.
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Affiliation(s)
- Ruth F Dubin
- Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Rajat Deo
- Division of Cardiovascular Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Yue Ren
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jianqiao Wang
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Zihe Zheng
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Haochang Shou
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alan S Go
- Division of Research, Kaiser Permanente Northern California, Oakland, the Department of Health Systems Science, Oakland, CA, USA
| | - Afshin Parsa
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - James P Lash
- Department of Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Mahboob Rahman
- Department of Medicine, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Chi-Yuan Hsu
- Division of Research, Kaiser Permanente Northern California, Oakland, the Department of Health Systems Science, Oakland, CA, USA
- Division of Nephrology, University of California San Francisco, San Francisco, CA, USA
| | - Matthew R Weir
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jing Chen
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
| | - Amanda Anderson
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
| | - Morgan E Grams
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Division of Precision Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Aditya Surapaneni
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Division of Precision Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Josef Coresh
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul L Kimmel
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ramachandran S Vasan
- University of Texas School of Public Health San Antonio and the University of Texas Health Sciences Center in San Antonio. Section of Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Harold Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark R Segal
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Peter Ganz
- Division of Cardiology, University of California, San Francisco, San Francisco, CA, USA
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45
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Farkona S, Pastrello C, Konvalinka A. Proteomics: Its Promise and Pitfalls in Shaping Precision Medicine in Solid Organ Transplantation. Transplantation 2023; 107:2126-2142. [PMID: 36808112 DOI: 10.1097/tp.0000000000004539] [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] [Indexed: 02/22/2023]
Abstract
Solid organ transplantation is an established treatment of choice for end-stage organ failure. However, all transplant patients are at risk of developing complications, including allograft rejection and death. Histological analysis of graft biopsy is still the gold standard for evaluation of allograft injury, but it is an invasive procedure and prone to sampling errors. The past decade has seen an increased number of efforts to develop minimally invasive procedures for monitoring allograft injury. Despite the recent progress, limitations such as the complexity of proteomics-based technology, the lack of standardization, and the heterogeneity of populations that have been included in different studies have hindered proteomic tools from reaching clinical transplantation. This review focuses on the role of proteomics-based platforms in biomarker discovery and validation in solid organ transplantation. We also emphasize the value of biomarkers that provide potential mechanistic insights into the pathophysiology of allograft injury, dysfunction, or rejection. Additionally, we forecast that the growth of publicly available data sets, combined with computational methods that effectively integrate them, will facilitate a generation of more informed hypotheses for potential subsequent evaluation in preclinical and clinical studies. Finally, we illustrate the value of combining data sets through the integration of 2 independent data sets that pinpointed hub proteins in antibody-mediated rejection.
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Affiliation(s)
- Sofia Farkona
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Ana Konvalinka
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON, Canada
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Canadian Donation and Transplantation Research Program, Edmonton, AB, Canada
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46
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Eldjarn GH, Ferkingstad E, Lund SH, Helgason H, Magnusson OT, Gunnarsdottir K, Olafsdottir TA, Halldorsson BV, Olason PI, Zink F, Gudjonsson SA, Sveinbjornsson G, Magnusson MI, Helgason A, Oddsson A, Halldorsson GH, Magnusson MK, Saevarsdottir S, Eiriksdottir T, Masson G, Stefansson H, Jonsdottir I, Holm H, Rafnar T, Melsted P, Saemundsdottir J, Norddahl GL, Thorleifsson G, Ulfarsson MO, Gudbjartsson DF, Thorsteinsdottir U, Sulem P, Stefansson K. Large-scale plasma proteomics comparisons through genetics and disease associations. Nature 2023; 622:348-358. [PMID: 37794188 PMCID: PMC10567571 DOI: 10.1038/s41586-023-06563-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 08/22/2023] [Indexed: 10/06/2023]
Abstract
High-throughput proteomics platforms measuring thousands of proteins in plasma combined with genomic and phenotypic information have the power to bridge the gap between the genome and diseases. Here we performed association studies of Olink Explore 3072 data generated by the UK Biobank Pharma Proteomics Project1 on plasma samples from more than 50,000 UK Biobank participants with phenotypic and genotypic data, stratifying on British or Irish, African and South Asian ancestries. We compared the results with those of a SomaScan v4 study on plasma from 36,000 Icelandic people2, for 1,514 of whom Olink data were also available. We found modest correlation between the two platforms. Although cis protein quantitative trait loci were detected for a similar absolute number of assays on the two platforms (2,101 on Olink versus 2,120 on SomaScan), the proportion of assays with such supporting evidence for assay performance was higher on the Olink platform (72% versus 43%). A considerable number of proteins had genomic associations that differed between the platforms. We provide examples where differences between platforms may influence conclusions drawn from the integration of protein levels with the study of diseases. We demonstrate how leveraging the diverse ancestries of participants in the UK Biobank helps to detect novel associations and refine genomic location. Our results show the value of the information provided by the two most commonly used high-throughput proteomics platforms and demonstrate the differences between them that at times provides useful complementarity.
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Affiliation(s)
| | | | - Sigrun H Lund
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Hannes Helgason
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Bjarni V Halldorsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Technology, Reykjavik University, Reykjavik, Iceland
| | | | | | | | | | | | - Agnar Helgason
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | | | | | - Magnus K Magnusson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Saedis Saevarsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Ingileif Jonsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Hilma Holm
- deCODE Genetics/Amgen, Reykjavik, Iceland
| | | | - Pall Melsted
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Magnus O Ulfarsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Electrical and Computer Engineering, University of Iceland, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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47
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Kimoto M, Tan HP, Matsunaga KI, Binte Mohd Mislan NA, Kawai G, Hirao I. Strict Interactions of Fifth Letters, Hydrophobic Unnatural Bases, in XenoAptamers with Target Proteins. J Am Chem Soc 2023; 145:20432-20441. [PMID: 37677157 PMCID: PMC10515488 DOI: 10.1021/jacs.3c06122] [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] [Received: 06/11/2023] [Indexed: 09/09/2023]
Abstract
XenoAptamers are DNA fragments containing additional letters (unnatural bases, UBs) that bind specifically to their target proteins with high affinities (sub-nanomolar KD values). One of the UBs is the highly hydrophobic 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds), which significantly increases XenoAptamers' affinities to targets. Originally, Ds was developed as a third base pair with a complementary UB, 2-nitro-4-propynylpyrrole (Px), for replication, and thus it can be used for aptamer generation by an evolutional engineering method involving PCR amplification. However, it is unclear whether the Ds base is the best component as the hydrophobic fifth-letter ligand for interactions with target proteins. To optimize the ligand structure of the fifth letter, we prepared 13 Ds variants and examined the affinities of XenoAptamers containing these variants to target proteins. The results obtained using four XenoAptamers prepared by the replacement of Ds bases with variants indicated that subtle changes in the chemical structure of Ds significantly affect the XenoAptamer affinities. Among the variants, placing either 4-(2-thienyl)pyrrolo[2,3-b]pyridine (Ys) or 4-(2-thienyl)benzimidazole (Bs) at specific Ds positions in each original XenoAptamer greatly improved their affinities to targets. The Ys and Bs bases are variants derived by replacing only one nitrogen with a carbon in the Ds base. These results demonstrate the strict intramolecular interactions, which are not simple hydrophobic contacts between UBs and targets, thus providing a method to mature XenoAptamers' affinities to targets.
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Affiliation(s)
- Michiko Kimoto
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | - Hui Pen Tan
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | - Ken-ichiro Matsunaga
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | | | - Gota Kawai
- Chiba
Institute of Technology (CIT), Tsudanuma 2-17-1, Narashino, Chiba 275-0016, Japan
| | - Ichiro Hirao
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
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48
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Kohn EM, Konovalov K, Gomez CA, Hoover GN, Yik AKH, Huang X, Martell JD. Terminal Alkyne-Modified DNA Aptamers with Enhanced Protein Binding Affinities. ACS Chem Biol 2023; 18:1976-1984. [PMID: 37531184 DOI: 10.1021/acschembio.3c00183] [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] [Indexed: 08/03/2023]
Abstract
Nucleic acid-based receptors, known as aptamers, are relatively fast to discover and manufacture but lack the diverse functional groups of protein receptors (e.g., antibodies). The binding properties of DNA aptamers can be enhanced by attaching abiotic functional groups; for example, aromatic groups such as naphthalene slow dissociation from proteins. Although the terminal alkyne is a π-electron-rich functional group that has been used in small molecule drugs to enhance binding to proteins through noncovalent interactions, it remains unexplored for enhancing DNA aptamer binding affinity. Here, we demonstrate the utility of the terminal alkyne for improving the binding of DNA to proteins. We prepared a library of 256 terminal-alkyne-bearing variants of HD22, a DNA aptamer that binds the protein thrombin with nanomolar affinity. After a one-step thrombin-binding selection, a high-affinity aptamer containing two alkynes was discovered, exhibiting 3.2-fold tighter thrombin binding than the corresponding unmodified sequence. The tighter binding was attributable to a slower rate of dissociation from thrombin (5.2-fold slower than HD22). Molecular dynamics simulations with enhanced sampling by Replica Exchange with Solute Tempering (REST2) suggest that the π-electron-rich alkyne interacts with an asparagine side chain N-H group on thrombin, forming a noncovalent interaction that stabilizes the aptamer-protein interface. Overall, this work represents the first case of terminal alkynes enhancing the binding properties of an aptamer and underscores the utility of the terminal alkyne as an atom economical π-electron-rich functional group to enhance binding affinity with minimal steric perturbation.
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Affiliation(s)
- Eric M Kohn
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kirill Konovalov
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Christian A Gomez
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Gillian N Hoover
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Andrew Kai-Hei Yik
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Xuhui Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D Martell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, United States
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49
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Paul AR, Falsaperna M, Lavender H, Garrett MD, Serpell CJ. Selection of optimised ligands by fluorescence-activated bead sorting. Chem Sci 2023; 14:9517-9525. [PMID: 37712023 PMCID: PMC10498682 DOI: 10.1039/d3sc03581f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023] Open
Abstract
The chemistry of aptamers is largely limited to natural nucleotides, and although modifications of nucleic acids can enhance target aptamer affinity, there has not yet been a technology for selecting the right modifications in the right locations out of the vast number of possibilities, because enzymatic amplification does not transmit sequence-specific modification information. Here we show the first method for the selection of specific nucleoside modifications that increase aptamer binding efficacy, using the oncoprotein EGFR as a model target. Using fluorescence-activated bead sorting (FABS), we have successfully selected optimized aptamers from a library of >65 000 variations. Hits were identified by tandem mass spectrometry and validated by using an EGFR binding assay and computational docking studies. Our results provide proof of concept for this novel strategy for the selection of chemically optimised aptamers and offer a new method for rapidly synthesising and screening large aptamer libraries to accelerate diagnostic and drug discovery.
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Affiliation(s)
- Alexandra R Paul
- School of Chemistry and Forensic Sciences, Division of Natural Sciences, University of Kent Canterbury CT2 7NH UK
| | - Mario Falsaperna
- School of Chemistry and Forensic Sciences, Division of Natural Sciences, University of Kent Canterbury CT2 7NH UK
| | - Helen Lavender
- Avvinity Therapeutics 66 Prescot Street London E1 8NN UK
| | - Michelle D Garrett
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury CT2 7NJ UK
| | - Christopher J Serpell
- School of Chemistry and Forensic Sciences, Division of Natural Sciences, University of Kent Canterbury CT2 7NH UK
- School of Pharmacy, University College London London WC1N 1AX UK
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50
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Helgason H, Eiriksdottir T, Ulfarsson MO, Choudhary A, Lund SH, Ivarsdottir EV, Hjorleifsson Eldjarn G, Einarsson G, Ferkingstad E, Moore KHS, Honarpour N, Liu T, Wang H, Hucko T, Sabatine MS, Morrow DA, Giugliano RP, Ostrowski SR, Pedersen OB, Bundgaard H, Erikstrup C, Arnar DO, Thorgeirsson G, Masson G, Magnusson OT, Saemundsdottir J, Gretarsdottir S, Steinthorsdottir V, Thorleifsson G, Helgadottir A, Sulem P, Thorsteinsdottir U, Holm H, Gudbjartsson D, Stefansson K. Evaluation of Large-Scale Proteomics for Prediction of Cardiovascular Events. JAMA 2023; 330:725-735. [PMID: 37606673 PMCID: PMC10445198 DOI: 10.1001/jama.2023.13258] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 06/29/2023] [Indexed: 08/23/2023]
Abstract
Importance Whether protein risk scores derived from a single plasma sample could be useful for risk assessment for atherosclerotic cardiovascular disease (ASCVD), in conjunction with clinical risk factors and polygenic risk scores, is uncertain. Objective To develop protein risk scores for ASCVD risk prediction and compare them to clinical risk factors and polygenic risk scores in primary and secondary event populations. Design, Setting, and Participants The primary analysis was a retrospective study of primary events among 13 540 individuals in Iceland (aged 40-75 years) with proteomics data and no history of major ASCVD events at recruitment (study duration, August 23, 2000 until October 26, 2006; follow-up through 2018). We also analyzed a secondary event population from a randomized, double-blind lipid-lowering clinical trial (2013-2016), consisting of individuals with stable ASCVD receiving statin therapy and for whom proteomic data were available for 6791 individuals. Exposures Protein risk scores (based on 4963 plasma protein levels and developed in a training set in the primary event population); polygenic risk scores for coronary artery disease and stroke; and clinical risk factors that included age, sex, statin use, hypertension treatment, type 2 diabetes, body mass index, and smoking status at the time of plasma sampling. Main Outcomes and Measures Outcomes were composites of myocardial infarction, stroke, and coronary heart disease death or cardiovascular death. Performance was evaluated using Cox survival models and measures of discrimination and reclassification that accounted for the competing risk of non-ASCVD death. Results In the primary event population test set (4018 individuals [59.0% women]; 465 events; median follow-up, 15.8 years), the protein risk score had a hazard ratio (HR) of 1.93 per SD (95% CI, 1.75 to 2.13). Addition of protein risk score and polygenic risk scores significantly increased the C index when added to a clinical risk factor model (C index change, 0.022 [95% CI, 0.007 to 0.038]). Addition of the protein risk score alone to a clinical risk factor model also led to a significantly increased C index (difference, 0.014 [95% CI, 0.002 to 0.028]). Among White individuals in the secondary event population (6307 participants; 432 events; median follow-up, 2.2 years), the protein risk score had an HR of 1.62 per SD (95% CI, 1.48 to 1.79) and significantly increased C index when added to a clinical risk factor model (C index change, 0.026 [95% CI, 0.011 to 0.042]). The protein risk score was significantly associated with major adverse cardiovascular events among individuals of African and Asian ancestries in the secondary event population. Conclusions and Relevance A protein risk score was significantly associated with ASCVD events in primary and secondary event populations. When added to clinical risk factors, the protein risk score and polygenic risk score both provided statistically significant but modest improvement in discrimination.
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Affiliation(s)
- Hannes Helgason
- deCODE genetics/Amgen, Inc, Reykjavik, Iceland
- University of Iceland, Reykjavik, Iceland
| | | | - Magnus O. Ulfarsson
- deCODE genetics/Amgen, Inc, Reykjavik, Iceland
- University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | | | - Huei Wang
- Amgen, Inc, Thousand Oaks, California
| | | | - Marc S. Sabatine
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - David A. Morrow
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Robert P. Giugliano
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Birger Pedersen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Henning Bundgaard
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology, The Heart Center, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - David O. Arnar
- deCODE genetics/Amgen, Inc, Reykjavik, Iceland
- University of Iceland, Reykjavik, Iceland
- Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland
| | - Gudmundur Thorgeirsson
- deCODE genetics/Amgen, Inc, Reykjavik, Iceland
- University of Iceland, Reykjavik, Iceland
- Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | | | - Hilma Holm
- deCODE genetics/Amgen, Inc, Reykjavik, Iceland
| | - Daniel Gudbjartsson
- deCODE genetics/Amgen, Inc, Reykjavik, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc, Reykjavik, Iceland
- University of Iceland, Reykjavik, Iceland
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