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Gudmundsdottir V, Frick E, Emilsson V, Jonmundsson T, Steindorsdottir A, Johnson ECB, Puerta R, Dammer E, Shantaraman A, Cano A, Boada M, Valero S, Garcia-Gonzalez P, Gudmundsson E, Gudjonsson A, Pitts R, Qiu X, Finkel N, Loureiro J, Orth A, Seyfried N, Levey A, Ruiz A, Aspelund T, Jennings L, Launer L, Gudnason V. Serum proteomics reveals APOE dependent and independent protein signatures in Alzheimer's disease. Res Sq 2024:rs.3.rs-3706206. [PMID: 38260284 PMCID: PMC10802738 DOI: 10.21203/rs.3.rs-3706206/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The current demand for early intervention, prevention, and treatment of late onset Alzheimer's disease (LOAD) warrants deeper understanding of the underlying molecular processes which could contribute to biomarker and drug target discovery. Utilizing high-throughput proteomic measurements in serum from a prospective population-based cohort of older adults (n = 5,294), we identified 303 unique proteins associated with incident LOAD (median follow-up 12.8 years). Over 40% of these proteins were associated with LOAD independently of APOE-ε4 carrier status. These proteins were implicated in neuronal processes and overlapped with protein signatures of LOAD in brain and cerebrospinal fluid. We found 17 proteins which LOAD-association was strongly dependent on APOE-ε4 carrier status. Most of them showed consistent associations with LOAD in cerebrospinal fluid and a third had brain-specific gene expression. Remarkably, four proteins in this group (TBCA, ARL2, S100A13 and IRF6) were downregulated by APOE-ε4 yet upregulated as a consequence of LOAD as determined in a bi-directional Mendelian randomization analysis, reflecting a potential response to the disease onset. Accordingly, the direct association of these proteins to LOAD was reversed upon APOE-ε4 genotype adjustment, a finding which we replicate in an external cohort (n = 719). Our findings provide an insight into the dysregulated pathways that may lead to the development and early detection of LOAD, including those both independent and dependent on APOE-ε4. Importantly, many of the LOAD-associated proteins we find in the circulation have been found to be expressed - and have a direct link with AD - in brain tissue. Thus, the proteins identified here, and their upstream modulating pathways, provide a new source of circulating biomarker and therapeutic target candidates for LOAD.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Merce Boada
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades-UIC, Barcelona
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lenore Launer
- National Institute on Aging, National Institutes of Health
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2
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Richards SM, Guo F, Zou H, Nigsch F, Baiges A, Pachori A, Zhang Y, Lens S, Pitts R, Finkel N, Loureiro J, Mongeon D, Ma S, Watkins M, Polus F, Albillos A, Tellez L, Martinez-González J, Bañares R, Turon F, Ferrusquía-Acosta J, Perez-Campuzano V, Magaz M, Forns X, Badman M, Sailer AW, Ukomadu C, Hernández-Gea V, Garcia-Pagán JC. Non-invasive candidate protein signature predicts hepatic venous pressure gradient reduction in cirrhotic patients after sustained virologic response. Liver Int 2023; 43:1984-1994. [PMID: 37443448 DOI: 10.1111/liv.15657] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/02/2023] [Accepted: 06/12/2023] [Indexed: 07/15/2023]
Abstract
BACKGROUND AND AIMS A reduction in hepatic venous pressure gradient (HVPG) is the most accurate marker for assessing the severity of portal hypertension and the effectiveness of intervention treatments. This study aimed to evaluate the prognostic potential of blood-based proteomic biomarkers in predicting HVPG response amongst cirrhotic patients with portal hypertension due to Hepatitis C virus (HCV) and had achieved sustained virologic response (SVR). METHODS The study comprised 59 patients from two cohorts. Patients underwent paired HVPG (pretreatment and after SVR), liver stiffness (LSM), and enhanced liver fibrosis scores (ELF) measurements, as well as proteomics-based profiling on serum samples using SomaScan® at baseline (BL) and after SVR (EOS). Machine learning with feature selection (Caret, Random Forest and RPART) methods were performed to determine the proteins capable of classifying HVPG responders. Model performance was evaluated using AUROC (pROC R package). RESULTS Patients were stratified by a change in HVPG (EOS vs. BL) into responders (greater than 20% decline in HVPG from BL, or <10 mmHg at EOS with >10 mmHg at BL) and non-responders. LSM and ELF decreased markedly after SVR but did not correlate with HVPG response. SomaScan (SomaLogic, Inc., Boulder, CO) analysis revealed a substantial shift in the peripheral proteome composition, reflected by 82 significantly differentially abundant proteins. Twelve proteins accurately distinguished responders from non-responders, with an AUROC of .86, sensitivity of 83%, specificity of 83%, accuracy of 83%, PPV of 83%, and NPV of 83%. CONCLUSIONS A combined non-invasive soluble protein signature was identified, capable of accurately predicting HVPG response in HCV liver cirrhosis patients after achieving SVR.
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Affiliation(s)
| | - Fang Guo
- Novartis Institutes for Biomedical Research, East Hannover, New Jersey, USA
| | - Heng Zou
- Novartis Institutes for Biomedical Research, East Hannover, New Jersey, USA
| | - Florian Nigsch
- Novartis Institutes of Biomedical Research, Basel, Switzerland
| | - Anna Baiges
- Barcelona Hepatic Hemodynamic Laboratory, Barcelona Health Care Provider of the European Reference Network on Rare Liver, Barcelona, Spain
- CIBEREHD (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Barcelona, Spain
- Liver Unit, Hospital Clínic, Institut de Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departament de Medicina. Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona., Barcelona, Spain
| | - Alok Pachori
- Novartis Institutes for Biomedical Research, East Hannover, New Jersey, USA
| | - Yiming Zhang
- Novartis Institutes for Biomedical Research, East Hannover, New Jersey, USA
| | - Sabela Lens
- CIBEREHD (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Barcelona, Spain
- Liver Unit, Hospital Clínic, Institut de Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departament de Medicina. Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona., Barcelona, Spain
| | - Rebecca Pitts
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Nancy Finkel
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Joseph Loureiro
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Dale Mongeon
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Shenglin Ma
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Mollie Watkins
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Florine Polus
- Novartis Institutes of Biomedical Research, Basel, Switzerland
| | - Agustin Albillos
- CIBEREHD (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Barcelona, Spain
- Servicio de Gastroenterología y Hepatología, Hospital Universitario Ramón y Cajal, Universidad de Alcalá, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Luis Tellez
- CIBEREHD (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Barcelona, Spain
- Servicio de Gastroenterología y Hepatología, Hospital Universitario Ramón y Cajal, Universidad de Alcalá, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Javier Martinez-González
- CIBEREHD (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Barcelona, Spain
- Servicio de Gastroenterología y Hepatología, Hospital Universitario Ramón y Cajal, Universidad de Alcalá, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Rafael Bañares
- CIBEREHD (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Barcelona, Spain
- Hospital General Universitario Gregorio Marañón, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Fanny Turon
- Barcelona Hepatic Hemodynamic Laboratory, Barcelona Health Care Provider of the European Reference Network on Rare Liver, Barcelona, Spain
- CIBEREHD (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Barcelona, Spain
- Liver Unit, Hospital Clínic, Institut de Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departament de Medicina. Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona., Barcelona, Spain
| | - José Ferrusquía-Acosta
- Barcelona Hepatic Hemodynamic Laboratory, Barcelona Health Care Provider of the European Reference Network on Rare Liver, Barcelona, Spain
| | - Valeria Perez-Campuzano
- Barcelona Hepatic Hemodynamic Laboratory, Barcelona Health Care Provider of the European Reference Network on Rare Liver, Barcelona, Spain
- CIBEREHD (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Barcelona, Spain
- Liver Unit, Hospital Clínic, Institut de Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departament de Medicina. Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona., Barcelona, Spain
| | - Marta Magaz
- Barcelona Hepatic Hemodynamic Laboratory, Barcelona Health Care Provider of the European Reference Network on Rare Liver, Barcelona, Spain
- CIBEREHD (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Barcelona, Spain
- Liver Unit, Hospital Clínic, Institut de Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departament de Medicina. Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona., Barcelona, Spain
| | - Xavier Forns
- CIBEREHD (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Barcelona, Spain
- Liver Unit, Hospital Clínic, Institut de Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departament de Medicina. Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona., Barcelona, Spain
| | - Michael Badman
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | | | - Chinweike Ukomadu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Virginia Hernández-Gea
- Barcelona Hepatic Hemodynamic Laboratory, Barcelona Health Care Provider of the European Reference Network on Rare Liver, Barcelona, Spain
- CIBEREHD (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Barcelona, Spain
- Liver Unit, Hospital Clínic, Institut de Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departament de Medicina. Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona., Barcelona, Spain
| | - Juan Carlos Garcia-Pagán
- Barcelona Hepatic Hemodynamic Laboratory, Barcelona Health Care Provider of the European Reference Network on Rare Liver, Barcelona, Spain
- CIBEREHD (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Barcelona, Spain
- Liver Unit, Hospital Clínic, Institut de Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departament de Medicina. Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona., Barcelona, Spain
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Emilsson V, Gudmundsson EF, Jonmundsson T, Jonsson BG, Twarog M, Gudmundsdottir V, Li Z, Finkel N, Poor S, Liu X, Esterberg R, Zhang Y, Jose S, Huang CL, Liao SM, Loureiro J, Zhang Q, Grosskreutz CL, Nguyen AA, Huang Q, Leehy B, Pitts R, Aspelund T, Lamb JR, Jonasson F, Launer LJ, Cotch MF, Jennings LL, Gudnason V, Walshe TE. A proteogenomic signature of age-related macular degeneration in blood. Nat Commun 2022; 13:3401. [PMID: 35697682 PMCID: PMC9192739 DOI: 10.1038/s41467-022-31085-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 06/01/2022] [Indexed: 12/28/2022] Open
Abstract
Age-related macular degeneration (AMD) is one of the most common causes of visual impairment in the elderly, with a complex and still poorly understood etiology. Whole-genome association studies have discovered 34 genomic regions associated with AMD. However, the genes and cognate proteins that mediate the risk, are largely unknown. In the current study, we integrate levels of 4782 human serum proteins with all genetic risk loci for AMD in a large population-based study of the elderly, revealing many proteins and pathways linked to the disease. Serum proteins are also found to reflect AMD severity independent of genetics and predict progression from early to advanced AMD after five years in this population. A two-sample Mendelian randomization study identifies several proteins that are causally related to the disease and are directionally consistent with the observational estimates. In this work, we present a robust and unique framework for elucidating the pathobiology of AMD. Age related macular degeneration is a common cause of visual impairment in the elderly, but the etiology is not fully understood. Here, the authors use genetic data, serum proteomics, and AMD phenotypic data from a large Icelandic cohort to discover proteins altered in, causally related to AMD or signifying progression of advanced AMD.
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Affiliation(s)
- Valur Emilsson
- Icelandic Heart Association, Holtasmari 1, IS-201, Kopavogur, Iceland. .,Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland.
| | | | | | | | - Michael Twarog
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Valborg Gudmundsdottir
- Icelandic Heart Association, Holtasmari 1, IS-201, Kopavogur, Iceland.,Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Zhiguang Li
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, MD, USA
| | - Nancy Finkel
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Stephen Poor
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Xin Liu
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Robert Esterberg
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Yiyun Zhang
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Sandra Jose
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Chia-Ling Huang
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Sha-Mei Liao
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Joseph Loureiro
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Qin Zhang
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Cynthia L Grosskreutz
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Andrew A Nguyen
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Qian Huang
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Barrett Leehy
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Rebecca Pitts
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Thor Aspelund
- Icelandic Heart Association, Holtasmari 1, IS-201, Kopavogur, Iceland
| | - John R Lamb
- Novartis Institutes for Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA
| | - Fridbert Jonasson
- Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland.,Department of Ophthalmology, University Hospital, Reykjavik, Iceland
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, MD, USA
| | - Mary Frances Cotch
- Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lori L Jennings
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Holtasmari 1, IS-201, Kopavogur, Iceland.,Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Tony E Walshe
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, 02139, USA.
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4
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Kashtan C, Schachter A, Klickstein L, Liu X, Jennings L, Finkel N. Urinary Monocyte Chemoattractant Protein-1 in Patients With Alport Syndrome. Kidney Int Rep 2022; 7:1112-1114. [PMID: 35571002 PMCID: PMC9091606 DOI: 10.1016/j.ekir.2022.01.1052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 01/29/2023] Open
Affiliation(s)
- Clifford Kashtan
- Division of Pediatric Nephrology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | | | | | - Xin Liu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Lori Jennings
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Nancy Finkel
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
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5
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Corey KE, Pitts R, Lai M, Loureiro J, Masia R, Osganian SA, Gustafson JL, Hutter MM, Gee DW, Meireles OR, Witkowski ER, Richards SM, Jacob J, Finkel N, Ngo D, Wang TJ, Gerszten RE, Ukomadu C, Jennings LL. ADAMTSL2 protein and a soluble biomarker signature identify at-risk non-alcoholic steatohepatitis and fibrosis in adults with NAFLD. J Hepatol 2022; 76:25-33. [PMID: 34600973 PMCID: PMC8688231 DOI: 10.1016/j.jhep.2021.09.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 09/14/2021] [Accepted: 09/18/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS Identifying fibrosis in non-alcoholic fatty liver disease (NAFLD) is essential to predict liver-related outcomes and guide treatment decisions. A protein-based signature of fibrosis could serve as a valuable, non-invasive diagnostic tool. This study sought to identify circulating proteins associated with fibrosis in NAFLD. METHODS We used aptamer-based proteomics to measure 4,783 proteins in 2 cohorts (Cohort A and B). Targeted, quantitative assays coupling aptamer-based protein pull down and mass spectrometry (SPMS) validated the profiling results in a bariatric and NAFLD cohort (Cohort C and D, respectively). Generalized linear modeling-logistic regression assessed the ability of candidate proteins to classify fibrosis. RESULTS From the multiplex profiling, 16 proteins differed significantly by fibrosis in cohorts A (n = 62) and B (n = 98). Quantitative and robust SPMS assays were developed for 8 proteins and validated in Cohorts C (n = 71) and D (n = 84). The A disintegrin and metalloproteinase with thrombospondin motifs like 2 (ADAMTSL2) protein accurately distinguished non-alcoholic fatty liver (NAFL)/non-alcoholic steatohepatitis (NASH) with fibrosis stage 0-1 (F0-1) from at-risk NASH with fibrosis stage 2-4, with AUROCs of 0.83 and 0.86 in Cohorts C and D, respectively, and from NASH with significant fibrosis (F2-3), with AUROCs of 0.80 and 0.83 in Cohorts C and D, respectively. An 8-protein panel distinguished NAFL/NASH F0-1 from at-risk NASH (AUROCs 0.90 and 0.87 in Cohort C and D, respectively) and NASH F2-3 (AUROCs 0.89 and 0.83 in Cohorts C and D, respectively). The 8-protein panel and ADAMTSL2 protein had superior performance to the NAFLD fibrosis score and fibrosis-4 score. CONCLUSION The ADAMTSL2 protein and an 8-protein soluble biomarker panel are highly associated with at-risk NASH and significant fibrosis; they exhibited superior diagnostic performance compared to standard of care fibrosis scores. LAY SUMMARY Non-alcoholic fatty liver disease (NAFLD) is one of the most common causes of liver disease worldwide. Diagnosing NAFLD and identifying fibrosis (scarring of the liver) currently requires a liver biopsy. Our study identified novel proteins found in the blood which may identify fibrosis without the need for a liver biopsy.
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Affiliation(s)
- Kathleen E. Corey
- Division of Gastroenterology, Massachusetts General Hospital (MGH) and Harvard Medical School (HMS), Boston, MA, USA
| | - Rebecca Pitts
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Michelle Lai
- Division of Hepatology, Beth Israel Deaconess Hospital (BIDMC) and HMS, Boston, MA, USA
| | - Joseph Loureiro
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Ricard Masia
- Department of Pathology, MGH and HMS, Boston, MA, USA
| | - Stephanie A. Osganian
- Division of Gastroenterology, Massachusetts General Hospital (MGH) and Harvard Medical School (HMS), Boston, MA, USA
| | - Jenna L. Gustafson
- Division of Gastroenterology, Massachusetts General Hospital (MGH) and Harvard Medical School (HMS), Boston, MA, USA
| | | | | | | | | | | | - Jaison Jacob
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Nancy Finkel
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Debby Ngo
- Department of Pulmonary/Critical Care, Cardiovascular Institute, BIDMC and HMS, Boston, MA, USA
| | - Thomas J Wang
- Department of Cardiology, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Robert E. Gerszten
- Division of Cardiovascular Medicine and Cardiovascular Institute, BIDMC and HMS, Boston, MA, USA
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6
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Emilsson V, Ilkov M, Lamb JR, Finkel N, Gudmundsson EF, Pitts R, Hoover H, Gudmundsdottir V, Horman SR, Aspelund T, Shu L, Trifonov V, Sigurdsson S, Manolescu A, Zhu J, Olafsson Ö, Jakobsdottir J, Lesley SA, To J, Zhang J, Harris TB, Launer LJ, Zhang B, Eiriksdottir G, Yang X, Orth AP, Jennings LL, Gudnason V. Co-regulatory networks of human serum proteins link genetics to disease. Science 2018; 361:769-773. [PMID: 30072576 PMCID: PMC6190714 DOI: 10.1126/science.aaq1327] [Citation(s) in RCA: 291] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 02/07/2018] [Accepted: 07/13/2018] [Indexed: 12/25/2022]
Abstract
Proteins circulating in the blood are critical for age-related disease processes; however, the serum proteome has remained largely unexplored. To this end, 4137 proteins covering most predicted extracellular proteins were measured in the serum of 5457 Icelanders over 65 years of age. Pairwise correlation between proteins as they varied across individuals revealed 27 different network modules of serum proteins, many of which were associated with cardiovascular and metabolic disease states, as well as overall survival. The protein modules were controlled by cis- and trans-acting genetic variants, which in many cases were also associated with complex disease. This revealed co-regulated groups of circulating proteins that incorporated regulatory control between tissues and demonstrated close relationships to past, current, and future disease states.
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Affiliation(s)
- Valur Emilsson
- Icelandic Heart Association, Holtasmari 1, IS-201 Kopavogur, Iceland.
- Faculty of Pharmacology, University of Iceland, 101 Reykjavik, Iceland
| | - Marjan Ilkov
- Icelandic Heart Association, Holtasmari 1, IS-201 Kopavogur, Iceland
| | - John R Lamb
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA.
| | - Nancy Finkel
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA 02139, USA
| | | | - Rebecca Pitts
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA 02139, USA
| | - Heather Hoover
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA 02139, USA
| | | | - Shane R Horman
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Thor Aspelund
- Icelandic Heart Association, Holtasmari 1, IS-201 Kopavogur, Iceland
- Centre of Public Health Sciences, University of Iceland, 101 Reykjavik, Iceland
| | - Le Shu
- Department of Integrative Biology and Physiology, University of California, Los Angeles CA, USA
| | - Vladimir Trifonov
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | | | - Andrei Manolescu
- School of Science and Engineering, Mentavegur 1, IS-101, Reykjavik University, 101 Reykjavik, Iceland
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Örn Olafsson
- Icelandic Heart Association, Holtasmari 1, IS-201 Kopavogur, Iceland
| | | | - Scott A Lesley
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Jeremy To
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Jia Zhang
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Tamara B Harris
- Laboratory of Epidemiology and Population Sciences, Intramural Research Program, National Institute on Aging, Bethesda, MD 20892-9205, USA
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, Intramural Research Program, National Institute on Aging, Bethesda, MD 20892-9205, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles CA, USA
| | - Anthony P Orth
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Lori L Jennings
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA 02139, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Holtasmari 1, IS-201 Kopavogur, Iceland.
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
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7
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Jacob J, Ngo D, Finkel N, Pitts R, Gleim S, Benson MD, Keyes MJ, Farrell LA, Morgan T, Jennings LL, Gerszten RE. Application of Large-Scale Aptamer-Based Proteomic Profiling to Planned Myocardial Infarctions. Circulation 2017; 137:1270-1277. [PMID: 29222138 DOI: 10.1161/circulationaha.117.029443] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 11/08/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Emerging proteomic technologies using novel affinity-based reagents allow for efficient multiplexing with high-sample throughput. To identify early biomarkers of myocardial injury, we recently applied an aptamer-based proteomic profiling platform that measures 1129 proteins to samples from patients undergoing septal alcohol ablation for hypertrophic cardiomyopathy, a human model of planned myocardial injury. Here, we examined the scalability of this approach using a markedly expanded platform to study a far broader range of human proteins in the context of myocardial injury. METHODS We applied a highly multiplexed, expanded proteomic technique that uses single-stranded DNA aptamers to assay 4783 human proteins (4137 distinct human gene targets) to derivation and validation cohorts of planned myocardial injury, individuals with spontaneous myocardial infarction, and at-risk controls. RESULTS We found 376 target proteins that significantly changed in the blood after planned myocardial injury in a derivation cohort (n=20; P<1.05E-05, 1-way repeated measures analysis of variance, Bonferroni threshold). Two hundred forty-seven of these proteins were validated in an independent planned myocardial injury cohort (n=15; P<1.33E-04, 1-way repeated measures analysis of variance); >90% were directionally consistent and reached nominal significance in the validation cohort. Among the validated proteins that were increased within 1 hour after planned myocardial injury, 29 were also elevated in patients with spontaneous myocardial infarction (n=63; P<6.17E-04). Many of the novel markers identified in our study are intracellular proteins not previously identified in the peripheral circulation or have functional roles relevant to myocardial injury. For example, the cardiac LIM protein, cysteine- and glycine-rich protein 3, is thought to mediate cardiac mechanotransduction and stress responses, whereas the mitochondrial ATP synthase F0 subunit component is a vasoactive peptide on its release from cells. Last, we performed aptamer-affinity enrichment coupled with mass spectrometry to technically verify aptamer specificity for a subset of the new biomarkers. CONCLUSIONS Our results demonstrate the feasibility of large-scale aptamer multiplexing at a level that has not previously been reported and with sample throughput that greatly exceeds other existing proteomic methods. The expanded aptamer-based proteomic platform provides a unique opportunity for biomarker and pathway discovery after myocardial injury.
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Affiliation(s)
- Jaison Jacob
- Novartis Institute for BioMedical Research, Chemical Biology and Therapeutics, Cambridge, MA (J.J., N.F., R.P., S.G., T.M., L.L.J.)
| | - Debby Ngo
- Division of Pulmonary, Critical Care and Sleep Medicine (D.N.).,Cardiovascular Research Center (D.N., M.J.K., L.A.F., R.E.G.)
| | - Nancy Finkel
- Novartis Institute for BioMedical Research, Chemical Biology and Therapeutics, Cambridge, MA (J.J., N.F., R.P., S.G., T.M., L.L.J.)
| | - Rebecca Pitts
- Novartis Institute for BioMedical Research, Chemical Biology and Therapeutics, Cambridge, MA (J.J., N.F., R.P., S.G., T.M., L.L.J.)
| | - Scott Gleim
- Novartis Institute for BioMedical Research, Chemical Biology and Therapeutics, Cambridge, MA (J.J., N.F., R.P., S.G., T.M., L.L.J.)
| | - Mark D Benson
- Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (M.D.B.)
| | | | | | - Thomas Morgan
- Novartis Institute for BioMedical Research, Chemical Biology and Therapeutics, Cambridge, MA (J.J., N.F., R.P., S.G., T.M., L.L.J.)
| | - Lori L Jennings
- Novartis Institute for BioMedical Research, Chemical Biology and Therapeutics, Cambridge, MA (J.J., N.F., R.P., S.G., T.M., L.L.J.)
| | - Robert E Gerszten
- Cardiovascular Research Center (D.N., M.J.K., L.A.F., R.E.G.) .,Division of Cardiovascular Medicine (R.E.G.), Beth Israel Deaconess Medical Center, Boston, MA
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Hoover H, Li J, Marchese J, Rothwell C, Borawoski J, Jeffery DA, Gaither LA, Finkel N. Quantitative Proteomic Verification of Membrane Proteins as Potential Therapeutic Targets Located in the 11q13 Amplicon in Cancers. J Proteome Res 2015; 14:3670-9. [PMID: 26151158 DOI: 10.1021/acs.jproteome.5b00508] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Tumor types can be defined cytologically by their regions of chromosomal amplification, which often results in the high expression of both mRNA and proteins of certain genes contained within the amplicon. An important strategy for defining therapeutically relevant targets in these situations is to ascertain which genes are amplified at the protein level and, concomitantly, are key drivers for tumor growth or maintenance. Furthermore, so-called passenger genes that are amplified with driver genes and a manifest on the cell surface can be attractive targets for an antibody-drug conjugate approach (ADC). We employed a tandem mass spectrometry proteomics approach using tumor cell lines to identify the cell surface proteins whose expression correlates with the 11q13 amplicon. The 11q13 amplicon is one of the most frequently amplified chromosomal regions in human cancer, being present in 45% of head and neck and oral squamous cell carcinoma (OSCC) and 13-21% of breast and liver carcinomas. Using a panel of tumor cell lines with defined 11q13 genomic amplification, we identified the membrane proteins that are differentially expressed in an 11q13 amplified cell line panel using membrane-enriched proteomic profiling. We found that DSG3, CD109, and CD14 were differentially overexpressed in head and neck and breast tumor cells with 11q13 amplification. The level of protein expression of each gene was confirmed by Western blot and FACS analysis. Because proteins with high cell surface expression on selected tumor cells could be potential antibody drug conjugate targets, we tested DSG3 and CD109 in antibody piggyback assays and validated that DSG3 and CD109 expression was sufficient to induce antibody internalization and cell killing in 11q13-amplified cell lines. Our results suggest that proteomic profiling using genetically stratified tumors can identify candidate antibody drug conjugate targets. Data are available via ProteomeXchange with the identifier PXD002486.
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Affiliation(s)
- Heather Hoover
- Novartis Institutes for Biomedical Research , Cambridge, Massachusetts 02139, United States
| | - Jun Li
- Novartis Institutes for Biomedical Research , Cambridge, Massachusetts 02139, United States
| | - Jason Marchese
- Novartis Institutes for Biomedical Research , Cambridge, Massachusetts 02139, United States
| | - Christopher Rothwell
- Novartis Institutes for Biomedical Research , Cambridge, Massachusetts 02139, United States
| | - Jason Borawoski
- Novartis Institutes for Biomedical Research , Cambridge, Massachusetts 02139, United States
| | - Douglas A Jeffery
- Novartis Institutes for Biomedical Research , Cambridge, Massachusetts 02139, United States
| | - L Alex Gaither
- Novartis Institutes for Biomedical Research , Cambridge, Massachusetts 02139, United States
| | - Nancy Finkel
- Novartis Institutes for Biomedical Research , Cambridge, Massachusetts 02139, United States
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Richieri-Costa A, Rogatko A, Levisky R, Finkel N, Frota-Pessoa O. Autosomal dominant late adult spinal muscular atrophy, type Finkel. Am J Med Genet 1981; 9:119-28. [PMID: 7258225 DOI: 10.1002/ajmg.1320090206] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We describe clinical and genetic data from the study of two families with 80 members affected with the autosomal dominant, slowly progressive spinal muscular atrophy of late onset (average 48.8 years), first described by Finkel in 1962. Electromyography and muscle biopsy of a number of patients confirmed the neurogenic nature of the conditions. Unusual findings in this disorder were cramps, spontaneous fits of suffocation, and symptomatic myotonia. Other manifestations are slow loss of muscle strength and progressive proximal atrophy, which starts in the lower limbs and progresses to the upper limbs; hypoactive or absent tendinous reflexes; and generalized fasciculations. Sensory and cranial nerve function is unimpaired. Probabilities for genetic counseling are evaluated by means of a method adequate to the late-onset nature of the condition.
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Rabinowitz FM, Moely BE, Finkel N, McClinton S. The Effects of Toy Novelty and Social Interaction on the Exploratory Behavior of Preschool Children. Child Dev 1975. [DOI: 10.2307/1128867] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Finkel N. Transient selective amnesia for merchandise prices. Mt Sinai J Med 1974; 41:125-6. [PMID: 4544500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Abstract
São relatados 4 casos de miopatia ocular descendente (MOD) com história familial levantada em três gerações. Biópsia musculares e eletromiografia em um caso confirmaram o caráter miogênico da doença. A MOD nada mais seria do que uma forma clínica especial de distrofia muscular, de início tardio.
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