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Menaker Y, van den Munckhof I, Scarpa A, Placek K, Brandes-Leibovitz R, Glantzspiegel Y, Joosten LAB, Rutten JHW, Netea MG, Gat-Viks I, Riksen NP. Stratification of Atherosclerosis based on Plasma Metabolic States. J Clin Endocrinol Metab 2024; 109:1250-1262. [PMID: 38044551 DOI: 10.1210/clinem/dgad672] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Indexed: 12/05/2023]
Abstract
CONTEXT Atherosclerosis is a dominant cause of cardiovascular disease (CVD), including myocardial infarction and stroke. OBJECTIVE To investigate metabolic states that are associated with the development of atherosclerosis. METHODS Cross-sectional cohort study at a university hospital in the Netherlands. A total of 302 adult subjects with a body mass index (BMI) ≥ 27 kg/m2 were included. We integrated plasma metabolomics with clinical metadata to quantify the "atherogenic state" of each individual, providing a continuous spectrum of atherogenic states that ranges between nonatherogenic states to highly atherogenic states. RESULTS Analysis of groups of individuals with different clinical conditions-such as metabolically healthy individuals with obesity, and individuals with metabolic syndrome-confirmed the generalizability of this spectrum; revealed a wide variation of atherogenic states within each condition; and allowed identification of metabolites that are associated with the atherogenic state regardless of the particular condition, such as gamma-glutamyl-glutamic acid and homovanillic acid sulfate. The analysis further highlighted metabolic pathways such as catabolism of phenylalanine and tyrosine and biosynthesis of estrogens and phenylpropanoids. Using validation cohorts, we confirmed variation in atherogenic states in healthy subjects (before atherosclerosis plaques become visible), and showed that metabolites associated with the atherogenic state were also associated with future CVD. CONCLUSION Our results provide a global view of atherosclerosis risk states using plasma metabolomics.
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Affiliation(s)
- Yuval Menaker
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Inge van den Munckhof
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Alice Scarpa
- Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
| | - Katarzyna Placek
- Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
| | - Rachel Brandes-Leibovitz
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yossef Glantzspiegel
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, 400000 Cluj-Napoca, Romania
| | - Joost H W Rutten
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
| | - Irit Gat-Viks
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Niels P Riksen
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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Payne T, Burgess T, Bradley S, Roscoe S, Sassani M, Dunning MJ, Hernandez D, Scholz S, McNeill A, Taylor R, Su L, Wilkinson I, Jenkins T, Mortiboys H, Bandmann O. Multimodal assessment of mitochondrial function in Parkinson's disease. Brain 2024; 147:267-280. [PMID: 38059801 PMCID: PMC10766247 DOI: 10.1093/brain/awad364] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 09/02/2023] [Accepted: 09/27/2023] [Indexed: 12/08/2023] Open
Abstract
The heterogenous aetiology of Parkinson's disease is increasingly recognized; both mitochondrial and lysosomal dysfunction have been implicated. Powerful, clinically applicable tools are required to enable mechanistic stratification for future precision medicine approaches. The aim of this study was to characterize bioenergetic dysfunction in Parkinson's disease by applying a multimodal approach, combining standardized clinical assessment with midbrain and putaminal 31-phosphorus magnetic resonance spectroscopy (31P-MRS) and deep phenotyping of mitochondrial and lysosomal function in peripheral tissue in patients with recent-onset Parkinson's disease and control subjects. Sixty participants (35 patients with Parkinson's disease and 25 healthy controls) underwent 31P-MRS for quantification of energy-rich metabolites [ATP, inorganic phosphate (Pi) and phosphocreatine] in putamen and midbrain. In parallel, skin biopsies were obtained from all research participants to establish fibroblast cell lines for subsequent quantification of total intracellular ATP and mitochondrial membrane potential (MMP) as well as mitochondrial and lysosomal morphology, using high content live cell imaging. Lower MMP correlated with higher intracellular ATP (r = -0.55, P = 0.0016), higher mitochondrial counts (r = -0.72, P < 0.0001) and higher lysosomal counts (r = -0.62, P = 0.0002) in Parkinson's disease patient-derived fibroblasts only, consistent with impaired mitophagy and mitochondrial uncoupling. 31P-MRS-derived posterior putaminal Pi/ATP ratio variance was considerably greater in Parkinson's disease than in healthy controls (F-tests, P = 0.0036). Furthermore, elevated 31P-MRS-derived putaminal, but not midbrain Pi/ATP ratios (indicative of impaired oxidative phosphorylation) correlated with both greater mitochondrial (r = 0.37, P = 0.0319) and lysosomal counts (r = 0.48, P = 0.0044) as well as lower MMP in both short (r = -0.52, P = 0.0016) and long (r = -0.47, P = 0.0052) mitochondria in Parkinson's disease. Higher 31P-MRS midbrain phosphocreatine correlated with greater risk of rapid disease progression (r = 0.47, P = 0.0384). Our data suggest that impaired oxidative phosphorylation in the striatal dopaminergic nerve terminals exceeds mitochondrial dysfunction in the midbrain of patients with early Parkinson's disease. Our data further support the hypothesis of a prominent link between impaired mitophagy and impaired striatal energy homeostasis as a key event in early Parkinson's disease.
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Affiliation(s)
- Thomas Payne
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Toby Burgess
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Stephen Bradley
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Sarah Roscoe
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Matilde Sassani
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, The University of Birmingham, Birmingham B15 2TT, UK
| | - Mark J Dunning
- The Bioinformatics Core, Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Dena Hernandez
- Molecular Genetics Section, Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD 20814, USA
| | - Sonja Scholz
- Neurodegenerative Diseases Research Unit, Laboratory of Neurogenetics, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD 21287, USA
| | - Alisdair McNeill
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Rosie Taylor
- Statistical Services Unit, The University of Sheffield, Shefield S3 7RH, UK
| | - Li Su
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
- Department of Psychiatry, University of Cambridge, Cambridge CB2 0SP, UK
| | - Iain Wilkinson
- Academic Unit of Radiology, University of Sheffield, Sheffield S10 2JF, UK
| | - Thomas Jenkins
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
- Department of Neurology, Royal Perth Hospital, Perth WA6000, Australia
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Oliver Bandmann
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Sheffield S10 2HQ, UK
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Lam MTY, Duttke SH, Odish MF, Le HD, Hansen EA, Nguyen CT, Trescott S, Kim R, Deota S, Chang MW, Patel A, Hepokoski M, Alotaibi M, Rolfsen M, Perofsky K, Warden AS, Foley J, Ramirez SI, Dan JM, Abbott RK, Crotty S, Crotty Alexander LE, Malhotra A, Panda S, Benner CW, Coufal NG. Dynamic activity in cis-regulatory elements of leukocytes identifies transcription factor activation and stratifies COVID-19 severity in ICU patients. Cell Rep Med 2023; 4:100935. [PMID: 36758547 PMCID: PMC9874047 DOI: 10.1016/j.xcrm.2023.100935] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 09/08/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023]
Abstract
Transcription factor programs mediating the immune response to coronavirus disease 2019 (COVID-19) are not fully understood. Capturing active transcription initiation from cis-regulatory elements such as enhancers and promoters by capped small RNA sequencing (csRNA-seq), in contrast to capturing steady-state transcripts by conventional RNA-seq, allows unbiased identification of the underlying transcription factor activity and regulatory pathways. Here, we profile transcription initiation in critically ill COVID-19 patients, identifying transcription factor motifs that correlate with clinical lung injury and disease severity. Unbiased clustering reveals distinct subsets of cis-regulatory elements that delineate the cell type, pathway-specific, and combinatorial transcription factor activity. We find evidence of critical roles of regulatory networks, showing that STAT/BCL6 and E2F/MYB regulatory programs from myeloid cell populations are activated in patients with poor disease outcomes and associated with COVID-19 susceptibility genetic variants. More broadly, we demonstrate how capturing acute, disease-mediated changes in transcription initiation can provide insight into the underlying molecular mechanisms and stratify patient disease severity.
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Affiliation(s)
- Michael Tun Yin Lam
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Laboratory of Regulatory Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Pulmonary and Critical Care Section, VA San Diego Healthcare System, La Jolla, CA 92161, USA.
| | - Sascha H Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99163, USA
| | - Mazen F Odish
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hiep D Le
- Laboratory of Regulatory Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Emily A Hansen
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Celina T Nguyen
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Samantha Trescott
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Roy Kim
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Shaunak Deota
- Laboratory of Regulatory Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Max W Chang
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Arjun Patel
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark Hepokoski
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mona Alotaibi
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark Rolfsen
- Internal Medicine Residency Program, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katherine Perofsky
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Anna S Warden
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | | | - Sydney I Ramirez
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jennifer M Dan
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Robert K Abbott
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Shane Crotty
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Laura E Crotty Alexander
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Pulmonary and Critical Care Section, VA San Diego Healthcare System, La Jolla, CA 92161, USA
| | - Atul Malhotra
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Satchidananda Panda
- Laboratory of Regulatory Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Christopher W Benner
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicole G Coufal
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Rady Children's Hospital, San Diego, CA 92123, USA
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Jones BE, Mkhaimer YG, Rangel LJ, Chedid M, Schulte PJ, Mohamed AK, Neal RM, Zubidat D, Randhawa AK, Hanna C, Gregory AV, Kline TL, Zoghby ZM, Senum SR, Harris PC, Torres VE, Chebib FT. Asymptomatic Pyuria as a Prognostic Biomarker in Autosomal Dominant Polycystic Kidney Disease. Kidney360 2022; 3:465-476. [PMID: 35582184 PMCID: PMC9034817 DOI: 10.34067/kid.0004292021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/06/2021] [Indexed: 06/15/2023]
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) has phenotypic variability only partially explained by established biomarkers that do not readily assess pathologically important factors of inflammation and kidney fibrosis. We evaluated asymptomatic pyuria (AP), a surrogate marker of inflammation, as a biomarker for disease progression. METHODS We performed a retrospective cohort study of adult patients with ADPKD. Patients were divided into AP and no pyuria (NP) groups. We evaluated the effect of pyuria on kidney function and kidney volume. Longitudinal models evaluating kidney function and kidney volume rate of change with respect to incidences of AP were created. RESULTS There were 687 included patients (347 AP, 340 NP). The AP group had more women (65% versus 49%). Median ages at kidney failure were 86 and 80 years in the NP and AP groups (log rank, P=0.49), respectively, for patients in Mayo Imaging Class (MIC) 1A-1B as compared with 59 and 55 years for patients in MIC 1C-1D-1E (log rank, P=0.02), respectively. Compared with the NP group, the rate of kidney function (ml/min per 1.73 m2 per year) decline shifted significantly after detection of AP in the models, including all patients (-1.48; P<0.001), patients in MIC 1A-1B (-1.79; P<0.001), patients in MIC 1C-1D-1E (-1.18; P<0.001), and patients with PKD1 (-1.04; P<0.001). Models evaluating kidney volume rate of growth showed no change after incidence of AP as compared with the NP group. CONCLUSIONS AP is associated with kidney failure and faster kidney function decline irrespective of the ADPKD gene, cystic burden, and cystic growth. These results support AP as an enriching prognostic biomarker for the rate of disease progression.
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Affiliation(s)
- Brian E. Jones
- Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Yaman G. Mkhaimer
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Laureano J. Rangel
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Maroun Chedid
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Phillip J. Schulte
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Alaa K. Mohamed
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Reem M. Neal
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Dalia Zubidat
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Amarjyot K. Randhawa
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Christian Hanna
- Division of Pediatric Nephrology, Department of Pediatrics, Mayo Clinic, Rochester, Minnesota
| | - Adriana V. Gregory
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Ziad M. Zoghby
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Sarah R. Senum
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Peter C. Harris
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Vicente E. Torres
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Fouad T. Chebib
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
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Chauhan G, Heemers HV. Somatic Alterations Impact AR Transcriptional Activity and Efficacy of AR-Targeting Therapies in Prostate Cancer. Cancers (Basel) 2021; 13:3947. [PMID: 34439101 DOI: 10.3390/cancers13163947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary For patients whose prostate cancer spreads beyond the confines of the prostate, treatment options continue to increase. However, we are missing the information that is needed to choose for each patient the best treatment at each step of his cancer progression so we can ensure that maximal remissions and prolonged survival are achieved. In this review, we examine whether a better understanding of how the activity of the target for the default first treatment, the androgen receptor, is regulated in prostate cancer tissues can improve prostate cancer treatment plans. We consider the evidence for variability of androgen receptor activity among patients and examine the molecular basis for this variable action. We summarize clinical evidence supporting that information on a prostate cancer’s genomic composition may inform on its level of androgen receptor action, which may facilitate choice for the most effective first-line therapy and ultimately improve prostate cancer treatment plans overall. Abstract Inhibiting the activity of the ligand-activated transcription factor androgen receptor (AR) is the default first-line treatment for metastatic prostate cancer (CaP). Androgen deprivation therapy (ADT) induces remissions, however, their duration varies widely among patients. The reason for this heterogeneity is not known. A better understanding of its molecular basis may improve treatment plans and patient survival. AR’s transcriptional activity is regulated in a context-dependent manner and relies on an interplay between its associated transcriptional regulators, DNA recognition motifs, and ligands. Alterations in one or more of these factors induce shifts in the AR cistrome and transcriptional output. Significant variability in AR activity is seen in both castration-sensitive (CS) and castration-resistant CaP (CRPC). Several AR transcriptional regulators undergo somatic alterations that impact their function in clinical CaPs. Some alterations occur in a significant fraction of cases, resulting in CaP subtypes, while others affect only a few percent of CaPs. Evidence is emerging that these alterations may impact the response to CaP treatments such as ADT, radiation therapy, and chemotherapy. Here, we review the contribution of recurring somatic alterations on AR cistrome and transcriptional output and the efficacy of CaP treatments and explore strategies to use these insights to improve treatment plans and outcomes for CaP patients.
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Yang C, Tang S, Zhu D, Ding Y, Qiao J. Classical Disease-Specific Autoantibodies in Systemic Sclerosis: Clinical Features, Gene Susceptibility, and Disease Stratification. Front Med (Lausanne) 2020; 7:587773. [PMID: 33330547 PMCID: PMC7710911 DOI: 10.3389/fmed.2020.587773] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/08/2020] [Indexed: 12/13/2022] Open
Abstract
Systemic sclerosis (SSc) is an autoimmune disease characterized by abnormalities in microcirculation, extracellular matrix accumulation, and immune activation. Autoantibodies are markers of immune abnormalities and provide diagnostic and predictive value in SSc. Anti-topoisomerase antibodies (ATAs), anticentromere antibodies (ACAs), and anti-RNA polymerase antibodies (ARAs) are the three classical specific antibodies with the highest availability and stability. In this review, we provide an overview of the recent progress in SSc research with respect to ATAs, ACAs, and ARAs, focusing on their application in distinguishing clinical phenotypes, such as malignancy and organ involvement, identifying genetic background in human leukocyte antigen (HLA) or non-HLA alleles, and their potential roles in disease pathogenesis based on the effects of antigen-antibody binding. We finally summarized the novel analysis using ATAs, ACAs, and ARAs on more detailed disease clusters. Considering these advantages, this review emphasizes that classical SSc-specific autoantibodies are still practical and have the potential for patient and risk stratification with applications in precise medicine for SSc.
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Affiliation(s)
- Changyi Yang
- Department of Dermatology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shunli Tang
- Department of Dermatology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dingxian Zhu
- Department of Dermatology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingguo Ding
- Department of Dermatology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianjun Qiao
- Department of Dermatology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Griffin H, Soneji Y, Van Baars R, Arora R, Jenkins D, van de Sandt M, Wu Z, Quint W, Jach R, Okon K, Huras H, Singer A, Doorbar J. Stratification of HPV-induced cervical pathology using the virally encoded molecular marker E4 in combination with p16 or MCM. Mod Pathol 2015; 28:977-93. [PMID: 25953390 DOI: 10.1038/modpathol.2015.52] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 03/05/2015] [Indexed: 01/07/2023]
Abstract
High-risk human papillomavirus (HPV) types cause cervical lesions of varying severity, ranging from transient productive infections to high-grade neoplasia. Disease stratification requires the examination of lesional pathology, and possibly also the detection of biomarkers. P16(INK4a) and MCM are established surrogates of high-risk HPV E6/E7 activity, and can be extensively expressed in high-grade lesions. Here we have combined these two cellular biomarkers with detection of the abundant HPV-encoded E4 protein in order to identify both productive and transforming lesions. This approach has allowed us to distinguish true papillomavirus infections from similar pathologies, and has allowed us to divide the heterogeneous CIN2 category into those that are CIN1-like and express E4, and those that more closely resemble nonproductive CIN3. To achieve this, 530 lesional areas were evaluated according to standard pathology criteria and by using a multiple staining approach that allows us to superimpose biomarker patterns either singly or in combination onto an annotated hematoxylin and eosin (H&E) image. Conventional grading of neoplasia was established by review panel, and compared directly with the composite molecular pathology visualized on the same tissue section. The detection of E4 coincided with the onset of vacuolation, becoming abundant in koilocytes as the MCM marker declined and cells lost their defined nuclear margins as visualized by standard H&E staining. Of the dual marker approaches, p16(INK4a) and E4 appeared most promising, with E4 generally identifying areas of low-grade disease even when p16(INK4a) was present. Extensive p16(INK4a) expression usually coincided with an absence of E4 expression or its focal retention in sporadic cells within the lesion. Our results suggest that a straightforward molecular evaluation of HPV life-cycle deregulation in cervical neoplasia may help improve disease stratification, and that this can be achieved using complementary molecular biomarker pairs such as MCM/E4 or, more promisingly, p16(INK4a)/E4 as an adjunct to conventional pathology.
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Abstract
Studying complex biological systems in a holistic rather than a "one gene or one protein" at a time approach requires the concerted effort of scientists from a wide variety of disciplines. The Institute for Systems Biology (ISB) has seamlessly integrated these disparate fields to create a cross-disciplinary platform and culture in which "biology drives technology drives computation." To achieve this platform/culture, it has been necessary for cross-disciplinary ISB scientists to learn one another's languages and work together effectively in teams. The focus of this "systems" approach on disease has led to a discipline denoted systems medicine. The advent of technological breakthroughs in the fields of genomics, proteomics, and, indeed, the other "omics" is catalyzing striking advances in systems medicine that have and are transforming diagnostic and therapeutic strategies. Systems medicine has united genomics and genetics through family genomics to more readily identify disease genes. It has made blood a window into health and disease. It is leading to the stratification of diseases (division into discrete subtypes) for proper impedance match against drugs and the stratification of patients into subgroups that respond to environmental challenges in a similar manner (e.g. response to drugs, response to toxins, etc.). The convergence of patient-activated social networks, big data and their analytics, and systems medicine has led to a P4 medicine that is predictive, preventive, personalized, and participatory. Medicine will focus on each individual. It will become proactive in nature. It will increasingly focus on wellness rather than disease. For example, in 10 years each patient will be surrounded by a virtual cloud of billions of data points, and we will have the tools to reduce this enormous data dimensionality into simple hypotheses about how to optimize wellness and avoid disease for each individual. P4 medicine will be able to detect and treat perturbations in healthy individuals long before disease symptoms appear, thus optimizing the wellness of individuals and avoiding disease. P4 medicine will 1) improve health care, 2) reduce the cost of health care, and 3) stimulate innovation and new company creation. Health care is not the only subject that can benefit from such integrative, cross-disciplinary, and systems-driven platforms and cultures. Many other challenges plaguing our planet, such as energy, environment, nutrition, and agriculture can be transformed by using such an integrated and systems-driven approach.
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Affiliation(s)
- Leroy Hood
- To whom correspondence should be addressed. E-mail:
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