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Kacar Z, Slud E, Levy D, Candia J, Budhu A, Forgues M, Wu X, Raziuddin A, Tran B, Shetty J, Pomyen Y, Chaisaingmongkol J, Rabibhadana S, Pupacdi B, Bhudhisawasdi V, Lertprasertsuke N, Auewarakul C, Sangrajrang S, Mahidol C, Ruchirawat M, Wang XW. Characterization of tumor evolution by functional clonality and phylogenetics in hepatocellular carcinoma. Commun Biol 2024; 7:383. [PMID: 38553628 DOI: 10.1038/s42003-024-06040-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/01/2023] [Accepted: 03/11/2024] [Indexed: 04/02/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a molecularly heterogeneous solid malignancy, and its fitness may be shaped by how its tumor cells evolve. However, ability to monitor tumor cell evolution is hampered by the presence of numerous passenger mutations that do not provide any biological consequences. Here we develop a strategy to determine the tumor clonality of three independent HCC cohorts of 524 patients with diverse etiologies and race/ethnicity by utilizing somatic mutations in cancer driver genes. We identify two main types of tumor evolution, i.e., linear, and non-linear models where non-linear type could be further divided into classes, which we call shallow branching and deep branching. We find that linear evolving HCC is less aggressive than other types. GTF2IRD2B mutations are enriched in HCC with linear evolution, while TP53 mutations are the most frequent genetic alterations in HCC with non-linear models. Furthermore, we observe significant B cell enrichment in linear trees compared to non-linear trees suggesting the need for further research to uncover potential variations in immune cell types within genomically determined phylogeny types. These results hint at the possibility that tumor cells and their microenvironment may collectively influence the tumor evolution process.
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Affiliation(s)
- Zeynep Kacar
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
- Department of Mathematics, University of Maryland, College Park, MD, 20742, USA
| | - Eric Slud
- Department of Mathematics, University of Maryland, College Park, MD, 20742, USA
| | - Doron Levy
- Department of Mathematics, University of Maryland, College Park, MD, 20742, USA
| | - Julián Candia
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, 21224, USA
| | - Anuradha Budhu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Xiaolin Wu
- Cancer Research Technology Program, Frederick, MD, 21702, USA
| | - Arati Raziuddin
- Cancer Research Technology Program, Frederick, MD, 21702, USA
| | - Bao Tran
- Cancer Research Technology Program, Frederick, MD, 21702, USA
| | - Jyoti Shetty
- Cancer Research Technology Program, Frederick, MD, 21702, USA
| | - Yotsawat Pomyen
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | | | - Siritida Rabibhadana
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Benjarath Pupacdi
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | | | | | - Chirayu Auewarakul
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
| | | | - Chulabhorn Mahidol
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Mathuros Ruchirawat
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA.
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA.
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2
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Dark HE, Paterson C, Daya GN, Peng Z, Duggan MR, Bilgel M, An Y, Moghekar A, Davatzikos C, Resnick SM, Loupy K, Simpson M, Candia J, Mosley T, Coresh J, Palta P, Ferrucci L, Shapiro A, Williams SA, Walker KA. Proteomic Indicators of Health Predict Alzheimer's Disease Biomarker Levels and Dementia Risk. Ann Neurol 2024; 95:260-273. [PMID: 37801487 PMCID: PMC10842994 DOI: 10.1002/ana.26817] [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: 05/05/2023] [Revised: 09/06/2023] [Accepted: 10/03/2023] [Indexed: 10/08/2023]
Abstract
OBJECTIVE Few studies have comprehensively examined how health and disease risk influence Alzheimer's disease (AD) biomarkers. The present study examined the association of 14 protein-based health indicators with plasma and neuroimaging biomarkers of AD and neurodegeneration. METHODS In 706 cognitively normal adults, we examined whether 14 protein-based health indices (ie, SomaSignal® tests) were associated with concurrently measured plasma-based biomarkers of AD pathology (amyloid-β [Aβ]42/40 , tau phosphorylated at threonine-181 [pTau-181]), neuronal injury (neurofilament light chain [NfL]), and reactive astrogliosis (glial fibrillary acidic protein [GFAP]), brain volume, and cortical Aβ and tau. In a separate cohort (n = 11,285), we examined whether protein-based health indicators associated with neurodegeneration also predict 25-year dementia risk. RESULTS Greater protein-based risk for cardiovascular disease, heart failure mortality, and kidney disease was associated with lower Aβ42/40 and higher pTau-181, NfL, and GFAP levels, even in individuals without cardiovascular or kidney disease. Proteomic indicators of body fat percentage, lean body mass, and visceral fat were associated with pTau-181, NfL, and GFAP, whereas resting energy rate was negatively associated with NfL and GFAP. Together, these health indicators predicted 12, 31, 50, and 33% of plasma Aβ42/40 , pTau-181, NfL, and GFAP levels, respectively. Only protein-based measures of cardiovascular risk were associated with reduced regional brain volumes; these measures predicted 25-year dementia risk, even among those without clinically defined cardiovascular disease. INTERPRETATION Subclinical peripheral health may influence AD and neurodegenerative disease processes and relevant biomarker levels, particularly NfL. Cardiovascular health, even in the absence of clinically defined disease, plays a central role in brain aging and dementia. ANN NEUROL 2024;95:260-273.
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Affiliation(s)
- Heather E. Dark
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | | | - Gulzar N. Daya
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Zhongsheng Peng
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Michael R. Duggan
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Murat Bilgel
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Yang An
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christos Davatzikos
- Section of Biomedical Image Analysis, Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan M. Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | | | | | - Julián Candia
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD USA
| | - Thomas Mosley
- University of Mississippi Medical Center, Jackson, MS, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Priya Palta
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
- Department of Epidemiology, Columbia Mailman School of Public Health, New York, New York, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD USA
| | - Allison Shapiro
- Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus
| | | | - Keenan A. Walker
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
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3
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Roberts JA, Basu-Roy S, Shin J, Varma VR, Williamson A, Blackshear C, Griswold ME, Candia J, Elango P, Karikkineth AC, Tanaka T, Ferrucci L, Thambisetty M. Serum Proteomic Signatures of Common Health Outcomes among Older Adults. Gerontology 2024; 70:269-278. [PMID: 38219723 DOI: 10.1159/000534753] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 10/09/2023] [Indexed: 01/16/2024] Open
Abstract
INTRODUCTION In aging populations, the coexistence of multiple health comorbidities represents a significant challenge for clinicians and researchers. Leveraging advances in omics techniques to characterize these health conditions may provide insight into disease pathogenesis as well as reveal biomarkers for monitoring, prognostication, and diagnosis. Researchers have previously established the utility of big data approaches with respect to comprehensive health outcome measurements in younger populations, identifying protein markers that may provide significant health information with a single blood sample. METHODS Here, we employed a similar approach in two cohorts of older adults, the Baltimore Longitudinal Study of Aging (mean age = 76.12 years) and InCHIANTI Study (mean age = 66.05 years), examining the relationship between levels of serum proteins and 5 key health outcomes: kidney function, fasting glucose, physical activity, lean body mass, and percent body fat. RESULTS Correlations between proteins and health outcomes were primarily shared across both older adult cohorts. We further identified that most proteins associated with health outcomes in the older adult cohorts were not associated with the same outcomes in a prior study of a younger population. A subset of proteins, adiponectin, MIC-1, and NCAM-120, were associated with at least three health outcomes in both older adult cohorts but not in the previously published younger cohort, suggesting that they may represent plausible markers of general health in older adult populations. CONCLUSION Taken together, these findings suggest that comprehensive protein health markers have utility in aging populations and are distinct from those identified in younger adults, indicating unique mechanisms of disease with aging.
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Affiliation(s)
- Jackson A Roberts
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA,
- Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA,
| | - Sayantani Basu-Roy
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Jong Shin
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Vijay R Varma
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Andrew Williamson
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Chad Blackshear
- University of Mississippi Medical Center, Jackson, Mississippi, USA
| | | | - Julián Candia
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Palchamy Elango
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Ajoy C Karikkineth
- Clinical Research Core, National Institute on Aging, National Institutes of Health Intramural Research Program, Baltimore, Maryland, USA
| | - Toshiko Tanaka
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Madhav Thambisetty
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
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Moaddel R, Ubaida‐Mohien C, Tanaka T, Tian Q, Candia J, Moore AZ, Lovett J, Fantoni G, Shehadeh N, Turek L, Collingham V, Kaileh M, Chia CW, Sen R, Egan JM, Ferrucci L. Cross-sectional analysis of healthy individuals across decades: Aging signatures across multiple physiological compartments. Aging Cell 2024; 23:e13902. [PMID: 37350292 PMCID: PMC10776121 DOI: 10.1111/acel.13902] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/28/2023] [Accepted: 05/27/2023] [Indexed: 06/24/2023] Open
Abstract
The study of age-related biomarkers from different biofluids and tissues within the same individual might provide a more comprehensive understanding of age-related changes within and between compartments as these changes are likely highly interconnected. Understanding age-related differences by compartments may shed light on the mechanism of their reciprocal interactions, which may contribute to the phenotypic manifestations of aging. To study such possible interactions, we carried out a targeted metabolomic analysis of plasma, skeletal muscle, and urine collected from healthy participants, age 22-92 years, and identified 92, 34, and 35 age-associated metabolites, respectively. The metabolic pathways that were identified across compartments included inflammation and cellular senescence, microbial metabolism, mitochondrial health, sphingolipid metabolism, lysosomal membrane permeabilization, vascular aging, and kidney function.
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Affiliation(s)
- Ruin Moaddel
- Biomedical Research CentreNational Institute on Aging, NIHBaltimoreMarylandUSA
| | | | - Toshiko Tanaka
- Biomedical Research CentreNational Institute on Aging, NIHBaltimoreMarylandUSA
| | - Qu Tian
- Biomedical Research CentreNational Institute on Aging, NIHBaltimoreMarylandUSA
| | - Julián Candia
- Biomedical Research CentreNational Institute on Aging, NIHBaltimoreMarylandUSA
| | - Ann Zenobia Moore
- Biomedical Research CentreNational Institute on Aging, NIHBaltimoreMarylandUSA
| | - Jacqueline Lovett
- Biomedical Research CentreNational Institute on Aging, NIHBaltimoreMarylandUSA
| | - Giovanna Fantoni
- Biomedical Research CentreNational Institute on Aging, NIHBaltimoreMarylandUSA
| | - Nader Shehadeh
- Biomedical Research CentreNational Institute on Aging, NIHBaltimoreMarylandUSA
| | - Lisa Turek
- Biomedical Research CentreNational Institute on Aging, NIHBaltimoreMarylandUSA
| | - Victoria Collingham
- Biomedical Research CentreNational Institute on Aging, NIHBaltimoreMarylandUSA
| | - Mary Kaileh
- Biomedical Research CentreNational Institute on Aging, NIHBaltimoreMarylandUSA
| | - Chee W. Chia
- Biomedical Research CentreNational Institute on Aging, NIHBaltimoreMarylandUSA
| | - Ranjan Sen
- Biomedical Research CentreNational Institute on Aging, NIHBaltimoreMarylandUSA
| | - Josephine M. Egan
- Biomedical Research CentreNational Institute on Aging, NIHBaltimoreMarylandUSA
| | - Luigi Ferrucci
- Biomedical Research CentreNational Institute on Aging, NIHBaltimoreMarylandUSA
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5
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Huth T, Dreher EC, Lemke S, Fritzsche S, Sugiyanto RN, Castven D, Ibberson D, Sticht C, Eiteneuer E, Jauch A, Pusch S, Albrecht T, Goeppert B, Candia J, Wang XW, Ji J, Marquardt JU, Nahnsen S, Schirmacher P, Roessler S. Chromosome 8p engineering reveals increased metastatic potential targetable by patient-specific synthetic lethality in liver cancer. Sci Adv 2023; 9:eadh1442. [PMID: 38134284 PMCID: PMC10745716 DOI: 10.1126/sciadv.adh1442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Large-scale chromosomal aberrations are prevalent in human cancer, but their function remains poorly understood. We established chromosome-engineered hepatocellular carcinoma cell lines using CRISPR-Cas9 genome editing. A 33-mega-base pair region on chromosome 8p (chr8p) was heterozygously deleted, mimicking a frequently observed chromosomal deletion. Using this isogenic model system, we delineated the functional consequences of chr8p loss and its impact on metastatic behavior and patient survival. We found that metastasis-associated genes on chr8p act in concert to induce an aggressive and invasive phenotype characteristic for chr8p-deleted tumors. Genome-wide CRISPR-Cas9 viability screening in isogenic chr8p-deleted cells served as a powerful tool to find previously unidentified synthetic lethal targets and vulnerabilities accompanying patient-specific chromosomal alterations. Using this target identification strategy, we showed that chr8p deletion sensitizes tumor cells to targeting of the reactive oxygen sanitizing enzyme Nudix hydrolase 17. Thus, chromosomal engineering allowed for the identification of novel synthetic lethalities specific to chr8p loss of heterozygosity.
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Affiliation(s)
- Thorben Huth
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Emely C. Dreher
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Steffen Lemke
- Quantitative Biology Center (QBiC), University of Tübingen, 72076 Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany
| | - Sarah Fritzsche
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Raisatun N. Sugiyanto
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Darko Castven
- Department of Medicine I, University Medical Center Schleswig Holstein, 23538 Lübeck, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, CellNetworks Excellence Cluster, Heidelberg University, 69120 Heidelberg, Germany
| | - Carsten Sticht
- NGS Core Facility, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Eva Eiteneuer
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Anna Jauch
- Institute of Human Genetics, Heidelberg University, 69120 Heidelberg, Germany
| | - Stefan Pusch
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas Albrecht
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Benjamin Goeppert
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Institute of Tissue Medicine and Pathology, University of Bern, 3008 Bern, Switzerland
- Institute of Pathology and Neuropathology, RKH Klinikum Ludwigsburg, 71640 Ludwigsburg, Germany
| | - Julián Candia
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis and Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Junfang Ji
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jens U. Marquardt
- Department of Medicine I, University Medical Center Schleswig Holstein, 23538 Lübeck, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany
- Biomedical Data Science, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
- The M3 Research Center, University of Tübingen, 72076 Tübingen, Germany
| | - Peter Schirmacher
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Stephanie Roessler
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
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Panigrahi G, Candia J, Dorsey TH, Tang W, Ohara Y, Byun JS, Minas TZ, Zhang A, Ajao A, Cellini A, Yfantis HG, Flis AL, Mann D, Ioffe O, Wang XW, Liu H, Loffredo CA, Napoles AM, Ambs S. Diabetes-associated breast cancer is molecularly distinct and shows a DNA damage repair deficiency. JCI Insight 2023; 8:e170105. [PMID: 37906280 PMCID: PMC10795835 DOI: 10.1172/jci.insight.170105] [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: 03/01/2023] [Accepted: 10/25/2023] [Indexed: 11/02/2023] Open
Abstract
Diabetes commonly affects patients with cancer. We investigated the influence of diabetes on breast cancer biology using a 3-pronged approach that included analysis of orthotopic human tumor xenografts, patient tumors, and breast cancer cells exposed to diabetes/hyperglycemia-like conditions. We aimed to identify shared phenotypes and molecular signatures by investigating the metabolome, transcriptome, and tumor mutational burden. Diabetes and hyperglycemia did not enhance cell proliferation but induced mesenchymal and stem cell-like phenotypes linked to increased mobility and odds of metastasis. They also promoted oxyradical formation and both a transcriptome and mutational signatures of DNA repair deficiency. Moreover, food- and microbiome-derived metabolites tended to accumulate in breast tumors in the presence of diabetes, potentially affecting tumor biology. Breast cancer cells cultured under hyperglycemia-like conditions acquired increased DNA damage and sensitivity to DNA repair inhibitors. Based on these observations, we conclude that diabetes-associated breast tumors may show an increased drug response to DNA damage repair inhibitors.
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Affiliation(s)
- Gatikrushna Panigrahi
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Tiffany H. Dorsey
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
- Data Science & Artificial Intelligence, R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Yuuki Ohara
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Jung S. Byun
- Division of Intramural Research, National Institute of Minority Health and Health Disparities, NIH, Bethesda, Maryland, USA
| | - Tsion Zewdu Minas
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Amy Zhang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Anuoluwapo Ajao
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Ashley Cellini
- Department of Pathology, University of Maryland Medical Center, Baltimore, Maryland, USA
| | - Harris G. Yfantis
- Department of Pathology, University of Maryland Medical Center and Veterans Affairs Maryland Care System, Baltimore, Maryland, USA
| | - Amy L. Flis
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Dean Mann
- Department of Pathology, University of Maryland Medical Center, Baltimore, Maryland, USA
| | - Olga Ioffe
- Department of Pathology, University of Maryland Medical Center, Baltimore, Maryland, USA
| | - Xin W. Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
- Liver Cancer Program, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Huaitian Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Christopher A. Loffredo
- Cancer Prevention and Control Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Anna Maria Napoles
- Division of Intramural Research, National Institute of Minority Health and Health Disparities, NIH, Bethesda, Maryland, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
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7
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Das JK, Banskota N, Candia J, Griswold ME, Orenduff M, de Cabo R, Corcoran DL, Das SK, De S, Huffman KM, Kraus VB, Kraus WE, Martin C, Racette SB, Redman LM, Schilling B, Belsky D, Ferrucci L. Calorie restriction modulates the transcription of genes related to stress response and longevity in human muscle: The CALERIE study. Aging Cell 2023; 22:e13963. [PMID: 37823711 PMCID: PMC10726900 DOI: 10.1111/acel.13963] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 06/19/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 10/13/2023] Open
Abstract
The lifespan extension induced by 40% caloric restriction (CR) in rodents is accompanied by postponement of disease, preservation of function, and increased stress resistance. Whether CR elicits the same physiological and molecular responses in humans remains mostly unexplored. In the CALERIE study, 12% CR for 2 years in healthy humans induced minor losses of muscle mass (leg lean mass) without changes of muscle strength, but mechanisms for muscle quality preservation remained unclear. We performed high-depth RNA-Seq (387-618 million paired reads) on human vastus lateralis muscle biopsies collected from the CALERIE participants at baseline, 12- and 24-month follow-up from the 90 CALERIE participants randomized to CR and "ad libitum" control. Using linear mixed effect model, we identified protein-coding genes and splicing variants whose expression was significantly changed in the CR group compared to controls, including genes related to proteostasis, circadian rhythm regulation, DNA repair, mitochondrial biogenesis, mRNA processing/splicing, FOXO3 metabolism, apoptosis, and inflammation. Changes in some of these biological pathways mediated part of the positive effect of CR on muscle quality. Differentially expressed splicing variants were associated with change in pathways shown to be affected by CR in model organisms. Two years of sustained CR in humans positively affected skeletal muscle quality, and impacted gene expression and splicing profiles of biological pathways affected by CR in model organisms, suggesting that attainable levels of CR in a lifestyle intervention can benefit muscle health in humans.
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Affiliation(s)
- Jayanta Kumar Das
- Longitudinal Studies Section, Translation Gerontology BranchNational Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
| | - Nirad Banskota
- Computational Biology and Genomics CoreNational Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
| | - Julián Candia
- Longitudinal Studies Section, Translation Gerontology BranchNational Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
| | | | - Melissa Orenduff
- Duke Molecular Physiology Institute and Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Rafael de Cabo
- Translation Gerontology Branch, National Institute on AgingNational Institutes of HealthBaltimoreMarylandUSA
| | - David L. Corcoran
- Department of GeneticsUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Sai Krupa Das
- Energy Metabolism, Jean Mayer USDA Human Nutrition Research Center on AgingTufts UniversityBostonMassachusettsUSA
| | - Supriyo De
- Computational Biology and Genomics CoreNational Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
| | - Kim Marie Huffman
- Duke Molecular Physiology Institute and Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Virginia B. Kraus
- Duke Molecular Physiology Institute and Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - William E. Kraus
- Duke Molecular Physiology Institute and Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Corby K. Martin
- Pennington Biomedical Research CenterLouisiana State UniversityBaton RougeLouisianaUSA
| | - Susan B. Racette
- College of Health SolutionsArizona State UniversityPhoenixArizonaUSA
| | - Leanne M. Redman
- Pennington Biomedical Research CenterLouisiana State UniversityBaton RougeLouisianaUSA
| | | | - Daniel W. Belsky
- Department of Epidemiology & Butler Columbia Aging CenterColumbia University Mailman School of Public HealthNew York CityNew YorkUSA
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translation Gerontology BranchNational Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
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8
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Tin A, Fohner AE, Yang Q, Brody JA, Davies G, Yao J, Liu D, Caro I, Lindbohm JV, Duggan MR, Meirelles O, Harris SE, Gudmundsdottir V, Taylor AM, Henry A, Beiser AS, Shojaie A, Coors A, Fitzpatrick AL, Langenberg C, Satizabal CL, Sitlani CM, Wheeler E, Tucker-Drob EM, Bressler J, Coresh J, Bis JC, Candia J, Jennings LL, Pietzner M, Lathrop M, Lopez OL, Redmond P, Gerszten RE, Rich SS, Heckbert SR, Austin TR, Hughes TM, Tanaka T, Emilsson V, Vasan RS, Guo X, Zhu Y, Tzourio C, Rotter JI, Walker KA, Ferrucci L, Kivimäki M, Breteler MMB, Cox SR, Debette S, Mosley TH, Gudnason VG, Launer LJ, Psaty BM, Seshadri S, Fornage M. Identification of circulating proteins associated with general cognitive function among middle-aged and older adults. Commun Biol 2023; 6:1117. [PMID: 37923804 PMCID: PMC10624811 DOI: 10.1038/s42003-023-05454-1] [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: 05/09/2023] [Accepted: 10/12/2023] [Indexed: 11/06/2023] Open
Abstract
Identifying circulating proteins associated with cognitive function may point to biomarkers and molecular process of cognitive impairment. Few studies have investigated the association between circulating proteins and cognitive function. We identify 246 protein measures quantified by the SomaScan assay as associated with cognitive function (p < 4.9E-5, n up to 7289). Of these, 45 were replicated using SomaScan data, and three were replicated using Olink data at Bonferroni-corrected significance. Enrichment analysis linked the proteins associated with general cognitive function to cell signaling pathways and synapse architecture. Mendelian randomization analysis implicated higher levels of NECTIN2, a protein mediating viral entry into neuronal cells, with higher Alzheimer's disease (AD) risk (p = 2.5E-26). Levels of 14 other protein measures were implicated as consequences of AD susceptibility (p < 2.0E-4). Proteins implicated as causes or consequences of AD susceptibility may provide new insight into the potential relationship between immunity and AD susceptibility as well as potential therapeutic targets.
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Grants
- N01 HC095163 NHLBI NIH HHS
- RC2 HL102419 NHLBI NIH HHS
- HHSN268201500003C NHLBI NIH HHS
- UH3 NS100605 NINDS NIH HHS
- R01 HL103612 NHLBI NIH HHS
- 75N92020D00002 NHLBI NIH HHS
- U01 HL096812 NHLBI NIH HHS
- MC_UU_00006/1 Medical Research Council
- UF1 NS125513 NINDS NIH HHS
- 75N92020D00005 NHLBI NIH HHS
- N01AG12100 NIA NIH HHS
- N01HC95160 NHLBI NIH HHS
- R01 AG054076 NIA NIH HHS
- R01 HL120393 NHLBI NIH HHS
- BB/F019394/1 Biotechnology and Biological Sciences Research Council
- RF1 AG059421 NIA NIH HHS
- R01 HL131136 NHLBI NIH HHS
- N01 HC095168 NHLBI NIH HHS
- UL1 RR025005 NCRR NIH HHS
- R01 AG015928 NIA NIH HHS
- HHSN268201800004I NHLBI NIH HHS
- U01 HL080295 NHLBI NIH HHS
- N01HC95163 NHLBI NIH HHS
- N01 AG012100 NIA NIH HHS
- HHSN268201500001C NHLBI NIH HHS
- UL1 TR001079 NCATS NIH HHS
- N01 HC085082 NHLBI NIH HHS
- U01 HL096917 NHLBI NIH HHS
- R01 HL059367 NHLBI NIH HHS
- U01 HL130114 NHLBI NIH HHS
- HHSN268200800007C NHLBI NIH HHS
- R01 HL085251 NHLBI NIH HHS
- N01HC95169 NHLBI NIH HHS
- R01 NS087541 NINDS NIH HHS
- 75N92020D00001 NHLBI NIH HHS
- R01 HL086694 NHLBI NIH HHS
- R01 AG054628 NIA NIH HHS
- U01 HL096902 NHLBI NIH HHS
- R01 HL087652 NHLBI NIH HHS
- N01 HC095162 NHLBI NIH HHS
- U01 HG004402 NHGRI NIH HHS
- N01HC95164 NHLBI NIH HHS
- N01 HC085086 NHLBI NIH HHS
- N01HC55222 NHLBI NIH HHS
- R01 AG049607 NIA NIH HHS
- R01 AG065596 NIA NIH HHS
- N01 HC095165 NHLBI NIH HHS
- N01HC95162 NHLBI NIH HHS
- MR/R024227/1 Medical Research Council
- N01HC85086 NHLBI NIH HHS
- 75N92020D00003 NHLBI NIH HHS
- R01 HL105756 NHLBI NIH HHS
- N01HC95168 NHLBI NIH HHS
- N01 HC095169 NHLBI NIH HHS
- HHSN268201800003I NHLBI NIH HHS
- P30 DK063491 NIDDK NIH HHS
- HHSN268201800007I NHLBI NIH HHS
- HHSN268201700002C NHLBI NIH HHS
- R01 AG066524 NIA NIH HHS
- RF1 AG063507 NIA NIH HHS
- HHSN268201200036C NHLBI NIH HHS
- R01 HL144483 NHLBI NIH HHS
- HHSN268201800001C NHLBI NIH HHS
- HHSN268201700001I NHLBI NIH HHS
- R01 AG056477 NIA NIH HHS
- HHSN268201700004I NHLBI NIH HHS
- N01HC95165 NHLBI NIH HHS
- N01 HC095159 NHLBI NIH HHS
- U01 AG058589 NIA NIH HHS
- N01HC95159 NHLBI NIH HHS
- N01 HC095161 NHLBI NIH HHS
- HHSN268201500001I NHLBI NIH HHS
- HHSN271201200022C NIDA NIH HHS
- N01 HC025195 NHLBI NIH HHS
- N01HC95161 NHLBI NIH HHS
- UL1 TR001420 NCATS NIH HHS
- 75N92020D00004 NHLBI NIH HHS
- U01 HL096814 NHLBI NIH HHS
- P30 AG066509 NIA NIH HHS
- R01 HL132320 NHLBI NIH HHS
- 75N92020D00007 NHLBI NIH HHS
- P30 AG066546 NIA NIH HHS
- R01 AG033040 NIA NIH HHS
- MR/S011676/1 Medical Research Council
- U01 AG052409 NIA NIH HHS
- HHSN268201500003I NHLBI NIH HHS
- K01 AG071689 NIA NIH HHS
- 75N92021D00006 NHLBI NIH HHS
- R01 AG026307 NIA NIH HHS
- R01 AG020098 NIA NIH HHS
- HHSN268201700005C NHLBI NIH HHS
- HHSN268201700001C NHLBI NIH HHS
- N01HC85082 NHLBI NIH HHS
- HHSN268201700003C NHLBI NIH HHS
- N01 HC095166 NHLBI NIH HHS
- N01HC95167 NHLBI NIH HHS
- N01HC85083 NHLBI NIH HHS
- UH2 NS100605 NINDS NIH HHS
- N01HC25195 NHLBI NIH HHS
- 75N92019D00031 NHLBI NIH HHS
- U01 HL096899 NHLBI NIH HHS
- HHSN268201700004C NHLBI NIH HHS
- UL1 TR000040 NCATS NIH HHS
- HHSN268201700002I NHLBI NIH HHS
- HHSN268201700005I NHLBI NIH HHS
- P30 AG072947 NIA NIH HHS
- R01 AG025941 NIA NIH HHS
- Chief Scientist Office
- 75N92020D00006 NHLBI NIH HHS
- N01HC95166 NHLBI NIH HHS
- R01 AG023629 NIA NIH HHS
- R01 HL087641 NHLBI NIH HHS
- N01HC85079 NHLBI NIH HHS
- N01 HC085080 NHLBI NIH HHS
- UL1 TR001881 NCATS NIH HHS
- N01 HC095167 NHLBI NIH HHS
- HHSN268201800005I NHLBI NIH HHS
- N01HC85080 NHLBI NIH HHS
- HHSN268201700003I NHLBI NIH HHS
- HHSN268201800006I NHLBI NIH HHS
- N01 HC095164 NHLBI NIH HHS
- N01HC85081 NHLBI NIH HHS
- N01 HC095160 NHLBI NIH HHS
- The ARIC study has been funded in whole or in part with Federal funds from the National Heart, Lung, and Blood Institute, National Institutes of Health, Department of Health and Human Services (contract numbers HHSN268201700001I, HHSN268201700002I, HHSN268201700003I, HHSN268201700004I and HHSN268201700005I), R01HL087641, R01HL059367 and R01HL086694; National Human Genome Research Institute contract U01HG004402; and National Institutes of Health contract HHSN268200625226C. Funding was also supported by 5RC2HL102419, R01NS087541 and R01HL131136. Neurocognitive data were collected by U01 2U01HL096812, 2U01HL096814, 2U01HL096899, 2U01HL096902, 2U01HL096917 from the NIH (NHLBI, NINDS, NIA and NIDCD). Infrastructure was partly supported by Grant Number UL1RR025005, a component of the National Institutes of Health and NIH Roadmap for Medical Research. This Cardiovascular Heath Study (CHS) research was supported by NHLBI contracts HHSN268201200036C, HHSN268200800007C, HHSN268201800001C, N01HC55222, N01HC85079, N01HC85080, N01HC85081, N01HC85082, N01HC85083, N01HC85086, 75N92021D00006; and NHLBI grants U01HL080295, R01HL087652, R01HL105756, R01HL103612, R01HL120393, R01HL085251, R01HL144483, and U01HL130114 with additional contribution from the National Institute of Neurological Disorders and Stroke (NINDS). Additional support was provided through R01AG023629, R01AG15928, and R01AG20098 from the National Institute on Aging (NIA). AEF is supported by K01AG071689. The Framingham Heart Study is conducted and supported by the National Heart, Lung, and Blood Institute (NHLBI) in collaboration with Boston University (Contract No. N01-HC-25195, HHSN268201500001I and 75N92019D00031). This work was also supported by grant R01AG063507, R01AG054076, R01AG049607, R01AG059421, R01AG033040, R01AG066524, P30AG066546, U01 AG052409, U01 AG058589 from from the National Institute on Aging and R01 AG017950, UH2/3 NS100605, UF1 NS125513 from National Institute of Neurological Disorders and Stroke and R01HL132320. AGES has been funded by NIA contracts N01-AG012100 and HSSN271201200022C, NIH Grant No. 1R01AG065596-01A1, Hjartavernd (the Icelandic Heart Association), and the Althingi (the Icelandic Parliament). M. R. Duggan, T. Tanaka, J. Candia, K. A. Walker, L. Ferrucci, L.J. Launer, O. Meirelles are funded by the National Institute on Aging Intramural Research Program. This study was funded, in part, by the National Institute on Aging Intramural Research Program. The Coronary Artery Risk Development in Young Adults Study (CARDIA) is supported by contracts HHSN268201800003I, HHSN268201800004I, HHSN268201800005I, HHSN268201800006I, and HHSN268201800007I from the National Heart, Lung, and Blood Institute (NHLBI). The LBC1921 was supported by the UK’s Biotechnology and Biological Sciences Research Council (BBSRC), The Royal Society, and The Chief Scientist Office of the Scottish Government. Genotyping was funded by the BBSRC (BB/F019394/1). LBC1936 is supported by the Biotechnology and Biological Sciences Research Council, and the Economic and Social Research Council [BB/W008793/1], Age UK (Disconnected Mind project), and the University of Edinburgh. Genotyping was funded by the BBSRC (BB/F019394/1). The Olink® Neurology Proteomics assay was supported by a National Institutes of Health (NIH) research grant R01AG054628. Phenotype harmonization, data management, sample-identity QC, and general study coordination, were provided by the TOPMed Data Coordinating Center (3R01HL-120393-02S1), and TOPMed MESA Multi-Omics (HHSN2682015000031/HSN26800004). The MESA projects are conducted and supported by the National Heart, Lung, and Blood Institute (NHLBI) in collaboration with MESA investigators. Support for the Multi-Ethnic Study of Atherosclerosis (MESA) projects are conducted and supported by the National Heart, Lung, and Blood Institute (NHLBI) in collaboration with MESA investigators. Support for MESA is provided by contracts 75N92020D00001, HHSN268201500003I, N01-HC-95159, 75N92020D00005, N01-HC-95160, 75N92020D00002, N01-HC-95161, 75N92020D00003, N01-HC-95162, 75N92020D00006, N01-HC-95163, 75N92020D00004, N01-HC-95164, 75N92020D00007, N01-HC-95165, N01-HC-95166, N01-HC-95167, N01-HC-95168, N01-HC-95169, UL1-TR-000040, UL1-TR-001079, UL1-TR-001420, UL1TR001881, DK063491, and R01HL105756. The Three City (3C) Study is conducted under a partnership agreement among the Institut National de la Santé et de la Recherche Médicale (INSERM), the University of Bordeaux, and Sanofi-Aventis. The Fondation pour la Recherche Médicale funded the preparation and initiation of the study. The 3C Study is also supported by the Caisse Nationale Maladie des Travailleurs Salariés, Direction Générale de la Santé, Mutuelle Générale de l’Education Nationale (MGEN), Institut de la Longévité, Conseils Régionaux of Aquitaine and Bourgogne, Fondation de France, and Ministry of Research–INSERM Programme “Cohortes et collections de données biologiques.” Ilana Caro received a grant from the EUR digital public health. This PhD program is supported within the framework of the PIA3 (Investment for the future). Project reference 17-EURE-0019.
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Affiliation(s)
- Adrienne Tin
- Memory Impairment and Neurodegenerative Dementia (MIND) Center, University of Mississippi Medical Center, Jackson, MS, USA.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Alison E Fohner
- Department of Epidemiology, University of Washington, Seattle, WA, USA.
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA.
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA.
| | - Qiong Yang
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Gail Davies
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Dan Liu
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Ilana Caro
- University of Bordeaux, Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux Population Health Research Center, UMR 1219, CHU Bordeaux, Bordeaux, France
| | - Joni V Lindbohm
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, The Klarman Cell Observatory, Cambridge, MA, USA
- Clinicum, Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Epidemiology and Public Health, University College London, London, UK
| | - Michael R Duggan
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
| | - Osorio Meirelles
- National Institute on Aging, National Institutes of Health, Laboratory of Epidemiology and Population Science, Bethesda, MD, USA
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Valborg Gudmundsdottir
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Icelandic Heart Association, Kopavogur, Iceland
| | - Adele M Taylor
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Albert Henry
- Institute of Cardiovascular Science, University of London, London, UK
| | - Alexa S Beiser
- Department of Biostatistics, Boston University, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Ali Shojaie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Annabell Coors
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Annette L Fitzpatrick
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Departments of Family Medicine, University of Washington, Seattle, WA, USA
| | - Claudia Langenberg
- Precision Healthcare Institute, Queen Mary University of London, London, UK
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Claudia L Satizabal
- Framingham Heart Study, Framingham, MA, USA
- Department of Population Health Sciences and Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Eleanor Wheeler
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | | | - Jan Bressler
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Julián Candia
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Lori L Jennings
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA, USA
| | - Maik Pietzner
- Precision Healthcare Institute, Queen Mary University of London, London, UK
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Oscar L Lopez
- Departments of Neurology and Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Paul Redmond
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Robert E Gerszten
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Thomas R Austin
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Timothy M Hughes
- Department of Internal Medicine, Section of Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Epidemiology and Prevention, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Valur Emilsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Icelandic Heart Association, Kopavogur, Iceland
| | - Ramachandran S Vasan
- Framingham Heart Study, Framingham, MA, USA
- University of Texas School of Public Health in San Antonio, San Antonio, TX, USA
- University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yineng Zhu
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - Christophe Tzourio
- University of Bordeaux, Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux Population Health Research Center, UMR 1219, CHU Bordeaux, Bordeaux, France
| | - 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, USA
| | - Keenan A Walker
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Mika Kivimäki
- UCL Brain Sciences, University College London, London, UK
- Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Monique M B Breteler
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Stephanie Debette
- University of Bordeaux, Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux Population Health Research Center, UMR 1219, CHU Bordeaux, Bordeaux, France
- Department of Neurology, Institute for Neurodegenerative Diseases, CHU de Bordeaux, Bordeaux, France
| | - Thomas H Mosley
- Memory Impairment and Neurodegenerative Dementia (MIND) Center, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Lenore J Launer
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Bruce M Psaty
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Sudha Seshadri
- Framingham Heart Study, Framingham, MA, USA
- Department of Population Health Sciences and Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Myriam Fornage
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
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Cordon J, Duggan MR, Gomez GT, Pucha K, Peng Z, Dark HE, Davatzikos C, Erus G, Lewis A, Moghekar A, Candia J, Ferrucci L, Kapogiannis D, Walker KA. Identification of Clinically Relevant Brain Endothelial Cell Biomarkers in Plasma. Stroke 2023; 54:2853-2863. [PMID: 37814955 PMCID: PMC10608795 DOI: 10.1161/strokeaha.123.043908] [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: 05/15/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND Proteins expressed by brain endothelial cells (BECs), the primary cell type of the blood-brain barrier, may serve as sensitive plasma biomarkers for neurological and neurovascular conditions, including cerebral small vessel disease. METHODS Using data from the BLSA (Baltimore Longitudinal Study of Aging; n=886; 2009-2020), BEC-enriched proteins were identified among 7268 plasma proteins (measured with SomaScanv4.1) using an automated annotation algorithm that filtered endothelial cell transcripts followed by cross-referencing with BEC-specific transcripts reported in single-cell RNA-sequencing studies. To identify BEC-enriched proteins in plasma most relevant to the maintenance of neurological and neurovascular health, we selected proteins significantly associated with 3T magnetic resonance imaging-defined white matter lesion volumes. We then examined how these candidate BEC biomarkers related to white matter lesion volumes, cerebral microhemorrhages, and lacunar infarcts in the ARIC study (Atherosclerosis Risk in Communities; US multisite; 1990-2017). Finally, we determined whether these candidate BEC biomarkers, when measured during midlife, were related to dementia risk over a 25-year follow-up period. RESULTS Of the 28 proteins identified as BEC-enriched, 4 were significantly associated with white matter lesion volumes (CDH5 [cadherin 5], CD93 [cluster of differentiation 93], ICAM2 [intracellular adhesion molecule 2], GP1BB [glycoprotein 1b platelet subunit beta]), while another approached significance (RSPO3 [R-Spondin 3]). A composite score based on 3 of these BEC proteins accounted for 11% of variation in white matter lesion volumes in BLSA participants. We replicated the associations between the BEC composite score, CDH5, and RSPO3 with white matter lesion volumes in ARIC, and further demonstrated that the BEC composite score and RSPO3 were associated with the presence of ≥1 cerebral microhemorrhages. We also showed that the BEC composite score, CDH5, and RSPO3 were associated with 25-year dementia risk. CONCLUSIONS In addition to identifying BEC proteins in plasma that relate to cerebral small vessel disease and dementia risk, we developed a composite score of plasma BEC proteins that may be used to estimate blood-brain barrier integrity and risk for adverse neurovascular outcomes.
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Affiliation(s)
- Jenifer Cordon
- Multimodal Imaging of Neurodegenerative Disease (MIND) Unit, NIA
| | | | | | | | - Zhongsheng Peng
- Multimodal Imaging of Neurodegenerative Disease (MIND) Unit, NIA
| | - Heather E. Dark
- Multimodal Imaging of Neurodegenerative Disease (MIND) Unit, NIA
| | | | | | | | | | | | | | | | - Keenan A. Walker
- Multimodal Imaging of Neurodegenerative Disease (MIND) Unit, NIA
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10
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Roy R, Kuo PL, Candia J, Sarantopoulou D, Ubaida-Mohien C, Hernandez D, Kaileh M, Arepalli S, Singh A, Bektas A, Kim J, Moore AZ, Tanaka T, McKelvey J, Zukley L, Nguyen C, Wallace T, Dunn C, Wood W, Piao Y, Coletta C, De S, Sen J, Weng NP, Sen R, Ferrucci L. Epigenetic signature of human immune aging in the GESTALT study. eLife 2023; 12:e86136. [PMID: 37589453 PMCID: PMC10506794 DOI: 10.7554/elife.86136] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023] Open
Abstract
Age-associated DNA methylation in blood cells convey information on health status. However, the mechanisms that drive these changes in circulating cells and their relationships to gene regulation are unknown. We identified age-associated DNA methylation sites in six purified blood-borne immune cell types (naive B, naive CD4+ and CD8+ T cells, granulocytes, monocytes, and NK cells) collected from healthy individuals interspersed over a wide age range. Of the thousands of age-associated sites, only 350 sites were differentially methylated in the same direction in all cell types and validated in an independent longitudinal cohort. Genes close to age-associated hypomethylated sites were enriched for collagen biosynthesis and complement cascade pathways, while genes close to hypermethylated sites mapped to neuronal pathways. In silico analyses showed that in most cell types, the age-associated hypo- and hypermethylated sites were enriched for ARNT (HIF1β) and REST transcription factor (TF) motifs, respectively, which are both master regulators of hypoxia response. To conclude, despite spatial heterogeneity, there is a commonality in the putative regulatory role with respect to TF motifs and histone modifications at and around these sites. These features suggest that DNA methylation changes in healthy aging may be adaptive responses to fluctuations of oxygen availability.
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Affiliation(s)
- Roshni Roy
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Pei-Lun Kuo
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| | - Julián Candia
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| | - Dimitra Sarantopoulou
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | | | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on AgingBethesdaUnited States
| | - Mary Kaileh
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Sampath Arepalli
- Laboratory of Neurogenetics, National Institute on AgingBethesdaUnited States
| | - Amit Singh
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Arsun Bektas
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| | - Jaekwan Kim
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Ann Z Moore
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| | - Julia McKelvey
- Clinical Research Core, National Institute on AgingBaltimoreUnited States
| | - Linda Zukley
- Clinical Research Core, National Institute on AgingBaltimoreUnited States
| | - Cuong Nguyen
- Flow Cytometry Unit, National Institute on AgingBaltimoreUnited States
| | - Tonya Wallace
- Flow Cytometry Unit, National Institute on AgingBaltimoreUnited States
| | - Christopher Dunn
- Flow Cytometry Unit, National Institute on AgingBaltimoreUnited States
| | - William Wood
- Laboratory of Genetics and Genomics, National Institute on AgingBaltimoreUnited States
| | - Yulan Piao
- Laboratory of Genetics and Genomics, National Institute on AgingBaltimoreUnited States
| | - Christopher Coletta
- Laboratory of Genetics and Genomics, National Institute on AgingBaltimoreUnited States
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on AgingBaltimoreUnited States
| | - Jyoti Sen
- Laboratory of Clinical Investigation, National Institute on AgingBaltimoreUnited States
| | - Nan-ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
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11
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Minas TZ, Lord BD, Zhang AL, Candia J, Dorsey TH, Baker FS, Tang W, Bailey-Whyte M, Smith CJ, Obadi OM, Ajao A, Jordan SV, Tettey Y, Biritwum RB, Adjei AA, Mensah JE, Hoover RN, Hsing AW, Liu J, Loffredo CA, Yates C, Cook MB, Ambs S. Circulating trans fatty acids are associated with prostate cancer in Ghanaian and American men. Nat Commun 2023; 14:4322. [PMID: 37468456 DOI: 10.1038/s41467-023-39865-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
The association between fatty acids and prostate cancer remains poorly explored in African-descent populations. Here, we analyze 24 circulating fatty acids in 2934 men, including 1431 prostate cancer cases and 1503 population controls from Ghana and the United States, using CLIA-certified mass spectrometry-based assays. We investigate their associations with population groups (Ghanaian, African American, European American men), lifestyle factors, the fatty acid desaturase (FADS) genetic locus, and prostate cancer. Blood levels of circulating fatty acids vary significantly between the three population groups, particularly trans, omega-3 and omega-6 fatty acids. FADS1/2 germline genetic variants and lifestyle factors explain some of the variation in fatty acid levels, with the FADS1/2 locus showing population-specific associations, suggesting differences in their control by germline genetic factors. All trans fatty acids, namely elaidic, palmitelaidic, and linoelaidic acids, associated with an increase in the odds of developing prostate cancer, independent of ancestry, geographic location, or potential confounders.
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Affiliation(s)
- Tsion Zewdu Minas
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, USA
- Center for Innovative Drug Development and Therapeutic Trials for Africa, Addis Ababa University, Addis Ababa, Ethiopia
| | - Brittany D Lord
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, USA
| | - Amy L Zhang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, USA
| | - Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, USA
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Tiffany H Dorsey
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, USA
| | - Francine S Baker
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, USA
- Data Science & Artificial Intelligence, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Maeve Bailey-Whyte
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, USA
- School of Medicine, University of Limerick, Limerick, Ireland
| | - Cheryl J Smith
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, USA
| | - Obadi M Obadi
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, USA
| | - Anuoluwapo Ajao
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, USA
| | - Symone V Jordan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, USA
| | - Yao Tettey
- University of Ghana Medical School, Accra, Ghana
| | | | | | | | - Robert N Hoover
- Division of Cancer Epidemiology & Genetics, NCI, Rockville, MD, USA
| | - Ann W Hsing
- Stanford Cancer Institute, Stanford University, Palo Alto, CA, USA
- Stanford Prevention Research Center, Stanford University, Palo Alto, CA, USA
| | - Jia Liu
- Cancer Genomics Research Laboratory, NCI, Rockville, MD, USA
| | | | - Clayton Yates
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Urology and the James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael B Cook
- Division of Cancer Epidemiology & Genetics, NCI, Rockville, MD, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, USA.
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12
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Roberts JA, Varma VR, Candia J, Tanaka T, Ferrucci L, Bennett DA, Thambisetty M. Unbiased proteomics and multivariable regularized regression techniques identify SMOC1, NOG, APCS, and NTN1 in an Alzheimer's disease brain proteomic signature. NPJ Aging 2023; 9:18. [PMID: 37414805 PMCID: PMC10326005 DOI: 10.1038/s41514-023-00112-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/18/2023] [Indexed: 07/08/2023]
Abstract
Advancements in omics methodologies have generated a wealth of high-dimensional Alzheimer's disease (AD) datasets, creating significant opportunities and challenges for data interpretation. In this study, we utilized multivariable regularized regression techniques to identify a reduced set of proteins that could discriminate between AD and cognitively normal (CN) brain samples. Utilizing eNetXplorer, an R package that tests the accuracy and significance of a family of elastic net generalized linear models, we identified 4 proteins (SMOC1, NOG, APCS, NTN1) that accurately discriminated between AD (n = 31) and CN (n = 22) middle frontal gyrus (MFG) tissue samples from Religious Orders Study participants with 83 percent accuracy. We then validated this signature in MFG samples from Baltimore Longitudinal Study of Aging participants using leave-one-out logistic regression cross-validation, finding that the signature again accurately discriminated AD (n = 31) and CN (n = 19) participants with a receiver operating characteristic curve area under the curve of 0.863. These proteins were strongly correlated with the burden of neurofibrillary tangle and amyloid pathology in both study cohorts. We additionally tested whether these proteins differed between AD and CN inferior temporal gyrus (ITG) samples and blood serum samples at the time of AD diagnosis in ROS and BLSA, finding that the proteins differed between AD and CN ITG samples but not in blood serum samples. The identified proteins may provide mechanistic insights into the pathophysiology of AD, and the methods utilized in this study may serve as the basis for further work with additional high-dimensional datasets in AD.
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Affiliation(s)
- Jackson A Roberts
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA.
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA.
| | - Vijay R Varma
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Julián Candia
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Toshiko Tanaka
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Madhav Thambisetty
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA.
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13
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Osawa Y, Candia J, Abe Y, Tajima T, Oguma Y, Arai Y. Plasma amino acid signature for sarcopenic phenotypes in community-dwelling octogenarians: Results from the Kawasaki Aging Wellbeing Project. Exp Gerontol 2023; 178:112230. [PMID: 37286061 DOI: 10.1016/j.exger.2023.112230] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/29/2023] [Accepted: 06/01/2023] [Indexed: 06/09/2023]
Abstract
Sarcopenia is one of the primary risk factors for various adverse health events in later life. However, its pathophysiology in the very old population remains unclear. Hence, this study aimed to examine whether plasma free amino acids (PFAAs) correlate with major sarcopenic phenotypes (i.e., muscle mass, muscle strength, and physical performance) in community-dwelling adults aged 85-89 years living in Japan. Cross-sectional data from the Kawasaki Aging Well-being Project were used. We included 133 adults aged 85-89 years. In this study, fasting blood was collected to measure 20 plasma PFAAs. Measures for the three major sarcopenic phenotypes included appendicular lean mass assessed by multifrequency bioimpedance, isometric handgrip strength, and gait speed from a 5 m walk at a usual pace. Furthermore, we used phenotype-specific elastic net regression models adjusted for age centered at 85 years, sex, body mass index, education level, smoking status, and drinking habit to identify significant PFAAs for each sarcopenic phenotype. Higher histidine and lower alanine levels were associated with poor gait speed, but no PFAAs correlated with muscle strength or mass. In conclusion, PFAAs such as plasma histidine and alanine are novel blood biomarkers associated with physical performance in community-dwelling adults aged 85 years or older.
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Affiliation(s)
- Yusuke Osawa
- Graduate School of Health Management, Keio University, Kanagawa, Japan; Sports Medicine Research Center, Keio University, Kanagawa, Japan; Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, United States.
| | - Julián Candia
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, United States
| | - Yukiko Abe
- Center for Supercentenarian Medical Research, Keio University School of Medicine, Tokyo, Japan
| | - Takayuki Tajima
- Sports Medicine Research Center, Keio University, Kanagawa, Japan; Graduate School of Human Health Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Yuko Oguma
- Graduate School of Health Management, Keio University, Kanagawa, Japan; Sports Medicine Research Center, Keio University, Kanagawa, Japan
| | - Yasumichi Arai
- Center for Supercentenarian Medical Research, Keio University School of Medicine, Tokyo, Japan; Faculty of Nursing and Medical Care, Keio University School of Medicine, Kanagawa, Japan.
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14
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Ferrucci L, Candia J, Ubaida-Mohien C, Lyaskov A, Banskota N, Leeuwenburgh C, Wohlgemuth S, Guralnik JM, Kaileh M, Zhang D, Sufit R, De S, Gorospe M, Munk R, Peterson CA, McDermott MM. Transcriptomic and Proteomic of Gastrocnemius Muscle in Peripheral Artery Disease. Circ Res 2023; 132:1428-1443. [PMID: 37154037 DOI: 10.1161/circresaha.122.322325] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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] [Indexed: 05/10/2023]
Abstract
BACKGROUND Few effective therapies exist to improve lower extremity muscle pathology and mobility loss due to peripheral artery disease (PAD), in part because mechanisms associated with functional impairment remain unclear. METHODS To better understand mechanisms of muscle impairment in PAD, we performed in-depth transcriptomic and proteomic analyses on gastrocnemius muscle biopsies from 31 PAD participants (mean age, 69.9 years) and 29 age- and sex-matched non-PAD controls (mean age, 70.0 years) free of diabetes or limb-threatening ischemia. RESULTS Transcriptomic and proteomic analyses suggested activation of hypoxia-compensatory mechanisms in PAD muscle, including inflammation, fibrosis, apoptosis, angiogenesis, unfolded protein response, and nerve and muscle repair. Stoichiometric proportions of mitochondrial respiratory proteins were aberrant in PAD compared to non-PAD, suggesting that respiratory proteins not in complete functional units are not removed by mitophagy, likely contributing to abnormal mitochondrial activity. Supporting this hypothesis, greater mitochondrial respiratory protein abundance was significantly associated with greater complex II and complex IV respiratory activity in non-PAD but not in PAD. Rate-limiting glycolytic enzymes, such as hexokinase and pyruvate kinase, were less abundant in muscle of people with PAD compared with non-PAD participants, suggesting diminished glucose metabolism. CONCLUSIONS In PAD muscle, hypoxia induces accumulation of mitochondria respiratory proteins, reduced activity of rate-limiting glycolytic enzymes, and an enhanced integrated stress response that modulates protein translation. These mechanisms may serve as targets for disease modification.
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Affiliation(s)
- Luigi Ferrucci
- National Institute on Aging, Intramural Research Program, Baltimore, MD (L.F., J.C., C.U.-M., A.L., N.B., M.K., S.D., M.G., R.M.)
| | - Julián Candia
- National Institute on Aging, Intramural Research Program, Baltimore, MD (L.F., J.C., C.U.-M., A.L., N.B., M.K., S.D., M.G., R.M.)
| | - Ceereena Ubaida-Mohien
- National Institute on Aging, Intramural Research Program, Baltimore, MD (L.F., J.C., C.U.-M., A.L., N.B., M.K., S.D., M.G., R.M.)
| | - Alexey Lyaskov
- National Institute on Aging, Intramural Research Program, Baltimore, MD (L.F., J.C., C.U.-M., A.L., N.B., M.K., S.D., M.G., R.M.)
| | - Nirad Banskota
- National Institute on Aging, Intramural Research Program, Baltimore, MD (L.F., J.C., C.U.-M., A.L., N.B., M.K., S.D., M.G., R.M.)
| | - Christiaan Leeuwenburgh
- Department of Physiology and Aging, University of Florida, Institute on Aging, Gainesville (C.L., S.W.)
| | - Stephanie Wohlgemuth
- Department of Physiology and Aging, University of Florida, Institute on Aging, Gainesville (C.L., S.W.)
| | - Jack M Guralnik
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD (J.M.G.)
| | - Mary Kaileh
- National Institute on Aging, Intramural Research Program, Baltimore, MD (L.F., J.C., C.U.-M., A.L., N.B., M.K., S.D., M.G., R.M.)
| | - Dongxue Zhang
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL. (D.Z., R.S.)
| | - Robert Sufit
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL. (D.Z., R.S.)
| | - Supriyo De
- National Institute on Aging, Intramural Research Program, Baltimore, MD (L.F., J.C., C.U.-M., A.L., N.B., M.K., S.D., M.G., R.M.)
| | - Myriam Gorospe
- National Institute on Aging, Intramural Research Program, Baltimore, MD (L.F., J.C., C.U.-M., A.L., N.B., M.K., S.D., M.G., R.M.)
| | - Rachel Munk
- National Institute on Aging, Intramural Research Program, Baltimore, MD (L.F., J.C., C.U.-M., A.L., N.B., M.K., S.D., M.G., R.M.)
| | - Charlotte A Peterson
- Center for Muscle Biology. College of Health Sciences, University of Kentucky, Lexington (C.A.P.)
| | - Mary M McDermott
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL. (M.M.D.)
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15
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Pat N, Wang Y, Bartonicek A, Candia J, Stringaris A. Explainable machine learning approach to predict and explain the relationship between task-based fMRI and individual differences in cognition. Cereb Cortex 2023; 33:2682-2703. [PMID: 35697648 PMCID: PMC10016053 DOI: 10.1093/cercor/bhac235] [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: 02/04/2021] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Despite decades of costly research, we still cannot accurately predict individual differences in cognition from task-based functional magnetic resonance imaging (fMRI). Moreover, aiming for methods with higher prediction is not sufficient. To understand brain-cognition relationships, we need to explain how these methods draw brain information to make the prediction. Here we applied an explainable machine-learning (ML) framework to predict cognition from task-based fMRI during the n-back working-memory task, using data from the Adolescent Brain Cognitive Development (n = 3,989). We compared 9 predictive algorithms in their ability to predict 12 cognitive abilities. We found better out-of-sample prediction from ML algorithms over the mass-univariate and ordinary least squares (OLS) multiple regression. Among ML algorithms, Elastic Net, a linear and additive algorithm, performed either similar to or better than nonlinear and interactive algorithms. We explained how these algorithms drew information, using SHapley Additive explanation, eNetXplorer, Accumulated Local Effects, and Friedman's H-statistic. These explainers demonstrated benefits of ML over the OLS multiple regression. For example, ML provided some consistency in variable importance with a previous study and consistency with the mass-univariate approach in the directionality of brain-cognition relationships at different regions. Accordingly, our explainable-ML framework predicted cognition from task-based fMRI with boosted prediction and explainability over standard methodologies.
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Affiliation(s)
- Narun Pat
- Corresponding author: Department of Psychology, University of Otago, William James Building, 275 Leith Walk, Dunedin 9016, New Zealand.
| | - Yue Wang
- Department of Psychology, University of Otago, William James Building, 275 Leith Walk, Dunedin 9016, New Zealand
| | - Adam Bartonicek
- Department of Psychology, University of Otago, William James Building, 275 Leith Walk, Dunedin 9016, New Zealand
| | - Julián Candia
- Longitudinal Studies Section, Translational Gerontology National Institute on Aging, National Institute of Health, Branch, 251 Bayview Boulevard, Rm 05B113A, Biomedical Research Center, Baltimore, MD 21224, USA
| | - Argyris Stringaris
- Division of Psychiatry and Department of Clinical, Educational – Health Psychology, University College London, 1-19 Torrington Pl, London WC1E 7HB, United Kingdom
- Department of Psychiatry, National and Kapodistrian University of Athens, Medical School, Mikras Asias 75, Athina 115 27, Greece
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16
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Tanaka T, Talegawkar SA, Jin Y, Candia J, Fantoni G, Bandinelli S, Ferrucci L. Proteomic Mediators of Overall Cardiovascular Health on All-Cause Mortality. Nutrients 2023; 15:781. [PMID: 36771486 PMCID: PMC9921082 DOI: 10.3390/nu15030781] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/25/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Measures of cardiovascular health (CVH) assessed by a combination of behavioral and biological factors has shown protective associations with all-cause mortality. The mechanisms underlying these associations have not been fully elucidated. In this study, we characterized the plasma proteomics profile of CVH and tested whether specific proteins mediated the associations between CVH and all-cause mortality in participants of the InCHIANTI study. Of the 1301 proteins tested, 92 proteins were associated with CVH (22 positively, 70 negatively). Proteins most strongly associated with CVH included leptin (LEP), fatty acid binding protein 3 (FABP3), Angiopoietin-2 (ANGPT2), and growth-differential factor 15 (GDF15). Of the 92 CVH-associated proteins, 33 proteins significantly mediated the associations between CVH and all-cause mortality, with percent mediation ranging from 5 to 30%. The most significant mediating proteins were GDF15 and insulin-like growth factor 2 (IGFBP2). Proteins associated with better CVH were enriched for proteins that reflect the suppression of the complement coagulation and GH/IGF pathways.
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Affiliation(s)
- Toshiko Tanaka
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - Sameera A. Talegawkar
- Department of Exercise and Nutrition Sciences, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
| | - Yichen Jin
- Department of Exercise and Nutrition Sciences, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
| | - Julián Candia
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - Giovanna Fantoni
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | | | - Luigi Ferrucci
- Department of Exercise and Nutrition Sciences, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
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17
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Sarto F, Stashuk DW, Franchi MV, Monti E, Zampieri S, Valli G, Sirago G, Candia J, Hartnell LM, Paganini M, McPhee JS, De Vito G, Ferrucci L, Reggiani C, Narici MV. Effects of short-term unloading and active recovery on human motor unit properties, neuromuscular junction transmission and transcriptomic profile. J Physiol 2022; 600:4731-4751. [PMID: 36071599 PMCID: PMC9828768 DOI: 10.1113/jp283381] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/26/2022] [Indexed: 01/12/2023] Open
Abstract
Electrophysiological alterations of the neuromuscular junction (NMJ) and motor unit potential (MUP) with unloading are poorly studied. We aimed to investigate these aspects and the underlying molecular mechanisms with short-term unloading and active recovery (AR). Eleven healthy males underwent a 10-day unilateral lower limb suspension (ULLS) period, followed by 21-day AR based on resistance exercise. Quadriceps femoris (QF) cross-sectional area (CSA) and isometric maximum voluntary contraction (MVC) were evaluated. Intramuscular electromyographic recordings were obtained during 10% and 25% MVC isometric contractions from the vastus lateralis (VL). Biomarkers of NMJ molecular instability (serum c-terminal agrin fragment, CAF), axonal damage (neurofilament light chain) and denervation status were assessed from blood samples and VL biopsies. NMJ and ion channel transcriptomic profiles were investigated by RNA-sequencing. QF CSA and MVC decreased with ULLS. Increased CAF and altered NMJ transcriptome with unloading suggested the emergence of NMJ molecular instability, which was not associated with impaired NMJ transmission stability. Instead, increased MUP complexity and decreased motor unit firing rates were found after ULLS. Downregulation of ion channel gene expression was found together with increased neurofilament light chain concentration and partial denervation. The AR period restored most of these neuromuscular alterations. In conclusion, the human NMJ is destabilized at the molecular level but shows functional resilience to a 10-day unloading period at least at relatively low contraction intensities. However, MUP properties are altered by ULLS, possibly due to alterations in ion channel dynamics and initial axonal damage and denervation. These changes are fully reversed by 21 days of AR. KEY POINTS: We used integrative electrophysiological and molecular approaches to comprehensively investigate changes in neuromuscular integrity and function after a 10-day unilateral lower limb suspension (ULLS), followed by 21 days of active recovery in young healthy men, with a particular focus on neuromuscular junction (NMJ) and motor unit potential (MUP) properties alterations. After 10-day ULLS, we found significant NMJ molecular alterations in the absence of NMJ transmission stability impairment. These findings suggest that the human NMJ is functionally resilient against insults and stresses induced by short-term disuse at least at relatively low contraction intensities, at which low-threshold, slow-type motor units are recruited. Intramuscular electromyography analysis revealed that unloading caused increased MUP complexity and decreased motor unit firing rates, and these alterations could be related to the observed changes in skeletal muscle ion channel pool and initial and partial signs of fibre denervation and axonal damage. The active recovery period restored these neuromuscular changes.
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Affiliation(s)
- Fabio Sarto
- Department of Biomedical SciencesUniversity of PadovaPadovaItaly
| | - Daniel W. Stashuk
- Department of Systems Design EngineeringUniversity of WaterlooOntarioCanada
| | - Martino V. Franchi
- Department of Biomedical SciencesUniversity of PadovaPadovaItaly,CIR‐MYO Myology CenterUniversity of PadovaPadovaItaly
| | - Elena Monti
- Department of Biomedical SciencesUniversity of PadovaPadovaItaly
| | - Sandra Zampieri
- Department of Biomedical SciencesUniversity of PadovaPadovaItaly,CIR‐MYO Myology CenterUniversity of PadovaPadovaItaly,Department of SurgeryOncology, and GastroenterologyUniversity of PadovaPadovaItaly
| | - Giacomo Valli
- Department of Biomedical SciencesUniversity of PadovaPadovaItaly
| | - Giuseppe Sirago
- Department of Biomedical SciencesUniversity of PadovaPadovaItaly
| | - Julián Candia
- Longitudinal Studies SectionTranslational Gerontology BranchNational Institute of AgingNational Institutes of HealthBaltimoreMDUSA
| | - Lisa M. Hartnell
- Longitudinal Studies SectionTranslational Gerontology BranchNational Institute of AgingNational Institutes of HealthBaltimoreMDUSA
| | - Matteo Paganini
- Department of Biomedical SciencesUniversity of PadovaPadovaItaly
| | - Jamie S. McPhee
- Department of Sport and Exercise SciencesManchester Metropolitan University Institute of SportManchesterUK
| | - Giuseppe De Vito
- Department of Biomedical SciencesUniversity of PadovaPadovaItaly,CIR‐MYO Myology CenterUniversity of PadovaPadovaItaly
| | - Luigi Ferrucci
- Longitudinal Studies SectionTranslational Gerontology BranchNational Institute of AgingNational Institutes of HealthBaltimoreMDUSA
| | - Carlo Reggiani
- Department of Biomedical SciencesUniversity of PadovaPadovaItaly,Science and Research Center KoperInstitute for Kinesiology ResearchKoperSlovenia
| | - Marco V. Narici
- Department of Biomedical SciencesUniversity of PadovaPadovaItaly,CIR‐MYO Myology CenterUniversity of PadovaPadovaItaly,Science and Research Center KoperInstitute for Kinesiology ResearchKoperSlovenia
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18
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Osawa Y, Tanaka T, Semba RD, Fantoni G, Moaddel R, Candia J, Simonsick EM, Bandinelli S, Ferrucci L. Plasma Growth and Differentiation Factor 15 Predict Longitudinal Changes in Bone Parameters in Women, but Not in Men. J Gerontol A Biol Sci Med Sci 2022; 77:1951-1958. [PMID: 35363860 PMCID: PMC9536444 DOI: 10.1093/gerona/glac079] [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: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Bone fragility can progress with aging, but biomarkers to detect emerging osteopenia have not been fully elucidated. Growth/differentiation factor 15 (GDF-15) has pleiotropic roles in a broad range of age-related conditions, but its association with osteopenia is unknown. We examined the relationship between plasma GDF-15 levels and rate of change in bone parameters over 9 years of follow-up in 596 adults in the InCHIANTI study (baseline age, 65-94 years; women, 52.4%; mean follow-up, 7.0 ± 3.0 years). Plasma GDF-15 concentrations were measured using the 1.3k HTS SOMAscan assay. Eight bone parameters were measured in the right tibia by peripheral quantitative computed tomography; total bone density, trabecular bone density, medullary plus trabecular bone density, cortical bone density, total bone area, cortical bone area, medullary bone area, and minimum moment of inertia (mMOI). We ran sex-specific linear mixed-effect models with random intercepts and slopes adjusted for age, age-squared, education, body mass index, the rate of change in weight, smoking, sedentary behavior, cross-sectional areas of calf muscles and fat, 25-hydroxyvitamin D, parathyroid hormone, calcium, diabetes mellitus, and follow-up time. We found a significant association of "baseline GDF-15 × time" in models predicting cortical bone density and the mMOI in women, suggesting that the rates of decline in these bone parameters increased with higher GDF-15 (false discovery rate <0.05). Higher plasma levels GDF-15 predicted an accelerated decline in bone parameters in women, but was less associated in men. Furthermore studies are needed to understand the mechanisms underlying these sex differences.
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Affiliation(s)
- Yusuke Osawa
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland,USA
- Graduate School of Health Management, Keio University, Kanagawa, Japan
| | - Toshiko Tanaka
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland,USA
| | - Richard D Semba
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland,USA
| | - Giovanna Fantoni
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland,USA
| | - Ruin Moaddel
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland,USA
| | - Julián Candia
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland,USA
| | - Eleanor M Simonsick
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland,USA
| | | | - Luigi Ferrucci
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland,USA
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19
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Wang L, Candia J, Ma L, Zhao Y, Imberti L, Sottini A, Quiros-Roldan E, Dobbs K, Burbelo PD, Cohen JI, Delmonte OM, Forgues M, Liu H, Matthews HF, Shaw E, Stack MA, Weber SE, Zhang Y, Lisco A, Sereti I, Su HC, Notarangelo LD, Wang XW. Serological responses to human virome define clinical outcomes of Italian patients infected with SARS-CoV-2. Int J Biol Sci 2022; 18:5591-5606. [PMID: 36263161 PMCID: PMC9576512 DOI: 10.7150/ijbs.78002] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/14/2022] [Accepted: 08/14/2022] [Indexed: 01/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the pandemic respiratory infectious disease COVID-19. However, clinical manifestations and outcomes differ significantly among COVID-19 patients, ranging from asymptomatic to extremely severe, and it remains unclear what drives these disparities. Here, we studied 159 sequentially enrolled hospitalized patients with COVID-19-associated pneumonia from Brescia, Italy using the VirScan phage-display method to characterize circulating antibodies binding to 96,179 viral peptides encoded by 1,276 strains of human viruses. SARS-CoV-2 infection was associated with a marked increase in immune antibody repertoires against many known pathogenic and non-pathogenic human viruses. This antiviral antibody response was linked to longitudinal trajectories of disease severity and was further confirmed in additional 125 COVID-19 patients from the same geographical region in Northern Italy. By applying a machine-learning-based strategy, a viral exposure signature predictive of COVID-19-related disease severity linked to patient survival was developed and validated. These results provide a basis for understanding the role of memory B-cell repertoire to viral epitopes in COVID-19-related symptoms and suggest that a unique anti-viral antibody repertoire signature may be useful to define COVID-19 clinical severity.
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Affiliation(s)
- Limin Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892,These authors contributed equally
| | - Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892,These authors contributed equally
| | - Lichun Ma
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892,These authors contributed equally
| | - Yongmei Zhao
- CCR-SF Bioinformatics Group, Advanced Biomedical and Computational Sciences, Frederick National Laboratory for Cancer Research, 8560 Progress Drive, Frederick, Maryland 21701,These authors contributed equally
| | - Luisa Imberti
- CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Alessandra Sottini
- CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili, Brescia, Italy
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Peter D. Burbelo
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland 20892
| | - Jeffrey I. Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Ottavia M. Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892
| | - Hui Liu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Helen F. Matthews
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Elana Shaw
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Michael A. Stack
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Sarah E. Weber
- Section of Molecular Development of the Immune System, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Andrea Lisco
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Irini Sereti
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Helen C. Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892,✉ Corresponding author: ; . Lead contact: Xin Wei Wang, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Building 37, Room 3044A, Bethesda, MD 20892; 240-760-6858;
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892,Liver Cancer Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892,Lead Contact,✉ Corresponding author: ; . Lead contact: Xin Wei Wang, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Building 37, Room 3044A, Bethesda, MD 20892; 240-760-6858;
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20
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Tanaka T, Talegawkar SA, Jin Y, Candia J, Tian Q, Moaddel R, Simonsick EM, Ferrucci L. Metabolomic Profile of Different Dietary Patterns and Their Association with Frailty Index in Community-Dwelling Older Men and Women. Nutrients 2022; 14:nu14112237. [PMID: 35684039 PMCID: PMC9182888 DOI: 10.3390/nu14112237] [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: 05/10/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 11/28/2022] Open
Abstract
Diet quality has been associated with slower rates of aging; however, the mechanisms underlying the role of a healthy diet in aging are not fully understood. To address this question, we aimed to identify plasma metabolomic biomarkers of dietary patterns and explored whether these metabolites mediate the relationship between diet and healthy aging, as assessed by the frailty index (FI) in 806 participants of the Baltimore Longitudinal Study of Aging. Adherence to different dietary patterns was evaluated using the Mediterranean diet score (MDS), Mediterranean–DASH Diet Intervention for Neurodegenerative Delay (MIND) score, and Alternate Healthy Eating Index-2010 (AHEI). Associations between diet, FI, and metabolites were assessed using linear regression models. Higher adherence to these dietary patterns was associated with lower FI. We found 236, 218, and 278 metabolites associated with the MDS, MIND, and AHEI, respectively, with 127 common metabolites, which included lipids, tri/di-glycerides, lyso/phosphatidylcholine, amino acids, bile acids, ceramides, cholesterol esters, fatty acids and acylcarnitines, indoles, and sphingomyelins. Metabolomic signatures of diet explained 28%, 37%, and 38% of the variance of the MDS, MIND, and AHEI, respectively. Signatures of MIND and AHEI mediated 55% and 61% of the association between each dietary pattern with FI, while the mediating effect of MDS signature was not statistically significant. The high number of metabolites associated with the different dietary patterns supports the notion of common mechanisms that underly the relationship between diet and frailty. The identification of multiple metabolite classes suggests that the effect of diet is complex and not mediated by any specific biomarkers. Furthermore, these metabolites may serve as biomarkers for poor diet quality to identify individuals for targeted dietary interventions.
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Affiliation(s)
- Toshiko Tanaka
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD 21224, USA; (J.C.); (Q.T.); (E.M.S.); (L.F.)
- Correspondence:
| | - Sameera A. Talegawkar
- Department of Exercise and Nutrition Sciences, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (S.A.T.); (Y.J.)
| | - Yichen Jin
- Department of Exercise and Nutrition Sciences, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (S.A.T.); (Y.J.)
| | - Julián Candia
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD 21224, USA; (J.C.); (Q.T.); (E.M.S.); (L.F.)
| | - Qu Tian
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD 21224, USA; (J.C.); (Q.T.); (E.M.S.); (L.F.)
| | - Ruin Moaddel
- Laboratory of Clinical Investigation, National Institute on Aging, Baltimore, MD 21224, USA;
| | - Eleanor M. Simonsick
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD 21224, USA; (J.C.); (Q.T.); (E.M.S.); (L.F.)
| | - Luigi Ferrucci
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD 21224, USA; (J.C.); (Q.T.); (E.M.S.); (L.F.)
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21
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Osawa Y, Tanaka T, Semba RD, Fantoni G, Moaddel R, Candia J, Simonsick EM, Bandinelli S, Ferrucci L. Proteins in the pathway from high red blood cell width distribution to all-cause mortality. EBioMedicine 2022; 76:103816. [PMID: 35065420 PMCID: PMC8784626 DOI: 10.1016/j.ebiom.2022.103816] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 09/17/2021] [Revised: 12/21/2021] [Accepted: 01/06/2022] [Indexed: 01/01/2023] Open
Abstract
Background The pathophysiological mechanisms underlying the association between red blood cell distribution width (RDW) and all-cause mortality are unknown. We conducted a data-driven discovery investigation to identify plasma proteins that mediate the association between RDW and time to death in community-dwelling adults. Methods At baseline, 962 adults (women, 54·4%; age range, 21–98 years) participated in the InCHIANTI, “Aging in the Chianti Area” study, and proteomics data were generated from their plasma specimens. Of these, 623 participants had proteomics data available at the 9-year follow-up. For each visit, a total of 1301 plasma proteins were measured using SOMAscan technology. Complete data on vital status were available up to the 15-year follow-up period. Protein-specific exponential distribution accelerated failure time, and linear regression analyses adjusted for possible covariates were used for mortality and mediation analyses, respectively (survival data analysis). Findings Baseline values of EGFR, GHR, NTRK3, SOD2, KLRF1, THBS2, TIMP1, IGFBP2, C9, APOB, and LRP1B mediated the association between baseline RDW and all-cause mortality. Changes in IGFBP2 and C7 over 9 years mediated the association between changes in RDW and 6-year all-cause mortality. Interpretation Cellular senescence may contribute to the association between RDW and mortality. Funding This study was funded by grants from the National Institutes of Health (NIH) and the National Institute on Aging (NIA) contract and was supported by the Intramural Research Program of the NIA, NIH. The InCHIANTI study was supported as a ‘targeted project’ by the Italian Ministry of Health and in part by the U.S. NIA.
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Affiliation(s)
- Yusuke Osawa
- National Institute on Aging, National Institutes of Health, MedStar Harbor Hospital 5th floor, 3001 S. Hanover Street, Baltimore, MD 21225 USA; Graduate School of Health Management, Keio University, Kanagawa, Japan; Sports Medicine Research Center, Keio University, Kanagawa, Japan.
| | - Toshiko Tanaka
- National Institute on Aging, National Institutes of Health, MedStar Harbor Hospital 5th floor, 3001 S. Hanover Street, Baltimore, MD 21225 USA
| | - Richard D Semba
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Giovanna Fantoni
- National Institute on Aging, National Institutes of Health, MedStar Harbor Hospital 5th floor, 3001 S. Hanover Street, Baltimore, MD 21225 USA
| | - Ruin Moaddel
- National Institute on Aging, National Institutes of Health, MedStar Harbor Hospital 5th floor, 3001 S. Hanover Street, Baltimore, MD 21225 USA
| | - Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Eleanor M Simonsick
- National Institute on Aging, National Institutes of Health, MedStar Harbor Hospital 5th floor, 3001 S. Hanover Street, Baltimore, MD 21225 USA
| | | | - Luigi Ferrucci
- National Institute on Aging, National Institutes of Health, MedStar Harbor Hospital 5th floor, 3001 S. Hanover Street, Baltimore, MD 21225 USA.
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22
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Minas TZ, Candia J, Dorsey TH, Baker F, Tang W, Kiely M, Smith CJ, Jordan SV, Obadi OM, Ajao A, Loffredo CA, Yates C, Cook MB, Ambs S. Abstract PR-11: Blood levels of TNFRSF9 and PTN predict lethal prostate cancer among African American men. Cancer Epidemiol Biomarkers Prev 2022. [DOI: 10.1158/1538-7755.disp21-pr-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
OBJECTIVE: Differentiating men who have lethal forms of prostate cancer from those with a more slow-growing disease remains a major challenge in clinical oncology. Risk stratification strategies are particularly needed for men of African descent who disproportionately bear the prostate cancer burden. Methods: Using a high throughput proximal extension assay, we simultaneously measured 82 immune-oncological proteins in the blood of 819 prostate cancer patients at diagnosis of whom 394 were African American (AA) and 425 were European American (EA). These patients were followed up for a median of 8.6 years since their diagnosis during which 57 died of prostate cancer while 202 died of all causes. To identify an immune-oncology protein signature predictive of lethal prostate cancer, we applied a cross-validated, regularized Cox regression model. Included in this model were the 82 immune-oncology proteins and 6 covariates of clinical significance (age, education, BMI, smoking history, aspirin use, and diabetes). Results: We did not identify a robust predictive signature of lethal prostate cancer for EA patients. However, for AA patients a signature primarily driven by tumor necrosis factor receptor superfamily member 9 (TNFRSF9) and pleiotrophin (PTN) (both positively associated with the risk of lethal disease) and regular aspirin use (negatively associated with risk) were the top predictors (P < 0.05) based on two selection criteria: the feature frequency and the weight of the features' contribution to the prediction. These features combined predicted prostate cancer-specific mortality with an accuracy of 83.7% (SE=3.8%). The two proteins alone, TNFRSF9 and PTN, predicted prostate cancer-specific mortality with an accuracy of 78.2% (SE=4.2%). AA prostate cancer patients with high levels (> median) of both TNFRSF9 and PTN in their blood at diagnosis had the worst prostate cancer-specific survival. By 10 years, 33% of cases with high levels of both TNFRSF9 and PTN died of prostate cancer compared to only 5% of cases with low levels of both or either of these proteins. Conclusions: Our study describes novel blood markers of lethal prostate cancer that can be used for risk stratification of AA patients at the time of diagnosis. AA patients with high levels of both TNFRSF9 and PTN in their sera had the highest risk of dying from prostate cancer. These markers may also be applicable to African prostate cancer patients since the blood-based immunome of Ghanaian and AA men are similar, as shown by our data.
Citation Format: Tsion Zewdu Minas, Julián Candia, Tiffany H. Dorsey, Francine Baker, Wei Tang, Maeve Kiely, Cheryl J. Smith, Symone V. Jordan, Obadi M. Obadi, Anuoluwapo Ajao, Christopher A. Loffredo, Clayton Yates, Michael B. Cook, Stefan Ambs. Blood levels of TNFRSF9 and PTN predict lethal prostate cancer among African American men [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PR-11.
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Affiliation(s)
| | | | | | | | - Wei Tang
- 1National Cancer Institute, Bethesda, MD,
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23
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Ma L, Wang L, Khatib SA, Chang CW, Heinrich S, Dominguez DA, Forgues M, Candia J, Hernandez MO, Kelly M, Zhao Y, Tran B, Hernandez JM, Davis JL, Kleiner DE, Wood BJ, Greten TF, Wang XW. Single-cell atlas of tumor cell evolution in response to therapy in hepatocellular carcinoma and intrahepatic cholangiocarcinoma. J Hepatol 2021; 75:1397-1408. [PMID: 34216724 PMCID: PMC8604764 DOI: 10.1016/j.jhep.2021.06.028] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [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: 11/24/2020] [Revised: 06/15/2021] [Accepted: 06/20/2021] [Indexed: 01/10/2023]
Abstract
BACKGROUND & AIMS Intratumor molecular heterogeneity is a key feature of tumorigenesis and is linked to treatment failure and patient prognosis. Herein, we aimed to determine what drives tumor cell evolution by performing single-cell transcriptomic analysis. METHODS We analyzed 46 hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA) biopsies from 37 patients enrolled in interventional studies at the NIH Clinical Center, with 16 biopsies collected before and after treatment from 7 patients. We developed a novel machine learning-based consensus clustering approach to track cellular states of 57,000 malignant and non-malignant cells including tumor cell transcriptome-based functional clonality analysis. We determined tumor cell relationships using RNA velocity and reverse graph embedding. We also studied longitudinal samples from 4 patients to determine tumor cellular state and its evolution. We validated our findings in bulk transcriptomic data from 488 patients with HCC and 277 patients with iCCA. RESULTS Using transcriptomic clusters as a surrogate for functional clonality, we observed an increase in tumor cell state heterogeneity which was tightly linked to patient prognosis. Furthermore, increased functional clonality was accompanied by a polarized immune cell landscape which included an increase in pre-exhausted T cells. We found that SPP1 expression was tightly associated with tumor cell evolution and microenvironmental reprogramming. Finally, we developed a user-friendly online interface as a knowledge base for a single-cell atlas of liver cancer. CONCLUSIONS Our study offers insight into the collective behavior of tumor cell communities in liver cancer as well as potential drivers of tumor evolution in response to therapy. LAY SUMMARY Intratumor molecular heterogeneity is a key feature of tumorigenesis that is linked to treatment failure and patient prognosis. In this study, we present a single-cell atlas of liver tumors from patients treated with immunotherapy and describe intratumoral cell states and their hierarchical relationship. We suggest osteopontin, encoded by the gene SPP1, as a candidate regulator of tumor evolution in response to treatment.
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Affiliation(s)
- Lichun Ma
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA
| | - Limin Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA
| | - Subreen A Khatib
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA
| | - Ching-Wen Chang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA
| | - Sophia Heinrich
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA
| | - Dana A Dominguez
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA
| | - Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA
| | - Maria O Hernandez
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 20701 USA
| | - Michael Kelly
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 20701 USA
| | - Yongmei Zhao
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 20701 USA
| | - Bao Tran
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 20701 USA
| | - Jonathan M Hernandez
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA
| | - Jeremy L Davis
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA
| | - David E Kleiner
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA
| | - Bradford J Wood
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA; NIH Center for Interventional Oncology, Bethesda, Maryland 20892 USA
| | - Tim F Greten
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA; Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA.
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892 USA.
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24
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Roberts JA, Varma VR, An Y, Varma S, Candia J, Fantoni G, Tiwari V, Anerillas C, Williamson A, Saito A, Loeffler T, Schilcher I, Moaddel R, Khadeer M, Lovett J, Tanaka T, Pletnikova O, Troncoso JC, Bennett DA, Albert MS, Yu K, Niu M, Haroutunian V, Zhang B, Peng J, Croteau DL, Resnick SM, Gorospe M, Bohr VA, Ferrucci L, Thambisetty M. A brain proteomic signature of incipient Alzheimer's disease in young APOE ε4 carriers identifies novel drug targets. Sci Adv 2021; 7:eabi8178. [PMID: 34757788 PMCID: PMC8580310 DOI: 10.1126/sciadv.abi8178] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aptamer-based proteomics revealed differentially abundant proteins in Alzheimer’s disease (AD) brains in the Baltimore Longitudinal Study of Aging and Religious Orders Study (mean age, 89 ± 9 years). A subset of these proteins was also differentially abundant in the brains of young APOE ε4 carriers relative to noncarriers (mean age, 39 ± 6 years). Several of these proteins represent targets of approved and experimental drugs for other indications and were validated using orthogonal methods in independent human brain tissue samples as well as in transgenic AD models. Using cell culture–based phenotypic assays, we showed that drugs targeting the cytokine transducer STAT3 and the Src family tyrosine kinases, YES1 and FYN, rescued molecular phenotypes relevant to AD pathogenesis. Our findings may accelerate the development of effective interventions targeting the earliest molecular triggers of AD.
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Affiliation(s)
- Jackson A Roberts
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Vijay R Varma
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yang An
- Brain Aging and Behavior Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | | | - Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Giovanna Fantoni
- Clinical Research Core, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Vinod Tiwari
- Section on DNA Repair, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Andrew Williamson
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Atsushi Saito
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Tina Loeffler
- QPS Austria GmbH, Parkring 12, 8074 Grambach, Austria
| | | | - Ruin Moaddel
- Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Mohammed Khadeer
- Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jacqueline Lovett
- Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Toshiko Tanaka
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Olga Pletnikova
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Marilyn S Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kaiwen Yu
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mingming Niu
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Vahram Haroutunian
- Departments of Psychiatry and Neuroscience, The Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research, Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences and Department of Pharmacological Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Deborah L Croteau
- Section on DNA Repair, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Susan M Resnick
- Brain Aging and Behavior Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Vilhelm A Bohr
- Section on DNA Repair, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Madhav Thambisetty
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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Yamaguchi Y, Zampino M, Tanaka T, Bandinelli S, Moaddel R, Fantoni G, Candia J, Ferrucci L, Semba RD. The Plasma Proteome Fingerprint Associated with Circulating Carotenoids and Retinol in Older Adults. J Nutr 2021; 152:40-48. [PMID: 34550359 PMCID: PMC8754576 DOI: 10.1093/jn/nxab340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/23/2021] [Accepted: 09/16/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Although diets rich in carotenoids are associated with reduced risks of cardiovascular disease, age-related macular degeneration, disability, and other adverse aging outcomes, the underlying biological mechanisms are not fully elucidated. OBJECTIVES To characterize the plasma proteome fingerprint associated with circulating carotenoid and retinol concentrations in older adults. METHODS In 728 adults ≥65 y participating in the Invecchiare in Chianti (InCHIANTI) Study, plasma α-carotene, β-carotene, β-cryptoxanthin, lutein, zeaxanthin, and lycopene were measured using HPLC. The SOMAscan assay was used to measure 1301 plasma proteins. Multivariable linear regression models were used to examine the relationship of individual carotenoids and retinol with plasma proteins. A false discovery rate approach was used to deal with multiple comparisons using a q-value < 0.05. RESULTS Plasma β-carotene, β-cryptoxanthin, lutein, zeaxanthin, and lycopene were associated with 85, 39, 4, 2, and 5 plasma proteins, respectively, in multivariable linear regression models adjusting for potential confounders (q < 0.05). No proteins were associated with α-carotene or retinol. Two or more carotenoids were positively associated with ferritin, 6-phosphogluconate dehydrogenase (decarboxylating), hepcidin, thrombospondin-2, and choline/ethanolamine kinase. The proteins associated with circulating carotenoids were related to energy metabolism, sirtuin signaling, inflammation and oxidative stress, iron metabolism, proteostasis, innate immunity, and longevity. CONCLUSIONS The plasma proteomic fingerprint associated with elevated circulating carotenoids in older adults provides insight into the mechanisms underlying the protective role of carotenoids on health.
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Affiliation(s)
| | - Marta Zampino
- National Institutes on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Toshiko Tanaka
- National Institutes on Aging, National Institutes of Health, Baltimore, MD, USA
| | | | - Ruin Moaddel
- National Institutes on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Giovanna Fantoni
- National Institutes on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Julián Candia
- National Institutes on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Luigi Ferrucci
- National Institutes on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Richard D Semba
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Center for a Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Han K, Singh K, Rodman MJ, Hassanzadeh S, Baumer Y, Huffstutler RD, Chen J, Candia J, Cheung F, Stagliano KER, Pirooznia M, Powell-Wiley TM, Sack MN. Identification and Validation of Nutrient State-Dependent Serum Protein Mediators of Human CD4 + T Cell Responsiveness. Nutrients 2021; 13:nu13051492. [PMID: 33924911 PMCID: PMC8146063 DOI: 10.3390/nu13051492] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023] Open
Abstract
Intermittent fasting and fasting mimetic diets ameliorate inflammation. Similarly, serum extracted from fasted healthy and asthmatic subjects' blunt inflammation in vitro, implicating serum components in this immunomodulation. To identify the proteins orchestrating these effects, SOMAScan technology was employed to evaluate serum protein levels in healthy subjects following an overnight, 24-h fast and 3 h after refeeding. Partial least square discriminant analysis identified several serum proteins as potential candidates to confer feeding status immunomodulation. The characterization of recombinant IGFBP1 (elevated following 24 h of fasting) and PYY (elevated following refeeding) in primary human CD4+ T cells found that they blunted and induced immune activation, respectively. Furthermore, integrated univariate serum protein analysis compared to RNA-seq analysis from peripheral blood mononuclear cells identified the induction of IL1RL1 and MFGE8 levels in refeeding compared to the 24-h fasting in the same study. Subsequent quantitation of these candidate proteins in lean versus obese individuals identified an inverse regulation of serum levels in the fasted subjects compared to the obese subjects. In parallel, IL1RL1 and MFGE8 supplementation promoted increased CD4+ T responsiveness to T cell receptor activation. Together, these data show that caloric load-linked conditions evoke serological protein changes, which in turn confer biological effects on circulating CD4+ T cell immune responsiveness.
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Affiliation(s)
- Kim Han
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.); (M.J.R.); (S.H.)
| | - Komudi Singh
- Bioinformatics and Computational Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.S.); (M.P.)
| | - Matthew J. Rodman
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.); (M.J.R.); (S.H.)
| | - Shahin Hassanzadeh
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.); (M.J.R.); (S.H.)
| | - Yvonne Baumer
- Determinants of Obesity and Cardiovascular Risk, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (Y.B.); (T.M.P.-W.)
| | - Rebecca D. Huffstutler
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Jinguo Chen
- Center of Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (J.C.); (J.C.); (F.C.); (K.E.R.S.)
| | - Julián Candia
- Center of Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (J.C.); (J.C.); (F.C.); (K.E.R.S.)
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Foo Cheung
- Center of Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (J.C.); (J.C.); (F.C.); (K.E.R.S.)
| | - Katherine E. R. Stagliano
- Center of Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (J.C.); (J.C.); (F.C.); (K.E.R.S.)
| | - Mehdi Pirooznia
- Bioinformatics and Computational Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.S.); (M.P.)
| | - Tiffany M. Powell-Wiley
- Determinants of Obesity and Cardiovascular Risk, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (Y.B.); (T.M.P.-W.)
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael N. Sack
- Laboratory of Mitochondrial Biology and Metabolism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.); (M.J.R.); (S.H.)
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA;
- Correspondence:
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Matsuda K, Migueles SA, Huang J, Bolkhovitinov L, Stuccio S, Griesman T, Pullano AA, Kang BH, Ishida E, Zimmerman M, Kashyap N, Martins KM, Stadlbauer D, Pederson J, Patamawenu A, Wright N, Shofner T, Evans S, Liang CJ, Candia J, Biancotto A, Fantoni G, Poole A, Smith J, Alexander J, Gurwith M, Krammer F, Connors M. A replication-competent adenovirus-vectored influenza vaccine induces durable systemic and mucosal immunity. J Clin Invest 2021; 131:140794. [PMID: 33529172 DOI: 10.1172/jci140794] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/07/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUNDTo understand the features of a replicating vaccine that might drive potent and durable immune responses to transgene-encoded antigens, we tested a replication-competent adenovirus type 4 encoding influenza virus H5 HA (Ad4-H5-Vtn) administered as an oral capsule or via tonsillar swab or nasal spray.METHODSViral shedding from the nose, mouth, and rectum was measured by PCR and culturing. H5-specific IgG and IgA antibodies were measured by bead array binding assays. Serum antibodies were measured by a pseudovirus entry inhibition, microneutralization, and HA inhibition assays.RESULTSAd4-H5-Vtn DNA was shed from most upper respiratory tract-immunized (URT-immunized) volunteers for 2 to 4 weeks, but cultured from only 60% of participants, with a median duration of 1 day. Ad4-H5-Vtn vaccination induced increases in H5-specific CD4+ and CD8+ T cells in the peripheral blood as well as increases in IgG and IgA in nasal, cervical, and rectal secretions. URT immunizations induced high levels of serum neutralizing antibodies (NAbs) against H5 that remained stable out to week 26. The duration of viral shedding correlated with the magnitude of the NAb response at week 26. Adverse events (AEs) were mild, and peak NAb titers were associated with overall AE frequency and duration. Serum NAb titers could be boosted to very high levels 2 to 5 years after Ad4-H5-Vtn vaccination with recombinant H5 or inactivated split H5N1 vaccine.CONCLUSIONReplicating Ad4 delivered to the URT caused prolonged exposure to antigen, drove durable systemic and mucosal immunity, and proved to be a promising platform for the induction of immunity against viral surface glycoprotein targets.TRIAL REGISTRATIONClinicalTrials.gov NCT01443936 and NCT01806909.FUNDINGIntramural and Extramural Research Programs of the NIAID, NIH (U19 AI109946) and the Centers of Excellence for Influenza Research and Surveillance (CEIRS), NIAID, NIH (contract HHSN272201400008C).
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Affiliation(s)
- Kenta Matsuda
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Stephen A Migueles
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Jinghe Huang
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Lyuba Bolkhovitinov
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Sarah Stuccio
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Trevor Griesman
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Alyssa A Pullano
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Byong H Kang
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Elise Ishida
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Matthew Zimmerman
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Neena Kashyap
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Kelly M Martins
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Daniel Stadlbauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jessica Pederson
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Andy Patamawenu
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Nathaniel Wright
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Tulley Shofner
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Sean Evans
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | | | - Julián Candia
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, Maryland, USA
| | - Angelique Biancotto
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, Maryland, USA
| | - Giovanna Fantoni
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, Maryland, USA
| | - April Poole
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Jon Smith
- Emergent Biosolutions Inc., Gaithersburg, Maryland, USA
| | | | - Marc Gurwith
- Emergent Biosolutions Inc., Gaithersburg, Maryland, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mark Connors
- HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
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Tanaka T, Basisty N, Fantoni G, Candia J, Moore AZ, Biancotto A, Schilling B, Bandinelli S, Ferrucci L. Plasma proteomic biomarker signature of age predicts health and life span. eLife 2020; 9:61073. [PMID: 33210602 PMCID: PMC7723412 DOI: 10.7554/elife.61073] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [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: 07/15/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022] Open
Abstract
Older age is a strong shared risk factor for many chronic diseases, and there is increasing interest in identifying aging biomarkers. Here, a proteomic analysis of 1301 plasma proteins was conducted in 997 individuals between 21 and 102 years of age. We identified 651 proteins associated with age (506 over-represented, 145 underrepresented with age). Mediation analysis suggested a role for partial cis-epigenetic control of protein expression with age. Of the age-associated proteins, 33.5% and 45.3%, were associated with mortality and multimorbidity, respectively. There was enrichment of proteins associated with inflammation and extracellular matrix as well as senescence-associated secretory proteins. A 76-protein proteomic age signature predicted accumulation of chronic diseases and all-cause mortality. These data support the use of proteomic biomarkers to monitor aging trajectories and to identify individuals at higher risk of disease to be targeted for in depth diagnostic procedures and early interventions.
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Affiliation(s)
- Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, United States
| | - Nathan Basisty
- The Buck Institute for Research on Aging, Novato, United States
| | - Giovanna Fantoni
- National Institute on Aging, Intramural Research Program, Clinical Research Core, NIH, Baltimore, United States
| | - Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, United States
| | - Ann Z Moore
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, United States
| | - Angelique Biancotto
- Precision Immunology, Immunology & Inflammation Research Therapeutic Area, Sanofi, Cambridge, United States
| | | | | | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, United States
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29
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Landino K, Tanaka T, Fantoni G, Candia J, Bandinelli S, Ferrucci L. Characterization of the plasma proteomic profile of frailty phenotype. GeroScience 2020; 43:1029-1037. [PMID: 33200349 PMCID: PMC8110642 DOI: 10.1007/s11357-020-00288-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022] Open
Abstract
Frailty is a risk factor for poor health outcomes in older adults. The aim of this study was to identify plasma proteomic biomarkers of frailty in 752 men and women older than 65 years of age from the InCHIANTI study. One thousand three hundred one plasma proteins were measured using an aptamer-based assay. Associations of each protein with frailty status were assessed using logistic regression and four proteins creatine kinase M-type (CKM), B-type (CKB), C-X-C motif chemokine ligand 13 (CXCL13), and thrombospondin 2 (THBS2) were associated with frailty status. Two proteins, cyclin-dependent kinase 5 (CDK5/CDK5R1) and interleukin 1 alpha (IL1A), were associated with worsening of frailty status over time in volunteers free of frailty at baseline. Using partial least squares discriminant analysis (PLS-DA), data of 1301 proteins was able to discriminate between frail and non-frail with a 2% error rate. The proteins with greater discriminatory ability represented the inflammation, blood coagulation, and cell growth pathways. The utility of these proteins as biomarkers of frailty should be further explored.
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Affiliation(s)
- Kristina Landino
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA.
| | - Giovanna Fantoni
- National Institute on Aging, Intramural Research Program, Clinical Research Core, NIH, Baltimore, MD, 21224, USA
| | - Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | | | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
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Wang L, Candia J, Ma L, Zhao Y, Imberti L, Sottini A, Dobbs K, Lisco A, Sereti I, Su HC, Notarangelo LD, Wang XW. Serological Responses to Human Virome Define Clinical Outcomes of Italian Patients Infected with SARS-CoV-2. medRxiv 2020:2020.09.04.20187088. [PMID: 32908997 PMCID: PMC7480049 DOI: 10.1101/2020.09.04.20187088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the pandemic respiratory infectious disease COVID-19. However, clinical manifestations and outcomes differ significantly among COVID-19 patients, ranging from asymptomatic to extremely severe, and it remains unclear what drives these disparities. Here, we studied 159 hospitalized Italian patients with pneumonia from the NIAID-NCI COVID-19 Consortium using a phage-display method to characterize circulating antibodies binding to 93,904 viral peptides encoded by 1,276 strains of human viruses. SARS-CoV-2 infection was associated with a marked increase in individual's immune memory antibody repertoires linked to trajectories of disease severity from the longitudinal analysis also including anti-spike protein antibodies. By applying a machine-learning-based strategy, we developed a viral exposure signature predictive of COVID-19-related disease severity linked to patient survival. These results provide a basis for understanding the roles of memory B-cell repertoires in COVID-19-related symptoms as well as a predictive tool for monitoring its clinical severity.
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Affiliation(s)
- Limin Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
- These authors contributed equally
| | - Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
- These authors contributed equally
| | - Lichun Ma
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
- These authors contributed equally
| | - Yongmei Zhao
- CCR-SF Bioinformatics Group, Advanced Biomedical and Computational Sciences, Frederick National Laboratory for Cancer Research, 8560 Progress Drive, Frederick, Maryland 21701
- These authors contributed equally
| | - Luisa Imberti
- CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Alessandra Sottini
- CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892
| | | | - Andrea Lisco
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892
| | - Irini Sereti
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892
| | - Helen C. Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
- Lead Contact
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Candia J, Bayarsaikhan E, Tandon M, Budhu A, Forgues M, Tovuu LO, Tudev U, Lack J, Chao A, Chinburen J, Wang XW. The genomic landscape of Mongolian hepatocellular carcinoma. Nat Commun 2020; 11:4383. [PMID: 32873799 PMCID: PMC7462863 DOI: 10.1038/s41467-020-18186-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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: 02/18/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023] Open
Abstract
Mongolia has the highest incidence of hepatocellular carcinoma (HCC) in the world, but its causative factors and underlying tumor biology remain unknown. Here, we describe molecular characteristics of HCC from 76 Mongolian patients by whole-exome and transcriptome sequencing. We present a comprehensive analysis of mutational signatures, driver genes, and molecular subtypes of Mongolian HCC compared to 373 HCC patients of different races and ethnicities and diverse etiologies. Mongolian HCC consists of prognostic molecular subtypes similar to those found in patients from other areas of Asia, Europe, and North America, as well as other unique subtypes, suggesting the presence of distinct etiologies linked to Mongolian patients. In addition to common driver mutations (TP53, CTNNB1) frequently found in pan-cancer analysis, Mongolian HCC exhibits unique drivers (most notably GTF2IRD2B, PNRC2, and SPTA1), the latter of which is associated with hepatitis D viral infection. These results suggest the existence of new molecular mechanisms at play in Mongolian hepatocarcinogenesis.
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Affiliation(s)
- Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Mayank Tandon
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anuradha Budhu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lkhagva-Ochir Tovuu
- General Laboratory Department, National Cancer Center, Ulaanbaatar, Mongolia
| | - Undarmaa Tudev
- Cancer Registry and Screening Department, National Cancer Center, Ulaanbaatar, Mongolia
| | - Justin Lack
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ann Chao
- Center for Global Health, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA
| | - Jigjidsuren Chinburen
- Hepato-Pancreatic-Biliary Surgical Department, National Cancer Center, Ulaanbaatar, Mongolia
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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Candia J, Bayarsaikhan E, Tandon M, Budhu A, Forgues M, Lack J, Chao A, Chinburen J, Wang XW. Abstract 5855: The genomic landscape of Mongolian hepatocellular carcinoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Mongolia has the highest incidence of-and mortality from- hepatocellular carcinoma (HCC) in the world, which is between three and seven times higher than that observed in other high-incidence populations, such as South Korea, Thailand, and China. In Mongolia, where cancer is the second most common cause of death accounting for nearly a fifth of deaths, HCC is the most prevalent cancer type at about 40% of all cancers. Despite the daunting proportion of this longstanding health crisis, the molecular landscape of Mongolian HCC has not been studied yet. Filling this gap, we aim to identify robust molecular subclasses and driver features informative of the etiology and progression of the disease. Here, we describe molecular characteristics of 76 Mongolian HCC patients by whole-exome and whole-transcriptome sequencing. We present a comprehensive comparison of mutational signatures, driver genes and molecular subtypes of Mongolian HCC versus 373 HCC patients of different ethnicities and diverse etiologies. Mongolian HCC consists of several similar prognostic molecular subtypes in patients from other areas of Asia, Europe and North America as well as several unique types, suggesting potentially the presence of unique etiologies linked to Mongolian patients. Consistently, Mongolian HCC exhibits several common driver mutations (TP53, CTNNB1) frequently found in pan-cancer analyses but also a unique driver (SPTA1) that may be linked to hepatitis D viral infection. Furthermore, unique hotspot missense mutations were identified in driver genes GTF2IRD2B and PNRC2. These results indicate the existence of novel molecular mechanisms at play in Mongolian hepatocarcinogenesis.
Citation Format: Julián Candia, Enkhjargal Bayarsaikhan, Mayank Tandon, Anuradha Budhu, Marshonna Forgues, Justin Lack, Ann Chao, Jigjidsuren Chinburen, Xin W. Wang. The genomic landscape of Mongolian hepatocellular carcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5855.
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Affiliation(s)
| | | | | | | | | | - Justin Lack
- 1National Institutes of Health, Bethesda, MD
| | - Ann Chao
- 1National Institutes of Health, Bethesda, MD
| | | | - Xin W. Wang
- 1National Institutes of Health, Bethesda, MD
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Liu J, Tang W, Budhu A, Forgues M, Hernandez MO, Candia J, Kim Y, Bowman ED, Ambs S, Zhao Y, Tran B, Wu X, Koh C, Surana P, Liang TJ, Guarnera M, Mann D, Rajaure M, Greten TF, Wang Z, Yu H, Wang XW. A Viral Exposure Signature Defines Early Onset of Hepatocellular Carcinoma. Cell 2020; 182:317-328.e10. [PMID: 32526205 DOI: 10.1016/j.cell.2020.05.038] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/20/2020] [Accepted: 05/20/2020] [Indexed: 12/25/2022]
Abstract
Hepatocellular carcinoma (HCC) is an aggressive malignancy with its global incidence and mortality rate continuing to rise, although early detection and surveillance are suboptimal. We performed serological profiling of the viral infection history in 899 individuals from an NCI-UMD case-control study using a synthetic human virome, VirScan. We developed a viral exposure signature and validated the results in a longitudinal cohort with 173 at-risk patients who had long-term follow-up for HCC development. Our viral exposure signature significantly associated with HCC status among at-risk individuals in the validation cohort (area under the curve: 0.91 [95% CI 0.87-0.96] at baseline and 0.98 [95% CI 0.97-1] at diagnosis). The signature identified cancer patients prior to a clinical diagnosis and was superior to alpha-fetoprotein. In summary, we established a viral exposure signature that can predict HCC among at-risk patients prior to a clinical diagnosis, which may be useful in HCC surveillance.
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Affiliation(s)
- Jinping Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Wei Tang
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Anuradha Budhu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Maria O Hernandez
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Yujin Kim
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Elise D Bowman
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stefan Ambs
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Yongmei Zhao
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Bao Tran
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Xiaolin Wu
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Christopher Koh
- Liver Diseases Branch, National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD 20892, USA
| | - Pallavi Surana
- Liver Diseases Branch, National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD 20892, USA
| | - T Jake Liang
- Liver Diseases Branch, National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD 20892, USA
| | - Maria Guarnera
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Dean Mann
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Manoj Rajaure
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tim F Greten
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Zhanwei Wang
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Herbert Yu
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
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Osawa Y, Semba RD, Fantoni G, Candia J, Biancotto A, Tanaka T, Bandinelli S, Ferrucci L. Plasma proteomic signature of the risk of developing mobility disability: A 9-year follow-up. Aging Cell 2020; 19:e13132. [PMID: 32157804 PMCID: PMC7189986 DOI: 10.1111/acel.13132] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 11/22/2019] [Revised: 02/10/2020] [Accepted: 02/18/2020] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION Mobility disability is a powerful indicator of poor health in older adults. The biological and pathophysiological mechanism underlying the development of mobility disability remains unknown. This study conducted a data-driven discovery phase investigation to identify plasma proteins that predict the incidence of mobility disability in community-dwelling older adults without mobility disability at baseline. METHODS We investigated 660 women and men, aged 71.9 ± 6.0 (60-94) years, who participated in the Invecchiare in Chianti, "Aging in the Chianti Area" study and completed the 400-m walk at fast pace (400-m walk) at enrollment. Median follow-up time was 8.57 [interquartile, 3.20-9.08] years. SOMAscan technology was used to measure 1,301 plasma proteins at enrollment. The incident of mobility disability was defined as inability to complete the 400-m walk. Protein-specific Cox proportional hazard model was adjusted for sex, age, and other important covariates. RESULTS Plasma levels of 75 proteins predicted mobility disability (p < .05). Significant proteins were enriched for the KEGG "PI3K-Akt signaling," "phagosomes," and "cytokine-cytokine receptor interaction" pathways. After multiple comparison adjustment, plasma cathepsin S (CTSS; hazard ratio [HR] 1.33, 95% CI: 1.17, 1.51, q = 0.007), growth/differentiation factor 15 (GDF15; HR: 1.45, 95% CI: 1.23, 1.72, q = 0.007), and thrombospondin-2 (THBS2; HR: 1.44, 95% CI: 1.22, 1.69, q = 0.007) remained significantly associated with high risk of losing mobility. CONCLUSION CTSS, GDF15, and THBS2 are novel blood biomarkers associated with new mobility disability in community-dwelling individuals. Overall, our analysis suggests that cellular senescence and inflammation should be targeted for prevention of mobility disability.
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Affiliation(s)
- Yusuke Osawa
- Longitudinal Study SectionTranslational Gerontology BranchNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Richard D. Semba
- Wilmer Eye InstituteJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Giovanna Fantoni
- Clinical Research CoreNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Julián Candia
- Laboratory of Human CarcinogenesisCenter for Cancer ResearchNational Cancer InstituteNIHBethesdaMDUSA
| | - Angélique Biancotto
- Precision Immunology, Immunology and Inflammation Research Therapeutic AreaSanofiCambridgeMAUSA
| | - Toshiko Tanaka
- Longitudinal Study SectionTranslational Gerontology BranchNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | | | - Luigi Ferrucci
- Longitudinal Study SectionTranslational Gerontology BranchNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
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Karmaus PW, Shi M, Perl S, Biancotto A, Candia J, Cheung F, Kotliarov Y, Young N, Fessler MB. Effects of rosuvastatin on the immune system in healthy volunteers with normal serum cholesterol. JCI Insight 2019; 4:131530. [PMID: 31573980 DOI: 10.1172/jci.insight.131530] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/25/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUNDHMG-CoA reductase inhibitors (statins) are prescribed to millions of people. Statins are antiinflammatory independent of their cholesterol-reducing effects. To date, most reports on the immune effects of statins have assayed a narrow array of variables and have focused on cell lines, rodent models, or patient cohorts. We sought to define the effect of rosuvastatin on the "immunome" of healthy, normocholesterolemic subjects.METHODSWe conducted a prospective study of rosuvastatin (20 mg/d × 28 days) in 18 statin-naive adults with LDL cholesterol <130 mg/dL. A panel of >180 immune/biochemical/endocrinologic variables was measured at baseline and on days 14, 28, and 42 (14 days after drug withdrawal). Drug effect was evaluated using linear mixed-effects models. Potential interactions between drug and baseline high-sensitivity C-reactive protein (hsCRP) were evaluated.RESULTSA wide array of immune measures changed (nominal P < 0.05) during rosuvastatin treatment, although the changes were modest in magnitude, and few met an FDR of 0.05. Among changes noted were a concordant increase in proinflammatory cytokines (IFN-γ, IL-1β, IL-5, IL-6, and TNF-α) and peripheral blood neutrophil frequency, and a decline in activated Treg frequency. Several drug effects were significantly modified by baseline hsCRP, and some did not resolve after drug withdrawal. Among other unexpected rosuvastatin effects were changes in erythrocyte indices, glucose-regulatory hormones, CD8+ T cells, and haptoglobin.CONCLUSIONRosuvastatin induces modest changes in immunologic and metabolic measures in normocholesterolemic subjects, with several effects dependent on baseline CRP. Future, larger studies are warranted to validate these changes and their physiological significance.TRIAL REGISTRATIONClinicalTrials.gov NCT01200836.FUNDINGThis research was supported by the Intramural Research Program of the NIH, National Institute of Environmental Health Sciences (Z01 ES102005), and the trans-NIH Center for Human Immunology.
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Affiliation(s)
| | - Min Shi
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Shira Perl
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, Maryland, USA
| | - Angélique Biancotto
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, Maryland, USA
| | - Julián Candia
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, Maryland, USA
| | - Foo Cheung
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, Maryland, USA
| | - Yuri Kotliarov
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, Maryland, USA
| | - Neal Young
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
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- The CHI Consortium is detailed in the supplemental material
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Popescu B, Lindblad K, Fantoni G, Gui G, Valdez J, Goswami M, DeStefano C, Lai C, Biancotto A, Candia J, Cheung F, Thompson J, Dillon LW, Hourigan CS. Abstract 3756: Highly multiplexed proteomic assessment of the human acute myeloid leukemia bone marrow microenvironment. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Acute myeloid leukemia (AML) is a genetically heterogenous and often fatal cancer of the hematopoietic system. Even after achieving an initial complete remission, more than half of such AML patients experience clinical relapse due to the persistence of “minimal” residual disease (MRD). Ex-vivo studies have hypothesized that the interactions between residual leukemic cells and the local microenvironment in the bone marrow may play a key role in their survival and chemoresistance.
Therefore, we performed for the first time a global examination of the proteomic profile of the bone marrow microenvironment in AML patients using a highly multiplexed method based on the ability of slow off-rate modified aptamers (modified small single-stranded oligonucleotides) to bind target proteins with high specificity and affinity at slow dissociation rates. Ten relapsed/refractory adult AML patients and age-matched healthy subject controls were recruited, under an IRB-approved protocol, for research bone marrow aspirate (BMA) and blood serum collection. The supernatant resulting from centrifugation of BMA and serum samples were processed and analyzed on a SOMAscan™ hybridization microarray platform for the detection and quantification of 1,305 target proteins (Somalogic, CO). Data was corrected using Hybridization Control and Median Signal Normalization methods. Significant differences were found between AML and healthy donor bone marrow, such that 133 analytes were differentially expressed in the AML group (Wilcoxon rank sum test FDR p<0.05, fold change >1.5); 85 over-expressed and 48 under-expressed. In addition to proteins already known to be elevated in AML patients (eg: Erythropoietin, Thrombopoietin, Hepcidin and Ferritin) and dysregulation of pathways previously identified as disease relevant (eg: Arginase), we also discovered multiple statistically significant differences in levels of soluble proteins that are not currently known to be associated with AML pathogenesis or treatment. Comparative analysis between blood serum and bone marrow determined that 82 of the 133 candidates have differential expression that was specifically restricted to the bone marrow. The STRING database was queried for pathway analysis of enriched protein sets in the AML group and clustered analytes with molecular functions including cytokine activity (GO:0005125, n=11, p=1.93e-08), cytokine receptor binding (GO:0005126, n=12, p=3.17e-08) and signal transducer activity (GO:0004871, n=19, p=9.23e-05).
Using a high-throughput proteomic technology we have identified an AML bone marrow microenvironment-specific profile comprised of both proteins with known implications in leukemic pathogenesis and also several novel candidates from biologically plausible pathways that, once validated, may provide mechanistic insight and opportunity for therapeutic targeting.
Citation Format: Bogdan Popescu, Katherine Lindblad, Giovanna Fantoni, Gege Gui, Janet Valdez, Meghali Goswami, Christin DeStefano, Catherine Lai, Angélique Biancotto, Julián Candia, Foo Cheung, Julie Thompson, Laura W. Dillon, Christopher S. Hourigan. Highly multiplexed proteomic assessment of the human acute myeloid leukemia bone marrow microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3756.
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Affiliation(s)
- Bogdan Popescu
- 1National Institutes of Health, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Katherine Lindblad
- 1National Institutes of Health, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Giovanna Fantoni
- 2National Institutes of Health, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Gege Gui
- 1National Institutes of Health, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Janet Valdez
- 1National Institutes of Health, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Meghali Goswami
- 1National Institutes of Health, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Christin DeStefano
- 1National Institutes of Health, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Catherine Lai
- 1National Institutes of Health, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Angélique Biancotto
- 2National Institutes of Health, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Julián Candia
- 2National Institutes of Health, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Foo Cheung
- 2National Institutes of Health, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Julie Thompson
- 1National Institutes of Health, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Laura W. Dillon
- 1National Institutes of Health, National Heart, Lung and Blood Institute, Bethesda, MD
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Candia J, Tsang JS. eNetXplorer: an R package for the quantitative exploration of elastic net families for generalized linear models. BMC Bioinformatics 2019; 20:189. [PMID: 30991955 PMCID: PMC6469092 DOI: 10.1186/s12859-019-2778-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 11/05/2018] [Accepted: 03/25/2019] [Indexed: 01/26/2023] Open
Abstract
Background Regularized generalized linear models (GLMs) are popular regression methods in bioinformatics, particularly useful in scenarios with fewer observations than parameters/features or when many of the features are correlated. In both ridge and lasso regularization, feature shrinkage is controlled by a penalty parameter λ. The elastic net introduces a mixing parameter α to tune the shrinkage continuously from ridge to lasso. Selecting α objectively and determining which features contributed significantly to prediction after model fitting remain a practical challenge given the paucity of available software to evaluate performance and statistical significance. Results eNetXplorer builds on top of glmnet to address the above issues for linear (Gaussian), binomial (logistic), and multinomial GLMs. It provides new functionalities to empower practical applications by using a cross validation framework that assesses the predictive performance and statistical significance of a family of elastic net models (as α is varied) and of the corresponding features that contribute to prediction. The user can select which quality metrics to use to quantify the concordance between predicted and observed values, with defaults provided for each GLM. Statistical significance for each model (as defined by α) is determined based on comparison to a set of null models generated by random permutations of the response; the same permutation-based approach is used to evaluate the significance of individual features. In the analysis of large and complex biological datasets, such as transcriptomic and proteomic data, eNetXplorer provides summary statistics, output tables, and visualizations to help assess which subset(s) of features have predictive value for a set of response measurements, and to what extent those subset(s) of features can be expanded or reduced via regularization. Conclusions This package presents a framework and software for exploratory data analysis and visualization. By making regularized GLMs more accessible and interpretable, eNetXplorer guides the process to generate hypotheses based on features significantly associated with biological phenotypes of interest, e.g. to identify biomarkers for therapeutic responsiveness. eNetXplorer is also generally applicable to any research area that may benefit from predictive modeling and feature identification using regularized GLMs. The package is available under GPL-3 license at the CRAN repository, https://CRAN.R-project.org/package=eNetXplorer. Electronic supplementary material The online version of this article (10.1186/s12859-019-2778-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. .,Trans-NIH Center for Human Immunology (CHI), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - John S Tsang
- Trans-NIH Center for Human Immunology (CHI), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. .,Systems Genomics and Bioinformatics Unit, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Sanhueza GE, Candia J. Access to healthcare in Chilean prisons: an inmates' perspective. Rev Esp Sanid Penit 2019; 21:5-10. [PMID: 31498860 PMCID: PMC6788202] [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] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 05/09/2018] [Indexed: 11/21/2022]
Abstract
OBJECTIVES To analyze the perception of access to Chilean prisons in a representative national sample of persons deprived of liberty as well as to examine the most important covariates of such access. MATERIALS AND METHODS This study uses secondary data from the First National Survey on the Quality of Prison Life (2014), which investigated inmates' perceptions regarding access to health services inside the prisons. To do this, it uses descriptive statistics and a logistic regression model. RESULTS Descriptive results at the national level show that access to health services in prisons tends to be "difficult" (44.7% of cases in this category). Multivariate logistic regression results indicate that men (OR=0.43) and those who reported better infrastructure (OR=0.70) were less likely to report "difficult access to health services". On the other hand, prison inmates (OR=1.61) and those who had reported higher levels of mistreatment (OR=1.26) were associated with a higher probability of reporting "difficult access to health services". DISCUSSION Our study suggests that access to health care is dynamically linked to other aspects of life within prisons such as the composition of the prison population (gender), some of the material aspects of prisons (infrastructure, type of facility), and even some relational aspects (level of mistreatment/abuse). Future studies could further extend the debate on healthcare in prisons, incorporating more complex both variables and analyses.
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Affiliation(s)
- GE Sanhueza
- Social Work Department. Faculty of Social Sciences. University of Chile.Universidad de ChileSocial Work DepartmentFaculty of Social SciencesUniversity of ChileChile
| | - J Candia
- San Sebastián University. Concepción. Chile.Universidad San SebastiánSan Sebastián UniversityConcepciónChile
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Shen Y, Kubben N, Candia J, Morozov AV, Misteli T, Losert W. RefCell: multi-dimensional analysis of image-based high-throughput screens based on 'typical cells'. BMC Bioinformatics 2018; 19:427. [PMID: 30445906 PMCID: PMC6240236 DOI: 10.1186/s12859-018-2454-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 05/28/2018] [Accepted: 10/31/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Image-based high-throughput screening (HTS) reveals a high level of heterogeneity in single cells and multiple cellular states may be observed within a single population. Currently available high-dimensional analysis methods are successful in characterizing cellular heterogeneity, but suffer from the "curse of dimensionality" and non-standardized outputs. RESULTS Here we introduce RefCell, a multi-dimensional analysis pipeline for image-based HTS that reproducibly captures cells with typical combinations of features in reference states and uses these "typical cells" as a reference for classification and weighting of metrics. RefCell quantitatively assesses heterogeneous deviations from typical behavior for each analyzed perturbation or sample. CONCLUSIONS We apply RefCell to the analysis of data from a high-throughput imaging screen of a library of 320 ubiquitin-targeted siRNAs selected to gain insights into the mechanisms of premature aging (progeria). RefCell yields results comparable to a more complex clustering-based single-cell analysis method; both methods reveal more potential hits than a conventional analysis based on averages.
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Affiliation(s)
- Yang Shen
- Department of Physics and Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742 USA
| | - Nard Kubben
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Julián Candia
- Trans-NIH Center for Human Immunology (CHI), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Alexandre V. Morozov
- Department of Physics and Astronomy and Center for Quantitative Biology, Rutgers University, Piscataway, NJ 08854 USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Wolfgang Losert
- Department of Physics and Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742 USA
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Giudice V, Biancotto A, Wu Z, Cheung F, Candia J, Fantoni G, Kajigaya S, Rios O, Townsley D, Feng X, Young NS. Aptamer-based proteomics of serum and plasma in acquired aplastic anemia. Exp Hematol 2018; 68:38-50. [PMID: 30312735 DOI: 10.1016/j.exphem.2018.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/18/2018] [Accepted: 09/29/2018] [Indexed: 11/25/2022]
Abstract
Single-stranded oligonucleotides containing deoxyuridine are aptamers (SOMAmers) that can bind proteins with high specificity and affinity and slow dissociation rates. SOMAscan, an aptamer-based proteomic technology, allows measurement of more than 1,300 proteins simultaneously for the identification of new disease biomarkers. The aim of the present study was to identify new serum and plasma protein markers for diagnosis of acquired aplastic anemia (AA) and response to immunosuppressive therapies (IST). SOMAscan was used to screen 1,141 serum proteins in 28 AA patients before and after therapy and 1,317 plasma proteins in seven SAA patients treated with standard IST and a thrombopoietin receptor agonist. From our analysis, 19 serum and 28 plasma proteins were identified as possible candidate diagnostic and prognostic markers. A custom immunobead-based multiplex assay with five selected serum proteins (BMP-10, CCL17, DKK1, HGF, and SELL) was used for validation in a verification set (n = 65) of samples obtained before and after IST and in a blinded validation cohort at baseline (n = 16). After technical validation, four biomarkers were employed to predict diagnosis (accuracy, 88%) and long-term response to IST (accuracy, 79%). In conclusion, SOMAscan is a powerful tool for the identification of new biomarkers. We propose further larger studies to validate new candidate serum and plasma diagnostic and prognostic markers of AA.
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Affiliation(s)
- Valentina Giudice
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Angélique Biancotto
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, MD, USA
| | - Zhijie Wu
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Foo Cheung
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, MD, USA
| | - Julián Candia
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, MD, USA
| | - Giovanna Fantoni
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, MD, USA
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Olga Rios
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Danielle Townsley
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Xingmin Feng
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, USA
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Brown D, Zingone A, Yu Y, Zhu B, Candia J, Cao L, Ryan BM. Relationship between Circulating Inflammation Proteins and Lung Cancer Diagnosis in the National Lung Screening Trial. Cancer Epidemiol Biomarkers Prev 2018; 28:110-118. [PMID: 30297515 DOI: 10.1158/1055-9965.epi-18-0598] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/09/2018] [Accepted: 09/27/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Previously, we observed a strong relationship between circulating serum inflammation proteins in relation to lung cancer diagnosis and risk, both in case-control and prospective cohorts. Low-dose computed tomography (LDCT) screening has a high prevalence of false-positive nodules, thus companion noninvasive biomarkers that can distinguish between benign and malignant nodules could have clinical utility and positive impact on patient outcomes. METHODS We conducted a nested case-control study within the National Lung Screening Trial. Concentrations of 30 inflammation proteins were measured on plasma samples of 262 cases and 528 controls using a highly sensitive and analytically validated electrochemiluminescence V-PLEX immunoassay. RESULTS Comparing the fourth quartile with the first quartile, we found increased IFNγ and IL12/IL23p40 associated with increased odds of a lung cancer diagnosis [OR 1.89, 95% confidence intervals (CI), 1.16-3.09; OR 2.49, 95% CI, 1.46-4.23, respectively]. Confirming our previous observations, we also detected a relationship between increased IL6, IL8, and C-reactive protein (CRP) with lung cancer diagnosis. These relationships were significant after adjustment for age, gender, race, smoking, body mass index (BMI), family history of lung cancer, and previous diagnoses of inflammatory conditions. However, none of these proteins could distinguish between a benign and malignant lung nodule (IL6: OR 1.25, 95% CI, 0.59-2.64; IL8: OR 1.40, 95% CI, 0.70-2.81; CRP: OR 0.98, 95% CI, 0.45-2.12). CONCLUSIONS We have discovered new associations for IFNγ and IL12/IL23p40 with lung cancer but have no evidence that these proteins can distinguish between benign and malignant lung nodules. IMPACT Circulating inflammation proteins are unlikely to have utility as companion LDCT biomarkers.
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Affiliation(s)
- Derek Brown
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Adriana Zingone
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Yunkai Yu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Bin Zhu
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Julián Candia
- Trans-NIH Center for Human Immunology (CHI), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Liang Cao
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.
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Tanaka T, Biancotto A, Moaddel R, Moore AZ, Gonzalez‐Freire M, Aon MA, Candia J, Zhang P, Cheung F, Fantoni G, Semba RD, Ferrucci L. Plasma proteomic signature of age in healthy humans. Aging Cell 2018; 17:e12799. [PMID: 29992704 PMCID: PMC6156492 DOI: 10.1111/acel.12799] [Citation(s) in RCA: 260] [Impact Index Per Article: 43.3] [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: 03/28/2018] [Revised: 05/13/2018] [Accepted: 06/01/2018] [Indexed: 12/30/2022] Open
Abstract
To characterize the proteomic signature of chronological age, 1,301 proteins were measured in plasma using the SOMAscan assay (SomaLogic, Boulder, CO, USA) in a population of 240 healthy men and women, 22-93 years old, who were disease- and treatment-free and had no physical and cognitive impairment. Using a p ≤ 3.83 × 10-5 significance threshold, 197 proteins were positively associated, and 20 proteins were negatively associated with age. Growth differentiation factor 15 (GDF15) had the strongest, positive association with age (GDF15; 0.018 ± 0.001, p = 7.49 × 10-56 ). In our sample, GDF15 was not associated with other cardiovascular risk factors such as cholesterol or inflammatory markers. The functional pathways enriched in the 217 age-associated proteins included blood coagulation, chemokine and inflammatory pathways, axon guidance, peptidase activity, and apoptosis. Using elastic net regression models, we created a proteomic signature of age based on relative concentrations of 76 proteins that highly correlated with chronological age (r = 0.94). The generalizability of our findings needs replication in an independent cohort.
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Affiliation(s)
- Toshiko Tanaka
- Longitudinal Study SectionTranslational Gerontology BranchNIANIHBaltimoreMaryland
| | - Angelique Biancotto
- Trans‐NIH Center for Human Immunology, Autoimmunity, and InflammationNIHBethesdaMaryland
| | - Ruin Moaddel
- Laboratory of Clinical InvestigationNIANIHBaltimoreMaryland
| | - Ann Zenobia Moore
- Longitudinal Study SectionTranslational Gerontology BranchNIANIHBaltimoreMaryland
| | | | - Miguel A. Aon
- Laboratory of Cardiovascular ScienceNational Institute on AgingNational Institutes of HealthBaltimoreMaryland
| | - Julián Candia
- Trans‐NIH Center for Human Immunology, Autoimmunity, and InflammationNIHBethesdaMaryland
| | - Pingbo Zhang
- Wilmer Eye InstituteJohns Hopkins University School of MedicineBaltimoreMaryland
| | - Foo Cheung
- Trans‐NIH Center for Human Immunology, Autoimmunity, and InflammationNIHBethesdaMaryland
| | - Giovanna Fantoni
- Trans‐NIH Center for Human Immunology, Autoimmunity, and InflammationNIHBethesdaMaryland
| | - Richard D. Semba
- Wilmer Eye InstituteJohns Hopkins University School of MedicineBaltimoreMaryland
| | - Luigi Ferrucci
- Longitudinal Study SectionTranslational Gerontology BranchNIANIHBaltimoreMaryland
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Cheung F, Fantoni G, Conner M, Sellers BA, Kotliarov Y, Candia J, Stagliano K, Biancotto A. Web Tool for Navigating and Plotting SomaLogic ADAT Files. J Open Res Softw 2017; 5:20. [PMID: 29951204 PMCID: PMC6017986 DOI: 10.5334/jors.166] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
SOMAscan™ is a complex proteomic platform created by SomaLogic. Experimental data resulting from the assay is provided by SomaLogic in a proprietary text-based format called ADAT. This manuscript describes a user-friendly point and click open source, platform-independent software tool designed to be used for navigating and plotting data from an ADAT file. This tool was used either alone or in conjunction with other tools as a first pass analysis of the data on several different on-going research projects. We have seen a need from our experience for a web interface to the ADAT file so that users can navigate, generate plots, perform QC and conduct statistical analysis on their own data in a point and click manner. After several rounds of interacting with biologists and their requirements with respect to data analysis, we present an online interactive Shiny Web Tool for Navigating and Plotting data contained within the ADAT file. Extensive video tutorials, example data, the tool and the source code are available online.
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Affiliation(s)
- Foo Cheung
- Trans-NIH Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, US
| | - Giovanna Fantoni
- Trans-NIH Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, US
| | - Maria Conner
- Trans-NIH Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, US
| | - Brian A Sellers
- Trans-NIH Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, US
| | - Yuri Kotliarov
- Trans-NIH Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, US
| | - Julián Candia
- Trans-NIH Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, US
| | - Katherine Stagliano
- Trans-NIH Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, US
| | - Angélique Biancotto
- Trans-NIH Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, US
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Tanaka T, Biancotto A, Foo C, Candia J, Kotlariov Y, Semba R, Ferrucci L. PROTEOMIC SIGNATURE OF AGE IN HEALTHY HUMANS. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.3293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- T. Tanaka
- National Institute on Aging, Baltimore, Maryland,
| | - A. Biancotto
- National institute of Health, Bethesda, District of Columbia,
| | - C. Foo
- National institute of Health, Bethesda, District of Columbia,
| | - J. Candia
- National institute of Health, Bethesda, District of Columbia,
| | - Y. Kotlariov
- National institute of Health, Bethesda, District of Columbia,
| | - R.D. Semba
- John Hopkins University, Baltimore, Maryland
| | - L. Ferrucci
- National Institute on Aging, Baltimore, Maryland,
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Dolatabadi S, Candia J, Akrap N, Vannas C, Tesan Tomic T, Losert W, Landberg G, Åman P, Ståhlberg A. Cell Cycle and Cell Size Dependent Gene Expression Reveals Distinct Subpopulations at Single-Cell Level. Front Genet 2017; 8:1. [PMID: 28179914 PMCID: PMC5263129 DOI: 10.3389/fgene.2017.00001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 06/07/2016] [Accepted: 01/06/2017] [Indexed: 12/22/2022] Open
Abstract
Cell proliferation includes a series of events that is tightly regulated by several checkpoints and layers of control mechanisms. Most studies have been performed on large cell populations, but detailed understanding of cell dynamics and heterogeneity requires single-cell analysis. Here, we used quantitative real-time PCR, profiling the expression of 93 genes in single-cells from three different cell lines. Individual unsynchronized cells from three different cell lines were collected in different cell cycle phases (G0/G1 - S - G2/M) with variable cell sizes. We found that the total transcript level per cell and the expression of most individual genes correlated with progression through the cell cycle, but not with cell size. By applying the random forests algorithm, a supervised machine learning approach, we show how a multi-gene signature that classifies individual cells into their correct cell cycle phase and cell size can be generated. To identify the most predictive genes we used a variable selection strategy. Detailed analysis of cell cycle predictive genes allowed us to define subpopulations with distinct gene expression profiles and to calculate a cell cycle index that illustrates the transition of cells between cell cycle phases. In conclusion, we provide useful experimental approaches and bioinformatics to identify informative and predictive genes at the single-cell level, which opens up new means to describe and understand cell proliferation and subpopulation dynamics.
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Affiliation(s)
- Soheila Dolatabadi
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg Gothenburg, Sweden
| | - Julián Candia
- Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of HealthBethesda, MD, USA; Department of Physics, University of MarylandCollege Park, MD, USA
| | - Nina Akrap
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg Gothenburg, Sweden
| | - Christoffer Vannas
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg Gothenburg, Sweden
| | - Tajana Tesan Tomic
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg Gothenburg, Sweden
| | - Wolfgang Losert
- Department of Physics, University of Maryland College Park, MD, USA
| | - Göran Landberg
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg Gothenburg, Sweden
| | - Pierre Åman
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg Gothenburg, Sweden
| | - Anders Ståhlberg
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg Gothenburg, Sweden
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Chen D, Sarkar S, Candia J, Florczyk SJ, Bodhak S, Driscoll MK, Simon CG, Dunkers JP, Losert W. Machine learning based methodology to identify cell shape phenotypes associated with microenvironmental cues. Biomaterials 2016; 104:104-18. [DOI: 10.1016/j.biomaterials.2016.06.040] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/17/2016] [Accepted: 06/19/2016] [Indexed: 01/02/2023]
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Candia J, Cherukuri S, Guo Y, Doshi KA, Banavar JR, Civin CI, Losert W. Uncovering low-dimensional, miR-based signatures of acute myeloid and lymphoblastic leukemias with a machine-learning-driven network approach. Converg Sci Phys Oncol 2015; 1. [PMID: 27274862 DOI: 10.1088/2057-1739/1/2/025002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Complex phenotypic differences among different acute leukemias cannot be fully captured by analyzing the expression levels of one single molecule, such as a miR, at a time, but requires systematic analysis of large sets of miRs. While a popular approach for analysis of such datasets is principal component analysis (PCA), this method is not designed to optimally discriminate different phenotypes. Moreover, PCA and other low-dimensional representation methods yield linear or non-linear combinations of all measured miRs. Global human miR expression was measured in AML, B-ALL, and TALL cell lines and patient RNA samples. By systematically applying support vector machines to all measured miRs taken in dyad and triad groups, we built miR networks using cell line data and validated our findings with primary patient samples. All the coordinately transcribed members of the miR-23a cluster (which includes also miR-24 and miR-27a), known to function as tumor suppressors of acute leukemias, appeared in the AML, B-ALL and T-ALL centric networks. Subsequent qRT-PCR analysis showed that the most connected miR in the B-ALL-centric network, miR-708, is highly and specifically expressed in B-ALLs, suggesting that miR-708 might serve as a biomarker for B-ALL. This approach is systematic, quantitative, scalable, and unbiased. Rather than a single signature, our approach yields a network of signatures reflecting the redundant nature of biological signaling pathways. The network representation allows for visual analysis of all signatures by an expert and for future integration of additional information. Furthermore, each signature involves only small sets of miRs, such as dyads and triads, which are well suited for in depth validation through laboratory experiments. In particular, loss-and gain-of-function assays designed to drive changes in leukemia cell survival, proliferation and differentiation will benefit from the identification of multi-miR signatures that characterize leukemia subtypes and their normal counterpart cells of origin.
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Affiliation(s)
- Julián Candia
- Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA; Center for Stem Cell Biology & Regenerative Medicine, Departments of Pediatrics and Physiology, University of Maryland School of Medicine, Baltimore MD 21201, USA
| | - Srujana Cherukuri
- Center for Stem Cell Biology & Regenerative Medicine, Departments of Pediatrics and Physiology, University of Maryland School of Medicine, Baltimore MD 21201, USA; Noble Life Sciences, 22 Firstfield Rd, Gaithersburg, MD 20878, USA
| | - Yin Guo
- Center for Stem Cell Biology & Regenerative Medicine, Departments of Pediatrics and Physiology, University of Maryland School of Medicine, Baltimore MD 21201, USA
| | - Kshama A Doshi
- Center for Stem Cell Biology & Regenerative Medicine, Departments of Pediatrics and Physiology, University of Maryland School of Medicine, Baltimore MD 21201, USA
| | - Jayanth R Banavar
- Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Curt I Civin
- Center for Stem Cell Biology & Regenerative Medicine, Departments of Pediatrics and Physiology, University of Maryland School of Medicine, Baltimore MD 21201, USA
| | - Wolfgang Losert
- Department of Physics, University of Maryland, College Park, MD 20742, USA
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Mazzitello KI, Candia J, Albano EV. Far-from-equilibrium growth of magnetic thin films with Blume-Capel impurities. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 91:042118. [PMID: 25974450 DOI: 10.1103/physreve.91.042118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Indexed: 06/04/2023]
Abstract
We investigate the irreversible growth of (2+1)-dimensional magnetic thin films. The spin variable can adopt three states (s(I)=±1,0), and the system is in contact with a thermal bath of temperature T. The deposition process depends on the change of the configuration energy, which, by analogy to the Blume-Capel Hamiltonian in equilibrium systems, depends on Ising-like couplings between neighboring spins (J) and has a crystal field (D) term that controls the density of nonmagnetic impurities (s(I)=0). Once deposited, particles are not allowed to flip, diffuse, or detach. By means of extensive Monte Carlo simulations, we obtain the phase diagram in the crystal field vs temperature parameter space. We show clear evidence of the existence of a tricritical point located at D(t)/J=1.145(10) and k(B)T(t)/J=0.425(10), which separates a first-order transition curve at lower temperatures from a critical second-order transition curve at higher temperatures, in analogy with the previously studied equilibrium Blume-Capel model. Furthermore, we show that, along the second-order transition curve, the critical behavior of the irreversible growth model can be described by means of the critical exponents of the two-dimensional Ising model under equilibrium conditions. Therefore, our findings provide a link between well-known theoretical equilibrium models and nonequilibrium growth processes that are of great interest for many experimental applications, as well as a paradigmatic topic of study in current statistical physics.
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Affiliation(s)
| | - Julián Candia
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET, UNLP), La Plata, Argentina
- Department of Physics, University of Maryland, College Park, Maryland 20742, USA
| | - Ezequiel V Albano
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET, UNLP), La Plata, Argentina
- Departamento de Física (UNLP), La Plata, Argentina
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Abstract
Current efforts in the biomedical sciences and related interdisciplinary fields are focused on gaining a molecular understanding of health and disease, which is a problem of daunting complexity that spans many orders of magnitude in characteristic length scales, from small molecules that regulate cell function to cell ensembles that form tissues and organs working together as an organism. In order to uncover the molecular nature of the emergent properties of a cell, it is essential to measure multiple-cell components simultaneously in the same cell. In turn, cell heterogeneity requires multiple-cells to be measured in order to understand health and disease in the organism. This review summarizes current efforts towards a data-driven framework that leverages single-cell technologies to build robust signatures of healthy and diseased phenotypes. While some approaches focus on multicolor flow cytometry data and other methods are designed to analyze high-content image-based screens, we emphasize the so-called Supercell/SVM paradigm (recently developed by the authors of this review and collaborators) as a unified framework that captures mesoscopic-scale emergence to build reliable phenotypes. Beyond their specific contributions to basic and translational biomedical research, these efforts illustrate, from a larger perspective, the powerful synergy that might be achieved from bringing together methods and ideas from statistical physics, data mining, and mathematics to solve the most pressing problems currently facing the life sciences.
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Affiliation(s)
- Julián Candia
- Department of Physics, University of Maryland, College Park, MD 20742, USA. School of Medicine, University of Maryland, Baltimore, MD 21201, USA. IFLYSIB and CONICET, University of La Plata, 1900 La Plata, Argentina
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Loscar ES, Candia J. Stochastic resonance and dynamic first-order pseudo-phase-transitions in the irreversible growth of thin films under spatially periodic magnetic fields. Phys Rev E Stat Nonlin Soft Matter Phys 2013; 88:042412. [PMID: 24229194 DOI: 10.1103/physreve.88.042412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Indexed: 06/02/2023]
Abstract
We study the irreversible growth of magnetic thin films under the influence of spatially periodic fields by means of extensive Monte Carlo simulations. We find first-order pseudo-phase-transitions that separate a dynamically disordered phase from a dynamically ordered phase. By analogy with time-dependent oscillating fields applied to Ising-type models, we qualitatively associate this dynamic transition with the localization-delocalization transition of spatial hysteresis loops. Depending on the relative width of the magnetic film L compared to the wavelength of the external field λ, different transition regimes are observed. For small systems (L < λ), the transition is associated with the standard stochastic resonance regime, while for large systems (L > λ), the transition is driven by anomalous stochastic resonance. The origin of the latter is identified as due to the emergence of an additional relevant length scale, namely, the roughness of the spin domain switching interface. The distinction between different stochastic resonance regimes is discussed at length both qualitatively by means of snapshot configurations and quantitatively via residence-length and order-parameter probability distributions.
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Affiliation(s)
- Ernesto S Loscar
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, CCT La Plata CONICET, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Sucursal 4, C.C. 16, 1900 La Plata, Buenos Aires, Argentina
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