1
|
Lin W, Wall JD, Li G, Newman D, Yang Y, Abney M, VandeBerg JL, Olivier M, Gilad Y, Cox LA. Genetic regulatory effects in response to a high-cholesterol, high-fat diet in baboons. Cell Genom 2024; 4:100509. [PMID: 38430910 PMCID: PMC10943580 DOI: 10.1016/j.xgen.2024.100509] [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] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/20/2023] [Accepted: 02/05/2024] [Indexed: 03/05/2024]
Abstract
Steady-state expression quantitative trait loci (eQTLs) explain only a fraction of disease-associated loci identified through genome-wide association studies (GWASs), while eQTLs involved in gene-by-environment (GxE) interactions have rarely been characterized in humans due to experimental challenges. Using a baboon model, we found hundreds of eQTLs that emerge in adipose, liver, and muscle after prolonged exposure to high dietary fat and cholesterol. Diet-responsive eQTLs exhibit genomic localization and genic features that are distinct from steady-state eQTLs. Furthermore, the human orthologs associated with diet-responsive eQTLs are enriched for GWAS genes associated with human metabolic traits, suggesting that context-responsive eQTLs with more complex regulatory effects are likely to explain GWAS hits that do not seem to overlap with standard eQTLs. Our results highlight the complexity of genetic regulatory effects and the potential of eQTLs with disease-relevant GxE interactions in enhancing the understanding of GWAS signals for human complex disease using non-human primate models.
Collapse
Affiliation(s)
- Wenhe Lin
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA.
| | - Jeffrey D Wall
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ge Li
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Deborah Newman
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78229, USA
| | - Yunqi Yang
- Committee on Genetics, Genomics and System Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Mark Abney
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - John L VandeBerg
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA
| | - Michael Olivier
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Yoav Gilad
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA; Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL 60637, USA.
| | - Laura A Cox
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78229, USA.
| |
Collapse
|
2
|
Cox LA, Puppala S, Chan J, Zimmerman KD, Hamid Z, Ampong I, Huber HF, Li G, Jadhav AYL, Wang B, Li C, Baxter MG, Shively C, Clarke GD, Register TC, Nathanielsz PW, Olivier M. Integrated multi-omics analysis of brain aging in female nonhuman primates reveals altered signaling pathways relevant to age-related disorders. Neurobiol Aging 2023; 132:109-119. [PMID: 37797463 PMCID: PMC10841409 DOI: 10.1016/j.neurobiolaging.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/25/2023] [Accepted: 08/27/2023] [Indexed: 10/07/2023]
Abstract
The prefrontal cortex (PFC) has been implicated as a key brain region responsible for age-related cognitive decline. Little is known about aging-related molecular changes in PFC that may mediate these effects. To date, no studies have used untargeted discovery methods with integrated analyses to determine PFC molecular changes in healthy female primates. We quantified PFC changes associated with healthy aging in female baboons by integrating multiple omics data types (transcriptomics, proteomics, metabolomics) from samples across the adult age span. Our integrated omics approach using unbiased weighted gene co-expression network analysis to integrate data and treat age as a continuous variable, revealed highly interconnected known and novel pathways associated with PFC aging. We found Gamma-aminobutyric acid (GABA) tissue content associated with these signaling pathways, providing 1 potential biomarker to assess PFC changes with age. These highly coordinated pathway changes during aging may represent early steps for aging-related decline in PFC functions, such as learning and memory, and provide potential biomarkers to assess cognitive status in humans.
Collapse
Affiliation(s)
- Laura A Cox
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA; Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA; Section on Comparative Medicine, Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA; Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Sobha Puppala
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA; Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jeannie Chan
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA; Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Kip D Zimmerman
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA; Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Zeeshan Hamid
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Isaac Ampong
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Hillary F Huber
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Ge Li
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Avinash Y L Jadhav
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Benlian Wang
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Cun Li
- Texas Pregnancy & Life-Course Health Research Center, Department of Animal Science, University of Wyoming, Laramie, WY, USA
| | - Mark G Baxter
- Section on Comparative Medicine, Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Carol Shively
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA; Section on Comparative Medicine, Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Geoffrey D Clarke
- Department of Radiology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Thomas C Register
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA; Section on Comparative Medicine, Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Peter W Nathanielsz
- Texas Pregnancy & Life-Course Health Research Center, Department of Animal Science, University of Wyoming, Laramie, WY, USA
| | - Michael Olivier
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA; Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| |
Collapse
|
3
|
Lin W, Wall JD, Li G, Newman D, Yang Y, Abney M, VandeBerg JL, Olivier M, Gilad Y, Cox LA. Genetic regulatory effects in response to a high cholesterol, high fat diet in baboons. bioRxiv 2023:2023.08.01.551489. [PMID: 37577666 PMCID: PMC10418186 DOI: 10.1101/2023.08.01.551489] [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] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Steady-state expression quantitative trait loci (eQTLs) explain only a fraction of disease-associated loci identified through genome-wide association studies (GWAS), while eQTLs involved in gene-by-environment (GxE) interactions have rarely been characterized in humans due to experimental challenges. Using a baboon model, we found hundreds of eQTLs that emerge in adipose, liver, and muscle after prolonged exposure to high dietary fat and cholesterol. Diet-responsive eQTLs exhibit genomic localization and genic features that are distinct from steady-state eQTLs. Furthermore, the human orthologs associated with diet-responsive eQTLs are enriched for GWAS genes associated with human metabolic traits, suggesting that context-responsive eQTLs with more complex regulatory effects are likely to explain GWAS hits that do not seem to overlap with standard eQTLs. Our results highlight the complexity of genetic regulatory effects and the potential of eQTLs with disease-relevant GxE interactions in enhancing the understanding of GWAS signals for human complex disease using nonhuman primate models.
Collapse
Affiliation(s)
- Wenhe Lin
- Department of Human Genetics, The University of Chicago, Chicago, USA
| | - Jeffrey D. Wall
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Present address: Galatea Bio, Hialeah, FL, USA
| | - Ge Li
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Deborah Newman
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Yunqi Yang
- Committee on Genetics, Genomics and System Biology, The University of Chicago, Chicago, USA
| | - Mark Abney
- Department of Human Genetics, The University of Chicago, Chicago, USA
| | - John L. VandeBerg
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grand Valley, Brownsville, TX, USA
| | - Michael Olivier
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Yoav Gilad
- Department of Human Genetics, The University of Chicago, Chicago, USA
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA
- Lead contact
| | - Laura A. Cox
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| |
Collapse
|
4
|
Grilo LF, Zimmerman KD, Puppala S, Chan J, Huber HF, Li G, Jadhav AYL, Wang B, Li C, Clarke GD, Register TC, Oliveira PJ, Nathanielsz PW, Olivier M, Pereira SP, Cox LA. Cardiac Molecular Analysis Reveals Aging-Associated Metabolic Alterations Promoting Glycosaminoglycans Accumulation Via Hexosamine Biosynthetic Pathway. bioRxiv 2023:2023.11.17.567640. [PMID: 38014295 PMCID: PMC10680868 DOI: 10.1101/2023.11.17.567640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Age is a prominent risk factor for cardiometabolic disease, and often leads to heart structural and functional changes. However, precise molecular mechanisms underlying cardiac remodeling and dysfunction resulting from physiological aging per se remain elusive. Understanding these mechanisms requires biological models with optimal translation to humans. Previous research demonstrated that baboons undergo age-related reduction in ejection fraction and increased heart sphericity, mirroring changes observed in humans. The goal of this study was to identify early cardiac molecular alterations that precede functional adaptations, shedding light on the regulation of age-associated changes. We performed unbiased transcriptomics of left ventricle (LV) samples from female baboons aged 7.5-22.1 years (human equivalent ~30-88 years). Weighted-gene correlation network and pathway enrichment analyses were performed to identify potential age-associated mechanisms in LV, with histological validation. Myocardial modules of transcripts negatively associated with age were primarily enriched for cardiac metabolism, including oxidative phosphorylation, tricarboxylic acid cycle, glycolysis, and fatty-acid β-oxidation. Transcripts positively correlated with age suggest upregulation of glucose uptake, pentose phosphate pathway, and hexosamine biosynthetic pathway (HBP), indicating a metabolic shift towards glucose-dependent anabolic pathways. Upregulation of HBP commonly results in increased glycosaminoglycan precursor synthesis. Transcripts involved in glycosaminoglycan synthesis, modification, and intermediate metabolism were also upregulated in older animals, while glycosaminoglycan degradation transcripts were downregulated with age. These alterations would promote glycosaminoglycan accumulation, which was verified histologically. Upregulation of extracellular matrix (ECM)-induced signaling pathways temporally coincided with glycosaminoglycan accumulation. We found a subsequent upregulation of cardiac hypertrophy-related pathways and an increase in cardiomyocyte width. Overall, our findings revealed a transcriptional shift in metabolism from catabolic to anabolic pathways that leads to ECM glycosaminoglycan accumulation through HBP prior to upregulation of transcripts of cardiac hypertrophy-related pathways. This study illuminates cellular mechanisms that precede development of cardiac hypertrophy, providing novel potential targets to remediate age-related cardiac diseases.
Collapse
Affiliation(s)
- Luís F. Grilo
- CNC-UC, Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
- CIBB, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal
- University of Coimbra, Institute for Interdisciplinary Research, PDBEB - Doctoral Programme in Experimental Biology and Biomedicine
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Kip D. Zimmerman
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Sobha Puppala
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jeannie Chan
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Hillary F. Huber
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Ge Li
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Avinash Y. L. Jadhav
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Benlian Wang
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Cun Li
- Texas Pregnancy & Life-Course Health Research Center, Department of Animal Science, University of Wyoming, Laramie, Wyoming, USA
| | - Geoffrey D. Clarke
- Department of Radiology, University of Texas Health Science Center, San Antonio, Texas
| | - Thomas C. Register
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
- Section on Comparative Medicine, Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Paulo J. Oliveira
- CNC-UC, Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
- CIBB, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal
| | - Peter W. Nathanielsz
- Texas Pregnancy & Life-Course Health Research Center, Department of Animal Science, University of Wyoming, Laramie, Wyoming, USA
| | - Michael Olivier
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Susana P. Pereira
- CNC-UC, Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
- CIBB, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal
- Laboratory of Metabolism and Exercise (LaMetEx), Research Centre in Physical Activity, Health and Leisure (CIAFEL), Laboratory for Integrative and Translational Research in Population Health (ITR), Faculty of Sports, University of Porto, Porto, Portugal
| | - Laura A. Cox
- Center for Precision Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
- Section on Comparative Medicine, Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| |
Collapse
|
5
|
Cox L, Olivier M. SIRT2 counteracts primate cardiac aging. Nat Aging 2023; 3:1178-1179. [PMID: 37783814 DOI: 10.1038/s43587-023-00496-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Affiliation(s)
- Laura Cox
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
| | - Michael Olivier
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| |
Collapse
|
6
|
Sluka KA, Wager TD, Sutherland SP, Labosky PA, Balach T, Bayman EO, Berardi G, Brummett CM, Burns J, Buvanendran A, Caffo B, Calhoun VD, Clauw D, Chang A, Coffey CS, Dailey DL, Ecklund D, Fiehn O, Fisch KM, Frey Law LA, Harris RE, Harte SE, Howard TD, Jacobs J, Jacobs JM, Jepsen K, Johnston N, Langefeld CD, Laurent LC, Lenzi R, Lindquist MA, Lokshin A, Kahn A, McCarthy RJ, Olivier M, Porter L, Qian WJ, Sankar CA, Satterlee J, Swensen AC, Vance CG, Waljee J, Wandner LD, Williams DA, Wixson RL, Zhou XJ. Predicting chronic postsurgical pain: current evidence and a novel program to develop predictive biomarker signatures. Pain 2023; 164:1912-1926. [PMID: 37326643 PMCID: PMC10436361 DOI: 10.1097/j.pain.0000000000002938] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 12/19/2022] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 06/17/2023]
Abstract
ABSTRACT Chronic pain affects more than 50 million Americans. Treatments remain inadequate, in large part, because the pathophysiological mechanisms underlying the development of chronic pain remain poorly understood. Pain biomarkers could potentially identify and measure biological pathways and phenotypical expressions that are altered by pain, provide insight into biological treatment targets, and help identify at-risk patients who might benefit from early intervention. Biomarkers are used to diagnose, track, and treat other diseases, but no validated clinical biomarkers exist yet for chronic pain. To address this problem, the National Institutes of Health Common Fund launched the Acute to Chronic Pain Signatures (A2CPS) program to evaluate candidate biomarkers, develop them into biosignatures, and discover novel biomarkers for chronification of pain after surgery. This article discusses candidate biomarkers identified by A2CPS for evaluation, including genomic, proteomic, metabolomic, lipidomic, neuroimaging, psychophysical, psychological, and behavioral measures. Acute to Chronic Pain Signatures will provide the most comprehensive investigation of biomarkers for the transition to chronic postsurgical pain undertaken to date. Data and analytic resources generatedby A2CPS will be shared with the scientific community in hopes that other investigators will extract valuable insights beyond A2CPS's initial findings. This article will review the identified biomarkers and rationale for including them, the current state of the science on biomarkers of the transition from acute to chronic pain, gaps in the literature, and how A2CPS will address these gaps.
Collapse
Affiliation(s)
- Kathleen A. Sluka
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Tor D. Wager
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH
| | - Stephani P. Sutherland
- Department of Biostatistics, Johns Hopkins Bloomberg Schools of Public Health, Baltimore, MD
| | - Patricia A. Labosky
- Office of Strategic Coordination, Division of Program Coordination, Planning and Strategic Initiatives, Office of the Director, National Institutes of Health, Bethesda, MD
| | - Tessa Balach
- Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago, Chicago, IL
| | - Emine O. Bayman
- Clinical Trials and Data Management Center, Department of Biostatistics, University of Iowa, Iowa City, IA
| | - Giovanni Berardi
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Chad M. Brummett
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI
| | - John Burns
- Division of Behavioral Sciences, Rush Medical College, Chicago, IL
| | | | - Brian Caffo
- Department of Biostatistics, Johns Hopkins Bloomberg Schools of Public Health, Baltimore, MD
| | - Vince D. Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State, Georgia Tech, and Emory University, Atlanta, GA
| | - Daniel Clauw
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI
| | - Andrew Chang
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI
| | - Christopher S. Coffey
- Clinical Trials and Data Management Center, Department of Biostatistics, University of Iowa, Iowa City, IA
| | - Dana L. Dailey
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Dixie Ecklund
- Clinical Trials and Data Management Center, Department of Biostatistics, University of Iowa, Iowa City, IA
| | - Oliver Fiehn
- University of California, Davis, Davis, CA, United States
| | - Kathleen M. Fisch
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, San Diego, CA, United States
- Center for Computational Biology and Bioinformatics, University of California San Diego, San Diego, CA, United States
| | - Laura A. Frey Law
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Richard E. Harris
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI
| | - Steven E. Harte
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI
| | - Timothy D. Howard
- Department of Biochemistry, Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
- Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
| | - Joshua Jacobs
- Department of Orthopedic Surgery, Rush Medical College, CHicago, IL
| | - Jon M. Jacobs
- Environmental and Molecular Sciences Laboratory, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | | | | | - Carl D. Langefeld
- Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
- Department of Biostatistics and Data Science, Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, San Diego, CA, United States
| | - Rebecca Lenzi
- Office of Strategic Coordination, Division of Program Coordination, Planning and Strategic Initiatives, Office of the Director, National Institutes of Health, Bethesda, MD
| | - Martin A. Lindquist
- Department of Biostatistics, Johns Hopkins Bloomberg Schools of Public Health, Baltimore, MD
| | | | - Ari Kahn
- Texas Advanced Computing Center, University of Texas, AUstin, TX
| | | | - Michael Olivier
- Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
- Department of Internal Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
| | - Linda Porter
- National Institute of Neurological Disorders and Stroke, Bethesda, MD
- Office of Pain Policy and Planning National Institutes of Health, Bethesda, MD
| | - Wei-Jun Qian
- Environmental and Molecular Sciences Laboratory, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Cheryse A. Sankar
- National Institute of Neurological Disorders and Stroke, Bethesda, MD
| | | | - Adam C. Swensen
- Environmental and Molecular Sciences Laboratory, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Carol G.T. Vance
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Jennifer Waljee
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI
| | - Laura D. Wandner
- National Institute of Neurological Disorders and Stroke, Bethesda, MD
| | - David A. Williams
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI
| | | | - Xiaohong Joe Zhou
- Center for MR Research and Departments of Radiology, Neurosurgery, and Bioengineering, University of Illinois College of Medicine at Chicago, Chicago, IL, United States
| |
Collapse
|
7
|
Puppala S, Chan J, Zimmerman KD, Hamid Z, Ampong I, Huber HF, Li G, Jadhav AYL, Li C, Nathanielsz PW, Olivier M, Cox LA. Multi-omics Analysis of Aging Liver Reveals Changes in Endoplasmic Stress and Degradation Pathways in Female Nonhuman Primates. bioRxiv 2023:2023.08.21.554149. [PMID: 37662261 PMCID: PMC10473634 DOI: 10.1101/2023.08.21.554149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The liver is critical for functions that support metabolism, immunity, digestion, detoxification, and vitamin storage. Aging is associated with severity and poor prognosis of various liver diseases such as nonalcoholic fatty liver disease (NAFLD). Previous studies have used multi-omic approaches to study liver diseases or to examine the effects of aging on the liver. However, to date, no studies have used an integrated omics approach to investigate aging-associated molecular changes in the livers of healthy female nonhuman primates. The goal of this study was to identify molecular changes associated with healthy aging in the livers of female baboons ( Papio sp., n=35) by integrating multiple omics data types (transcriptomics, proteomics, metabolomics) from samples across the adult age span. To integrate omics data, we performed unbiased weighted gene co-expression network analysis (WGCNA), and the results revealed 3 modules containing 3,149 genes and 33 proteins were positively correlated with age, and 2 modules containing 37 genes and 216 proteins were negatively correlated with age. Pathway enrichment analysis showed that unfolded protein response (UPR) and endoplasmic reticulum (ER) stress were positively associated with age, whereas xenobiotic metabolism and melatonin and serotonin degradation pathways were negatively associated with age. The findings of our study suggest that UPR and a reduction in reactive oxygen species generated from serotonin degradation could protect the liver from oxidative stress during the aging process in healthy female baboons.
Collapse
|
8
|
Zimmerman KD, Chan J, Glenn JP, Birnbaum S, Li C, Nathanielsz PW, Olivier M, Cox LA. Moderate maternal nutrient reduction in pregnancy alters fatty acid oxidation and RNA splicing in the nonhuman primate fetal liver. J Dev Orig Health Dis 2023; 14:381-388. [PMID: 36924159 PMCID: PMC10202844 DOI: 10.1017/s204017442300003x] [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] [Indexed: 03/18/2023]
Abstract
Fetal liver tissue collected from a nonhuman primate (NHP) baboon model of maternal nutrient reduction (MNR) at four gestational time points (90, 120, 140, and 165 days gestation [dG], term in the baboon is ∼185 dG) was used to quantify MNR effects on the fetal liver transcriptome. 28 transcripts demonstrated different expression patterns between MNR and control livers during the second half of gestation, a developmental period when the fetus undergoes rapid weight gain and fat accumulation. Differentially expressed transcripts were enriched for fatty acid oxidation and RNA splicing-related pathways. Increased RNA splicing activity in MNR was reflected in greater abundances of transcript splice variant isoforms in the MNR group. It can be hypothesized that the increase in splice variants is deployed in an effort to adapt to the poor in utero environment and ensure near-normal development and energy metabolism. This study is the first to study developmental programming across four critical gestational stages during primate fetal liver development and reveals a potentially novel cellular response mechanism mediating fetal programming in response to MNR.
Collapse
Affiliation(s)
- Kip D. Zimmerman
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jeannie Chan
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jeremy P. Glenn
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA and
| | - Shifra Birnbaum
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA and
| | - Cun Li
- Animal Science, University of Wyoming, Laramie, WY, USA
| | - Peter W. Nathanielsz
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA and
- Animal Science, University of Wyoming, Laramie, WY, USA
| | - Michael Olivier
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Laura A. Cox
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA and
| |
Collapse
|
9
|
Gawrieh S, Karns R, Kleiner DE, Olivier M, Jenkins T, Inge TH, Chalasani NP, Xanthakos S. Comparative Analysis of Global Hepatic Gene Expression in Adolescents and Adults with Non-alcoholic Fatty Liver Disease. Arch Clin Biomed Res 2023; 7:112-119. [PMID: 37583647 PMCID: PMC10426795 DOI: 10.26502/acbr.50170323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Introduction To gain insights into the mechanisms underlying distinct nonalcoholic fatty liver disease (NAFLD) histological phenotypes between children and adults, we compared hepatic gene expression profiles associated with NAFLD phenotypes between the two age groups. Methods Histological characteristics of intra-operative liver biopsies from adolescents and adults undergoing bariatric surgery were assessed by the same pathologist using the non-alcoholic steatohepatitis (NASH) Clinical Research Network scoring system. Hepatic gene expression was measured by microarray analysis. Transcriptomic signatures of histological phenotypes between the two groups were compared, with significance defined as p-value <0.05 and a fold change >1.5. Results In 67 adolescents and 76 adults, distribution of histological phenotypes was: not-NAFLD (controls) 51% vs 39%, NAFL 39% vs 37%, and NASH 10% vs 24%, respectively. There were 279 differentially expressed genes in adolescents and 213 in adults with NAFLD vs controls. In adolescents, transcriptomes for NAFL vs controls, and borderline vs definite NASH were undifferentiable, whereas in adults, NAFL and borderline NASH demonstrated a transcriptomic gradient between controls and definite NASH. When applied to adolescents, significant adult genes discriminated borderline and definite NASH from control and NAFL, but the majority of significant pediatric genes were not portable to adults. Genes associated with NASH in adolescents and adults showed some ontological consistency but notable differences. Conclusions There is some similarity but major differences in the transcriptomic profiles associated with NAFLD between adolescents and adults with severe obesity. These data suggest different mechanisms contribute to the pathogenesis of NAFLD severity at different stages in life.
Collapse
Affiliation(s)
- Samer Gawrieh
- Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rebekah Karns
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital, Cincinnati, OH, USA
| | - David E Kleiner
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Michael Olivier
- Center for Precision Medicine, Department of Internal Medicine - Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Todd Jenkins
- Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Thomas H Inge
- Department of Surgery, Lurie Children’s Hospital of Chicago, and Northwestern University, Chicago, IL, USA
| | - Naga P Chalasani
- Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Stavra Xanthakos
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| |
Collapse
|
10
|
Nazli S, Zimmerman KD, Riojas AM, Cox LA, Olivier M. An Isobaric Labeling Approach to Enhance Detection and Quantification of Tissue-Derived Plasma Proteins as Potential Early Disease Biomarkers. Biomolecules 2023; 13:215. [PMID: 36830584 PMCID: PMC9952993 DOI: 10.3390/biom13020215] [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: 12/10/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
The proteomic analysis of plasma holds great promise to advance precision medicine and identify biomarkers of disease. However, it is likely that many potential biomarkers circulating in plasma originate from other tissues and are only present in low abundances in the plasma. Accurate detection and quantification of low abundance proteins by standard mass spectrometry approaches remain challenging. In addition, it is difficult to link low abundance plasma proteins back to their specific tissues or organs of origin with confidence. To address these challenges, we developed a mass spectrometry approach based on the use of tandem mass tags (TMT) and a tissue reference sample. By applying this approach to nonhuman primate plasma samples, we were able to identify and quantify 820 proteins by using a kidney tissue homogenate as reference. On average, 643 ± 16 proteins were identified per plasma sample. About 58% of proteins identified in replicate experiments were identified both times. A ratio of 50 μg kidney protein to 10 μg plasma protein, and the use of the TMT label with the highest molecular weight (131) for the kidney reference yielded the largest number of proteins in the analysis, and identified low abundance proteins in plasma that are prominently found in the kidney. Overall, this methodology promises efficient quantification of plasma proteins potentially released from specific tissues, thereby increasing the number of putative disease biomarkers for future study.
Collapse
Affiliation(s)
- Sumaiya Nazli
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Kip D. Zimmerman
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Angelica M. Riojas
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Laura A. Cox
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Michael Olivier
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| |
Collapse
|
11
|
Ampong I, Zimmerman KD, Perumalla DS, Wallis KE, Li G, Huber HF, Li C, Nathanielsz PW, Cox LA, Olivier M. Maternal obesity alters offspring liver and skeletal muscle metabolism in early post-puberty despite maintaining a normal post-weaning dietary lifestyle. FASEB J 2022; 36:e22644. [PMID: 36415994 PMCID: PMC9827852 DOI: 10.1096/fj.202201473r] [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: 09/11/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 11/24/2022]
Abstract
Maternal obesity (MO) during pregnancy is linked to increased and premature risk of age-related metabolic diseases in the offspring. However, the underlying molecular mechanisms still remain not fully understood. Using a well-established nonhuman primate model of MO, we analyzed tissue biopsies and plasma samples obtained from post-pubertal offspring (3-6.5 y) of MO mothers (n = 19) and from control animals born to mothers fed a standard diet (CON, n = 13). All offspring ate a healthy chow diet after weaning. Using untargeted gas chromatography-mass spectrometry metabolomics analysis, we quantified a total of 351 liver, 316 skeletal muscle, and 423 plasma metabolites. We identified 58 metabolites significantly altered in the liver and 46 in the skeletal muscle of MO offspring, with 8 metabolites shared between both tissues. Several metabolites were changed in opposite directions in males and females in both liver and skeletal muscle. Several tissue-specific and 4 shared metabolic pathways were identified from these dysregulated metabolites. Interestingly, none of the tissue-specific metabolic changes were reflected in plasma. Overall, our study describes characteristic metabolic perturbations in the liver and skeletal muscle in MO offspring, indicating that metabolic programming in utero persists postnatally, and revealing potential novel mechanisms that may contribute to age-related metabolic diseases later in life.
Collapse
Affiliation(s)
- Isaac Ampong
- Center for Precision MedicineWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
- Department of Internal Medicine, Section on Molecular MedicineWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Kip D. Zimmerman
- Center for Precision MedicineWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
- Department of Internal Medicine, Section on Molecular MedicineWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Danu S. Perumalla
- Center for Precision MedicineWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
- Department of Internal Medicine, Section on Molecular MedicineWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Katharyn E. Wallis
- Center for Precision MedicineWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
- Department of Internal Medicine, Section on Molecular MedicineWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Ge Li
- Center for Precision MedicineWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
- Department of Internal Medicine, Section on Molecular MedicineWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Hillary F. Huber
- Southwest National Primate Research CenterTexas Biomedical Research InstituteSan AntonioTexasUSA
| | - Cun Li
- Center for Pregnancy & Newborn ResearchUniversity of WyomingLaramieWyomingUSA
| | - Peter W. Nathanielsz
- Southwest National Primate Research CenterTexas Biomedical Research InstituteSan AntonioTexasUSA
- Center for Pregnancy & Newborn ResearchUniversity of WyomingLaramieWyomingUSA
| | - Laura A. Cox
- Center for Precision MedicineWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
- Department of Internal Medicine, Section on Molecular MedicineWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
- Southwest National Primate Research CenterTexas Biomedical Research InstituteSan AntonioTexasUSA
| | - Michael Olivier
- Center for Precision MedicineWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
- Department of Internal Medicine, Section on Molecular MedicineWake Forest University School of MedicineWinston‐SalemNorth CarolinaUSA
| |
Collapse
|
12
|
Dillenhöfer S, Gruber W, Stehling F, Blosch C, Olivier M, Sutharsan S, Welsner M, Brinkmann F. Körperliche Aktivität und motorische
Leistungsfähigkeit bei Kindern mit Cystischer Fibrose –
verbessern sie sich unter der Therapie mit
Elexacaftor-Tezacaftor-Ivacaftor. Klinische Pädiatrie 2022. [DOI: 10.1055/s-0042-1754505] [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] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- S Dillenhöfer
- St. Josef Hospital Universitätsklinikum Bochum, Klinik
für Kinder- und Jugendmedizin, Abteilung Kinderpneumologie und
Mukoviszidosezentrum, Bochum, Germany
| | - W Gruber
- Kinderklinik, Universität Duisburg-Essen, Pädiatrische
Pulmologie und Schlafmedizin, Mukoviszidosezentrum, Essen, Germany
| | - F Stehling
- Kinderklinik, Universität Duisburg-Essen, Pädiatrische
Pulmologie und Schlafmedizin, Mukoviszidosezentrum, Essen, Germany
| | - C Blosch
- Kinderklinik, Universität Duisburg-Essen, Pädiatrische
Pulmologie und Schlafmedizin, Mukoviszidosezentrum, Essen, Germany
| | - M Olivier
- Kinderklinik, Universität Duisburg-Essen, Pädiatrische
Pulmologie und Schlafmedizin, Mukoviszidosezentrum, Essen, Germany
| | - S Sutharsan
- Universitätsklinikum Essen – Ruhrlandklinik, Abteilung
für Lungenheilkunde, Mukoviszidosezentrum, Essen, Germany
| | - M Welsner
- Universitätsklinikum Essen – Ruhrlandklinik, Abteilung
für Lungenheilkunde, Mukoviszidosezentrum, Essen, Germany
| | - F Brinkmann
- St. Josef Hospital Universitätsklinikum Bochum, Klinik
für Kinder- und Jugendmedizin, Abteilung Kinderpneumologie und
Mukoviszidosezentrum, Bochum, Germany
| |
Collapse
|
13
|
Puppala S, Spradling-Reeves KD, Chan J, Birnbaum S, Newman DE, Comuzzie AG, Mahaney MC, VandeBerg JL, Olivier M, Cox LA. Hepatic transcript signatures predict atherosclerotic lesion burden prior to a 2-year high cholesterol, high fat diet challenge. PLoS One 2022; 17:e0271514. [PMID: 35925965 PMCID: PMC9352111 DOI: 10.1371/journal.pone.0271514] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 07/04/2022] [Indexed: 11/19/2022] Open
Abstract
The purpose of this study was to identify molecular mechanisms by which the liver influences total lesion burden in a nonhuman primate model (NHP) of cardiovascular disease with acute and chronic feeding of a high cholesterol, high fat (HCHF) diet. Baboons (47 females, 64 males) were fed a HCHF diet for 2 years (y); liver biopsies were collected at baseline, 7 weeks (w) and 2y, and lesions were quantified in aortic arch, descending aorta, and common iliac at 2y. Unbiased weighted gene co-expression network analysis (WGCNA) revealed several modules of hepatic genes correlated with lesions at different time points of dietary challenge. Pathway and network analyses were performed to study the roles of hepatic module genes. More significant pathways were observed in males than females. In males, we found modules enriched for genes in oxidative phosphorylation at baseline, opioid signaling at 7w, and EIF2 signaling and HNF1A and HNF4A networks at baseline and 2y. One module enriched for fatty acid β oxidation pathway genes was found in males and females at 2y. To our knowledge, this is the first study of a large NHP cohort to identify hepatic genes that correlate with lesion burden. Correlations of baseline and 7w module genes with lesions at 2y were observed in males but not in females. Pathway analyses of baseline and 7w module genes indicate EIF2 signaling, oxidative phosphorylation, and μ-opioid signaling are possible mechanisms that predict lesion formation induced by HCHF diet consumption in males. Our findings of coordinated hepatic transcriptional response in male baboons but not female baboons indicate underlying molecular mechanisms differ between female and male primate atherosclerosis.
Collapse
Affiliation(s)
- Sobha Puppala
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Kimberly D. Spradling-Reeves
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Jeannie Chan
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Shifra Birnbaum
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Deborah E. Newman
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | | | - Michael C. Mahaney
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, The University of Texas Rio Grande Valley School of Medicine, Brownsville, Texas, United States of America
| | - John L. VandeBerg
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, The University of Texas Rio Grande Valley School of Medicine, Brownsville, Texas, United States of America
| | - Michael Olivier
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Laura A. Cox
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| |
Collapse
|
14
|
Hamid Z, Zimmerman KD, Guillen-Ahlers H, Li C, Nathanielsz P, Cox LA, Olivier M. Assessment of label-free quantification and missing value imputation for proteomics in non-human primates. BMC Genomics 2022; 23:496. [PMID: 35804317 PMCID: PMC9264528 DOI: 10.1186/s12864-022-08723-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 06/23/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Reliable and effective label-free quantification (LFQ) analyses are dependent not only on the method of data acquisition in the mass spectrometer, but also on the downstream data processing, including software tools, query database, data normalization and imputation. In non-human primates (NHP), LFQ is challenging because the query databases for NHP are limited since the genomes of these species are not comprehensively annotated. This invariably results in limited discovery of proteins and associated Post Translational Modifications (PTMs) and a higher fraction of missing data points. While identification of fewer proteins and PTMs due to database limitations can negatively impact uncovering important and meaningful biological information, missing data also limits downstream analyses (e.g., multivariate analyses), decreases statistical power, biases statistical inference, and makes biological interpretation of the data more challenging. In this study we attempted to address both issues: first, we used the MetaMorphues proteomics search engine to counter the limits of NHP query databases and maximize the discovery of proteins and associated PTMs, and second, we evaluated different imputation methods for accurate data inference. We used a generic approach for missing data imputation analysis without distinguising the potential source of missing data (either non-assigned m/z or missing values across runs). RESULTS Using the MetaMorpheus proteomics search engine we obtained quantitative data for 1622 proteins and 10,634 peptides including 58 different PTMs (biological, metal and artifacts) across a diverse age range of NHP brain frontal cortex. However, among the 1622 proteins identified, only 293 proteins were quantified across all samples with no missing values, emphasizing the importance of implementing an accurate and statiscaly valid imputation method to fill in missing data. In our imputation analysis we demonstrate that Single Imputation methods that borrow information from correlated proteins such as Generalized Ridge Regression (GRR), Random Forest (RF), local least squares (LLS), and a Bayesian Principal Component Analysis methods (BPCA), are able to estimate missing protein abundance values with great accuracy. CONCLUSIONS Overall, this study offers a detailed comparative analysis of LFQ data generated in NHP and proposes strategies for improved LFQ in NHP proteomics data.
Collapse
Affiliation(s)
- Zeeshan Hamid
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Kip D Zimmerman
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Hector Guillen-Ahlers
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Cun Li
- Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, University of Wyoming, Laramie, WY, USA
| | - Peter Nathanielsz
- Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, University of Wyoming, Laramie, WY, USA
| | - Laura A Cox
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Southwest National Primate Research Center, San Antonio, TX, USA
| | - Michael Olivier
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
| |
Collapse
|
15
|
Olivier M, Rey S, Voilmy D, Ganascia JG, Lan Hing Ting K. Combining Cultural Probes and Interviews with Caregivers to Co-Design a Social Mobile Robotic Solution. Ing Rech Biomed 2022. [DOI: 10.1016/j.irbm.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
16
|
Dillenhöfer S, Gruber W, Stehling F, Blosch C, Olivier M, Sutharsan S, Taube C, Mellies U, Welsner M, Brinkmann F. P209 Physical fitness and habitual physical activity in children with cystic fibrosis - do they improve with elexacaftor/tezacaftor/ivacaftor therapy? J Cyst Fibros 2022. [DOI: 10.1016/s1569-1993(22)00538-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
17
|
Ampong I, Zimmerman KD, Nathanielsz PW, Cox LA, Olivier M. Optimization of Imputation Strategies for High-Resolution Gas Chromatography-Mass Spectrometry (HR GC-MS) Metabolomics Data. Metabolites 2022; 12:429. [PMID: 35629933 PMCID: PMC9144635 DOI: 10.3390/metabo12050429] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 12/17/2022] Open
Abstract
Gas chromatography-coupled mass spectrometry (GC-MS) has been used in biomedical research to analyze volatile, non-polar, and polar metabolites in a wide array of sample types. Despite advances in technology, missing values are still common in metabolomics datasets and must be properly handled. We evaluated the performance of ten commonly used missing value imputation methods with metabolites analyzed on an HR GC-MS instrument. By introducing missing values into the complete (i.e., data without any missing values) National Institute of Standards and Technology (NIST) plasma dataset, we demonstrate that random forest (RF), glmnet ridge regression (GRR), and Bayesian principal component analysis (BPCA) shared the lowest root mean squared error (RMSE) in technical replicate data. Further examination of these three methods in data from baboon plasma and liver samples demonstrated they all maintained high accuracy. Overall, our analysis suggests that any of the three imputation methods can be applied effectively to untargeted metabolomics datasets with high accuracy. However, it is important to note that imputation will alter the correlation structure of the dataset and bias downstream regression coefficients and p-values.
Collapse
Affiliation(s)
- Isaac Ampong
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University, Winston-Salem, NC 27157, USA; (I.A.); (K.D.Z.); (L.A.C.)
| | - Kip D. Zimmerman
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University, Winston-Salem, NC 27157, USA; (I.A.); (K.D.Z.); (L.A.C.)
| | - Peter W. Nathanielsz
- Center for the Study of Fetal Programming, University of Wyoming, Laramie, WY 82071, USA;
- Southwest National Primate Research Center, San Antonio, TX 78227, USA
| | - Laura A. Cox
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University, Winston-Salem, NC 27157, USA; (I.A.); (K.D.Z.); (L.A.C.)
- Southwest National Primate Research Center, San Antonio, TX 78227, USA
| | - Michael Olivier
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University, Winston-Salem, NC 27157, USA; (I.A.); (K.D.Z.); (L.A.C.)
| |
Collapse
|
18
|
Berardi G, Frey-Law L, Sluka KA, Bayman EO, Coffey CS, Ecklund D, Vance CGT, Dailey DL, Burns J, Buvanendran A, McCarthy RJ, Jacobs J, Zhou XJ, Wixson R, Balach T, Brummett CM, Clauw D, Colquhoun D, Harte SE, Harris RE, Williams DA, Chang AC, Waljee J, Fisch KM, Jepsen K, Laurent LC, Olivier M, Langefeld CD, Howard TD, Fiehn O, Jacobs JM, Dakup P, Qian WJ, Swensen AC, Lokshin A, Lindquist M, Caffo BS, Crainiceanu C, Zeger S, Kahn A, Wager T, Taub M, Ford J, Sutherland SP, Wandner LD. Multi-Site Observational Study to Assess Biomarkers for Susceptibility or Resilience to Chronic Pain: The Acute to Chronic Pain Signatures (A2CPS) Study Protocol. Front Med (Lausanne) 2022; 9:849214. [PMID: 35547202 PMCID: PMC9082267 DOI: 10.3389/fmed.2022.849214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic pain has become a global health problem contributing to years lived with disability and reduced quality of life. Advances in the clinical management of chronic pain have been limited due to incomplete understanding of the multiple risk factors and molecular mechanisms that contribute to the development of chronic pain. The Acute to Chronic Pain Signatures (A2CPS) Program aims to characterize the predictive nature of biomarkers (brain imaging, high-throughput molecular screening techniques, or "omics," quantitative sensory testing, patient-reported outcome assessments and functional assessments) to identify individuals who will develop chronic pain following surgical intervention. The A2CPS is a multisite observational study investigating biomarkers and collective biosignatures (a combination of several individual biomarkers) that predict susceptibility or resilience to the development of chronic pain following knee arthroplasty and thoracic surgery. This manuscript provides an overview of data collection methods and procedures designed to standardize data collection across multiple clinical sites and institutions. Pain-related biomarkers are evaluated before surgery and up to 3 months after surgery for use as predictors of patient reported outcomes 6 months after surgery. The dataset from this prospective observational study will be available for researchers internal and external to the A2CPS Consortium to advance understanding of the transition from acute to chronic postsurgical pain.
Collapse
Affiliation(s)
- Giovanni Berardi
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Laura Frey-Law
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Kathleen A. Sluka
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Emine O. Bayman
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Christopher S. Coffey
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Dixie Ecklund
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Carol G. T. Vance
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Dana L. Dailey
- Department of Physical Therapy, St. Ambrose University, Davenport, IA, United States
| | - John Burns
- Department of Psychiatry, Rush University Medical Center, Chicago, IL, United States
| | - Asokumar Buvanendran
- Department of Anesthesiology, Rush University Medical Center, Chicago, IL, United States
| | - Robert J. McCarthy
- Department of Anesthesiology, Rush University Medical Center, Chicago, IL, United States
| | - Joshua Jacobs
- Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, United States
| | - Xiaohong Joe Zhou
- Departments of Radiology, Neurosurgery, and Bioengineering, University of Illinois College of Medicine at Chicago, Chicago, IL, United States
| | - Richard Wixson
- NorthShore Orthopaedic and Spine Institute, NorthShore University HealthSystem, Skokie, IL, United States
| | - Tessa Balach
- Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago, Chicago, IL, United States
| | - Chad M. Brummett
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
| | - Daniel Clauw
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, United States
| | - Douglas Colquhoun
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
| | - Steven E. Harte
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
| | - Richard E. Harris
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
| | - David A. Williams
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, United States
- Department of Psychology, University of Michigan, Ann Arbor, MI, United States
| | - Andrew C. Chang
- Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI, United States
| | - Jennifer Waljee
- Section of Plastic and Reconstructive Surgery, University of Michigan, Ann Arbor, MI, United States
| | - Kathleen M. Fisch
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Kristen Jepsen
- Institute of Genomic Medicine Genomics Center, University of California, San Diego, La Jolla, CA, United States
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Michael Olivier
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Timothy D. Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, United States
| | - Jon M. Jacobs
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Panshak Dakup
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Wei-Jun Qian
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Adam C. Swensen
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Anna Lokshin
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Martin Lindquist
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Brian S. Caffo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Ciprian Crainiceanu
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Scott Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Ari Kahn
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX, United States
| | - Tor Wager
- Presidential Cluster in Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, United States
| | - Margaret Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - James Ford
- Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Stephani P. Sutherland
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Laura D. Wandner
- National Institute of Neurological Disorders and Stroke, The National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
19
|
Cox LA, Chan J, Rao P, Hamid Z, Glenn JP, Jadhav A, Das V, Karere GM, Quillen E, Kavanagh K, Olivier M. Integrated omics analysis reveals sirtuin signaling is central to hepatic response to a high fructose diet. BMC Genomics 2021; 22:870. [PMID: 34861817 PMCID: PMC8641221 DOI: 10.1186/s12864-021-08166-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 06/29/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Dietary high fructose (HFr) is a known metabolic disruptor contributing to development of obesity and diabetes in Western societies. Initial molecular changes from exposure to HFr on liver metabolism may be essential to understand the perturbations leading to insulin resistance and abnormalities in lipid and carbohydrate metabolism. We studied vervet monkeys (Clorocebus aethiops sabaeus) fed a HFr (n=5) or chow diet (n=5) for 6 weeks, and obtained clinical measures of liver function, blood insulin, cholesterol and triglycerides. In addition, we performed untargeted global transcriptomics, proteomics, and metabolomics analyses on liver biopsies to determine the molecular impact of a HFr diet on coordinated pathways and networks that differed by diet. RESULTS We show that integration of omics data sets improved statistical significance for some pathways and networks, and decreased significance for others, suggesting that multiple omics datasets enhance confidence in relevant pathway and network identification. Specifically, we found that sirtuin signaling and a peroxisome proliferator activated receptor alpha (PPARA) regulatory network were significantly altered in hepatic response to HFr. Integration of metabolomics and miRNAs data further strengthened our findings. CONCLUSIONS Our integrated analysis of three types of omics data with pathway and regulatory network analysis demonstrates the usefulness of this approach for discovery of molecular networks central to a biological response. In addition, metabolites aspartic acid and docosahexaenoic acid (DHA), protein ATG3, and genes ATG7, and HMGCS2 link sirtuin signaling and the PPARA network suggesting molecular mechanisms for altered hepatic gluconeogenesis from consumption of a HFr diet.
Collapse
Affiliation(s)
- Laura A Cox
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA.
- Department of Genetics, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA.
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA.
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, 27157, Winston-Salem, NC, USA.
| | - Jeannie Chan
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA
- Department of Genetics, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA
| | - Prahlad Rao
- University of Tennessee Health Science Center, TN, Memphis, USA
| | - Zeeshan Hamid
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA
| | - Jeremy P Glenn
- Department of Genetics, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA
| | - Avinash Jadhav
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA
- Department of Genetics, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA
| | - Vivek Das
- Novo Nordisk Research Center, Seattle, WA, USA
| | - Genesio M Karere
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA
- Department of Genetics, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA
| | - Ellen Quillen
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA
- Department of Genetics, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA
| | - Kylie Kavanagh
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, 27157, Winston-Salem, NC, USA
| | - Michael Olivier
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, NRC, G-floor, NC, 27157, Winston-Salem, USA
- Department of Genetics, Texas Biomedical Research Institute, 78245, San Antonio, TX, USA
| |
Collapse
|
20
|
Lesvenan C, Simoni M, Olivier M, Winer N, Banaszkiewicz N, Collin R, Coutin AS, Dochez V, Flamant C, Gascoin G, Gillard P, Legendre G, Arthuis CJ. [Prolonged and post-term pregnancies: a regional survey of French clinical practices]. Gynecol Obstet Fertil Senol 2021; 49:580-586. [PMID: 33639281 DOI: 10.1016/j.gofs.2021.02.007] [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] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Indexed: 06/12/2023]
Abstract
OBJECTIVE To assess professional practices of prolonged and post-term pregnancies in accordance to French guidelines. The secondary outcome was to evaluate neonatal and maternal morbidity during prolonged pregnancy. METHODS Descriptive retrospective study was conducted in the 23 maternity hospitals of perinatal network between September and December 2018. The inclusion criterion was a birth term of≥41+0 weeks of gestation. Primary outcome was conformity to the national guidelines based on 10 items (conformity score≥80%). The secondary outcome was a composite criteria of neonatal morbidity (ventilation, resuscitation and/or Apgar score<7 at 5minutes) and maternal morbidity (obstetrical anal sphincter injury and/or postpartum hemorrhage). RESULTS A total of 596 patients were included and the conformity was obtained in 65.3% of cases. Inconsistent criteria were amniotic fluid evaluation by the deepest vertical pocket (46.8%, n=279), and information of patients on prolonged pregnancy management (14.8%, n=88). Adverse perinatal outcome occurred for 40 newborns (6.0%) with shoulder dystocia (OR=5.2; CI 95%: 1.4-19.7) as a principal risk factor. Maternal morbidity outcome occurred in 70 cases (10.6%) primarily with increase in labour duration (OR=1.1 by hour of labour; CI 95%: 1.02-1.24) and prior caesarian section (OR=4.4; CI 95%: 1.8-11.0). CONCLUSIONS Management of prolonged and post-term pregnancies matching with the French national guidelines. Points of improvement are amniotic fluid evaluation at term by a single deepest vertical pocket, and the information about induction of labour at term.
Collapse
Affiliation(s)
- C Lesvenan
- Service de gynécologie obstétrique, centre hospitalier universitaire d'Angers, 4, rue Larrey, 49933 Angers, France
| | - M Simoni
- UMR 1280, PhAN, NUN, INRAE, service de gynécologie obstétrique, université de Nantes. physiologie des adaptations nutritionnelles, CIC et Hôpital mère-enfant-adolescent, centre hospitalier universitaire de Nantes, 38, boulevard Jean-Monnet, 44000 Nantes, France
| | - M Olivier
- Réseau sécurité naissance, naître ensemble, 2, rue de la Loire, 44200 Nantes, France
| | - N Winer
- UMR 1280, PhAN, NUN, INRAE, service de gynécologie obstétrique, université de Nantes. physiologie des adaptations nutritionnelles, CIC et Hôpital mère-enfant-adolescent, centre hospitalier universitaire de Nantes, 38, boulevard Jean-Monnet, 44000 Nantes, France
| | - N Banaszkiewicz
- Réseau sécurité naissance, naître ensemble, 2, rue de la Loire, 44200 Nantes, France
| | - R Collin
- Réseau sécurité naissance, naître ensemble, 2, rue de la Loire, 44200 Nantes, France
| | - A-S Coutin
- Réseau sécurité naissance, naître ensemble, 2, rue de la Loire, 44200 Nantes, France
| | - V Dochez
- UMR 1280, PhAN, NUN, INRAE, service de gynécologie obstétrique, université de Nantes. physiologie des adaptations nutritionnelles, CIC et Hôpital mère-enfant-adolescent, centre hospitalier universitaire de Nantes, 38, boulevard Jean-Monnet, 44000 Nantes, France
| | - C Flamant
- Service de pédiatrie, centre hospitalier universitaire de Nantes, CIC et hôpital mère-enfant-adolescent, 38, boulevard Jean-Monnet, 44000 Nantes, France
| | - G Gascoin
- Service de pédiatrie, centre hospitalier universitaire d'Angers, 4, rue Larrey, 49933 Angers, France
| | - P Gillard
- Réseau sécurité naissance, naître ensemble, 2, rue de la Loire, 44200 Nantes, France
| | - G Legendre
- Service de gynécologie obstétrique, centre hospitalier universitaire d'Angers, 4, rue Larrey, 49933 Angers, France
| | - C-J Arthuis
- UMR 1280, PhAN, NUN, INRAE, service de gynécologie obstétrique, université de Nantes. physiologie des adaptations nutritionnelles, CIC et Hôpital mère-enfant-adolescent, centre hospitalier universitaire de Nantes, 38, boulevard Jean-Monnet, 44000 Nantes, France.
| |
Collapse
|
21
|
Chan J, Yao W, Howard TD, Hawkins GA, Olivier M, Jorgensen MJ, Cheeseman IH, Cole SA, Cox LA. Efficiency of whole-exome sequencing in old world and new world primates using human capture reagents. J Med Primatol 2021; 50:176-181. [PMID: 33876458 DOI: 10.1111/jmp.12524] [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: 01/18/2021] [Revised: 03/10/2021] [Accepted: 04/06/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Whole-exome sequencing (WES) can expedite research on genetic variation in non-human primate (NHP) models of human diseases. However, NHP-specific reagents for exome capture are not available. This study reports the use of human-specific capture reagents in WES for olive baboons, marmosets, and vervet monkeys. METHODS Exome capture was carried out using the SureSelect Human All Exon V6 panel from Agilent Technologies, followed by high-throughput sequencing. Capture of protein-coding genes and detection of single nucleotide variants were evaluated. RESULTS Exome capture and sequencing results showed that more than 97% of old world and 93% of new world monkey protein coding genes were detected. Single nucleotide variants were detected across the genomes and missense variants were found in genes associated with human diseases. CONCLUSIONS A cost-effective approach based on commercial, human-specific reagents can be used to perform WES for the discovery of genetic variants in these NHP species.
Collapse
Affiliation(s)
- Jeannie Chan
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Wen Yao
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Timothy D Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Gregory A Hawkins
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Michael Olivier
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Matthew J Jorgensen
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | - Shelley A Cole
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Laura A Cox
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| |
Collapse
|
22
|
Hayes MG, Urbanek M, Ehrmann DA, Armstrong LL, Lee JY, Sisk R, Karaderi T, Barber TM, McCarthy MI, Franks S, Lindgren CM, Welt CK, Diamanti-Kandarakis E, Panidis D, Goodarzi MO, Azziz R, Zhang Y, James RG, Olivier M, Kissebah AH, Stener-Victorin E, Legro RS, Dunaif A. Publisher Correction: Genome-wide association of polycystic ovary syndrome implicates alterations in gonadotropin secretion in European ancestry populations. Nat Commun 2020; 11:2158. [PMID: 32345980 PMCID: PMC7188886 DOI: 10.1038/s41467-020-15793-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Collapse
Affiliation(s)
- M Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611, USA. .,Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611, USA. .,Department of Anthropology, Northwestern University, Evanston, Illinois, 60208, USA.
| | - Margrit Urbanek
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611, USA.,Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611, USA
| | - David A Ehrmann
- Section of Endocrinology, Diabetes, and Metabolism, The University of Chicago, Chicago, Illinois, 60637, USA
| | - Loren L Armstrong
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611, USA
| | - Ji Young Lee
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611, USA
| | - Ryan Sisk
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611, USA
| | - Tugce Karaderi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Thomas M Barber
- Warwick Medical School, University of Warwick, Warwick, CV4 7AL, UK
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LE, UK.,Oxford NIHR Biomedical Research Centre, Churchill Hospital, Headington, OX3 7LE, UK
| | - Stephen Franks
- Institute of Reproductive & Developmental Biology, Hammersmith Hospital, Imperial College London, London, W12 0NN, UK
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Corrine K Welt
- Division of Endocrinology, Metabolism and Diabetes, University of Utah, Salt Lake City, Utah, 84112, USA
| | | | - Dimitrios Panidis
- Division of Endocrinology and Human Reproduction, 2nd Department of Obstetrics and Gynecology, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, 90048, USA
| | - Ricardo Azziz
- Departments of Obstetrics and Gynecology and Medicine, Medical College of Georgia, Georgia Regents University, Augusta, Georgia, 30912, USA
| | - Yi Zhang
- TOPS Obesity and Metabolic Research Center, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA.,Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA
| | - Roland G James
- TOPS Obesity and Metabolic Research Center, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA.,Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA
| | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, 78256, USA
| | - Ahmed H Kissebah
- TOPS Obesity and Metabolic Research Center, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA.,Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA
| | | | | | - Richard S Legro
- Department of Obstetrics and Gynecology, Penn State College of Medicine, Hershey, Pennsylvania, 17033, USA
| | - Andrea Dunaif
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611, USA.,Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611, USA
| |
Collapse
|
23
|
Misra BB, Olivier M. High Resolution GC-Orbitrap-MS Metabolomics Using Both Electron Ionization and Chemical Ionization for Analysis of Human Plasma. J Proteome Res 2020; 19:2717-2731. [DOI: 10.1021/acs.jproteome.9b00774] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Biswapriya B. Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157, United States
| | - Michael Olivier
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157, United States
| |
Collapse
|
24
|
Olivier M, Asmis R, Hawkins GA, Howard TD, Cox LA. The Need for Multi-Omics Biomarker Signatures in Precision Medicine. Int J Mol Sci 2019; 20:ijms20194781. [PMID: 31561483 PMCID: PMC6801754 DOI: 10.3390/ijms20194781] [Citation(s) in RCA: 232] [Impact Index Per Article: 46.4] [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: 08/23/2019] [Revised: 09/11/2019] [Accepted: 09/25/2019] [Indexed: 12/12/2022] Open
Abstract
Recent advances in omics technologies have led to unprecedented efforts characterizing the molecular changes that underlie the development and progression of a wide array of complex human diseases, including cancer. As a result, multi-omics analyses—which take advantage of these technologies in genomics, transcriptomics, epigenomics, proteomics, metabolomics, and other omics areas—have been proposed and heralded as the key to advancing precision medicine in the clinic. In the field of precision oncology, genomics approaches, and, more recently, other omics analyses have helped reveal several key mechanisms in cancer development, treatment resistance, and recurrence risk, and several of these findings have been implemented in clinical oncology to help guide treatment decisions. However, truly integrated multi-omics analyses have not been applied widely, preventing further advances in precision medicine. Additional efforts are needed to develop the analytical infrastructure necessary to generate, analyze, and annotate multi-omics data effectively to inform precision medicine-based decision-making.
Collapse
Affiliation(s)
- Michael Olivier
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest Baptist Health Comprehensive Cancer Center, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA.
| | - Reto Asmis
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest Baptist Health Comprehensive Cancer Center, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA.
| | - Gregory A Hawkins
- Center for Precision Medicine, Department of Biochemistry, Wake Forest Baptist Health Comprehensive Cancer Center, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA.
| | - Timothy D Howard
- Center for Precision Medicine, Department of Biochemistry, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA.
| | - Laura A Cox
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest Baptist Health Comprehensive Cancer Center, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA.
| |
Collapse
|
25
|
Jimenez H, Wang M, Zimmerman JW, Pennison MJ, Sharma S, Surratt T, Xu ZX, Brezovich I, Absher D, Myers RM, DeYoung B, Caudell DL, Chen D, Lo HW, Lin HK, Godwin DW, Olivier M, Ghanekar A, Chen K, Miller LD, Gong Y, Capstick M, D'Agostino RB, Munden R, Merle P, Barbault A, Blackstock AW, Bonkovsky HL, Yang GY, Jin G, Liu L, Zhang W, Watabe K, Blackman CF, Pasche BC. Tumour-specific amplitude-modulated radiofrequency electromagnetic fields induce differentiation of hepatocellular carcinoma via targeting Ca v3.2 T-type voltage-gated calcium channels and Ca 2+ influx. EBioMedicine 2019; 44:209-224. [PMID: 31160272 PMCID: PMC6604666 DOI: 10.1016/j.ebiom.2019.05.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 03/27/2019] [Revised: 04/30/2019] [Accepted: 05/14/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Administration of amplitude modulated 27·12 MHz radiofrequency electromagnetic fields (AM RF EMF) by means of a spoon-shaped applicator placed on the patient's tongue is a newly approved treatment for advanced hepatocellular carcinoma (HCC). The mechanism of action of tumour-specific AM RF EMF is largely unknown. METHODS Whole body and organ-specific human dosimetry analyses were performed. Mice carrying human HCC xenografts were exposed to AM RF EMF using a small animal AM RF EMF exposure system replicating human dosimetry and exposure time. We performed histological analysis of tumours following exposure to AM RF EMF. Using an agnostic genomic approach, we characterized the mechanism of action of AM RF EMF. FINDINGS Intrabuccal administration results in systemic delivery of athermal AM RF EMF from head to toe at levels lower than those generated by cell phones held close to the body. Tumour shrinkage results from differentiation of HCC cells into quiescent cells with spindle morphology. AM RF EMF targeted antiproliferative effects and cancer stem cell inhibiting effects are mediated by Ca2+ influx through Cav3·2 T-type voltage-gated calcium channels (CACNA1H) resulting in increased intracellular calcium concentration within HCC cells only. INTERPRETATION Intrabuccally-administered AM RF EMF is a systemic therapy that selectively block the growth of HCC cells. AM RF EMF pronounced inhibitory effects on cancer stem cells may explain the exceptionally long responses observed in several patients with advanced HCC. FUND: Research reported in this publication was supported by the National Cancer Institute's Cancer Centre Support Grant award number P30CA012197 issued to the Wake Forest Baptist Comprehensive Cancer Centre (BP) and by funds from the Charles L. Spurr Professorship Fund (BP). DWG is supported by R01 AA016852 and P50 AA026117.
Collapse
Affiliation(s)
- Hugo Jimenez
- Department of Cancer Biology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Minghui Wang
- Department of Cancer Biology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Jacquelyn W Zimmerman
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, MD, United States of America; Division of Haematology/Oncology, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Michael J Pennison
- Department of Cancer Biology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Sambad Sharma
- Department of Cancer Biology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Trevor Surratt
- Department of Cancer Biology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Zhi-Xiang Xu
- Division of Haematology/Oncology, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Ivan Brezovich
- Department of Radiation Oncology, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Barry DeYoung
- Department of Pathology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - David L Caudell
- Department of Pathology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Dongquan Chen
- Division of Preventive Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Hui-Wen Lo
- Department of Cancer Biology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Hui-Kuan Lin
- Department of Cancer Biology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Dwayne W Godwin
- Department of Neurobiology and Anatomy, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Michael Olivier
- Section of Molecular Medicine, Department of Medicine, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Anand Ghanekar
- Department of Surgery, University Health Network, Toronto, Ontario, Canada
| | - Kui Chen
- Toronto General Hospital Research Institute, Toronto, Ontario, Canada
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Yijian Gong
- IT'IS Foundation, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Myles Capstick
- IT'IS Foundation, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Ralph B D'Agostino
- Department of Biostatistical Sciences, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Reginald Munden
- Department of Radiology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Philippe Merle
- Croix-Rousse University Hospital, Hepato-Gastroenterology and Digestive Oncology, Lyon, France
| | | | - Arthur W Blackstock
- Department of Radiation Oncology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Herbert L Bonkovsky
- Section on Gastroenterology, Department of Medicine, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Guang-Yu Yang
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL, United States of America
| | - Guangxu Jin
- Department of Cancer Biology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Liang Liu
- Department of Cancer Biology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Wei Zhang
- Department of Cancer Biology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Kounosuke Watabe
- Department of Cancer Biology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America
| | - Carl F Blackman
- Department of Cancer Biology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America.
| | - Boris C Pasche
- Department of Cancer Biology, Wake Forest Baptist Medical Centre, Winston-Salem, NC, United States of America.
| |
Collapse
|
26
|
Misra BB, Puppala SR, Comuzzie AG, Mahaney MC, VandeBerg JL, Olivier M, Cox LA. Analysis of serum changes in response to a high fat high cholesterol diet challenge reveals metabolic biomarkers of atherosclerosis. PLoS One 2019; 14:e0214487. [PMID: 30951537 PMCID: PMC6450610 DOI: 10.1371/journal.pone.0214487] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/13/2019] [Indexed: 01/19/2023] Open
Abstract
Atherosclerotic plaques are characterized by an accumulation of macrophages, lipids, smooth muscle cells, and fibroblasts, and, in advanced stages, necrotic debris within the arterial walls. Dietary habits such as high fat and high cholesterol (HFHC) consumption are known risk factors for atherosclerosis. However, the key metabolic contributors to diet-induced atherosclerosis are far from established. Herein, we investigate the role of a 2-year HFHC diet challenge in the metabolic changes of development and progression of atherosclerosis. We used a non-human primate (NHP) model (baboons, n = 60) fed a HFHC diet for two years and compared metabolomic profiles in serum from animals on baseline chow with serum collected after the challenge diet using two-dimensional gas chromatography time-of-flight mass-spectrometry (2D GC-ToF-MS) for untargeted metabolomic analysis, to quantify metabolites that contribute to atherosclerotic lesion formation. Further, clinical biomarkers associated with atherosclerosis, lipoprotein measures, fat indices, and arterial plaque formation (lesions) were quantified. Using two chemical derivatization (i.e., silylation) approaches, we quantified 321 metabolites belonging to 66 different metabolic pathways, which revealed significantly different metabolic profiles of HFHC diet and chow diet fed baboon sera. We found heritability of two important metabolites, lactic acid and asparagine, in the context of diet-induced metabolic changes. In addition, abundance of cholesterol, lactic acid, and asparagine were sex-dependent. Finally, 35 metabolites correlated (R2, 0.068-0.271, P < 0.05) with total lesion burden assessed in three arteries (aortic arch, common iliac artery, and descending aorta) which could serve as potential biomarkers pending further validation. This study demonstrates the feasibility of detecting sex-specific and heritable metabolites in NHPs with diet-induced atherosclerosis using untargeted metabolomics allowing understanding of atherosclerotic disease progression in humans.
Collapse
Affiliation(s)
- Biswapriya B. Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina United States of America
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
- * E-mail:
| | - Sobha R. Puppala
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina United States of America
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | | | - Michael C. Mahaney
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, The University of Texas Rio Grande Valley School of Medicine, Brownsville, Texas, United States of America
| | - John L. VandeBerg
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, The University of Texas Rio Grande Valley School of Medicine, Brownsville, Texas, United States of America
| | - Michael Olivier
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina United States of America
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Laura A. Cox
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina United States of America
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| |
Collapse
|
27
|
Cox LA, Olivier M, Spradling-Reeves K, Karere GM, Comuzzie AG, VandeBerg JL. Nonhuman Primates and Translational Research-Cardiovascular Disease. ILAR J 2018; 58:235-250. [PMID: 28985395 DOI: 10.1093/ilar/ilx025] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Indexed: 12/18/2022] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of morbidity and mortality in the United States. Human epidemiological studies provide challenges for understanding mechanisms that regulate initiation and progression of CVD due to variation in lifestyle, diet, and other environmental factors. Studies describing metabolic and physiologic aspects of CVD, and those investigating genetic and epigenetic mechanisms influencing CVD initiation and progression, have been conducted in multiple Old World nonhuman primate (NHP) species. Major advantages of NHPs as models for understanding CVD are their genetic, metabolic, and physiologic similarities with humans, and the ability to control diet, environment, and breeding. These NHP species are also genetically and phenotypically heterogeneous, providing opportunities to study gene by environment interactions that are not feasible in inbred animal models. Each Old World NHP species included in this review brings unique strengths as models to better understand human CVD. All develop CVD without genetic manipulation providing multiple models to discover genetic variants that influence CVD risk. In addition, as each of these NHP species age, their age-related comorbidities such as dyslipidemia and diabetes are accelerated proportionally 3 to 4 times faster than in humans.In this review, we discuss current CVD-related research in NHPs focusing on selected aspects of CVD for which nonprimate model organism studies have left gaps in our understanding of human disease. We include studies on current knowledge of genetics, epigenetics, calorie restriction, maternal calorie restriction and offspring health, maternal obesity and offspring health, nonalcoholic steatohepatitis and steatosis, Chagas disease, microbiome, stem cells, and prevention of CVD.
Collapse
Affiliation(s)
- Laura A Cox
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas.,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
| | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas.,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
| | | | - Genesio M Karere
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - Anthony G Comuzzie
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - John L VandeBerg
- South Texas Diabetes and Obesity Center, School of Medicine, University of Texas Rio Grande Valley, Edinburg/Harlingen/Brownsville, Texas
| |
Collapse
|
28
|
Olivier M, Aludaat C, Di Cesare A, Droandi G, Amr G, Torossian F, Caplan B, Poncet A, Tassan S, Metz D, Ruggieri V. OC41 MID-TERM RESULTS OF TRANSCATHETER AORTIC VALVE IMPLANTATION BY TRANS-CAROTID APPROACH UNDER LOCO-REGIONAL ANAESTHESIA. SINGLE CENTER EXPERIENCE. J Cardiovasc Med (Hagerstown) 2018. [DOI: 10.2459/01.jcm.0000549883.72251.cd] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
29
|
Misra BB, Bassey E, Bishop AC, Kusel DT, Cox LA, Olivier M. High-resolution gas chromatography/mass spectrometry metabolomics of non-human primate serum. Rapid Commun Mass Spectrom 2018; 32:1497-1506. [PMID: 29874398 PMCID: PMC6395519 DOI: 10.1002/rcm.8197] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Metabolomics analyses using gas chromatography/mass spectrometry (GC/MS)-based metabolomics are heavily impeded by the lack of high-resolution mass spectrometers and limited spectral libraries to complement the excellent chromatography that GC platforms offer, a challenge that is being addressed with the implementation of high-resolution (HR) platforms such as 1D-GC/Orbitrap-MS. METHODS We used serum samples from a non-human primate (NHP), a baboon (Papio hamadryas), with suitable quality controls to quantify the chemical space using an advanced HRMS platform for confident metabolite identification and robust quantification to assess the suitability of the platform for routine clinical metabolomics research. In a complementary approach, we also analyzed the same serum samples using two-dimensional gas chromatography/time-of-flight mass spectrometry (2D-GC/TOF-MS) for metabolite identification and quantification following established standard protocols. RESULTS Overall, the 2D-GC/TOF-MS (~5000 peaks per sample) and 1D-GC/Orbitrap-MS (~500 peaks per sample) analyses enabled identification and quantification of a total of 555 annotated metabolites from the NHP serum with a spectral similarity score Rsim ≥ 900 and signal-to-noise (S/N) ratio of >25. A common set of 30 metabolites with HMDB and KEGG IDs was quantified in the serum samples by both platforms where 2D-GC/TOF-MS enabled quantification of a total 384 metabolites (118 HMDB IDs) and 1D-GC/Orbitrap-MS analysis quantification of a total 200 metabolites (47 HMDB IDs). Thus, roughly 30-70% of the peaks remain unidentified or un-annotated across both platforms. CONCLUSIONS Our study provides insights into the benefits and limitations of the use of a higher mass resolution and mass accuracy instrument for untargeted GC/MS-based metabolomics with multi-dimensional chromatography in future studies addressing clinical conditions or exposome studies.
Collapse
Affiliation(s)
- Biswapriya B. Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem 27157, NC USA
- Department of Genetics, Texas Biomedical Research Institute, San Antonio 78227, TX, USA
| | - Ekong Bassey
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose 95134, CA, USA
| | - Andrew C. Bishop
- Department of Genetics, Texas Biomedical Research Institute, San Antonio 78227, TX, USA
| | - David T. Kusel
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose 95134, CA, USA
| | - Laura A. Cox
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem 27157, NC USA
- Department of Genetics, Texas Biomedical Research Institute, San Antonio 78227, TX, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio 78227, Texas USA
| | - Michael Olivier
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem 27157, NC USA
- Department of Genetics, Texas Biomedical Research Institute, San Antonio 78227, TX, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio 78227, Texas USA
| |
Collapse
|
30
|
Misra BB, Langefeld CD, Olivier M, Cox LA. Integrated Omics: Tools, Advances, and Future Approaches. J Mol Endocrinol 2018; 62:JME-18-0055. [PMID: 30006342 DOI: 10.1530/jme-18-0055] [Citation(s) in RCA: 187] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 07/02/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022]
Abstract
With the rapid adoption of high-throughput omic approaches to analyze biological samples such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can generate tera- to peta-byte sized data files on a daily basis. These data file sizes, together with differences in nomenclature among these data types, make the integration of these multi-dimensional omics data into biologically meaningful context challenging. Variously named as integrated omics, multi-omics, poly-omics, trans-omics, pan-omics, or shortened to just 'omics', the challenges include differences in data cleaning, normalization, biomolecule identification, data dimensionality reduction, biological contextualization, statistical validation, data storage and handling, sharing, and data archiving. The ultimate goal is towards the holistic realization of a 'systems biology' understanding of the biological question in hand. Commonly used approaches in these efforts are currently limited by the 3 i's - integration, interpretation, and insights. Post integration, these very large datasets aim to yield unprecedented views of cellular systems at exquisite resolution for transformative insights into processes, events, and diseases through various computational and informatics frameworks. With the continued reduction in costs and processing time for sample analyses, and increasing types of omics datasets generated such as glycomics, lipidomics, microbiomics, and phenomics, an increasing number of scientists in this interdisciplinary domain of bioinformatics face these challenges. We discuss recent approaches, existing tools, and potential caveats in the integration of omics datasets for development of standardized analytical pipelines that could be adopted by the global omics research community.
Collapse
Affiliation(s)
- Biswapriya B Misra
- B Misra, Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, United States
| | - Carl D Langefeld
- C Langefeld, Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, United States
| | - Michael Olivier
- M Olivier, Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, United States
| | - Laura A Cox
- L Cox, Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, United States
| |
Collapse
|
31
|
Guillen-Ahlers H, Rao PK, Perumalla DS, Montoya MJ, Jadhav AYL, Shortreed MR, Smith LM, Olivier M. Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells. J Vis Exp 2018. [PMID: 29912191 DOI: 10.3791/57140] [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: 10/31/2022] Open
Abstract
The hybridization capture of chromatin-associated proteins for proteomics (HyCCAPP) technology was initially developed to uncover novel DNA-protein interactions in yeast. It allows analysis of a target region of interest without the need for prior knowledge about likely proteins bound to the target region. This, in theory, allows HyCCAPP to be used to analyze any genomic region of interest, and it provides sufficient flexibility to work in different cell systems. This method is not meant to study binding sites of known transcription factors, a task better suited for Chromatin Immunoprecipitation (ChIP) and ChIP-like methods. The strength of HyCCAPP lies in its ability to explore DNA regions for which there is limited or no knowledge about the proteins bound to it. It can also be a convenient method to avoid biases (present in ChIP-like methods) introduced by protein-based chromatin enrichment using antibodies. Potentially, HyCCAPP can be a powerful tool to uncover truly novel DNA-protein interactions. To date, the technology has been predominantly applied to yeast cells or to high copy repeat sequences in mammalian cells. In order to become the powerful tool we envision, HyCCAPP approaches need to be optimized to efficiently capture single-copy loci in mammalian cells. Here, we present our adaptation of the initial yeast HyCCAPP capture protocol to human cell lines, and show that single-copy chromatin regions can be efficiently isolated with this modified protocol.
Collapse
Affiliation(s)
- Hector Guillen-Ahlers
- Department of Genetics, Texas Biomedical Research Institute; Department of Internal Medicine-Molecular Medicine, Wake Forest University School of Medicine
| | - Prahlad K Rao
- Department of Genetics, Texas Biomedical Research Institute
| | | | | | | | | | | | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute; Department of Internal Medicine-Molecular Medicine, Wake Forest University School of Medicine;
| |
Collapse
|
32
|
Lueong S, Villar S, Cahais V, Heguy A, Wanibuchi H, Gi M, Totsuka Y, Herbert R, Zavadil J, Olivier M. PO-319 Mutational signatures of 1,2-dichloropropane and dichloromethane identified in mouse carcinogenicity assays. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
33
|
Olivier M, Bouaoun L, Torres-Mejia G, Garmendia M, Sanchez G, Porras C, Romieu I, Porter P, Rinaldi S. PO-310 Genomic features of premenopausal breast cancers in latin american women: the PRECAMA study. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
34
|
Cavalin C, Ballerie A, Lescoat A, Macchi O, Catinon M, Chemarin C, Olivier M, Semerano L, Vincent M, Boissier M, Jego P, Rosental P. Analyse sociodémographique des expositions à des particules inorganiques dans la sclérodermie systémique et la polyarthrite rhumatoïde : une enquête en population générale (n= 2911) croisée avec le suivi de patients en CHU. Rev Med Interne 2018. [DOI: 10.1016/j.revmed.2018.03.280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
35
|
Abstract
INTRODUCTION Metabolomics is a promising approach for discovery of relevant biomarkers in cells, tissues, organs, and biofluids for disease identification and prediction. The field has mostly relied on blood-based biofluids (serum, plasma, urine) as non-invasive sources of samples as surrogates of tissue or organ-specific conditions. However, the tissue specificity of metabolites pose challenges in translating blood metabolic profiles to organ-specific pathophysiological changes, and require further downstream analysis of the metabolites. OBJECTIVES As part of this project, we aim to develop and optimize an efficient extraction protocol for the analysis of kidney tissue metabolites representative of key primate metabolic pathways. METHODS Kidney cortex and medulla tissues of a baboon were homogenized and extracted using eight different extraction protocols including methanol/water, dichloromethane/methanol, pure methanol, pure water, water/methanol/chloroform, methanol/chloroform, methanol/acetonitrile/water, and acetonitrile/isopropanol/water. The extracts were analyzed by a two-dimensional gas chromatography time-of-flight mass-spectrometer (2D GC-ToF-MS) platform after methoximation and silylation. RESULTS Our analysis quantified 110 shared metabolites in kidney cortex and medulla tissues from hundreds of metabolites found among the eight different solvent extractions spanning low to high polarities. The results revealed that medulla is metabolically richer compared to the cortex. Dichloromethane and methanol mixture (3:1) yielded highest number of metabolites across both the tissue types. Depending on the metabolites of interest, tissue type, and the biological question, different solvents can be used to extract specific groups of metabolites. CONCLUSION This investigation provides insights into selection of extraction solvents for detection of classes of metabolites in renal cortex and medulla, which is fundamentally important for identification of prognostic and diagnostic metabolic kidney biomarkers for future therapeutic applications.
Collapse
Affiliation(s)
- Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA.
| | - Ram P Upadhayay
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Laura A Cox
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Michael Olivier
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| |
Collapse
|
36
|
Bishop AC, Libardoni M, Choudary A, Misra B, Lange K, Bernal J, Nijland M, Li C, Olivier M, Nathanielsz PW, Cox LA. Nonhuman primate breath volatile organic compounds associate with developmental programming and cardio-metabolic status. J Breath Res 2018; 12:036016. [PMID: 29593130 PMCID: PMC6364675 DOI: 10.1088/1752-7163/aaba84] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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] [Indexed: 01/11/2023]
Abstract
Rodent and nonhuman primate studies indicate that developmental programming by reduced perinatal nutrition negatively impacts life course cardio-metabolic health. We have developed a baboon model in which we feed control mothers (CON) ad libitum while nutrient restricted mothers are fed 70% of ad libitum global feed in pregnancy and lactation. Offspring of nutrient restricted mothers are intrauterine growth restricted (IUGR) at term. By 3.5 years IUGR baboons showed signs of insulin resistance, indicating a pre-diabetic phenotype, in contrast to healthy CON offspring. We hypothesized that a novel breath analysis approach would provide markers of the altered cardio-metabolic state in a non-invasive manner. Here we assess whether exhaled breath volatile organic compounds (VOCs) collected from this unique cohort of juvenile baboons with documented cardio-metabolic dysfunction resulting from in utero programming can be detected from their breath signatures. Breath was collected from male and female CON and IUGR baboons at 4.8 ± 0.2 years (human equivalent ~13 years). Breath VOCs were quantified using a two-dimensional gas chromatography mass spectrometer. Two-way ANOVA, on 76 biologically relevant VOCs identified 27 VOCs (p < 0.05) with altered abundances between groups (sex, birthweight, and sex x birthweight). The 27 VOCs included 2-pentanone, 2-octanone, 2,2,7,7-tetramethyloctane and 3-methyl-1-heptene, which have not previously been associated with cardio-metabolic disease. Unsupervised principal component analysis of these VOCs could discriminate the four clusters defining males, females, CON and IUGR. This study, which is the first to assess quantifiable breath signatures associated with cardio-metabolic programing for any model of IUGR, demonstrates the translational value of this unique model to identify metabolites of programmed cardio-metabolic dysfunction in breath signatures. Future studies are required to validate the translatability of these findings to humans.
Collapse
Affiliation(s)
- Andrew C Bishop
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Guillen‐Ahlers H, Erbe CB, Chevalier FD, Montoya MJ, Zimmerman KD, Langefeld CD, Olivier M, Runge CL. TMTC2 variant associated with sensorineural hearing loss and auditory neuropathy spectrum disorder in a family dyad. Mol Genet Genomic Med 2018; 6:653-659. [PMID: 29671961 PMCID: PMC6081214 DOI: 10.1002/mgg3.397] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 02/02/2018] [Revised: 02/02/2018] [Accepted: 03/09/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Sensorineural hearing loss (SNHL) is a common form of hearing loss that can be inherited or triggered by environmental insults; auditory neuropathy spectrum disorder (ANSD) is a SNHL subtype with unique diagnostic criteria. The genetic factors associated with these impairments are vast and diverse, but causal genetic factors are rarely characterized. METHODS A family dyad, both cochlear implant recipients, presented with a hearing history of bilateral, progressive SNHL, and ANSD. Whole-exome sequencing was performed to identify coding sequence variants shared by both family members, and screened against genes relevant to hearing loss and variants known to be associated with SNHL and ANSD. RESULTS Both family members are successful cochlear implant users, demonstrating effective auditory nerve stimulation with their devices. Genetic analyses revealed a mutation (rs35725509) in the TMTC2 gene, which has been reported previously as a likely genetic cause of SNHL in another family of Northern European descent. CONCLUSION This study represents the first confirmation of the rs35725509 variant in an independent family as a likely cause for the complex hearing loss phenotype (SNHL and ANSD) observed in this family dyad.
Collapse
Affiliation(s)
- Hector Guillen‐Ahlers
- Department of GeneticsTexas Biomedical Research InstituteSan AntonioTXUSA
- Present address:
Department of Internal MedicineSection of Molecular MedicineWake Forest University School of MedicineWinston‐SalemNCUSA
| | - Christy B. Erbe
- Department of Otolaryngology and Communication SciencesMedical College of WisconsinMilwaukeeWIUSA
| | | | - Maria J. Montoya
- Department of GeneticsTexas Biomedical Research InstituteSan AntonioTXUSA
| | - Kip D. Zimmerman
- Department of Biostatistical SciencesWake Forest University School of MedicineWinston‐SalemNCUSA
| | - Carl D. Langefeld
- Department of Biostatistical SciencesWake Forest University School of MedicineWinston‐SalemNCUSA
| | - Michael Olivier
- Department of GeneticsTexas Biomedical Research InstituteSan AntonioTXUSA
- Present address:
Department of Internal MedicineSection of Molecular MedicineWake Forest University School of MedicineWinston‐SalemNCUSA
| | - Christina L. Runge
- Department of Otolaryngology and Communication SciencesMedical College of WisconsinMilwaukeeWIUSA
| |
Collapse
|
38
|
Interian Y, Valdes G, Vincent R, Joey C, Vasant K, Olivier M, Gennatas E, Solberg T. EP-2163: Deep Neural Networks vs Medical Physicists: An IMRT QA case study. Radiother Oncol 2018. [DOI: 10.1016/s0167-8140(18)32472-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
39
|
Rao PK, Merath K, Drigalenko E, Jadhav AYL, Komorowski RA, Goldblatt MI, Rohatgi A, Sarzynski MA, Gawrieh S, Olivier M. Proteomic characterization of high-density lipoprotein particles in patients with non-alcoholic fatty liver disease. Clin Proteomics 2018. [PMID: 29527140 PMCID: PMC5839024 DOI: 10.1186/s12014-018-9186-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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] [Indexed: 02/02/2023] Open
Abstract
Background Metabolic diseases such as obesity and diabetes are associated with changes in high-density lipoprotein (HDL) particles, including changes in particle size and protein composition, often resulting in abnormal function. Recent studies suggested that patients with non-alcoholic fatty liver disease (NAFLD), including individuals with non-alcoholic steatohepatitis (NASH), have smaller HDL particles when compared to individuals without liver pathologies. However, no studies have investigated potential changes in HDL particle protein composition in patients with NAFLD, in addition to changes related to obesity, to explore putative functional changes of HDL which may increase the risk of cardiovascular complications. Methods From a cohort of morbidly obese females who were diagnosed with simple steatosis (SS), NASH, or normal liver histology, we selected five matched individuals from each condition for a preliminary pilot HDL proteome analysis. HDL particles were enriched using size-exclusion chromatography, and the proteome of the resulting fraction was analyzed by liquid chromatography tandem mass spectrometry. Differences in the proteomes between the three conditions (normal, SS, NASH) were assessed using label-free quantitative analysis. Gene ontology term analysis was performed to assess the potential impact of proteomic changes on specific functions of HDL particles. Results Of the 95 proteins identified, 12 proteins showed nominally significant differences between the three conditions. Gene ontology term analysis revealed that severity of the liver pathology may significantly impact the anti-thrombotic functions of HDL particles, as suggested by changes in the abundance of HDL-associated proteins such as antithrombin III and plasminogen. Conclusions The pilot data from this study suggest that changes in the HDL proteome may impact the functionality of HDL particles in NAFLD and NASH patients. These proteome changes may alter cardio-protective properties of HDL, potentially contributing to the increased cardiovascular disease risk in affected individuals. Further validation of these protein changes by orthogonal approaches is key to confirming the role of alterations in the HDL proteome in NAFLD and NASH. This will help elucidate the mechanistic effects of the altered HDL proteome on cardioprotective properties of HDL particles.
Collapse
Affiliation(s)
- Prahlad K Rao
- 1Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX USA.,2Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI USA.,3Present Address: Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38103 USA
| | - Kate Merath
- 2Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI USA
| | - Eugene Drigalenko
- 1Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX USA
| | - Avinash Y L Jadhav
- 1Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX USA.,4Present Address: Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC USA
| | - Richard A Komorowski
- 5Department of Pathology, Froedtert and Medical College of Wisconsin, Milwaukee, WI USA
| | - Matthew I Goldblatt
- 6Department of Surgery, Froedtert and Medical College of Wisconsin, Milwaukee, WI USA
| | - Anand Rohatgi
- 7Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Mark A Sarzynski
- 8Department of Exercise Science, University of South Carolina, Columbia, SC USA
| | - Samer Gawrieh
- 9Department of Medicine, Indiana University, Indianapolis, IN USA
| | - Michael Olivier
- 1Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX USA.,2Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI USA.,4Present Address: Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC USA
| |
Collapse
|
40
|
Cavalin C, Lescoat A, Ballerie A, Macchi O, Catinon M, Chemarin C, Olivier M, Jego P, Vincent M, Rosental P. ELIPSSilice : une enquête en population générale pour explorer le rôle possible des expositions aux particules inorganiques dans la survenue de maladies systémiques. Rev Med Interne 2017. [DOI: 10.1016/j.revmed.2017.10.319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
41
|
Proffitt JM, Glenn J, Cesnik AJ, Jadhav A, Shortreed MR, Smith LM, Kavanagh K, Cox LA, Olivier M. Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys. BMC Genomics 2017; 18:877. [PMID: 29132314 PMCID: PMC5683380 DOI: 10.1186/s12864-017-4279-0] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 11/03/2017] [Indexed: 01/05/2023] Open
Abstract
Background Shotgun proteomics utilizes a database search strategy to compare detected mass spectra to a library of theoretical spectra derived from reference genome information. As such, the robustness of proteomics results is contingent upon the completeness and accuracy of the gene annotation in the reference genome. For animal models of disease where genomic annotation is incomplete, such as non-human primates, proteogenomic methods can improve the detection of proteins by incorporating transcriptional data from RNA-Seq to improve proteomics search databases used for peptide spectral matching. Customized search databases derived from RNA-Seq data are capable of identifying unannotated genetic and splice variants while simultaneously reducing the number of comparisons to only those transcripts actively expressed in the tissue. Results We collected RNA-Seq and proteomic data from 10 vervet monkey liver samples and used the RNA-Seq data to curate sample-specific search databases which were analyzed in the program Morpheus. We compared these results against those from a search database generated from the reference vervet genome. A total of 284 previously unannotated splice junctions were predicted by the RNA-Seq data, 92 of which were confirmed by peptide spectral matches. More than half (53/92) of these unannotated splice variants had orthologs in other non-human primates, suggesting that failure to match these peptides in the reference analyses likely arose from incomplete gene model information. The sample-specific databases also identified 101 unique peptides containing single amino acid substitutions which were missed by the reference database. Because the sample-specific searches were restricted to actively expressed transcripts, the search databases were smaller, more computationally efficient, and identified more peptides at the empirically derived 1 % false discovery rate. Conclusion Proteogenomic approaches are ideally suited to facilitate the discovery and annotation of proteins in less widely studies animal models such as non-human primates. We expect that these approaches will help to improve existing genome annotations of non-human primate species such as vervet. Electronic supplementary material The online version of this article (doi: 10.1186/s12864-017-4279-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- J Michael Proffitt
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Jeremy Glenn
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Anthony J Cesnik
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Avinash Jadhav
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA.,Current address: Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, NRC Building, G-55, Winston-Salem, North Carolina, 27157, USA
| | | | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA.,Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, USA
| | - Kylie Kavanagh
- Department of Pathology and Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Laura A Cox
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA.,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA. .,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA. .,Current address: Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, NRC Building, G-55, Winston-Salem, North Carolina, 27157, USA.
| |
Collapse
|
42
|
Huskova H, Ardin M, Weninger A, Vargova K, Barrin S, Villar S, Olivier M, Stopka T, Herceg Z, Hollstein M, Zavadil J, Korenjak M. Modeling cancer driver events in vitro using barrier bypass-clonal expansion assays and massively parallel sequencing. Oncogene 2017; 36:6041-6048. [PMID: 28692054 PMCID: PMC5666318 DOI: 10.1038/onc.2017.215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 03/30/2017] [Accepted: 05/12/2017] [Indexed: 12/14/2022]
Abstract
The information on candidate cancer driver alterations available from public databases is often descriptive and of limited mechanistic insight, which poses difficulties for reliable distinction between true driver and passenger events. To address this challenge, we performed in-depth analysis of whole-exome sequencing data from cell lines generated by a barrier bypass-clonal expansion (BBCE) protocol. The employed strategy is based on carcinogen-driven immortalization of primary mouse embryonic fibroblasts and recapitulates early steps of cell transformation. Among the mutated genes were almost 200 COSMIC Cancer Gene Census genes, many of which were recurrently affected in the set of 25 immortalized cell lines. The alterations affected pathways regulating DNA damage response and repair, transcription and chromatin structure, cell cycle and cell death, as well as developmental pathways. The functional impact of the mutations was strongly supported by the manifestation of several known cancer hotspot mutations among the identified alterations. We identified a new set of genes encoding subunits of the BAF chromatin remodeling complex that exhibited Ras-mediated dependence on PRC2 histone methyltransferase activity, a finding that is similar to what has been observed for other BAF subunits in cancer cells. Among the affected BAF complex subunits, we determined Smarcd2 and Smarcc1 as putative driver candidates not yet fully identified by large-scale cancer genome sequencing projects. In addition, Ep400 displayed characteristics of a driver gene in that it showed a mutually exclusive mutation pattern when compared with mutations in the Trrap subunit of the TIP60 complex, both in the cell line panel and in a human tumor data set. We propose that the information generated by deep sequencing of the BBCE cell lines coupled with phenotypic analysis of the mutant cells can yield mechanistic insights into driver events relevant to human cancer development.
Collapse
Affiliation(s)
- H Huskova
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - M Ardin
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
| | - A Weninger
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - K Vargova
- Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - S Barrin
- Dynamics of T cell Interactions Team, Institut Cochin, Inserm U1016, Paris, France
| | - S Villar
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
| | - M Olivier
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
| | - T Stopka
- Biocev, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Z Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - M Hollstein
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
- Faculty of Medicine and Health, University of Leeds, LIGHT Laboratories, Leeds, UK
| | - J Zavadil
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
| | - M Korenjak
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
| |
Collapse
|
43
|
Buxton KE, Kennedy-Darling J, Shortreed MR, Zaidan NZ, Olivier M, Scalf M, Sridharan R, Smith LM. Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry. J Proteome Res 2017; 16:3433-3442. [PMID: 28704058 DOI: 10.1021/acs.jproteome.7b00448] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The centromere is the chromosomal locus where the kinetochore forms and is critical for ensuring proper segregation of sister chromatids during cell division. A substantial amount of effort has been devoted to understanding the characteristic features and roles of the centromere, yet some fundamental aspects of the centromere, such as the complete list of elements that define it, remain obscure. It is well-known that human centromeres include a highly repetitive class of DNA known as alpha satellite, or alphoid, DNA. We present here the first DNA-centric examination of human protein-alpha satellite interactions, employing an approach known as HyCCAPP (hybridization capture of chromatin-associated proteins for proteomics) to identify the protein components of alphoid chromatin in a human cell line. Using HyCCAPP, cross-linked alpha satellite chromatin was isolated from cell lysate, and captured proteins were analyzed via mass spectrometry. After being compared to proteins identified in control pulldown experiments, 90 proteins were identified as enriched at alphoid DNA. This list included many known centromere-binding proteins in addition to multiple novel alpha satellite-binding proteins, such as LRIF1, a heterochromatin-associated protein. The ability of HyCCAPP to reveal both known as well as novel alphoid DNA-interacting proteins highlights the validity and utility of this approach.
Collapse
Affiliation(s)
| | | | | | | | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute , San Antonio, Texas 78227, United States
| | | | | | | |
Collapse
|
44
|
Runge CL, Indap A, Zhou Y, Kent JW, King E, Erbe CB, Cole R, Littrell J, Merath K, James R, Rüschendorf F, Kerschner JE, Marth G, Hübner N, Göring HHH, Friedland DR, Kwok WM, Olivier M. Association of TMTC2 With Human Nonsyndromic Sensorineural Hearing Loss. JAMA Otolaryngol Head Neck Surg 2017; 142:866-72. [PMID: 27311106 DOI: 10.1001/jamaoto.2016.1444] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
IMPORTANCE Sensorineural hearing loss (SNHL) is commonly caused by conditions that affect cochlear structures or the auditory nerve, and the genes identified as causing SNHL to date only explain a fraction of the overall genetic risk for this debilitating disorder. It is likely that other genes and mutations also cause SNHL. OBJECTIVE To identify a candidate gene that causes bilateral, symmetric, progressive SNHL in a large multigeneration family of Northern European descent. DESIGN, SETTING, AND PARTICIPANTS In this prospective genotype and phenotype study performed from January 1, 2006, through April 1, 2016, a 6-generation family of Northern European descent with 19 individuals having reported early-onset hearing loss suggestive of an autosomal dominant inheritance were studied at a tertiary academic medical center. In addition, 179 unrelated adult individuals with SNHL and 186 adult individuals reporting nondeafness were examined. MAIN OUTCOMES AND MEASURES Sensorineural hearing loss. RESULTS Nine family members (5 women [55.6%]) provided clinical audiometric and medical records that documented hearing loss. The hearing loss is characterized as bilateral, symmetric, progressive SNHL that reached severe to profound loss in childhood. Audiometric configurations demonstrated a characteristic dip at 1000 to 2000 Hz. All affected family members wear hearing aids or have undergone cochlear implantation. Exome sequencing and linkage and association analyses identified a fully penetrant sequence variant (rs35725509) on chromosome 12q21 (logarithm of odds, 3.3) in the TMTC2 gene region that segregates with SNHL in this family. This gene explains the SNHL occurrence in this family. The variant is also associated with SNHL in a cohort of 363 unrelated individuals (179 patients with confirmed SNHL and 184 controls, P = 7 × 10-4). CONCLUSIONS AND RELEVANCE A previously uncharacterized gene, TMTC2, has been identified as a candidate for causing progressive SNHL in humans. This finding identifies a novel locus that causes autosomal dominant SNHL and therefore a more detailed understanding of the genetic basis of SNHL. Because TMTC2 has not been previously reported to regulate auditory function, the discovery reveals a potentially new, uncharacterized mechanism of hearing loss.
Collapse
Affiliation(s)
- Christina L Runge
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee
| | - Amit Indap
- Department of Biology, Boston College, Chestnut Hill, Massachusetts
| | - Yifan Zhou
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee
| | - Jack W Kent
- Department of Genetics, Texas Biomedical Research Institute, San Antonio
| | - Ericka King
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee
| | - Christy B Erbe
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee
| | - Regina Cole
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee
| | - Jack Littrell
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee
| | - Kate Merath
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee
| | - Roland James
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee
| | | | - Joseph E Kerschner
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee
| | - Gabor Marth
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Harald H H Göring
- Department of Genetics, Texas Biomedical Research Institute, San Antonio
| | - David R Friedland
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee
| | - Wai-Meng Kwok
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee8Department of Anesthesiology, Medical College of Wisconsin, Milwaukee
| | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute, San Antonio5Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee
| |
Collapse
|
45
|
Musani SK, Martin LJ, Woo JG, Olivier M, Gurka MJ, DeBoer MD. Heritability of the Severity of the Metabolic Syndrome in Whites and Blacks in 3 Large Cohorts. ACTA ACUST UNITED AC 2017; 10:CIRCGENETICS.116.001621. [PMID: 28408709 DOI: 10.1161/circgenetics.116.001621] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 09/16/2016] [Accepted: 03/06/2017] [Indexed: 02/02/2023]
Abstract
BACKGROUND Although dichotomous criteria for the metabolic syndrome (MetS) appear heritable, it is not known whether MetS severity as assessed by a continuous MetS score is heritable and whether this varies by race. METHODS AND RESULTS We used SOLAR (Sequential Oligogenic Linkage Analysis Routines) to evaluate heritability of Adult Treatment Panel-III MetS and a sex- and race-specific MetS severity Z score among 3 large familial cohorts: the JHS (Jackson Heart Study, 1404 black participants), TOPS (Take Off Pounds Sensibly, 1947 white participants), and PLRS (Princeton Lipid Research Study, 229 black and 527 white participants). Heritability estimates were larger for Adult Treatment Panel-III MetS among black compared with white cohort members (JHS 0.48; 95% confidence interval [CI], 0.28-0.68 and PLRS blacks 0.93 [95% CI, 0.73-1.13] versus TOPS 0.21 [95% CI, -0.18 to 0.60] and PLRS whites 0.27 [95% CI, -0.04 to 0.58]). The difference by race narrowed when assessing heritability of the MetS severity score (JHS 0.52 [95% CI, 0.38, 0.66] and PLRS blacks 0.64 [95% CI, 0.13-1.15] versus TOPS 0.23 [95% CI, 0.15-0.31] and PLRS whites 0.60 [95% CI, 0.33-0.87]). There was a high degree of genetic and phenotypic correlation between MetS severity and the individual components of MetS among all groups, although the genetic correlations failed to reach statistical significance among PLRS blacks. Meta-analyses revealed a combined heritability estimate for Adult Treatment Panel-III MetS of 0.24 (95% CI, 0.11-0.36) and for the MetS severity score of 0.50 (95% CI, -0.05 to 0.99). CONCLUSIONS MetS severity seems highly heritable among whites and blacks. This continuous MetS severity Z score may provide a more useful means of characterizing phenotypic MetS in genetic studies by minimizing racial differences.
Collapse
Affiliation(s)
- Solomon K Musani
- From the Jackson Heart Study, University of Mississippi Medical Center, Jackson (S.K.M.); Division of Human Genetics (L.J.M.) and Division of Epidemiology & Biostatistics (J.G.W.), Cincinnati Children's Hospital Medical Center, OH; Department of Pediatrics, University of Cincinnati, OH (L.J.M., J.G.W.); Texas Biomedical Research Institute, San Antonio (M.O.); Department of Health Outcomes & Policy, University of Florida, Gainesville (M.J.G.); and Department of Pediatrics, University of Virginia, Charlottesville (M.D.D.)
| | - Lisa J Martin
- From the Jackson Heart Study, University of Mississippi Medical Center, Jackson (S.K.M.); Division of Human Genetics (L.J.M.) and Division of Epidemiology & Biostatistics (J.G.W.), Cincinnati Children's Hospital Medical Center, OH; Department of Pediatrics, University of Cincinnati, OH (L.J.M., J.G.W.); Texas Biomedical Research Institute, San Antonio (M.O.); Department of Health Outcomes & Policy, University of Florida, Gainesville (M.J.G.); and Department of Pediatrics, University of Virginia, Charlottesville (M.D.D.)
| | - Jessica G Woo
- From the Jackson Heart Study, University of Mississippi Medical Center, Jackson (S.K.M.); Division of Human Genetics (L.J.M.) and Division of Epidemiology & Biostatistics (J.G.W.), Cincinnati Children's Hospital Medical Center, OH; Department of Pediatrics, University of Cincinnati, OH (L.J.M., J.G.W.); Texas Biomedical Research Institute, San Antonio (M.O.); Department of Health Outcomes & Policy, University of Florida, Gainesville (M.J.G.); and Department of Pediatrics, University of Virginia, Charlottesville (M.D.D.)
| | - Michael Olivier
- From the Jackson Heart Study, University of Mississippi Medical Center, Jackson (S.K.M.); Division of Human Genetics (L.J.M.) and Division of Epidemiology & Biostatistics (J.G.W.), Cincinnati Children's Hospital Medical Center, OH; Department of Pediatrics, University of Cincinnati, OH (L.J.M., J.G.W.); Texas Biomedical Research Institute, San Antonio (M.O.); Department of Health Outcomes & Policy, University of Florida, Gainesville (M.J.G.); and Department of Pediatrics, University of Virginia, Charlottesville (M.D.D.)
| | - Matthew J Gurka
- From the Jackson Heart Study, University of Mississippi Medical Center, Jackson (S.K.M.); Division of Human Genetics (L.J.M.) and Division of Epidemiology & Biostatistics (J.G.W.), Cincinnati Children's Hospital Medical Center, OH; Department of Pediatrics, University of Cincinnati, OH (L.J.M., J.G.W.); Texas Biomedical Research Institute, San Antonio (M.O.); Department of Health Outcomes & Policy, University of Florida, Gainesville (M.J.G.); and Department of Pediatrics, University of Virginia, Charlottesville (M.D.D.)
| | - Mark D DeBoer
- From the Jackson Heart Study, University of Mississippi Medical Center, Jackson (S.K.M.); Division of Human Genetics (L.J.M.) and Division of Epidemiology & Biostatistics (J.G.W.), Cincinnati Children's Hospital Medical Center, OH; Department of Pediatrics, University of Cincinnati, OH (L.J.M., J.G.W.); Texas Biomedical Research Institute, San Antonio (M.O.); Department of Health Outcomes & Policy, University of Florida, Gainesville (M.J.G.); and Department of Pediatrics, University of Virginia, Charlottesville (M.D.D.).
| |
Collapse
|
46
|
Wang S, Lim J, Choi D, Dickman K, Olivier M, Villar S, Sidorenko V, Yun B, Turesky R, Zavadil J, Grollman A. New Molecular Evidence of Exposure to Aristolochic Acid in South Korea:
Implications for Global Public Health Hazard Linked to Nephrotoxic and
Carcinogenic Herbal Medicines. Ann Glob Health 2017. [DOI: 10.1016/j.aogh.2017.03.416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
|
47
|
Archambault M, Olivier M, Foiry B, Diarra M, Paradis SÉ, Jacques M. Effects of pig hemoglobin binding on some physical and biological properties of Actinobacillus pleuropneumoniae lipopolysaccharides. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/096805199700400107] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Binding of pig hemoglobin (Hb) to Actinobacillus pleuropneumoniae lipopolysaccharide (LPS), either extracted or present at the surface of whole cells, was studied. After a short incubation period, pig Hb seemed to cover the bacterial cell surface and enhanced the cells' contrast when examined by transmission electron microscopy (TEM). Energy-dispersive X-ray spectroscopy analysis showed that the amount of elemental iron detected was increased when cells of A. pleuropneumoniae were incubated with pig Hb. Coating with pig Hb, however, did not interfere with the accessibility of O- and capsular antigens to antibodies on the bacterial cell surface. Binding of pig Hb and polymyxin B to lipid A of A. pleuropneumoniae was confirmed with a fluorescent probe (dansylcadaverine) displacement assay. The binding of pig Hb to extracted LPS resulted in a disaggregation of LPS as observed by TEM after negative staining. Additional evidence for a direct physical interaction between pig Hb and A. pleuropneumoniae LPS was demonstrated by a shift in the sedimentation velocity of LPS-Hb complexes determined by sucrose gradient centrifugation. Pig Hb binding to extracted LPS or to bacterial cells resulted in a significant decrease of chromogenic Limulus amebocyte lysate activation. Finally, the capacity of extracted LPS to induce NO2-in the presence of pig Hb was tested by using cell line J774 and determined by the Greiss' reaction. LPS alone induced, as expected, NO2- production, whereas the presence of pig Hb significantly reduced NO2-production by murine macrophages. Taken together, our results indicate that binding of pig Hb affected some physical and biological properties of A. pleuropneumoniae LPS.
Collapse
Affiliation(s)
- M. Archambault
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - M. Olivier
- Pavillon CHUL, Laboratoire et Service d'Infectiologie
| | - B. Foiry
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - M.S. Diarra
- Pavillon St-François d'Assise, Centre Hospitalier Universitaire de Québec, Québec, Canada
| | - S.-É. Paradis
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - M. Jacques
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada,
| |
Collapse
|
48
|
Jacobsen S, Olivier M, Smith F, Knutti D, Johnson R, Colvin G, Scroggin W. Research Robots for Applications in Artificial Intelligence, Teleoperation and Entertainment. Int J Rob Res 2016. [DOI: 10.1177/0278364904042198] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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
Sarcos Research Corporation, and the Center for Engineering Design at the University of Utah, have long been interested in both the fundamental and the applied aspects of robots and other computationally driven machines. We have produced substantial numbers of systems that function as products for commercial applications, and as advanced research tools specifically designed for experimental use. This paper reviews various aspects of the design and control of a number of robot-like machines ranging from our first projects, the Utah Arm and the Utah/MIT Dextrous Hand, to present work on humanoid robots and the Wearable Energetically Autonomous Robot (WEAR). Our systems have been used in: entertainment, operator remotization from hazardous environments, R&D, and medicine. In addition to the robots and their subsystems, extensive work has been devoted to command systems that drive the robots. Command systems have been: playback supervisors, teleoperation masters, and various higher level approaches based on work from the AI community. Playback interfaces have included motion capture mechanisms that provide movement-stream information to storage systems configured for later, repeated and coordinated, operation of many robots and associated mechanisms. Play-back command systems use human commands, from an “earlier” time, to command motions that are played out, over and over, mindlessly. Teleoperation “masters”, that operate in real-time with the robot, have ranged from simple motion capture devices, to more complex force reflective exoskeletal masters. Teleoperation interfaces have been composed of complex kinematic structures designed to perform motions compatible with operator movements and are attached via appropriate soft tissue interfaces. The masters emit lower level commands (joint angles) in real-time using the natural intelligence and sensory systems of the operator. AI-based command sources, blend higher level (simple) commands, with system and existing environmental states, to make decisions for the management of the robot. As with the playback systems, AI-based systems are programmed earlier to perform later operations. In the AI case, however, adaptive intelligence and sensory capabilities reside in the robot. Our general design approach has been to begin with the definition of desired objective behaviors, rather than the use of available components with their predefined technical specifications. With the technical specifications of the components necessary to achieve the desired behaviors defined, the components are either acquired, or in most cases, developed and built. The control system, which includes the operation of feedback approaches, acting in collaboration with physical machinery, is then defined and implemented. Control is considered a function of both feedback, and the designed-in performance of the robot’s physical machinery. It has not been true that bad performance from physical machine elements can be simply compensated out via innovative control methods and faster computers. After the completion of many projects we believe that the final frontier(s) of robotics reside at both ends of the brain and brawn spectrum. Both frontiers (barriers) are related to autonomy—intelligence/computation and energy/power. Recently, energetic autonomy has become a major interest at Sarcos and projects are underway to develop appropriate fuel-based servo-actuators to satisfy that need. Our objective is to develop power systems that are capable producing high performance servo-quality actuation for extended operating times without reenergizing the system. At the other end of the spectrum, we are working in collaboration with various groups to supply physical robots capable of operation under the control of advanced AI-based systems.
Collapse
Affiliation(s)
- S.C. Jacobsen
- Sarcos Research Corporation (SRC) 360 Wakara Way, SLC, Utah 84108, USA and Center for Engineering Design (CED) University of Utah, SLC, Utah 84104, USA
| | - M. Olivier
- Sarcos Research Corporation (SRC) 360 Wakara Way, SLC, Utah 84108, USA and Center for Engineering Design (CED) University of Utah, SLC, Utah 84104, USA
| | - F.M. Smith
- Sarcos Research Corporation (SRC) 360 Wakara Way, SLC, Utah 84108, USA and Center for Engineering Design (CED) University of Utah, SLC, Utah 84104, USA
| | - D.F. Knutti
- Sarcos Research Corporation (SRC) 360 Wakara Way, SLC, Utah 84108, USA and Center for Engineering Design (CED) University of Utah, SLC, Utah 84104, USA
| | - R.T. Johnson
- Sarcos Research Corporation (SRC) 360 Wakara Way, SLC, Utah 84108, USA and Center for Engineering Design (CED) University of Utah, SLC, Utah 84104, USA
| | - G.E. Colvin
- Sarcos Research Corporation (SRC) 360 Wakara Way, SLC, Utah 84108, USA and Center for Engineering Design (CED) University of Utah, SLC, Utah 84104, USA
| | - W.B. Scroggin
- Sarcos Research Corporation (SRC) 360 Wakara Way, SLC, Utah 84108, USA and Center for Engineering Design (CED) University of Utah, SLC, Utah 84104, USA
| |
Collapse
|
49
|
Olivier M, Bouaoun L, Sonkin D, Ardin M, Hollstein M, Byrnes G, Zavadil J. TP53 variations in human cancers: new lessons from the IARC TP53 Database and genomic studies. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)61042-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
50
|
Guillen-Ahlers H, Rao PK, Levenstein ME, Kennedy-Darling J, Perumalla DS, Jadhav AYL, Glenn JP, Ludwig-Kubinski A, Drigalenko E, Montoya MJ, Göring HH, Anderson CD, Scalf M, Gildersleeve HIS, Cole R, Greene AM, Oduro AK, Lazarova K, Cesnik AJ, Barfknecht J, Cirillo LA, Gasch AP, Shortreed MR, Smith LM, Olivier M. HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae. Genomics 2016; 107:267-73. [PMID: 27184763 DOI: 10.1016/j.ygeno.2016.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 04/05/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 11/30/2022]
Abstract
Currently available methods for interrogating DNA-protein interactions at individual genomic loci have significant limitations, and make it difficult to work with unmodified cells or examine single-copy regions without specific antibodies. In this study, we describe a physiological application of the Hybridization Capture of Chromatin-Associated Proteins for Proteomics (HyCCAPP) methodology we have developed. Both novel and known locus-specific DNA-protein interactions were identified at the ENO2 and GAL1 promoter regions of Saccharomyces cerevisiae, and revealed subgroups of proteins present in significantly different levels at the loci in cells grown on glucose versus galactose as the carbon source. Results were validated using chromatin immunoprecipitation. Overall, our analysis demonstrates that HyCCAPP is an effective and flexible technology that does not require specific antibodies nor prior knowledge of locally occurring DNA-protein interactions and can now be used to identify changes in protein interactions at target regions in the genome in response to physiological challenges.
Collapse
Affiliation(s)
- Hector Guillen-Ahlers
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Prahlad K Rao
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Mark E Levenstein
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | | | - Danu S Perumalla
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Avinash Y L Jadhav
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Jeremy P Glenn
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Amy Ludwig-Kubinski
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Eugene Drigalenko
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Maria J Montoya
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Harald H Göring
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Corianna D Anderson
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | | | - Regina Cole
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Alexandra M Greene
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Akua K Oduro
- Department of Cell Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Katarina Lazarova
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anthony J Cesnik
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Jared Barfknecht
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Lisa A Cirillo
- Department of Cell Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Audrey P Gasch
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | | | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| |
Collapse
|