1
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Wheeler MM, Stilp AM, Rao S, Halldórsson BV, Beyter D, Wen J, Mihkaylova AV, McHugh CP, Lane J, Jiang MZ, Raffield LM, Jun G, Sedlazeck FJ, Metcalf G, Yao Y, Bis JB, Chami N, de Vries PS, Desai P, Floyd JS, Gao Y, Kammers K, Kim W, Moon JY, Ratan A, Yanek LR, Almasy L, Becker LC, Blangero J, Cho MH, Curran JE, Fornage M, Kaplan RC, Lewis JP, Loos RJF, Mitchell BD, Morrison AC, Preuss M, Psaty BM, Rich SS, Rotter JI, Tang H, Tracy RP, Boerwinkle E, Abecasis GR, Blackwell TW, Smith AV, Johnson AD, Mathias RA, Nickerson DA, Conomos MP, Li Y, Þorsteinsdóttir U, Magnússon MK, Stefansson K, Pankratz ND, Bauer DE, Auer PL, Reiner AP. Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program. Nat Commun 2022; 13:7592. [PMID: 36481753 PMCID: PMC9732337 DOI: 10.1038/s41467-022-35354-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies have identified thousands of single nucleotide variants and small indels that contribute to variation in hematologic traits. While structural variants are known to cause rare blood or hematopoietic disorders, the genome-wide contribution of structural variants to quantitative blood cell trait variation is unknown. Here we utilized whole genome sequencing data in ancestrally diverse participants of the NHLBI Trans Omics for Precision Medicine program (N = 50,675) to detect structural variants associated with hematologic traits. Using single variant tests, we assessed the association of common and rare structural variants with red cell-, white cell-, and platelet-related quantitative traits and observed 21 independent signals (12 common and 9 rare) reaching genome-wide significance. The majority of these associations (N = 18) replicated in independent datasets. In genome-editing experiments, we provide evidence that a deletion associated with lower monocyte counts leads to disruption of an S1PR3 monocyte enhancer and decreased S1PR3 expression.
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Affiliation(s)
- Marsha M Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, 98105, USA
| | - Shuquan Rao
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Boston, MA, 02138, USA
- Broad Institute, Cambridge, MA, 02142, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Bjarni V Halldórsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Technology, Reykjavik University, Reykjavík, Iceland
| | | | - Jia Wen
- Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Anna V Mihkaylova
- Department of Biostatistics, University of Washington, Seattle, WA, 98105, USA
| | - Caitlin P McHugh
- Department of Biostatistics, University of Washington, Seattle, WA, 98105, USA
| | - John Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Min-Zhi Jiang
- Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Goo Jun
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Yao Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Boston, MA, 02138, USA
- Broad Institute, Cambridge, MA, 02142, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Joshua B Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Paul S de Vries
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Pinkal Desai
- Division of Hematology and Oncology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Yan Gao
- Jackson Heart Study, Department of Medicine, University of Mississippi, Jackson, MS, 39216, USA
| | - Kai Kammers
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, 2115, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Laura Almasy
- Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Lewis C Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, 2115, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Russell P Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, Larner College of Medicine at the University of Vermont, Colchester, VT, 5446, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Goncalo R Abecasis
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI, 48109, USA
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI, 48109, USA
| | - Albert V Smith
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI, 48109, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, 1702, USA
| | - Rasika A Mathias
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, 98105, USA
| | - Yun Li
- Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Unnur Þorsteinsdóttir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Magnús K Magnússon
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Nathan D Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Boston, MA, 02138, USA
- Broad Institute, Cambridge, MA, 02142, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, 98105, USA.
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2
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DeVeaux SA, Ogle ME, Vyshnya S, Chiappa NF, Leitmann B, Rudy R, Day A, Mortensen LJ, Kurtzberg J, Roy K, Botchwey EA. Characterizing human mesenchymal stromal cells' immune-modulatory potency using targeted lipidomic profiling of sphingolipids. Cytotherapy 2022; 24:608-618. [PMID: 35190267 PMCID: PMC10725732 DOI: 10.1016/j.jcyt.2021.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/29/2021] [Accepted: 12/06/2021] [Indexed: 12/17/2022]
Abstract
Cell therapies are expected to increase over the next decade owing to increasing demand for clinical applications. Mesenchymal stromal cells (MSCs) have been explored to treat a number of diseases, with some successes in early clinical trials. Despite early successes, poor MSC characterization results in lessened therapeutic capacity once in vivo. Here, we characterized MSCs derived from bone marrow (BM), adipose tissue and umbilical cord tissue for sphingolipids (SLs), a class of bioactive lipids, using liquid chromatography/tandem mass spectrometry. We found that ceramide levels differed based on the donor's sex in BM-MSCs. We detected fatty acyl chain variants in MSCs from all three sources. Linear discriminant analysis revealed that MSCs separated based on tissue source. Principal component analysis showed that interferon-γ-primed and unstimulated MSCs separated according to their SL signature. Lastly, we detected higher ceramide levels in low indoleamine 2,3-dioxygenase MSCs, indicating that sphingomyelinase or ceramidase enzymatic activity may be involved in their immune potency.
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Affiliation(s)
- S’Dravious A. DeVeaux
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory, Atlanta, GA
- Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA
| | - Molly E. Ogle
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory, Atlanta, GA
- Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA
| | - Sofiya Vyshnya
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory, Atlanta, GA
- Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA
| | - Nathan F. Chiappa
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory, Atlanta, GA
- Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA
| | - Bobby Leitmann
- Regenerative Bioscience Center, Rhodes Center for ADS, University of Georgia, Athens, GA
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA
| | - Ryan Rudy
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory, Atlanta, GA
- Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA
| | - Abigail Day
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory, Atlanta, GA
- Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA
| | - Luke J. Mortensen
- Regenerative Bioscience Center, Rhodes Center for ADS, University of Georgia, Athens, GA
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA
| | - Joanne Kurtzberg
- Marcus Center for Cellular Cures, Duke University School of Medicine, Durham, NC
| | - Krishnendu Roy
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory, Atlanta, GA
- Marcus Center for Therapeutic Cell Characterization and Manufacturing, Georgia Institute of Technology, Atlanta, GA
- NSF Engineering Research Center (ERC) for Cell Manufacturing Technologies (CMaT), Georgia Institute of Technology, Atlanta, GA
| | - Edward A. Botchwey
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory, Atlanta, GA
- Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA
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3
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Rothe R, Schulze S, Neuber C, Hauser S, Rammelt S, Pietzsch J. Adjuvant drug-assisted bone healing: Part II - Modulation of angiogenesis. Clin Hemorheol Microcirc 2020; 73:409-438. [PMID: 31177206 DOI: 10.3233/ch-199103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The treatment of critical-size bone defects following complicated fractures, infections or tumor resections is a major challenge. The same applies to fractures in patients with impaired bone healing due to systemic inflammatory and metabolic diseases. Despite considerable progress in development and establishment of new surgical techniques, design of bone graft substitutes and imaging techniques, these scenarios still represent unresolved clinical problems. However, the development of new active substances offers novel potential solutions for these issues. This work discusses therapeutic approaches that influence angiogenesis or hypoxic situations in healing bone and surrounding tissue. In particular, literature on sphingosine-1-phosphate receptor modulators and nitric oxide (NO•) donors, including bi-functional (hybrid) compounds like NO•-releasing cyclooxygenase-2 inhibitors, was critically reviewed with regard to their local and systemic mode of action.
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Affiliation(s)
- Rebecca Rothe
- Department of Radiopharmaceutical and Chemical Biology, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Sabine Schulze
- University Center of Orthopaedics and Traumatology (OUC), University Hospital Carl Gustav Carus, Dresden, Germany.,Center for Translational Bone, Joint and Soft Tissue Research, University Hospital Carl Gustav Carus and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Christin Neuber
- Department of Radiopharmaceutical and Chemical Biology, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Sandra Hauser
- Department of Radiopharmaceutical and Chemical Biology, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Stefan Rammelt
- University Center of Orthopaedics and Traumatology (OUC), University Hospital Carl Gustav Carus, Dresden, Germany.,Center for Translational Bone, Joint and Soft Tissue Research, University Hospital Carl Gustav Carus and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Tatzberg 4, Dresden, Germany
| | - Jens Pietzsch
- Department of Radiopharmaceutical and Chemical Biology, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Institute of Radiopharmaceutical Cancer Research, Dresden, Germany.,Technische Universität Dresden, School of Science, Faculty of Chemistry and Food Chemistry, Dresden, Germany
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