1
|
Fang R, Zhang RS, Wang XT, Ye SB, Xia QY, Rao Q. [Clinicopathological and molecular genetic characteristics of 10 cases of epithelioid sarcoma]. Zhonghua Bing Li Xue Za Zhi 2024; 53:293-295. [PMID: 38433059 DOI: 10.3760/cma.j.cn112151-20231016-00266] [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] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Affiliation(s)
- R Fang
- Department of Pathology, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - R S Zhang
- Department of Pathology, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - X T Wang
- Department of Pathology, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - S B Ye
- Department of Pathology, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Q Y Xia
- Department of Pathology, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Q Rao
- Department of Pathology, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| |
Collapse
|
2
|
deBoer RJ, Febbraro M, Bardayan DW, Boomershine C, Brandenburg K, Brune C, Coil S, Couder M, Derkin J, Dede S, Fang R, Fritsch A, Gula A, Gyürky G, Hackett B, Hamad G, Jones-Alberty Y, Kelmar R, Manukyan K, Matney M, McDonaugh J, Meisel Z, Moylan S, Nattress J, Odell D, O'Malley P, Paris MW, Robertson D, Shahina, Singh N, Smith K, Smith MS, Stech E, Tan W, Wiescher M. Measurement of the ^{13}C(α, n_{0})^{16}O Differential Cross Section from 0.8 to 6.5 MeV. Phys Rev Lett 2024; 132:062702. [PMID: 38394565 DOI: 10.1103/physrevlett.132.062702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 09/05/2023] [Accepted: 01/17/2024] [Indexed: 02/25/2024]
Abstract
The cross section of the ^{13}C(α,n)^{16}O reaction is needed for nuclear astrophysics and applications to a precision of 10% or better, yet inconsistencies among 50 years of experimental studies currently lead to an uncertainty of ≈15%. Using a state-of-the-art neutron detection array, we have performed a high resolution differential cross section study covering a broad energy range. These measurements result in a dramatic improvement in the extrapolation of the cross section to stellar energies potentially reducing the uncertainty to ≈5% and resolving long standing discrepancies in higher energy data.
Collapse
Affiliation(s)
- R J deBoer
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - M Febbraro
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - D W Bardayan
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - C Boomershine
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - K Brandenburg
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701, USA
| | - C Brune
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701, USA
| | - S Coil
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - M Couder
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - J Derkin
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701, USA
| | - S Dede
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - R Fang
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - A Fritsch
- Department of Physics, Gonzaga University, Spokane, Washington 99258, USA
| | - A Gula
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Gy Gyürky
- Institute for Nuclear Research (Atomki), P.O.B 51, H-4001 Debrecen, Hungary
| | - B Hackett
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - G Hamad
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701, USA
| | - Y Jones-Alberty
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701, USA
| | - R Kelmar
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - K Manukyan
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - M Matney
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - J McDonaugh
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Z Meisel
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701, USA
| | - S Moylan
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - J Nattress
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - D Odell
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701, USA
| | - P O'Malley
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - M W Paris
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - D Robertson
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Shahina
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - N Singh
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701, USA
| | - K Smith
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - M S Smith
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - E Stech
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - W Tan
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - M Wiescher
- Department of Physics and Astronomy, University of Notre Dame, Notre Dame, Indiana 46556, USA
| |
Collapse
|
3
|
Hawrylycz M, Martone ME, Ascoli GA, Bjaalie JG, Dong HW, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Hof PR, Kim Y, Lein E, Liu Y, Miller JA, Mitra PP, Mukamel E, Ng L, Osumi-Sutherland D, Peng H, Ray PL, Sanchez R, Regev A, Ropelewski A, Scheuermann RH, Tan SZK, Thompson CL, Tickle T, Tilgner H, Varghese M, Wester B, White O, Zeng H, Aevermann B, Allemang D, Ament S, Athey TL, Baker C, Baker KS, Baker PM, Bandrowski A, Banerjee S, Bishwakarma P, Carr A, Chen M, Choudhury R, Cool J, Creasy H, D’Orazi F, Degatano K, Dichter B, Ding SL, Dolbeare T, Ecker JR, Fang R, Fillion-Robin JC, Fliss TP, Gee J, Gillespie T, Gouwens N, Zhang GQ, Halchenko YO, Harris NL, Herb BR, Hintiryan H, Hood G, Horvath S, Huo B, Jarecka D, Jiang S, Khajouei F, Kiernan EA, Kir H, Kruse L, Lee C, Lelieveldt B, Li Y, Liu H, Liu L, Markuhar A, Mathews J, Mathews KL, Mezias C, Miller MI, Mollenkopf T, Mufti S, Mungall CJ, Orvis J, Puchades MA, Qu L, Receveur JP, Ren B, Sjoquist N, Staats B, Tward D, van Velthoven CTJ, Wang Q, Xie F, Xu H, Yao Z, Yun Z, Zhang YR, Zheng WJ, Zingg B. A guide to the BRAIN Initiative Cell Census Network data ecosystem. PLoS Biol 2023; 21:e3002133. [PMID: 37390046 PMCID: PMC10313015 DOI: 10.1371/journal.pbio.3002133] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023] Open
Abstract
Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.
Collapse
Affiliation(s)
- Michael Hawrylycz
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Maryann E. Martone
- Department of Neuroscience, University of California San Diego, San Diego, California, United States of America
- San Francisco Veterans Affairs Medical Center, San Francisco, California, United States of America
| | - Giorgio A. Ascoli
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, Volgenau School of Engineering, George Mason University, Fairfax, Virginia, United States of America
| | - Jan G. Bjaalie
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Hong-Wei Dong
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America
| | - Satrajit S. Ghosh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jesse Gillis
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Ronna Hertzano
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - David R. Haynor
- Department of Radiology, University of Washington, Seattle, Washington, United States of America
| | - Patrick R. Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Yongsoo Kim
- Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania, United States of America
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Yufeng Liu
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Jeremy A. Miller
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Partha P. Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Eran Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, California, United States of America
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - David Osumi-Sutherland
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Hanchuan Peng
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Patrick L. Ray
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Raymond Sanchez
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Aviv Regev
- Genentech, South San Francisco, California, United States of America
| | - Alex Ropelewski
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | | | - Shawn Zheng Kai Tan
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Carol L. Thompson
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Timothy Tickle
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Hagen Tilgner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, United States of America
| | - Merina Varghese
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Brock Wester
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, United States of America
| | - Owen White
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Brian Aevermann
- Chan Zuckerberg Initiative, Redwood City, California, United States of America
| | - David Allemang
- Kitware Inc., Albany, New York, United States of America
| | - Seth Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Thomas L. Athey
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Cody Baker
- CatalystNeuro, Benicia, California, United States of America
| | - Katherine S. Baker
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Pamela M. Baker
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Anita Bandrowski
- Department of Neuroscience, University of California San Diego, San Diego, California, United States of America
| | - Samik Banerjee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Prajal Bishwakarma
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Ambrose Carr
- Chan Zuckerberg Initiative, Redwood City, California, United States of America
| | - Min Chen
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Roni Choudhury
- Kitware Inc., Albany, New York, United States of America
| | - Jonah Cool
- Chan Zuckerberg Initiative, Redwood City, California, United States of America
| | - Heather Creasy
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Florence D’Orazi
- Chan Zuckerberg Initiative, Redwood City, California, United States of America
| | - Kylee Degatano
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Song-Lin Ding
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Joseph R. Ecker
- Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies La Jolla, California, United States of America
| | - Rongxin Fang
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
| | | | - Timothy P. Fliss
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - James Gee
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tom Gillespie
- Department of Neuroscience, University of California San Diego, San Diego, California, United States of America
| | - Nathan Gouwens
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Guo-Qiang Zhang
- Texas Institute for Restorative Neurotechnologies, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Yaroslav O. Halchenko
- Department of Psychological and Brain Sciences, Dartmouth College, Hannover, New Hampshire, United States of America
| | - Nomi L. Harris
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Brian R. Herb
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Houri Hintiryan
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America
| | - Gregory Hood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Sam Horvath
- Kitware Inc., Albany, New York, United States of America
| | - Bingxing Huo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Dorota Jarecka
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Shengdian Jiang
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Farzaneh Khajouei
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Elizabeth A. Kiernan
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Huseyin Kir
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Boudewijn Lelieveldt
- Department of Intelligent Systems, Delft University of Technology, Delft, the Netherlands
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Yang Li
- Center for Epigenomics, Department of Cellular and Molecular Medicine, UC San Diego School of Medicine, La Jolla, California, United States of America
| | - Hanqing Liu
- Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies La Jolla, California, United States of America
| | - Lijuan Liu
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Anup Markuhar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - James Mathews
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Kaylee L. Mathews
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Chris Mezias
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Michael I. Miller
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tyler Mollenkopf
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Shoaib Mufti
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Christopher J. Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Joshua Orvis
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Maja A. Puchades
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Lei Qu
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Joseph P. Receveur
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Bing Ren
- Center for Epigenomics, Department of Cellular and Molecular Medicine, UC San Diego School of Medicine, La Jolla, California, United States of America
- Ludwig Institute for Cancer Research, La Jolla, California, United States of America
| | - Nathan Sjoquist
- Microsoft Corporation, Seattle, Washington, United States of America
| | - Brian Staats
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Daniel Tward
- UCLA Brain Mapping Center, University of California, Los Angeles, California, United States of America
| | | | - Quanxin Wang
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Fangming Xie
- Department of Chemistry and Biochemistry, University of California Los Angeles, California, United States of America
| | - Hua Xu
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Zhixi Yun
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Yun Renee Zhang
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - W. Jim Zheng
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Brian Zingg
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America
| |
Collapse
|
4
|
Raviram R, Raman A, Preissl S, Ning J, Wu S, Koga T, Zhang K, Brennan CW, Zhu C, Luebeck J, Van Deynze K, Han JY, Hou X, Ye Z, Mischel AK, Li YE, Fang R, Baback T, Mugford J, Han CZ, Glass CK, Barr CL, Mischel PS, Bafna V, Escoubet L, Ren B, Chen CC. Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity. Proc Natl Acad Sci U S A 2023; 120:e2210991120. [PMID: 37155843 PMCID: PMC10194019 DOI: 10.1073/pnas.2210991120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 03/09/2023] [Indexed: 05/10/2023] Open
Abstract
In 2021, the World Health Organization reclassified glioblastoma, the most common form of adult brain cancer, into isocitrate dehydrogenase (IDH)-wild-type glioblastomas and grade IV IDH mutant (G4 IDHm) astrocytomas. For both tumor types, intratumoral heterogeneity is a key contributor to therapeutic failure. To better define this heterogeneity, genome-wide chromatin accessibility and transcription profiles of clinical samples of glioblastomas and G4 IDHm astrocytomas were analyzed at single-cell resolution. These profiles afforded resolution of intratumoral genetic heterogeneity, including delineation of cell-to-cell variations in distinct cell states, focal gene amplifications, as well as extrachromosomal circular DNAs. Despite differences in IDH mutation status and significant intratumoral heterogeneity, the profiled tumor cells shared a common chromatin structure defined by open regions enriched for nuclear factor 1 transcription factors (NFIA and NFIB). Silencing of NFIA or NFIB suppressed in vitro and in vivo growths of patient-derived glioblastomas and G4 IDHm astrocytoma models. These findings suggest that despite distinct genotypes and cell states, glioblastoma/G4 astrocytoma cells share dependency on core transcriptional programs, yielding an attractive platform for addressing therapeutic challenges associated with intratumoral heterogeneity.
Collapse
Affiliation(s)
- Ramya Raviram
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Anugraha Raman
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jiangfang Ning
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
| | - Shaoping Wu
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
| | - Tomoyuki Koga
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
| | - Kai Zhang
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Cameron W. Brennan
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Chenxu Zhu
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Jens Luebeck
- Department of Computer Science and Engineering, Halicioglu Data Science Institute, University of California San Diego, La Jolla, CA92093
| | - Kinsey Van Deynze
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Jee Yun Han
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
| | - Xiaomeng Hou
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
| | - Zhen Ye
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Anna K. Mischel
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Yang Eric Li
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Rongxin Fang
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Tomas Baback
- Department of Computer Science and Engineering, Biomedical Sciences Graduate Program, San Diego, CA92121
| | - Joshua Mugford
- Department of Computer Science and Engineering, Biomedical Sciences Graduate Program, San Diego, CA92121
| | - Claudia Z. Han
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Department of Medicine, University of California San Diego, La Jolla, CA92093
| | - Cathy L. Barr
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Division of Experimental & Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ONM5T 0S8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ONM5T 0S8, Canada
- Department of Physiology, University of Toronto, Toronto, ONM5T 0S8, Canada
| | - Paul S. Mischel
- Department of Pathology, Stanford University, Stanford, CA94305
| | - Vineet Bafna
- Department of Computer Science and Engineering, Halicioglu Data Science Institute, University of California San Diego, La Jolla, CA92093
| | - Laure Escoubet
- Department of Computer Science and Engineering, Biomedical Sciences Graduate Program, San Diego, CA92121
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Clark C. Chen
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
| |
Collapse
|
5
|
Raviram R, Raman A, Preissl S, Wu S, Koga T, Zhu C, Luebeck J, Van Deynze K, Han JY, Hou X, Ye Z, Mischel A, Li YE, Fang R, Baback T, Mugford J, Han C, Glass C, Barr C, Mischel P, Bafna V, Escoubet L, Ren B, Chen C. DDDR-24. INTEGRATED ANALYSIS OF SINGLE CELL CHROMATIN ACCESSIBILITY AND RNA EXPRESSION IDENTIFIED COMMON VULNERABILITY DESPITE GLIOBLASTOMA HETEROGENEITY. Neuro Oncol 2022. [PMCID: PMC9660535 DOI: 10.1093/neuonc/noac209.389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
INTRODUCTION
In 2021, the World Health Organization (WHO) reclassified glioblastoma, the most common form of adult brain cancer, into isocitrate dehydrogenase (IDH) wild-type glioblastomas and grade IV IDH mutant (G4 IDHm) astrocytomas. For both tumor types, intra-tumoral heterogeneity is a key contributor to therapeutic failure.
METHODS
we applied integrated genome-wide chromatin accessibility (snATACseq) and transcription (snRNAseq) profiles to clinical specimens derived IDHwt glioblastomas and G4 IDHm) astrocytomas, with goal of therapeutic target discovery.
RESULTS
The integrated analysis achieved resolution of intra-tumoral heterogeneity not previously possible, providing a molecular landscape of extensive regional and cellular variability. snATACseq delineated focal amplification down to an ~40 KB resolution. The snRNA analysis elucidated distinct cell types and cell states (neural progenitor/oligodendrocyte cell-like or astrocyte/mesenchymal cell-like) that were superimposable onto the snATACseq landscape. Paired-seq (parallel snATACseq and snRNAseq using the same clinical sample) provided high resolution delineation of extrachromosomal circular DNA (ecDNA), harboring oncogenes including CCND1 and EGFR. Importantly, the copy number of ecDNA genes correlated closely with the level of RNA expression. Integrated analysis across all specimens profiled suggests that IDHm grade 4 astrocytoma and IDHwt glioblastoma cells shared a common chromatin structure defined by open regions enriched for Nuclear Factor 1 transcription factors (NFIA and NFIB). Silencing of NF1A or NF1B suppressed in vitro and in vivo growth of patient-derived IDHwt glioblastomas and G4 IDHm astrocytoma models that mimic distinct glioblastoma cell states.
CONCLUSION
Our findings suggest despite distinct genotypes and cell states, glablastoma/G4 astrocytoma cells share dependency on core transcriptional programs, yielding an attractive platform for addressing therapeutic challenges associated with intra-tumoral heterogeneity.
Collapse
Affiliation(s)
| | - Anugraha Raman
- University of California, San Diego , San Diego, CA , USA
| | | | - Shaoping Wu
- University of Minnesota , Minneapolis, MN , USA
| | | | - Chenxu Zhu
- University of California, San Diego , San Diego, CA , USA
| | - Jens Luebeck
- University of California, San Diego , San, CA , USA
| | | | - Jee Yun Han
- University of California, San Diego , San Diego, CA , USA
| | - Xioameng Hou
- University of California, San Diego , San Diego, CA , USA
| | - Zhen Ye
- University of California, San Diego , San Diego, CA , USA
| | - Anna Mischel
- University of California, San Diego , San Diego , USA
| | - Yang Eric Li
- University of California, San Diego , San Diego , USA
| | - Rongxin Fang
- University of California, San Diego , San Diego , USA
| | - Tomas Baback
- University of California, San Diego , San Diego, CA , USA
| | - Joshua Mugford
- University of California, San Diego , San Diego, CA , USA
| | - Claudia Han
- University of California, San Diego , San Diego, CA , USA
| | | | - Cathy Barr
- University of California, San Diego , San Diego, CA , USA
| | - Paul Mischel
- University of California, San Diego , San Diego , USA
| | - Vineet Bafna
- University of California, San Diego , San Diego , USA
| | | | - Bing Ren
- University of California, San Diego , San Diego, CA , USA
| | - Clark Chen
- University of Minnesota Medical School, Department of Neurosurgery , Minneapolis, MN , USA
| |
Collapse
|
6
|
Gong T, Lu T, Mi JX, Fang R, Shan C. [Research progress on the mechanisms of cryotherapy and its application in laryngopharyngeal diseases]. Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2022; 57:1023-1027. [PMID: 36058675 DOI: 10.3760/cma.j.cn115330-20211221-00811] [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] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- T Gong
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - T Lu
- Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - J X Mi
- Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - R Fang
- the Department of Otolaryngology-Head and Neck Surgery, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai 200031, China
| | - Chunlei Shan
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China Center of Rehabilitation Medicine, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China Engineering Research Center of Traditional Chinese Medicine Intelligent Rehabilitation, Ministry of Education, Shanghai 201203, China
| |
Collapse
|
7
|
Fang R, Xia C, Close JL, Zhang M, He J, Huang Z, Halpern AR, Long B, Miller JA, Lein ES, Zhuang X. Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH. Science 2022; 377:56-62. [PMID: 35771910 PMCID: PMC9262715 DOI: 10.1126/science.abm1741] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [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: 12/21/2022]
Abstract
The human cerebral cortex has tremendous cellular diversity. How different cell types are organized in the human cortex and how cellular organization varies across species remain unclear. In this study, we performed spatially resolved single-cell profiling of 4000 genes using multiplexed error-robust fluorescence in situ hybridization (MERFISH), identified more than 100 transcriptionally distinct cell populations, and generated a molecularly defined and spatially resolved cell atlas of the human middle and superior temporal gyrus. We further explored cell-cell interactions arising from soma contact or proximity in a cell type-specific manner. Comparison of the human and mouse cortices showed conservation in the laminar organization of cells and differences in somatic interactions across species. Our data revealed human-specific cell-cell proximity patterns and a markedly increased enrichment for interactions between neurons and non-neuronal cells in the human cortex.
Collapse
Affiliation(s)
- Rongxin Fang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Chenglong Xia
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Jennie L Close
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Meng Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Jiang He
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Zhengkai Huang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Aaron R Halpern
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| |
Collapse
|
8
|
Li YE, Preissl S, Hou X, Zhang Z, Zhang K, Qiu Y, Poirion OB, Li B, Chiou J, Liu H, Pinto-Duarte A, Kubo N, Yang X, Fang R, Wang X, Han JY, Lucero J, Yan Y, Miller M, Kuan S, Gorkin D, Gaulton KJ, Shen Y, Nunn M, Mukamel EA, Behrens MM, Ecker JR, Ren B. An atlas of gene regulatory elements in adult mouse cerebrum. Nature 2021; 598:129-136. [PMID: 34616068 PMCID: PMC8494637 DOI: 10.1038/s41586-021-03604-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 04/30/2021] [Indexed: 12/21/2022]
Abstract
The mammalian cerebrum performs high-level sensory perception, motor control and cognitive functions through highly specialized cortical and subcortical structures1. Recent surveys of mouse and human brains with single-cell transcriptomics2-6 and high-throughput imaging technologies7,8 have uncovered hundreds of neural cell types distributed in different brain regions, but the transcriptional regulatory programs that are responsible for the unique identity and function of each cell type remain unknown. Here we probe the accessible chromatin in more than 800,000 individual nuclei from 45 regions that span the adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei, and use the resulting data to map the state of 491,818 candidate cis-regulatory DNA elements in 160 distinct cell types. We find high specificity of spatial distribution for not only excitatory neurons, but also most classes of inhibitory neurons and a subset of glial cell types. We characterize the gene regulatory sequences associated with the regional specificity within these cell types. We further link a considerable fraction of the cis-regulatory elements to putative target genes expressed in diverse cerebral cell types and predict transcriptional regulators that are involved in a broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Our results provide a foundation for comprehensive analysis of gene regulatory programs of the mammalian brain and assist in the interpretation of noncoding risk variants associated with various neurological diseases and traits in humans.
Collapse
Affiliation(s)
- Yang Eric Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Sebastian Preissl
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Xiaomeng Hou
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Ziyang Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Kai Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Olivier B Poirion
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Bin Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Joshua Chiou
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Antonio Pinto-Duarte
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Naoki Kubo
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Xiaoyu Yang
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Rongxin Fang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Xinxin Wang
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Jee Yun Han
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Jacinta Lucero
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yiming Yan
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Michael Miller
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Samantha Kuan
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - David Gorkin
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Kyle J Gaulton
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Yin Shen
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Michael Nunn
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
9
|
Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Yanny AM, Zhang R, Ament SA, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preissl S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, Zeng H, Zhang K, Feng G, Ecker JR, Linnarsson S, Lein ES. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature 2021; 598:111-119. [PMID: 34616062 PMCID: PMC8494640 DOI: 10.1038/s41586-021-03465-8] [Citation(s) in RCA: 258] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 03/17/2021] [Indexed: 12/11/2022]
Abstract
The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch-seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.
Collapse
Affiliation(s)
| | | | - Qiwen Hu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Blue B Lake
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Wei Tian
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Brian E Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Megan Crow
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Fenna M Krienen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Jeroen Eggermont
- LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Andrew I Aldridge
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | - Rosa G Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nikolai Dembrow
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
- Epilepsy Center of Excellence, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Dinh Diep
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | | | - Weixiu Dong
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Rongxin Fang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Stephan Fischer
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Melissa Goldman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Brian R Herb
- Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Xiaomeng Hou
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jayaram Kancherla
- Department of Computer Science, University of Maryland College Park, College Park, MD, USA
| | | | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Baldur van Lew
- LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Yang Eric Li
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Christine S Liu
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Biomedical Sciences Program, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Anup Mahurkar
- Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | | | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Sheng-Yong Niu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Computer Science and Engineering Program, University of California, San Diego, La Jolla, CA, USA
| | - Joshua Orvis
- Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Julia K Osteen
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Scott Owen
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Carter R Palmer
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Biomedical Sciences Program, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Thanh Pham
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nongluk Plongthongkum
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivier Poirion
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nora M Reed
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Angeline Rivkin
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - William J Romanow
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Kimberly Siletti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Xinxin Wang
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Fangming Xie
- Department of Physics, University of California, San Diego, La Jolla, CA, USA
| | | | - Renee Zhang
- J. Craig Venter Institute, La Jolla, CA, USA
| | - Seth A Ament
- Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Hector Corrada Bravo
- Department of Computer Science, University of Maryland College Park, College Park, MD, USA
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Ronna Hertzano
- Departments of Otorhinolaryngology, Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Höllt
- Computer Graphics and Visualization Group, Delt University of Technology, Delft, The Netherlands
| | - Gregory D Horwitz
- Department of Physiology and Biophysics, Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA
- Regional Epilepsy Center, Harborview Medical Center, Seattle, WA, USA
| | - Boudewijn P Lelieveldt
- LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Pattern Recognition and Bioinformatics group, Delft University of Technology, Delft, The Netherlands
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA
| | | | - Sebastian Preissl
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bing Ren
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pathology, University of California, San Diego, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - William J Spain
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
- Epilepsy Center of Excellence, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Owen R White
- Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | | | | | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
| |
Collapse
|
10
|
Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, Casper T, Colantuoni C, Crabtree J, Creasy H, Crichton K, Crow M, Dee N, Dougherty EL, Doyle WI, Dudoit S, Fang R, Felix V, Fong O, Giglio M, Goldy J, Hawrylycz M, Herb BR, Hertzano R, Hou X, Hu Q, Kancherla J, Kroll M, Lathia K, Li YE, Lucero JD, Luo C, Mahurkar A, McMillen D, Nadaf NM, Nery JR, Nguyen TN, Niu SY, Ntranos V, Orvis J, Osteen JK, Pham T, Pinto-Duarte A, Poirion O, Preissl S, Purdom E, Rimorin C, Risso D, Rivkin AC, Smith K, Street K, Sulc J, Svensson V, Tieu M, Torkelson A, Tung H, Vaishnav ED, Vanderburg CR, van Velthoven C, Wang X, White OR, Huang ZJ, Kharchenko PV, Pachter L, Ngai J, Regev A, Tasic B, Welch JD, Gillis J, Macosko EZ, Ren B, Ecker JR, Zeng H, Mukamel EA. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature 2021; 598:103-110. [PMID: 34616066 PMCID: PMC8494649 DOI: 10.1038/s41586-021-03500-8] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [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: 03/05/2020] [Accepted: 03/26/2021] [Indexed: 12/30/2022]
Abstract
Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain1-3. With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of cell-type organization. Here we generated transcriptomes and epigenomes from more than 500,000 individual cells in the mouse primary motor cortex, a structure that has an evolutionarily conserved role in locomotion. We developed computational and statistical methods to integrate multimodal data and quantitatively validate cell-type reproducibility. The resulting reference atlas-containing over 56 neuronal cell types that are highly replicable across analysis methods, sequencing technologies and modalities-is a comprehensive molecular and genomic account of the diverse neuronal and non-neuronal cell types in the mouse primary motor cortex. The atlas includes a population of excitatory neurons that resemble pyramidal cells in layer 4 in other cortical regions4. We further discovered thousands of concordant marker genes and gene regulatory elements for these cell types. Our results highlight the complex molecular regulation of cell types in the brain and will directly enable the design of reagents to target specific cell types in the mouse primary motor cortex for functional analysis.
Collapse
Affiliation(s)
- Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Fangming Xie
- Department of Physics, University of California, San Diego, La Jolla, CA, USA
| | - Stephan Fischer
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Ricky S Adkins
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrew I Aldridge
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Koen Van den Berge
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium
| | | | - Hector Roux de Bézieux
- Division of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Héctor Corrada Bravo
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | | | - Carlo Colantuoni
- Johns Hopkins School of Medicine, Department of Neurology, Baltimore, MD, USA
- Johns Hopkins School of Medicine, Department of Neuroscience, Baltimore, MD, USA
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Heather Creasy
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Megan Crow
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Wayne I Doyle
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA
| | - Sandrine Dudoit
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Rongxin Fang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, San Diego, CA, USA
| | - Victor Felix
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Michelle Giglio
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Brian R Herb
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ronna Hertzano
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Otorhinolaryngology, Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Xiaomeng Hou
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Qiwen Hu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jayaram Kancherla
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | | | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Yang Eric Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Jacinta D Lucero
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Chongyuan Luo
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anup Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Naeem M Nadaf
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Sheng-Yong Niu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Vasilis Ntranos
- University of California, San Francisco, San Francisco, CA, USA
| | - Joshua Orvis
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Julia K Osteen
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Thanh Pham
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Antonio Pinto-Duarte
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Olivier Poirion
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| | | | - Davide Risso
- Department of Statistical Sciences, University of Padova, Padova, Italy
| | - Angeline C Rivkin
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Kelly Street
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Xinxin Wang
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Owen R White
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Lior Pachter
- California Institute of Technology, Pasadena, CA, USA
| | - John Ngai
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA, USA
| | | | - Joshua D Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Bing Ren
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA.
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
11
|
Callaway EM, Dong HW, Ecker JR, Hawrylycz MJ, Huang ZJ, Lein ES, Ngai J, Osten P, Ren B, Tolias AS, White O, Zeng H, Zhuang X, Ascoli GA, Behrens MM, Chun J, Feng G, Gee JC, Ghosh SS, Halchenko YO, Hertzano R, Lim BK, Martone ME, Ng L, Pachter L, Ropelewski AJ, Tickle TL, Yang XW, Zhang K, Bakken TE, Berens P, Daigle TL, Harris JA, Jorstad NL, Kalmbach BE, Kobak D, Li YE, Liu H, Matho KS, Mukamel EA, Naeemi M, Scala F, Tan P, Ting JT, Xie F, Zhang M, Zhang Z, Zhou J, Zingg B, Armand E, Yao Z, Bertagnolli D, Casper T, Crichton K, Dee N, Diep D, Ding SL, Dong W, Dougherty EL, Fong O, Goldman M, Goldy J, Hodge RD, Hu L, Keene CD, Krienen FM, Kroll M, Lake BB, Lathia K, Linnarsson S, Liu CS, Macosko EZ, McCarroll SA, McMillen D, Nadaf NM, Nguyen TN, Palmer CR, Pham T, Plongthongkum N, Reed NM, Regev A, Rimorin C, Romanow WJ, Savoia S, Siletti K, Smith K, Sulc J, Tasic B, Tieu M, Torkelson A, Tung H, van Velthoven CTJ, Vanderburg CR, Yanny AM, Fang R, Hou X, Lucero JD, Osteen JK, Pinto-Duarte A, Poirion O, Preissl S, Wang X, Aldridge AI, Bartlett A, Boggeman L, O’Connor C, Castanon RG, Chen H, Fitzpatrick C, Luo C, Nery JR, Nunn M, Rivkin AC, Tian W, Dominguez B, Ito-Cole T, Jacobs M, Jin X, Lee CT, Lee KF, Miyazaki PA, Pang Y, Rashid M, Smith JB, Vu M, Williams E, Biancalani T, Booeshaghi AS, Crow M, Dudoit S, Fischer S, Gillis J, Hu Q, Kharchenko PV, Niu SY, Ntranos V, Purdom E, Risso D, de Bézieux HR, Somasundaram S, Street K, Svensson V, Vaishnav ED, Van den Berge K, Welch JD, An X, Bateup HS, Bowman I, Chance RK, Foster NN, Galbavy W, Gong H, Gou L, Hatfield JT, Hintiryan H, Hirokawa KE, Kim G, Kramer DJ, Li A, Li X, Luo Q, Muñoz-Castañeda R, Stafford DA, Feng Z, Jia X, Jiang S, Jiang T, Kuang X, Larsen R, Lesnar P, Li Y, Li Y, Liu L, Peng H, Qu L, Ren M, Ruan Z, Shen E, Song Y, Wakeman W, Wang P, Wang Y, Wang Y, Yin L, Yuan J, Zhao S, Zhao X, Narasimhan A, Palaniswamy R, Banerjee S, Ding L, Huilgol D, Huo B, Kuo HC, Laturnus S, Li X, Mitra PP, Mizrachi J, Wang Q, Xie P, Xiong F, Yu Y, Eichhorn SW, Berg J, Bernabucci M, Bernaerts Y, Cadwell CR, Castro JR, Dalley R, Hartmanis L, Horwitz GD, Jiang X, Ko AL, Miranda E, Mulherkar S, Nicovich PR, Owen SF, Sandberg R, Sorensen SA, Tan ZH, Allen S, Hockemeyer D, Lee AY, Veldman MB, Adkins RS, Ament SA, Bravo HC, Carter R, Chatterjee A, Colantuoni C, Crabtree J, Creasy H, Felix V, Giglio M, Herb BR, Kancherla J, Mahurkar A, McCracken C, Nickel L, Olley D, Orvis J, Schor M, Hood G, Dichter B, Grauer M, Helba B, Bandrowski A, Barkas N, Carlin B, D’Orazi FD, Degatano K, Gillespie TH, Khajouei F, Konwar K, Thompson C, Kelly K, Mok S, Sunkin S. A multimodal cell census and atlas of the mammalian primary motor cortex. Nature 2021; 598:86-102. [PMID: 34616075 PMCID: PMC8494634 DOI: 10.1038/s41586-021-03950-0] [Citation(s) in RCA: 205] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 08/25/2021] [Indexed: 12/14/2022]
Abstract
Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
Collapse
|
12
|
Yu M, Abnousi A, Zhang Y, Li G, Lee L, Chen Z, Fang R, Lagler TM, Yang Y, Wen J, Sun Q, Li Y, Ren B, Hu M. SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data. Nat Methods 2021; 18:1056-1059. [PMID: 34446921 PMCID: PMC8440170 DOI: 10.1038/s41592-021-01231-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/30/2021] [Indexed: 11/30/2022]
Abstract
Single-cell Hi-C (scHi-C) analysis has been increasingly used to map chromatin architecture in diverse tissue contexts, but computational tools to define chromatin loops at high resolution from scHi-C data are still lacking. Here, we describe Single-Nucleus Analysis Pipeline for Hi-C (SnapHiC), a method that can identify chromatin loops at high resolution and accuracy from scHi-C data. Using scHi-C data from 742 mouse embryonic stem cells, we benchmark SnapHiC against a number of computational tools developed for mapping chromatin loops and interactions from bulk Hi-C. We further demonstrate its use by analyzing single-nucleus methyl-3C-seq data from 2,869 human prefrontal cortical cells, which uncovers cell type-specific chromatin loops and predicts putative target genes for noncoding sequence variants associated with neuropsychiatric disorders. Our results indicate that SnapHiC could facilitate the analysis of cell type-specific chromatin architecture and gene regulatory programs in complex tissues. SnapHiC offers a computational tool for improving detection of chromatin loops from single-cell Hi-C data.
Collapse
Affiliation(s)
- Miao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Armen Abnousi
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Guoqiang Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Lindsay Lee
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Ziyin Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Rongxin Fang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.,Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Taylor M Lagler
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Yuchen Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA.,McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.,Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA. .,Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
| |
Collapse
|
13
|
Fang R, Preissl S, Li Y, Hou X, Lucero J, Wang X, Motamedi A, Shiau AK, Zhou X, Xie F, Mukamel EA, Zhang K, Zhang Y, Behrens MM, Ecker JR, Ren B. Comprehensive analysis of single cell ATAC-seq data with SnapATAC. Nat Commun 2021; 12:1337. [PMID: 33637727 PMCID: PMC7910485 DOI: 10.1038/s41467-021-21583-9] [Citation(s) in RCA: 183] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 02/01/2021] [Indexed: 01/17/2023] Open
Abstract
Identification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. Single cell analysis of accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volume of data pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nyström method, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC is applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis reveals ~370,000 candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate cell-type specific transcriptional regulators.
Collapse
Affiliation(s)
- Rongxin Fang
- grid.1052.60000000097371625Ludwig Institute for Cancer Research, La Jolla, CA USA ,grid.38142.3c000000041936754XDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA USA
| | - Sebastian Preissl
- grid.266100.30000 0001 2107 4242Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA USA
| | - Yang Li
- grid.1052.60000000097371625Ludwig Institute for Cancer Research, La Jolla, CA USA
| | - Xiaomeng Hou
- grid.266100.30000 0001 2107 4242Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA USA
| | - Jacinta Lucero
- grid.250671.70000 0001 0662 7144The Salk Institute for Biological Studies, La Jolla, CA USA
| | - Xinxin Wang
- grid.266100.30000 0001 2107 4242Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA USA
| | - Amir Motamedi
- grid.1052.60000000097371625Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA USA
| | - Andrew K. Shiau
- grid.1052.60000000097371625Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA USA
| | - Xinzhu Zhou
- grid.266100.30000 0001 2107 4242Biomedical Science Graduate Program, University of California San Diego, La Jolla, CA USA
| | - Fangming Xie
- grid.266100.30000 0001 2107 4242Department of Physics, University of California, San Diego, La Jolla, CA USA
| | - Eran A. Mukamel
- grid.266100.30000 0001 2107 4242Department of Physics, University of California, San Diego, La Jolla, CA USA
| | - Kai Zhang
- grid.1052.60000000097371625Ludwig Institute for Cancer Research, La Jolla, CA USA
| | - Yanxiao Zhang
- grid.1052.60000000097371625Ludwig Institute for Cancer Research, La Jolla, CA USA
| | - M. Margarita Behrens
- grid.250671.70000 0001 0662 7144The Salk Institute for Biological Studies, La Jolla, CA USA
| | - Joseph R. Ecker
- grid.250671.70000 0001 0662 7144The Salk Institute for Biological Studies, La Jolla, CA USA ,grid.250671.70000 0001 0662 7144Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA. .,Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA. .,Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, UCSD Moores Cancer Center, La Jolla, CA, USA.
| |
Collapse
|
14
|
Shoshani O, Brunner SF, Yaeger R, Ly P, Nechemia-Arbely Y, Kim DH, Fang R, Castillon GA, Yu M, Li JSZ, Sun Y, Ellisman MH, Ren B, Campbell PJ, Cleveland DW. Chromothripsis drives the evolution of gene amplification in cancer. Nature 2020; 591:137-141. [PMID: 33361815 PMCID: PMC7933129 DOI: 10.1038/s41586-020-03064-z] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 11/26/2020] [Indexed: 12/15/2022]
Abstract
Focal chromosomal amplification is an important route to generating cancer through mediating over-expression of oncogenes1–3 or to developing cancer therapy resistance by increasing expression of a gene whose action diminishes efficacy of an anti-cancer drug. Here we used whole-genome sequencing of clonal isolates developing chemotherapeutic resistance to identify chromothripsis as a major driver of extrachromosomal DNA (ecDNA) amplification into circular double minutes (DMs) through PARP- and DNA-PKcs-dependent mechanisms. Longitudinal analyses revealed that DMs undergo continuing structural evolution to promote increased drug tolerance through additional chromothriptic events. In-situ Hi-C sequencing is used to demonstrate that DMs preferentially tether near chromosome ends where they re-integrate when DNA damage is present. Intrachromosomal amplifications formed initially under low-level drug selection undergo continuing breakage-fusion-bridge cycles, generating >100 megabase-long amplicons that we show become trapped within interphase bridges and then shattered, producing micronuclei that mediate DM formation. Similar genome rearrangement profiles linked to localized gene amplification are identified in human cancers with acquired drug resistance or with oncogene amplifications. We propose that chromothripsis is a primary mechanism accelerating genomic DNA amplification and which enables rapid acquisition of tolerance to altered growth conditions.
Collapse
Affiliation(s)
- Ofer Shoshani
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | | | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter Ly
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.,Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yael Nechemia-Arbely
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.,Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dong Hyun Kim
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Rongxin Fang
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Guillaume A Castillon
- National Center for Microscopy and Imaging Research (NCMIR), University of California at San Diego, La Jolla, CA, USA
| | - Miao Yu
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Julia S Z Li
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ying Sun
- Department of Pediatrics, University of California at San Diego, La Jolla, CA, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research (NCMIR), University of California at San Diego, La Jolla, CA, USA.,Department of Neurosciences, University of California at San Diego, La Jolla, CA, USA.,Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
| | - Bing Ren
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Peter J Campbell
- Wellcome Sanger Institute, Hinxton, UK. .,Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Don W Cleveland
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA. .,Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.
| |
Collapse
|
15
|
Robledo EA, Schutzman R, Fang R, Fernandez C, Kwasinski R, Leiva K, Perez-Clavijo F, Godavarty A. Physiological wound assessment from coregistered and segmented tissue hemoglobin maps. J Opt Soc Am A Opt Image Sci Vis 2020; 37:1249-1256. [PMID: 32749259 DOI: 10.1364/josaa.394985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
A handheld near-infrared optical scanner (NIROS) was recently developed to map for effective changes in oxy- and deoxyhemoglobin concentration in diabetic foot ulcers (DFUs) across weeks of treatment. Herein, a coregistration and image segmentation approach was implemented to overlay hemoglobin maps onto the white light images of ulcers. Validation studies demonstrated over 97% accuracy in coregistration. Coregistration was further applied to a healing DFU across weeks of healing. The potential to predict changes in wound healing was observed when comparing the coregistered and segmented hemoglobin concentration area maps to the visual area of the wound.
Collapse
|
16
|
He Y, Hariharan M, Gorkin DU, Dickel DE, Luo C, Castanon RG, Nery JR, Lee AY, Zhao Y, Huang H, Williams BA, Trout D, Amrhein H, Fang R, Chen H, Li B, Visel A, Pennacchio LA, Ren B, Ecker JR. Spatiotemporal DNA methylome dynamics of the developing mouse fetus. Nature 2020; 583:752-759. [PMID: 32728242 PMCID: PMC7398276 DOI: 10.1038/s41586-020-2119-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 06/11/2019] [Indexed: 01/10/2023]
Abstract
Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited1,2. Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 168 methylomes from 12 mouse tissues or organs at 9 developmental stages from embryogenesis to adulthood. We identified 1,808,810 genomic regions that showed variations in CG methylation by comparing the methylomes of different tissues or organs from different developmental stages. These DNA elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. During late stages of fetal development, non-CG methylation accumulated within the bodies of key developmental transcription factor genes, coinciding with their transcriptional repression. Integration of genome-wide DNA methylation, histone modification and chromatin accessibility data enabled us to predict 461,141 putative developmental tissue-specific enhancers, the human orthologues of which were enriched for disease-associated genetic variants. These spatiotemporal epigenome maps provide a resource for studies of gene regulation during tissue or organ progression, and a starting point for investigating regulatory elements that are involved in human developmental disorders. Analysis of 168 methylomes from 12 mouse tissues at 9 developmental stages sheds light on the epigenetic and regulatory landscape during mammalian fetal development.
Collapse
Affiliation(s)
- Yupeng He
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.,Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Manoj Hariharan
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - David U Gorkin
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chongyuan Luo
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rosa G Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Yuan Zhao
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA.,Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Hui Huang
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.,Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Brian A Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Diane Trout
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Henry Amrhein
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rongxin Fang
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA.,Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Huaming Chen
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bin Li
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,School of Natural Sciences, University of California, Merced, Merced, CA, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Comparative Biochemistry Program, University of California, Berkeley, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA. .,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| |
Collapse
|
17
|
Xia NB, Lu Y, Zhao PF, Wang CF, Li YY, Tan L, Fang R, Zhou YQ, Shen B, Zhao JL. Genotyping and characterization of Toxoplasma gondii strain isolated from pigs in Hubei province, central China. Trop Biomed 2020; 37:489-498. [PMID: 33612818] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Toxoplasma gondii, a ubiquitous pathogen that infects nearly all warm-blooded animals and humans, can cause severe complications to the infected people and animals as well as serious economic losses and social problems. Here, one local strain (TgPIG-WH1) was isolated from an aborted pig fetus, and the genotype of this strain was identified as ToxoDB #3 by the PCR RFLP typing method using 10 molecular markers (SAG1, SAG2, alternative SAG2, SAG3, BTUB, GRA6, L358, PK1, C22-8, C29-2 and Apico). A comparison of the virulence of this isolate with other strains in both mice and piglets showed that TgPIG-WH1 was less virulent than type 1 strain RH and type 2 strain ME49 in mice, and caused similar symptoms to those of ME49 such as fever in piglets. Additionally, in piglet infection with both strains, the TgPIG-WH1 caused a higher IgG response and more severe pathological damages than ME49. Furthermore, TgPIG-WH1 caused one death in the 5 infected piglets, whereas ME49 did not, suggesting the higher virulence of TgPIG-WH1 than ME49 during piglet infection. Experimental infections indicate that the virulence of TgPIG-WH1 relative to ME49 is weaker in mice, but higher in pigs. This is probably the first report regarding a ToxoDB #3 strain from pigs in Hubei, China. These data will facilitate the understanding of genetic diversity of Toxoplasma strains in China as well as the prevention and control of porcine toxoplasmosis in the local region.
Collapse
Affiliation(s)
- N B Xia
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - Y Lu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - P F Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - C F Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - Y Y Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - L Tan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - R Fang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - Y Q Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - B Shen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
- Key Laboratory of Preventive Medicine in Hubei Province, Wuhan, Hubei Province, PR China
| | - J L Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
- Hubei Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, PR China
- Key Laboratory of Preventive Medicine in Hubei Province, Wuhan, Hubei Province, PR China
| |
Collapse
|
18
|
Chiu WC, Powers DB, Hirshon JM, Shackelford SA, Hu PF, Chen SY, Chen HH, Mackenzie CF, Miller CH, DuBose JJ, Carroll C, Fang R, Scalea TM. Impact of trauma centre capacity and volume on the mortality risk of incoming new admissions. BMJ Mil Health 2020; 168:212-217. [PMID: 32474436 DOI: 10.1136/bmjmilitary-2020-001483] [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: 04/03/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Trauma centre capacity and surge volume may affect decisions on where to transport a critically injured patient and whether to bypass the closest facility. Our hypothesis was that overcrowding and high patient acuity would contribute to increase the mortality risk for incoming admissions. METHODS For a 6-year period, we merged and cross-correlated our institutional trauma registry with a database on Trauma Resuscitation Unit (TRU) patient admissions, movement and discharges, with average capacity of 12 trauma bays. The outcomes of overall hospital and 24 hours mortality for new trauma admissions (NEW) were assessed by multivariate logistic regression. RESULTS There were 42 003 (mean=7000/year) admissions having complete data sets, with 36 354 (87%) patients who were primary trauma admissions, age ≥18 and survival ≥15 min. In the logistic regression model for the entire cohort, NEW admission hospital mortality was only associated with NEW admission age and prehospital Glasgow Coma Scale (GCS) and Shock Index (SI) (all p<0.05). When TRU occupancy reached ≥16 patients, the factors associated with increased NEW admission hospital mortality were existing patients (TRU >1 hour) with SI ≥0.9, recent admissions (TRU ≤1 hour) with age ≥65, NEW admission age and prehospital GCS and SI (all p<0.05). CONCLUSION The mortality of incoming patients is not impacted by routine trauma centre overcapacity. In conditions of severe overcrowding, the number of admitted patients with shock physiology and a recent surge of elderly/debilitated patients may influence the mortality risk of a new trauma admission.
Collapse
Affiliation(s)
- William C Chiu
- R Adams Cowley Shock Trauma Center, Baltimore, Maryland, USA
| | - D B Powers
- Director, Craniomaxillofacial Trauma Program, Duke University Hospital, Durham, North Carolina, USA
| | - J M Hirshon
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - P F Hu
- University of Maryland Medical Center, Baltimore, Maryland, USA
| | - S Y Chen
- National Yunlin University of Science and Technology, Douliou, Taiwan
| | - H H Chen
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - C F Mackenzie
- Shock Trauma and Anesthesiology Research - Organized Research Center (STAR-ORC), University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - C H Miller
- US Air Force Materiel Command, Wright-Patterson AFB, Ohio, USA
| | - J J DuBose
- R Adams Cowley Shock Trauma Center, Baltimore, Maryland, USA.,Center for Sustainment of Trauma and Readiness Skills - Baltimore, US Air Force Medical Service, Baltimore, Maryland, USA
| | | | - R Fang
- Surgery, Johns Hopkins Bayview Medical Center, Baltimore, Maryland, USA
| | - T M Scalea
- R Adams Cowley Shock Trauma Center, Baltimore, Maryland, USA
| |
Collapse
|
19
|
Zhang H, Tang K, Fang R, Sun Q. What dermatologists could do to cope with the novel coronavirus (SARS-CoV-2): a dermatologist's perspective from China. J Eur Acad Dermatol Venereol 2020; 34:e211-e212. [PMID: 32220020 DOI: 10.1111/jdv.16389] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- H Zhang
- Department of Dermatology, Peking Union Medical College Hospital, Beijing, China
| | - K Tang
- Department of Dermatology, Peking Union Medical College Hospital, Beijing, China
| | - R Fang
- Department of Dermatology, Peking Union Medical College Hospital, Beijing, China
| | - Q Sun
- Department of Dermatology, Peking Union Medical College Hospital, Beijing, China
| |
Collapse
|
20
|
Wang Y, Zhang H, Fang R, Tang K, Sun Q. The top 100 most cited articles in rosacea: a bibliometric analysis. J Eur Acad Dermatol Venereol 2020; 34:2177-2182. [PMID: 32078196 DOI: 10.1111/jdv.16305] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/06/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Y. Wang
- Department of Dermatology Peking Union Medical College Hospital Beijing China
- Eight‐year MD Program Peking Union Medical College Beijing China
| | - H. Zhang
- Department of Dermatology Peking Union Medical College Hospital Beijing China
- Eight‐year MD Program Peking Union Medical College Beijing China
| | - R. Fang
- Department of Dermatology Peking Union Medical College Hospital Beijing China
| | - K. Tang
- Department of Dermatology Peking Union Medical College Hospital Beijing China
- Eight‐year MD Program Peking Union Medical College Beijing China
| | - Q. Sun
- Department of Dermatology Peking Union Medical College Hospital Beijing China
| |
Collapse
|
21
|
Fang R, Zhao NN, Zeng KX, Wen Q, Xiao P, Luo X, Liu XW, Wang YL. MicroRNA-544 inhibits inflammatory response and cell apoptosis after cerebral ischemia reperfusion by targeting IRAK4. Eur Rev Med Pharmacol Sci 2019; 22:5605-5613. [PMID: 30229835 DOI: 10.26355/eurrev_201809_15825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Stroke remains the most common malignant cerebrovascular event in the world. The correlation between the expression of miR-544 and the degree of cerebral ischemia reperfusion (CIR) injury has not been well recognized in recent years. This study focuses on the effect of miR-544 on inflammation and apoptosis after CIR. PATIENTS AND METHODS Plasma expression of miR-544 in ischemic stroke (IS) patients and healthy controls was determined by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). The effects of miR-544 on cerebral infarction and neurological deficits were verified in vitro by tail vein injection of Ago-miR-544. Western blotting was utilized to examine protein expressions of key proteins involving in inflammation and apoptosis in mouse brain. Western blotting, immunofluorescence staining and luciferase assays were used to demonstrate whether miR-544 influences the expression of interleukin-1 receptor-associated kinase 4 (IRAK4), downstream inflammatory and apoptosis-related proteins. RESULTS MiR-544 was found decreased in peripheral blood of IS patients compared with healthy controls. MiR-544 has been shown to relieve neurological deficits and reduce the volume of cerebral infarction in mice. Overexpression of miR-544 ameliorated the inflammation and apoptotic responses in brain tissue after ischemia reperfusion by down-regulating the expression of IRAK4, whereas the low expression was opposite in vivo and in vitro. CONCLUSIONS We found that miR-544 may participate in controlling inflammation and apoptosis after ischemia-reperfusion by targeting IRAK4, providing possible diagnostic indicators and therapeutic targets for IS.
Collapse
Affiliation(s)
- R Fang
- Department of Rehabilitation, The First Affiliated Hospital, Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China.
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Xiao P, Liu XW, Zhao NN, Fang R, Wen Q, Zeng KX, Wang YL. Correlations of neuronal apoptosis with expressions of c-Fos and c-Jun in rats with post-ischemic reconditioning damage. Eur Rev Med Pharmacol Sci 2019; 22:2832-2838. [PMID: 29771436 DOI: 10.26355/eurrev_201805_14984] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Transcription factors (c-Fos and c-Jun) have been considered to play roles in the initiation of programmed nerve cell death. However, the roles of c-Fos and c-Jun protein expressions in neuronal apoptosis of rats with post-ischemic reconditioning damage were not clarified. Therefore, the aim of this study was to investigate the correlations of protein expressions of c-Fos and c-Jun with neuronal apoptosis of rats with post-ischemic reconditioning damage. MATERIALS AND METHODS Rat models of post-ischemic reconditioning were established firstly. Then, apoptosis was assessed by terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate-biotin nick end labeling (TUNEL) assay, and the gene expression levels of apoptosis-related proteins [cytochrome c (Cyt c), B-cell lymphoma 2 (Bcl-2) and Bcl-2-associated X protein (Bax)] were detected by reverse transcription-polymerase chain reaction (RT-PCR). Lastly, Western blotting was used to determine the protein expression levels of c-Fos and c-Jun, and the expressions of c-Fos and c-Jun in brain tissues of models were measured by immunohistochemistry. RESULTS Treatment group had significantly increased malonaldehyde (MDA) level and significantly decreased superoxide dismutase (SOD) activity in rat cortex compared with those in control group (p<0.05). The number of TUNEL positive cells in the right cortex of rats in the treatment group was clearly higher than that in control group. Among them, post-ischemic reperfusion group had reduced level of Bax in the cytoplasm, but increased Bax level in the mitochondrion, and lowered expression level of Bcl-2 in both mitochondrion and cytoplasm in comparison with control group. Dynamic detection results of c-Jun were in synchronization with those of apoptosis proteins, and maximum expression occurred at 24 h after treatment. CONCLUSIONS c-Jun may play a role in the initiation of apoptotic cell death in these neurons.
Collapse
Affiliation(s)
- P Xiao
- Department of Rehabilitation, Shenzhen Dapeng New District Nan'ao People's Hospital, Shenzhen, China.
| | | | | | | | | | | | | |
Collapse
|
23
|
Zhang Y, Li T, Preissl S, Amaral ML, Grinstein JD, Farah EN, Destici E, Qiu Y, Hu R, Lee AY, Chee S, Ma K, Ye Z, Zhu Q, Huang H, Fang R, Yu L, Izpisua Belmonte JC, Wu J, Evans SM, Chi NC, Ren B. Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. Nat Genet 2019; 51:1380-1388. [PMID: 31427791 PMCID: PMC6722002 DOI: 10.1038/s41588-019-0479-7] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [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: 01/31/2019] [Accepted: 07/09/2019] [Indexed: 12/24/2022]
Abstract
Chromatin architecture has been implicated in cell type-specific gene regulatory programs, yet how chromatin remodels during development remains to be fully elucidated. Here, by interrogating chromatin reorganization during human pluripotent stem cell (hPSC) differentiation, we discover a role for the primate-specific endogenous retrotransposon human endogenous retrovirus subfamily H (HERV-H) in creating topologically associating domains (TADs) in hPSCs. Deleting these HERV-H elements eliminates their corresponding TAD boundaries and reduces the transcription of upstream genes, while de novo insertion of HERV-H elements can introduce new TAD boundaries. The ability of HERV-H to create TAD boundaries depends on high transcription, as transcriptional repression of HERV-H elements prevents the formation of boundaries. This ability is not limited to hPSCs, as these actively transcribed HERV-H elements and their corresponding TAD boundaries also appear in pluripotent stem cells from other hominids but not in more distantly related species lacking HERV-H elements. Overall, our results provide direct evidence for retrotransposons in actively shaping cell type- and species-specific chromatin architecture.
Collapse
Affiliation(s)
- Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Ting Li
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Sebastian Preissl
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Jonathan D Grinstein
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Elie N Farah
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Eugin Destici
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Sora Chee
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Kaiyue Ma
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Zhen Ye
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Quan Zhu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Hui Huang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Rongxin Fang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Leqian Yu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sylvia M Evans
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Neil C Chi
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
24
|
Jiang Q, Isquith J, Zipeto MA, Diep RH, Pham J, Delos Santos N, Reynoso E, Chau J, Leu H, Lazzari E, Melese E, Ma W, Fang R, Minden M, Morris S, Ren B, Pineda G, Holm F, Jamieson C. Hyper-Editing of Cell-Cycle Regulatory and Tumor Suppressor RNA Promotes Malignant Progenitor Propagation. Cancer Cell 2019; 35:81-94.e7. [PMID: 30612940 PMCID: PMC6333511 DOI: 10.1016/j.ccell.2018.11.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 10/20/2018] [Accepted: 11/26/2018] [Indexed: 12/26/2022]
Abstract
Adenosine deaminase associated with RNA1 (ADAR1) deregulation contributes to therapeutic resistance in many malignancies. Here we show that ADAR1-induced hyper-editing in normal human hematopoietic progenitors impairs miR-26a maturation, which represses CDKN1A expression indirectly via EZH2, thereby accelerating cell-cycle transit. However, in blast crisis chronic myeloid leukemia progenitors, loss of EZH2 expression and increased CDKN1A oppose cell-cycle transit. Moreover, A-to-I editing of both the MDM2 regulatory microRNA and its binding site within the 3' UTR region stabilizes MDM2 transcripts, thereby enhancing blast crisis progenitor propagation. These data reveal a dual mechanism governing malignant transformation of progenitors that is predicated on hyper-editing of cell-cycle-regulatory miRNAs and the 3' UTR binding site of tumor suppressor miRNAs.
Collapse
Affiliation(s)
- Qingfei Jiang
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA.
| | - Jane Isquith
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Maria Anna Zipeto
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Raymond H Diep
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Jessica Pham
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Nathan Delos Santos
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Eduardo Reynoso
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Julisia Chau
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Heather Leu
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Elisa Lazzari
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Etienne Melese
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Wenxue Ma
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Rongxin Fang
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark Minden
- Princess Margaret Hospital, Toronto, ON M5T 2M9, Canada
| | - Sheldon Morris
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093, USA
| | - Gabriel Pineda
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Health Sciences, School of Health and Human Services, National University, San Diego, CA, USA
| | - Frida Holm
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Catriona Jamieson
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA.
| |
Collapse
|
25
|
Link VM, Duttke SH, Chun HB, Holtman IR, Westin E, Hoeksema MA, Abe Y, Skola D, Romanoski CE, Tao J, Fonseca GJ, Troutman TD, Spann NJ, Strid T, Sakai M, Yu M, Hu R, Fang R, Metzler D, Ren B, Glass CK. Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell 2018; 173:1796-1809.e17. [PMID: 29779944 PMCID: PMC6003872 DOI: 10.1016/j.cell.2018.04.018] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [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: 01/03/2018] [Revised: 04/06/2018] [Accepted: 04/13/2018] [Indexed: 12/22/2022]
Abstract
Non-coding genetic variation is a major driver of phenotypic diversity and allows the investigation of mechanisms that control gene expression. Here, we systematically investigated the effects of >50 million variations from five strains of mice on mRNA, nascent transcription, transcription start sites, and transcription factor binding in resting and activated macrophages. We observed substantial differences associated with distinct molecular pathways. Evaluating genetic variation provided evidence for roles of ∼100 TFs in shaping lineage-determining factor binding. Unexpectedly, a substantial fraction of strain-specific factor binding could not be explained by local mutations. Integration of genomic features with chromatin interaction data provided evidence for hundreds of connected cis-regulatory domains associated with differences in transcription factor binding and gene expression. This system and the >250 datasets establish a substantial new resource for investigation of how genetic variation affects cellular phenotypes.
Collapse
Affiliation(s)
- Verena M Link
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Faculty of Biology, Division of Evolutionary Biology, Ludwig-Maximilian University of Munich, Munich, Germany
| | - Sascha H Duttke
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hyun B Chun
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Inge R Holtman
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Neuroscience, Section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Emma Westin
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marten A Hoeksema
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yohei Abe
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Dylan Skola
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Casey E Romanoski
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Jenhan Tao
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gregory J Fonseca
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ty D Troutman
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tobias Strid
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Miao Yu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Rongxin Fang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Dirk Metzler
- Faculty of Biology, Division of Evolutionary Biology, Ludwig-Maximilian University of Munich, Munich, Germany
| | - Bing Ren
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
26
|
Li H, Sun J, Du J, Wang F, Fang R, Yu C, Xiong J, Chen W, Lu Z, Liu J. Clostridium butyricum exerts a neuroprotective effect in a mouse model of traumatic brain injury via the gut-brain axis. Neurogastroenterol Motil 2018; 30:e13260. [PMID: 29193450 DOI: 10.1111/nmo.13260] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 11/06/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Traumatic brain injury (TBI) is a common occurrence following gastrointestinal dysfunction. Recently, more and more attentions are being focused on gut microbiota in brain and behavior. Glucagon-like peptide-1 (GLP-1) is considered as a mediator that links the gut-brain axis. The aim of this study was to explore the neuroprotective effects of Clostridium butyricum (Cb) on brain damage in a mouse model of TBI. METHODS Male C57BL/6 mice were subjected to a model of TBI-induced by weight-drop impact head injury and were treated intragastrically with Cb. The cognitive deficits, brain water content, neuronal death, and blood-brain barrier (BBB) permeability were evaluated. The expression of tight junction (TJ) proteins, Bcl-2, Bax, GLP-1 receptor (GLP-1R), and phosphorylation of Akt (p-Akt) in the brain were also measured. Moreover, the intestinal barrier permeability, the expression of TJ protein and GLP-1, and IL-6 level in the intestine were detected. RESULTS Cb treatment significantly improved neurological dysfunction, brain edema, neurodegeneration, and BBB impairment. Meanwhile, Cb treatment also significantly increased the expression of TJ proteins (occludin and zonula occluden-1), p-Akt and Bcl-2, but decreased expression of Bax. Moreover, Cb treatment exhibited more prominent effects on decreasing the levels of plasma d-lactate and colonic IL-6, upregulating expression of Occludin, and protecting intestinal barrier integrity. Furthermore, Cb-treated mice showed increased the secretion of intestinal GLP-1 and upregulated expression of cerebral GLP-1R. CONCLUSIONS Our findings demonstrated the neuroprotective effect of Cb in TBI mice and the involved mechanisms were partially attributed to the elevating GLP-1 secretion through the gut-brain axis.
Collapse
Affiliation(s)
- H Li
- Department of Emergency Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - J Sun
- Department of Neurology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - J Du
- Department of Clinical Microbiology and Immunology, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - F Wang
- Departments of Pathophysiology, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - R Fang
- Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - C Yu
- Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - J Xiong
- Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - W Chen
- Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Z Lu
- Department of Emergency Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - J Liu
- Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| |
Collapse
|
27
|
Amico AL, Fang R, Raoul A, Wroblewski K, Nielsen S, Weipert C, Abe H, Sheth D, Romero I, Kulkarni K, Schacht D, Patrick-Miller L, Verp M, Bradbury AR, Hlubocky F, Olopade OI. Abstract P5-19-04: Psychosocial impact of a multi-modality surveillance program for women at high-risk for breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p5-19-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose: To evaluate the psychosocial impact of semi-annual dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) screening in women at high-risk for breast cancer.
Background: For women with BRCA1 and BRCA2 mutations and/or a personal or family history of breast cancer, annual breast MRI has shown improved sensitivity and cancer detection compared to mammography. However, MRI's heightened sensitivity may lead to increased: false positives requiring additional follow-up biopsy/imaging; iatrogenic risk; and psychosocial distress, which all may negatively impact women's overall health-related quality of life.
Methods: Between 2004 and 2016, we assembled a prospective cohort of high-risk women undergoing semi-annual DCE-MRI and annual mammography. We reviewed a subset of this group. Participants completed psychosocial assessments at baseline and 6-month visits using the following measures: coping (MBSS); state/trait anxiety (STAI-S/T); depression (BDI-II); risk perception; and mental health (SF-36). Participants were classified according to Monitor or Blunter coping style. Mixed-effects logistic regressions models examined effects of demographics on psychosocial changes over time.
Results: 295 women were recruited to the study; 44% of the study participants had pathogenic mutations in BRCA1 or BRCA2 genes. 232 of 295 enrolled participants (78.6%) completed psychosocial assessments. For the total population: median age 44y (range: 21-73), 71% ≥college/post-graduate education; 84% Caucasian; 8% African American; 2% Latino; 99% with health insurance; 72% annual income of >$60,000. One third of women had a personal cancer history. Participants were evenly split between baseline Monitoring and Blunting coping style (49% and 51%, respectively). No significant differences were found between demographics (age, race, income, mutation, cancer type, cancer history) or psychosocial factors (baseline trait anxiety (p =0.64), depression (p =0.65), SF36 global health (p=0.66). After adjusting for education, race, cancer history and coping, women with ≥$60,000 income had lower trait anxiety (p<0.000) and greater mental health (p<0.001) than those with <$60,000 income. Over time, change in trait anxiety varied by coping (p=0.0006): Blunters did not experience significant changes in trait anxiety (p=0.072) while Monitors had significant diminished trait anxiety over time (p<0.001). For depression, women with ≥$60,000 income and college educated had lower BDI-II depression (p<0.000). Yet, women with a cancer history had significantly greater BDH-II depression (p= 0.048). Mental health over time varied by race as non-whites had greater gains in mental health (p=0.001) over time than whites (p=0.03).
Conclusion: Semi-annual DCE-MRI did not cause a significantly elevated state anxiety or depression, nor was there a significant decline in mental health over time for groups regardless of cancer history and genetic mutation status. Coping style may have an impact on psychosocial outcomes for those undergoing heightened surveillance over time.
Citation Format: Amico AL, Fang R, Raoul A, Wroblewski K, Nielsen S, Weipert C, Abe H, Sheth D, Romero I, Kulkarni K, Schacht D, Patrick-Miller L, Verp M, Bradbury AR, Hlubocky F, Olopade OI. Psychosocial impact of a multi-modality surveillance program for women at high-risk for breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-19-04.
Collapse
Affiliation(s)
- AL Amico
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| | - R Fang
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| | - A Raoul
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| | - K Wroblewski
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| | - S Nielsen
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| | - C Weipert
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| | - H Abe
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| | - D Sheth
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| | - I Romero
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| | - K Kulkarni
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| | - D Schacht
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| | - L Patrick-Miller
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| | - M Verp
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| | - AR Bradbury
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| | - F Hlubocky
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| | - OI Olopade
- The University of Chicago, Chicago, IL; University of Pennsylvania, Philadelphia, PA; Independent Contractor
| |
Collapse
|
28
|
Liyi C, Lu S, Fang R, Zhao X. Noninvasive chromosome screening improves the clinical outcomes in frozen-thawed single blastocyst transfer cycles. Fertil Steril 2017. [DOI: 10.1016/j.fertnstert.2017.07.824] [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: 10/18/2022]
|
29
|
Affiliation(s)
- S Yang
- Department of Cardiology, The Central Hospital of Linyi, Yishui, China
| | - C Fu
- Department of Cardiology, The Central Hospital of Linyi, Yishui, China
| | - R Xu
- Department of Cardiology, The Central Hospital of Linyi, Yishui, China
- Department of Cardiology, People’s Hospital of Weifang, Weifang, China
| | - Z Xun
- Department of Cardiology, People’s Hospital of Weifang, Weifang, China
| | - X Zhao
- Department of Clinical Laboratory, People’s Hospital of Weifang, Weifang, China
| | - R Fang
- Department of Cardiology, The Central Hospital of Linyi, Yishui, China
| |
Collapse
|
30
|
Fang R, Wang XT, Xia QY, Zhou XJ, Rao Q. [Immunohistochemistry provides genetic information on tumors]. Zhonghua Bing Li Xue Za Zhi 2017; 46:356-361. [PMID: 28468051 DOI: 10.3760/cma.j.issn.0529-5807.2017.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
|
31
|
Go J, Sy J, Santos A, Soll B, Davis J, Fang R. P194 Chronic obstructive pulmonary disease hospitalizations and emergency department visits among queen Emma clinic patients: a quality improvement initiative. Chest 2017. [DOI: 10.1016/j.chest.2017.04.098] [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] Open
|
32
|
Yang X, Qi MW, Zhang ZZ, Gao C, Wang CQ, Lei WQ, Tan L, Zhao JL, Fang R, Hu M. Development and Evaluation of a Loop-Mediated Isothermal Amplification (Lamp) Assay for the Detection of Haemonchus contortus in Goat Fecal Samples. J Parasitol 2017; 103:161-167. [PMID: 28098507 DOI: 10.1645/16-157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Haemonchus contortus is one of the most significant strongylid nematodes infecting small ruminants, and it causes great economic losses to the livestock industry worldwide. Accurate diagnosis of H. contortus is crucial to control strategies. Traditional microscopic examinations are the most common methods for the diagnosis of H. contortus , but they are time-consuming and inaccurate. Molecular methods based on PCR are more accurate, but need expensive machines usually only used in the laboratory. Loop-mediated isothermal amplification (LAMP) is a rapid, simple, specific, and sensitive method that has been widely used to detect viruses, bacteria, and parasites. In the present study, a LAMP method targeting ribosomal ITS-2 gene for detection of the H. contortus in goat fecal samples has been established. The established LAMP method was H. contortus specific, and the sensitivity of LAMP was the same as that of the H. contortus species-specific PCR, with the lowest DNA level detected as being 1 pg. Examination of the clinical samples indicated that the positive rate of LAMP was higher than that of PCR, but no statistical difference was observed between LAMP and PCR (χ2 = 17.991, P = 0.053). In conclusion, a LAMP assay with a high specificity and a good sensitivity has been developed to detect H. contortus infection in goats. The established LAMP assay is useful for clinical diagnosis of H. contortus .
Collapse
Affiliation(s)
- X Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - M W Qi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - Z Z Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - C Gao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - C Q Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - W Q Lei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - L Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - J L Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - R Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - M Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| |
Collapse
|
33
|
Geng T, Su X, Fang R, Xie X, Zhao Q, Liu J. BDS Precise Point Positioning for Seismic Displacements Monitoring: Benefit from the High-Rate Satellite Clock Corrections. Sensors (Basel) 2016; 16:s16122192. [PMID: 27999384 PMCID: PMC5191171 DOI: 10.3390/s16122192] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 11/16/2022]
Abstract
In order to satisfy the requirement of high-rate high-precision applications, 1 Hz BeiDou Navigation Satellite System (BDS) satellite clock corrections are generated based on precise orbit products, and the quality of the generated clock products is assessed by comparing with those from the other analysis centers. The comparisons show that the root mean square (RMS) of clock errors of geostationary Earth orbits (GEO) is about 0.63 ns, whereas those of inclined geosynchronous orbits (IGSO) and medium Earth orbits (MEO) are about 0.2–0.3 ns and 0.1 ns, respectively. Then, the 1 Hz clock products are used for BDS precise point positioning (PPP) to retrieve seismic displacements of the 2015 Mw 7.8 Gorkha, Nepal, earthquake. The derived seismic displacements from BDS PPP are consistent with those from the Global Positioning System (GPS) PPP, with RMS of 0.29, 0.38, and 1.08 cm in east, north, and vertical components, respectively. In addition, the BDS PPP solutions with different clock intervals of 1 s, 5 s, 30 s, and 300 s are processed and compared with each other. The results demonstrate that PPP with 300 s clock intervals is the worst and that with 1 s clock interval is the best. For the scenario of 5 s clock intervals, the precision of PPP solutions is almost the same to 1 s results. Considering the time consumption of clock estimates, we suggest that 5 s clock interval is competent for high-rate BDS solutions.
Collapse
Affiliation(s)
- Tao Geng
- GNSS Research Center, Wuhan University, 129 Luoyu Road, Wuhan 430079, China.
| | - Xing Su
- GNSS Research Center, Wuhan University, 129 Luoyu Road, Wuhan 430079, China.
| | - Rongxin Fang
- GNSS Research Center, Wuhan University, 129 Luoyu Road, Wuhan 430079, China.
| | - Xin Xie
- GNSS Research Center, Wuhan University, 129 Luoyu Road, Wuhan 430079, China.
| | - Qile Zhao
- GNSS Research Center, Wuhan University, 129 Luoyu Road, Wuhan 430079, China.
| | - Jingnan Liu
- GNSS Research Center, Wuhan University, 129 Luoyu Road, Wuhan 430079, China.
| |
Collapse
|
34
|
Xing T, Tan X, Yu Q, Yang T, Fang R. Identifying the location of epidermal growth factor-responsive element involved in the regulation of type IIb sodium-phosphate cotransporter expression in porcine intestinal epithelial cells. J Anim Physiol Anim Nutr (Berl) 2016; 101:1249-1258. [PMID: 27896869 DOI: 10.1111/jpn.12645] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 08/08/2016] [Accepted: 10/16/2016] [Indexed: 12/14/2022]
Abstract
Phosphate is an important mineral nutrient for both human and animals in growth and physiological functions; thus, much effort in the past has been made to clarify the mechanisms governing its absorption. Previous studies have found that epidermal growth factor (EGF) inhibits phosphate absorption in human intestinal cells via modulating the interaction of transcriptional factor c-myb with sodium-phosphate cotransporter (NaPi-IIb) gene promoter. This finding provoked our interest in determining the effect of EGF on NaPi-IIb gene expression in intestinal cells of pigs and the location of EGF-responsive element in the gene promoter. Using quantitative PCR, it was observed that EGF significantly reduced NaPi-IIb gene expression in porcine intestinal epithelial IPEC-J2 cells. Transfection with a series of constructs that contain different lengths of the 5'-flanking promoter region of the NaPi-IIb gene manifested that EGF-responsive element is located in the -1200 to -800 region. Further, c-myb was extracted from the cell nucleus of IPEC cells that were exposed to EGF or not via immunoprecipitation. The electrophoretic mobility shift assay showed a specific binding of transcription factor c-myb to labelled probes encompassing DNA sequence from -1092 to -1085 (-TCCAGTTG-). This protein-DNA complex was decreased with cells exposed to EGF and abrogated when c-myb was pre-incubated with excessive unlabelled competitive probes. Results from mutagenesis studies demonstrated that the c-myb-binding site is the EGF-responsive element involved in the regulation of NaPi-IIb expression. Identifying the location of EGF-responsive element contributes to understanding mechanisms underlying EGF down-regulated NaPi-IIb gene expression and provides a foundation for further investigating EGF-regulatory functions in phosphate absorption in pig intestine.
Collapse
Affiliation(s)
- T Xing
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - X Tan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Q Yu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - T Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - R Fang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| |
Collapse
|
35
|
Fang R, Yu M, Li G, Chee S, Liu T, Schmitt AD, Ren B. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res 2016; 26:1345-1348. [PMID: 27886167 DOI: 10.1038/cr.2016.137] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Rongxin Fang
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.,Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Miao Yu
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Guoqiang Li
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Sora Chee
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Tristin Liu
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Anthony D Schmitt
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.,Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
36
|
Zhang F, Li Q, Chen X, Huo Y, Guo H, Song Z, Cui F, Zhang L, Fang R. Roles of the Laodelphax striatellus Down syndrome cell adhesion molecule in Rice stripe virus infection of its insect vector. Insect Mol Biol 2016; 25:413-421. [PMID: 26991800 DOI: 10.1111/imb.12226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The arthropod Down syndrome cell adhesion molecule (Dscam) mediates pathogen-specific recognition via an extensive protein isoform repertoire produced by alternative splicing. To date, most studies have focused on the subsequent pathogen-specific immune response, and few have investigated the entry into cells of viruses or endosymbionts. In the present study, we cloned and characterized the cDNA of Laodelphax striatellus Dscam (LsDscam) and investigated the function of LsDscam in rice stripe virus (RSV) infection and the influence on the endosymbiont Wolbachia. LsDscam displayed a typical Dscam domain architecture, including 10 immunoglobulin (Ig) domains, six fibronectin type III domains, one transmembrane domain and a cytoplasmic tail. Alternative splicing occurred at the N-termini of the Ig2 and Ig3 domains, the complete Ig7 domain, the transmembrane domain and the C-terminus, comprising 10, 51, 35, two and two variable exons, respectively. Potentially LsDscam could encode at least 71 400 unique isoforms and 17 850 types of extracellular regions. LsDscam was expressed in various L. striatellus tissues. Knockdown of LsDscam mRNA via RNA interference decreased the titres of both RSV and Wolbachia, but did not change the numbers of the extracellular symbiotic bacterium Acinetobacter rhizosphaerae. Specific Dscam isoforms may play roles in enhancing the infection of vector-borne viruses or endosymbionts.
Collapse
Affiliation(s)
- F Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Q Li
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - X Chen
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
| | - Y Huo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
| | - H Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
| | - Z Song
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
| | - F Cui
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - L Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
| | - R Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
| |
Collapse
|
37
|
Li L, Fang R, Liu B, Shi H, Wang Y, Zhang W, Zhang X, Ye L. Deacetylation of tumor-suppressor MST1 in Hippo pathway induces its degradation through HBXIP-elevated HDAC6 in promotion of breast cancer growth. Oncogene 2015; 35:4048-57. [PMID: 26657153 DOI: 10.1038/onc.2015.476] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/25/2015] [Accepted: 11/17/2015] [Indexed: 12/12/2022]
Abstract
Reduction or loss of tumor-suppressor mammalian STE20-like kinase 1 (MST1) in Hippo pathway contributes to the tumorigenesis. However, the mechanism leading to reduction of MST1 in cancers remains poorly understood. In this study, we explored the hypothesis that the oncoprotein hepatitis B X-interacting protein (HBXIP) is involved in the reduction of MST1 in breast cancer. Immunohistochemical analysis of tissue microarrays revealed that the expression of HBXIP was negatively associated with that of MST1 in 98 clinical breast tissue samples. Then we found that HBXIP could posttranslationally downregulate MST1 in breast cancer cells. Mechanistically, we identified that MST1 could be acetylated on its lysine 35 residue in the cells. Strikingly, the treatment with trichostatin A, an inhibitor of histone deacetylases (HDACs), markedly increased the levels of MST1 acetylation and protein in the cells. Interestingly, the oncoprotein HBXIP could significantly inhibit acetylation of MST1, resulting in the reduction of MST1 protein. Notably, we revealed that the HDAC6 could reduce the protein levels of MST1 through deacetylation modification of MST1 in the cells. Moreover, our data revealed that HBXIP upregulated HDAC6 at the levels of mRNA and protein by activating transcription factor nuclear factor-κB. Deacetylation of MST1 promoted the interaction of MST1 with HSC70 in the cells, resulting in a lysosome-dependent degradation of MST1 via chaperone-mediated autophagy (CMA). Functionally, the reduction of tumor-suppressor MST1 mediated by HBXIP promoted the growth of breast cancer cells in vitro and in vivo. Thus we conclude that the deacetylation of MST1 mediated by HBXIP-enhanced HDAC6 results in MST1 degradation in a CMA manner in promotion of breast cancer growth. Our finding provides new insights into the mechanism of tumor-suppressor MST1 reduction in breast cancer.
Collapse
Affiliation(s)
- L Li
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
| | - R Fang
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
| | - B Liu
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
| | - H Shi
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
| | - Y Wang
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
| | - W Zhang
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
| | - X Zhang
- State Key Laboratory of Medicinal Chemical Biology, Department of Cancer Research, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
| | - L Ye
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
| |
Collapse
|
38
|
Fang R, Cui Q, Sun J, Duan X, Ma X, Wang W, Cheng B, Liu Y, Hou Y, Bai G. PDK1/Akt/PDE4D axis identified as a target for asthma remedy synergistic with β2 AR agonists by a natural agent arctigenin. Allergy 2015; 70:1622-32. [PMID: 26335809 DOI: 10.1111/all.12763] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Asthma is a heterogenetic disorder characterized by chronic inflammation with variable airflow obstruction and airway hyper-responsiveness. As the most potent and popular bronchodilators, β2 adrenergic receptor (β2 AR) agonists bind to the β2 ARs that are coupled via a stimulatory G protein to adenylyl cyclase, thereby improving cAMP accumulation and resulting in airway smooth muscle relaxation. We previously demonstrated arctigenin had a synergistic function with the β2 AR agonist, but the target for this remained elusive. METHOD Chemical proteomics capturing was used to enrich and uncover the target of arctigenin in human bronchial smooth muscle cells, and reverse docking and molecular dynamic stimulation were performed to evaluate the binding of arctigenin and its target. In vitro enzyme activities and protein levels were demonstrated with special kits and Western blotting. Finally, guinea pig tracheal muscle segregation and ex vivo function were analysed. RESULTS Arctigenin bound to PDK1 with an ideal binding free energy -25.45 kcal/mol and inhibited PDK1 kinase activity without changing its protein level. Additionally, arctigenin reduced PKB/Akt-induced phosphorylation of PDE4D, which was first identified in this study. Attenuation of PDE4D resulted in cAMP accumulation in human bronchial smooth muscle. The inhibition of PDK1 showed a synergistic function with β2 AR agonists and relaxed the constriction of segregated guinea pig tracheal muscle. CONCLUSIONS The PDK1/Akt/PDE4D axis serves as a novel asthma target, which may benefit airflow obstruction.
Collapse
Affiliation(s)
- R. Fang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy; Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin China
- State Key Laboratory of Natural and Biomimetic Drugs; Peking University; Beijing China
- State Key Laboratory of Medicinal Chemical Biology; Department of Biochemistry; College of Life Sciences; Nankai University; Tianjin China
| | - Q. Cui
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy; Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin China
| | - J. Sun
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy; Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin China
| | - X. Duan
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy; Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin China
| | - X. Ma
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy; Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin China
| | - W. Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy; Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin China
| | - B. Cheng
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy; Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin China
| | - Y. Liu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy; Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin China
| | - Y. Hou
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy; Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin China
- State Key Laboratory of Natural and Biomimetic Drugs; Peking University; Beijing China
| | - G. Bai
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy; Tianjin Key Laboratory of Molecular Drug Research; Nankai University; Tianjin China
| |
Collapse
|
39
|
Milhano N, Saito TB, Bechelli J, Fang R, Vilhena M, DE Sousa R, Walker DH. The role of Rhipicephalus sanguineus sensu lato saliva in the dissemination of Rickettsia conorii in C3H/HeJ mice. Med Vet Entomol 2015; 29:225-229. [PMID: 26011701 DOI: 10.1111/mve.12118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 12/24/2014] [Accepted: 01/05/2015] [Indexed: 06/04/2023]
Abstract
Animal models have been developed for the study of rickettsial pathogenesis. However, to understand what occurs during the natural route of rickettsial transmission via the tick bite, the role of tick saliva should be considered in these models. To address this, we analysed the role of tick saliva in the transmission of Rickettsia conorii (Rickettsiales: Rickettsiaceae) in a murine host by intradermally (i.d.) inoculating two groups of susceptible C3H/HeJ mice with this Rickettsia, and infesting one group with nymphal Rhipicephalus sanguineus sensu lato (Ixodida: Ixodidae) ticks. Quantification of bacterial loads and mRNA levels of interleukin-1β (IL-1β), IL-10 and NF-κB was performed in C3H/HeJ lung samples by real-time quantitative polymerase chain reaction (PCR) and real-time reverse transcriptase PCR, respectively. Lung histology was examined to evaluate the pathological manifestations of infection. No statistically significant difference in bacterial load in the lungs of mice was observed between these two groups; however, a statistically significant difference was observed in levels of IL-1β and NF-κB, both of which were higher in the group inoculated with rickettsiae but not infected with ticks. Lung histology in both groups of animals revealed infiltration of inflammatory cells. Overall, this study showed that i.d. inoculation of R. conorii caused infection in the lungs of C3H/HeJ mice and tick saliva inhibited proinflammatory effects.
Collapse
Affiliation(s)
- N Milhano
- Centre for the Study of Vectors and Infectious Diseases Dr Francisco Cambournac, National Institute of Health Dr Ricardo Jorge, Águas de Moura, Portugal
| | - T B Saito
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, U.S.A
| | - J Bechelli
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, U.S.A
| | - R Fang
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, U.S.A
| | - M Vilhena
- Department of Veterinary Medicine, University of Évora, Évora, Portugal
| | - R DE Sousa
- Centre for the Study of Vectors and Infectious Diseases Dr Francisco Cambournac, National Institute of Health Dr Ricardo Jorge, Águas de Moura, Portugal
| | - D H Walker
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, U.S.A
| |
Collapse
|
40
|
Abstract
BACKGROUND The CCCTC-binding factor (CTCF) has diverse regulatory functions. However, the definitive characteristics of the CTCF binding motif required for its functional diversity still remains elusive. RESULTS Here, we describe a new motif discovery workflow by which we have identified three CTCF binding motif variations with highly divergent functionalities. Supported by transcriptomic, epigenomic and chromatin-interactomic data, we show that the functional diversity of the CTCF binding motifs is strongly associated with their GC content, CpG dinucleotide coverage and relative DNA methylation level at the 12th position of the motifs. Further analysis suggested that the co-localization of cohesin, the key factor in cohesion of sister chromatids, is negatively correlated with the CpG coverage and the relative DNA methylation level at the 12th position. Finally, we present evidences for a hypothetical model in which chromatin interactions between promoters and distal regulatory regions are likely mediated by CTCFs binding to sequences with high CpG. CONCLUSION These results demonstrate the existence of definitive CTCF binding motifs corresponding to CTCF's diverse functions, and that the functional diversity of the motifs is strongly associated with genetic and epigenetic features at the 12th position of the motifs.
Collapse
Affiliation(s)
- Rongxin Fang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Chengqi Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Geir Skogerbo
- Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Zhihua Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
41
|
Wang GY, Zhang CC, Ren K, Zhang PP, Liu CH, Zheng ZA, Chen Y, Fang R. Treatment of vertebral body compression fractures using percutaneous kyphoplasty guided by a combination of computed tomography and C-arm fluoroscopy with finger-touch guidance to determine the needle entry point. Genet Mol Res 2015; 14:1546-56. [PMID: 25867298 DOI: 10.4238/2015.march.6.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This study aimed to evaluate the results and complications of image-guided percutaneous kyphoplasty (PKP) using computed tomography (CT) and C-arm fluoroscopy, with finger-touch guidance to determine the needle entry point. Of the 86 patients (106 PKP) examined, 56 were treated for osteoporotic vertebral compression fractures and 30 for vertebral tumors. All patients underwent image-guided treatment using CT and conventional fluoroscopy, with finger-touch identification of a puncture point within a small incision (1.5 to 2 cm). Partial or complete pain relief was achieved in 98% of patients within 24 h of treatment. Moreover, a significant improvement in functional mobility and reduction in analgesic use was observed. CT allowed the detection of cement leakage in 20.7% of the interventions. No bone cement leakages with neurologic symptoms were noted. All work channels were made only once, and bone cement was distributed near the center of the vertebral body. Our study confirms the efficacy of PKP treatment in osteoporotic and oncological patients. The combination of CT and C-arm fluoroscopy with finger-touch guidance reduces the risk of complications compared with conventional fluoroscopy alone, facilitates the detection of minor cement leakage, improves the operative procedure, and results in a favorable bone cement distribution.
Collapse
Affiliation(s)
- G Y Wang
- Department of Orthopedics, Wuhu No. 2 People's Hospital, Wannan Medical College, Anhui, China
| | - C C Zhang
- Department of Orthopedics, Changhai Hospital, Second Military Medical University of Chinese PLA, Shanghai, China
| | - K Ren
- Department of Orthopedics, Gen Hospital of Nanjin Military Area Command, Nanjin, Jiangsu, China
| | - P P Zhang
- Department of Orthopedics, Wuhu No. 2 People's Hospital, Wannan Medical College, Anhui, China
| | - C H Liu
- Department of Orthopedics, Wuhu No. 2 People's Hospital, Wannan Medical College, Anhui, China
| | - Z A Zheng
- Department of Orthopedics, Wuhu No. 2 People's Hospital, Wannan Medical College, Anhui, China
| | - Y Chen
- Department of Orthopedics, Wuhu No. 2 People's Hospital, Wannan Medical College, Anhui, China
| | - R Fang
- Department of Orthopedics, Wuhu No. 2 People's Hospital, Wannan Medical College, Anhui, China
| |
Collapse
|
42
|
Liu Z, Asila A, Aikenmu K, Zhao J, Meng Q, Fang R. Influence of ERCC2 gene polymorphisms on the treatment outcome of osteosarcoma. Genet Mol Res 2015; 14:12967-72. [DOI: 10.4238/2015.october.21.17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
43
|
|
44
|
Williams JS, Chamarthi B, Goodarzi MO, Pojoga LH, Sun B, Garza AE, Raby BA, Adler GK, Hopkins PN, Brown NJ, Jeunemaitre X, Ferri C, Fang R, Leonor T, Cui J, Guo X, Taylor KD, Chen YDI, Xiang A, Raffel LJ, Buchanan TA, Rotter JI, Williams GH, Shi Y. Lysine-specific demethylase 1: an epigenetic regulator of salt-sensitive hypertension. Am J Hypertens 2012; 25:812-7. [PMID: 22534796 DOI: 10.1038/ajh.2012.43] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Hypertension (HTN) represents a complex heritable disease in which environmental factors may directly affect gene function via epigenetic mechanisms. The aim of this study was to test the hypothesis that dietary salt influences the activity of a histone-modifying enzyme, lysine-specific demethylase 1 (LSD-1), which in turn is associated with salt-sensitivity of blood pressure (BP). METHODS Animal and human studies were performed. Salt-sensitivity of LSD-1 expression was assessed in wild-type (WT) and LSD-1 heterozygote knockout (LSD-1(+/-)) mice. Clinical relevance was tested by multivariate associations between single-nuclear polymorphisms (SNPs) in the LSD-1 gene and salt-sensitivity of BP, with control of dietary sodium, in a primary African-American hypertensive cohort and two replication hypertensive cohorts (Caucasian and Mexican-American). RESULTS LSD-1 expression was modified by dietary salt in WT mice with lower levels associated with liberal salt intake. LSD-1(+/-) mice expressed lower LSD-1 protein levels than WT mice in kidney tissue. Similar to LSD-1(+/-) mice, African-American minor allele carriers of two LSD-1 SNPs displayed greater change in systolic BP (SBP) in response to change from low to liberal salt diet (rs671357, P = 0.01; rs587168, P = 0.005). This association was replicated in the Hispanic (rs587168, P = 0.04) but not the Caucasian cohort. Exploratory analyses demonstrated decreased serum aldosterone concentrations in African-American minor allele carriers similar to findings in the LSD-1(+/-) mice, decreased α-EnaC expression in LSD-1(+/-) mice, and impaired renovascular responsiveness to salt loading in minor allele carriers. CONCLUSION The results of this translational research study support a role for LSD-1 in the pathogenesis of salt-sensitive HTN.
Collapse
|
45
|
Zhen YH, Fang R, Ding C, Jin LJ, Li XY, Diao YP, Shu XH, Ma XC, Xu YP. Efficacy of specific IgY for treatment of lipopolysaccharide-induced endotoxemia using a mouse model. J Appl Microbiol 2011; 111:1524-32. [PMID: 21933310 DOI: 10.1111/j.1365-2672.2011.05155.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To estimate the efficacy of specific egg yolk immunoglobulin (IgY) for the treatment of lipopolysaccharide (LPS)-induced endotoxemia using a mouse model. METHODS AND RESULTS Specific IgY was obtained from the yolk of hens immunized with formaldehyde-killed Escherichia coli O111 and showed a high binding activity to LPS when subjected to an ELISA. Endotoxemia was induced in mice by intraperitoneal injection of LPS at a dose of 20 mg kg(-1) for measuring survival rate and 10 mg kg(-1) for cytokine measurement. The survival rate of mice treated with 200 mg kg(-1) specific IgY or 5 mg kg(-1) dexamethasone was 70% while none of the mice in the normal saline-treated group survived more than 7 days. Specific IgY significantly (P < 0.05) decreased tumour necrosis factor-α (TNF-α) level and increased interleukin-10 (IL-10) level in the serum of endotoxemia mice. Specific IgY had less of an effect on TNF-α than dexamethasone, while its effect on increasing IL-10 was stronger than dexamethasone. Haematoxylin and eosin-stained sections indicated that IgY attenuated the damage to the lung and liver observed in mice with endotoxemia. CONCLUSIONS The specific IgY increased the survival rate of mice with endotoxemia induced by LPS, down-regulated TNF-α and up-regulated IL-10 in serum and attenuated the extent of damage to the lung and liver. SIGNIFICANCE AND IMPACT OF THE STUDY The specific IgY has potential for the treatment of LPS-induced endotoxemia.
Collapse
Affiliation(s)
- Y-H Zhen
- College of Pharmacy, Dalian Medical University, Dalian, China
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Bai XP, Zheng HX, Fang R, Wang TR, Hou XL, Li Y, Chen XB, Tian WM. Fabrication of engineered heart tissue grafts from alginate/collagen barium composite microbeads. Biomed Mater 2011; 6:045002. [DOI: 10.1088/1748-6041/6/4/045002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
47
|
Gu H, Fang R, O'Keefe TJ, O'Keefe MJ, Shih WS, Snook JAM, Leedy KD, Cortez R. Organic Solution Deposition of Copper Seed Layers onto Barrier Metals. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-612-d9.19.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractSpontaneous deposition of copper seed layers from metal bearing organic based solutions onto sputter deposited titanium, titanium nitride, and tantalum diffusion barrier thin films has been demonstrated. Based on electrochemically driven cementation exchange reactions, the process was used to produce adherent, selectively deposited copper metal particulate films on blanket and patterned barrier metal thin films on silicon substrates. The organic solution deposited copper films were capable of acting as seed layers for subsequent electrolytic and electroless copper deposition processes using standard plating baths. Electroless and electrolytic copper films from 0.1µm to 1.0µm thick were produced on a variety of samples on which the organic solution copper acted as the initial catalytic seed layer. The feasibility of using organic solution deposited palladium as a seed layer followed by electroless copper deposition has also been demonstrated. In addition, experiments conducted on patterned barrier metal samples with exposed areas of dielectric such as polyimide indicated that no organic solution copper or palladium deposition occurred on the insulating materials.
Collapse
|
48
|
Tomas C, Axler-DiPerte G, Budimlija ZM, Børsting C, Coble MD, Decker AE, Eisenberg A, Fang R, Fondevila M, Fredslund SF, Gonzalez S, Hansen AJ, Hoff-Olsen P, Haas C, Kohler P, Kriegel AK, Lindblom B, Manohar F, Maroñas O, Mogensen HS, Neureuther K, Nilsson H, Scheible MK, Schneider PM, Sonntag ML, Stangegaard M, Syndercombe-Court D, Thacker CR, Vallone PM, Westen AA, Morling N. Autosomal SNP typing of forensic samples with the GenPlex™ HID System: results of a collaborative study. Forensic Sci Int Genet 2010; 5:369-75. [PMID: 20650697 DOI: 10.1016/j.fsigen.2010.06.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 06/24/2010] [Accepted: 06/24/2010] [Indexed: 10/19/2022]
Abstract
The GenPlex™ HID System (Applied Biosystems - AB) offers typing of 48 of the 52 SNPforID SNPs and amelogenin. Previous studies have shown a high reproducibility of the GenPlex™ HID System using 250-500pg DNA of good quality. An international exercise was performed by 14 laboratories (9 in Europe and 5 in the US) in order to test the robustness and reliability of the GenPlex™ HID System on forensic samples. Three samples with partly degraded DNA and 10 samples with low amounts of DNA were analyzed in duplicates using various amounts of DNA. In order to compare the performance of the GenPlex™ HID System with the most commonly used STR kits, 500pg of partly degraded DNA from three samples was typed by the laboratories using one or more STR kits. The median SNP typing success rate was 92.3% with 500pg of partly degraded DNA. Three of the fourteen laboratories counted for more than two thirds of the locus dropouts. The median percentage of discrepant results was 0.2% with 500pg degraded DNA. An increasing percentage of locus dropouts and discrepant results were observed when lower amounts of DNA were used. Different success rates were observed for the various SNPs. The rs763869 SNP was the least successful. With the exception of the MiniFiler™ kit (AB), GenPlex™ HID performed better than five other tested STR kits. When partly degraded DNA was analyzed, GenPlex™ HID showed a very low mean mach probability, while all STR kits except MiniFiler™ had very limited discriminatory power.
Collapse
Affiliation(s)
- C Tomas
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 11 Frederik V's Vej, DK-2100 Copenhagen, Denmark.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Wang L, He L, Fang R, Song Q, Tu P, Jenkins A, Zhou Y, Zhao J. Loop-mediated isothermal amplification (LAMP) assay for detection of Theileria sergenti infection targeting the p33 gene. Vet Parasitol 2010; 171:159-62. [DOI: 10.1016/j.vetpar.2010.02.046] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2009] [Revised: 02/18/2010] [Accepted: 02/25/2010] [Indexed: 11/30/2022]
|
50
|
Zhen YH, Jin LJ, Guo J, Li XY, Li Z, Fang R, Xu YP. Characterization of specific egg yolk immunoglobulin (IgY) against mastitis-causing Staphylococcus aureus. J Appl Microbiol 2010; 105:1529-35. [PMID: 19146490 DOI: 10.1111/j.1365-2672.2008.03920.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To evaluate the in vitro activity of egg yolk immunoglobulin (IgY) against mastitis-causing Staphylococcus aureus. METHODS AND RESULTS Specific IgY was produced by immunizing hens with formaldehyde-killed Staph. aureus, using a bacterial strain known to cause mastitis. The IgY, of 94% purity, was obtained from yolks by water dilution, salt precipitations, ultrafiltration and gel filtration. ELISA indicated that the IgY produced was specific to the antigen and five Staph. aureus isolates obtained from mastitic cows. The growth of Staph. aureus was inhibited by specific IgY at concentrations from 1 to 10 mg ml(-1) in a dose-dependent manner. The phagocytosis of Staph. aureus by milk macrophages was enhanced in the presence of specific IgY with the highest phagocytic percentage being 30% higher than that without IgY (P < 0.05). CONCLUSIONS The specific IgY against mastitis-causing Staph. aureus inhibited the growth of Staph. aureus and enhanced the phagocytosis of Staph. aureus by milk macrophages. SIGNIFICANCE AND IMPACT OF THE STUDY Specific IgY would be a potential treatment for bovine mastitis.
Collapse
Affiliation(s)
- Y-H Zhen
- Department of Bioscience and Biotechnology, Dalian University of Technology, Dalian, China
| | | | | | | | | | | | | |
Collapse
|