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Buswinka CJ, Rosenberg DB, Simikyan RG, Osgood RT, Fernandez K, Nitta H, Hayashi Y, Liberman LW, Nguyen E, Yildiz E, Kim J, Jarysta A, Renauld J, Wesson E, Wang H, Thapa P, Bordiga P, McMurtry N, Llamas J, Kitcher SR, López-Porras AI, Cui R, Behnammanesh G, Bird JE, Ballesteros A, Vélez-Ortega AC, Edge ASB, Deans MR, Gnedeva K, Shrestha BR, Manor U, Zhao B, Ricci AJ, Tarchini B, Basch ML, Stepanyan R, Landegger LD, Rutherford MA, Liberman MC, Walters BJ, Kros CJ, Richardson GP, Cunningham LL, Indzhykulian AA. Large-scale annotated dataset for cochlear hair cell detection and classification. Sci Data 2024; 11:416. [PMID: 38653806 PMCID: PMC11039649 DOI: 10.1038/s41597-024-03218-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Our sense of hearing is mediated by cochlear hair cells, of which there are two types organized in one row of inner hair cells and three rows of outer hair cells. Each cochlea contains 5-15 thousand terminally differentiated hair cells, and their survival is essential for hearing as they do not regenerate after insult. It is often desirable in hearing research to quantify the number of hair cells within cochlear samples, in both pathological conditions, and in response to treatment. Machine learning can be used to automate the quantification process but requires a vast and diverse dataset for effective training. In this study, we present a large collection of annotated cochlear hair-cell datasets, labeled with commonly used hair-cell markers and imaged using various fluorescence microscopy techniques. The collection includes samples from mouse, rat, guinea pig, pig, primate, and human cochlear tissue, from normal conditions and following in-vivo and in-vitro ototoxic drug application. The dataset includes over 107,000 hair cells which have been identified and annotated as either inner or outer hair cells. This dataset is the result of a collaborative effort from multiple laboratories and has been carefully curated to represent a variety of imaging techniques. With suggested usage parameters and a well-described annotation procedure, this collection can facilitate the development of generalizable cochlear hair-cell detection models or serve as a starting point for fine-tuning models for other analysis tasks. By providing this dataset, we aim to give other hearing research groups the opportunity to develop their own tools with which to analyze cochlear imaging data more fully, accurately, and with greater ease.
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Affiliation(s)
- Christopher J Buswinka
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
- Speech and Hearing Biosciences and Technology graduate program, Harvard University, Cambridge, MA, 02138, USA
| | - David B Rosenberg
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rubina G Simikyan
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
| | - Richard T Osgood
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - Katharine Fernandez
- Section on Sensory Cell Biology, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Hidetomi Nitta
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
| | - Yushi Hayashi
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Leslie W Liberman
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Emily Nguyen
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
| | - Erdem Yildiz
- Department of Otolaryngology, Head and Neck Surgery, Vienna General Hospital and Medical University of Vienna, 1090, Vienna, Austria
| | - Jinkyung Kim
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Justine Renauld
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Ella Wesson
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
| | - Haobing Wang
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Punam Thapa
- The University of Mississippi Medical Center, Department of Otolaryngology - Head and Neck Surgery, Jackson, MS, 39216, USA
| | - Pierrick Bordiga
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Noah McMurtry
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Juan Llamas
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, 90033, USA
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery, University of Southern California, Los Angeles, CA, 90033, USA
| | - Siân R Kitcher
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - Ana I López-Porras
- Department of Physiology, University of Kentucky, Lexington, KY, 40536, USA
| | - Runjia Cui
- Section on Sensory Physiology and Biophysics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Ghazaleh Behnammanesh
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, 32610, USA
| | - Jonathan E Bird
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, 32610, USA
| | - Angela Ballesteros
- Section on Sensory Physiology and Biophysics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20814, USA
| | | | - Albert S B Edge
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Michael R Deans
- Department of Neurobiology, Spencer Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT, 84112, USA
- Department of Otolaryngology - Head & Neck Surgery, Spencer Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT, 84132, USA
| | - Ksenia Gnedeva
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, 90033, USA
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery, University of Southern California, Los Angeles, CA, 90033, USA
| | - Brikha R Shrestha
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Uri Manor
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Bo Zhao
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Anthony J Ricci
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Basile Tarchini
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
- Tufts University School of Medicine, Boston, 02111, MA, USA
- Graduate School of Biomedical Science and Engineering (GSBSE), University of Maine, Orono, ME, 04469, USA
| | - Martín L Basch
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Ruben Stepanyan
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Lukas D Landegger
- Department of Otolaryngology, Head and Neck Surgery, Vienna General Hospital and Medical University of Vienna, 1090, Vienna, Austria
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Mark A Rutherford
- Department of Otolaryngology, Washington University, 660 S. Euclid Avenue, Campus Box 8115, St. Louis, MO, 63110, USA
| | - M Charles Liberman
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
- Speech and Hearing Biosciences and Technology graduate program, Harvard University, Cambridge, MA, 02138, USA
| | - Bradley J Walters
- The University of Mississippi Medical Center, Department of Otolaryngology - Head and Neck Surgery, Jackson, MS, 39216, USA
| | - Corné J Kros
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - Guy P Richardson
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - Lisa L Cunningham
- Section on Sensory Cell Biology, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Artur A Indzhykulian
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA.
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA.
- Speech and Hearing Biosciences and Technology graduate program, Harvard University, Cambridge, MA, 02138, USA.
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Zhang X, Pearsall VM, Carver CM, Atkinson EJ, Clarkson BDS, Grund EM, Baez-Faria M, Pavelko KD, Kachergus JM, White TA, Johnson RK, Malo CS, Gonzalez-Suarez AM, Ayasoufi K, Johnson KO, Tritz ZP, Fain CE, Khadka RH, Ogrodnik M, Jurk D, Zhu Y, Tchkonia T, Revzin A, Kirkland JL, Johnson AJ, Howe CL, Thompson EA, LeBrasseur NK, Schafer MJ. Rejuvenation of the aged brain immune cell landscape in mice through p16-positive senescent cell clearance. Nat Commun 2022; 13:5671. [PMID: 36167854 PMCID: PMC9515187 DOI: 10.1038/s41467-022-33226-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [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: 08/17/2021] [Accepted: 09/06/2022] [Indexed: 11/10/2022] Open
Abstract
Cellular senescence is a plausible mediator of inflammation-related tissue dysfunction. In the aged brain, senescent cell identities and the mechanisms by which they exert adverse influence are unclear. Here we used high-dimensional molecular profiling, coupled with mechanistic experiments, to study the properties of senescent cells in the aged mouse brain. We show that senescence and inflammatory expression profiles increase with age and are brain region- and sex-specific. p16-positive myeloid cells exhibiting senescent and disease-associated activation signatures, including upregulation of chemoattractant factors, accumulate in the aged mouse brain. Senescent brain myeloid cells promote peripheral immune cell chemotaxis in vitro. Activated resident and infiltrating immune cells increase in the aged brain and are partially restored to youthful levels through p16-positive senescent cell clearance in female p16-InkAttac mice, which is associated with preservation of cognitive function. Our study reveals dynamic remodeling of the brain immune cell landscape in aging and suggests senescent cell targeting as a strategy to counter inflammatory changes and cognitive decline.
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Affiliation(s)
- Xu Zhang
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | | | - Chase M Carver
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Elizabeth J Atkinson
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Benjamin D S Clarkson
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ethan M Grund
- Mayo Graduate School and Medical Scientist Training Program, Mayo Clinic, Rochester, MN, USA
| | - Michelle Baez-Faria
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Jennifer M Kachergus
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Jacksonville, FL, USA
| | - Thomas A White
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | - Kurt O Johnson
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | | | - Cori E Fain
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Roman H Khadka
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Mikolaj Ogrodnik
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
- Ludwig Boltzmann Research Group Senescence and Healing of Wounds, Vienna, Austria
| | - Diana Jurk
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Yi Zhu
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Tamara Tchkonia
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Alexander Revzin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - James L Kirkland
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Department of General Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Charles L Howe
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
- Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, MN, USA
- Division of Experimental Neurology, Mayo Clinic, Rochester, MN, USA
| | - E Aubrey Thompson
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Jacksonville, FL, USA
| | - Nathan K LeBrasseur
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Marissa J Schafer
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA.
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA.
- Department of Neurology, Mayo Clinic, Rochester, MN, USA.
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Jindal S, Pennock ND, Klug A, Narasimhan J, Calhoun A, Roberts MR, Tamimi RM, Eliassen AH, Weinmann S, Borges VF, Schedin P. S-nitrosylated and non-nitrosylated COX2 have differential expression and distinct subcellular localization in normal and breast cancer tissue. NPJ Breast Cancer 2020; 6:62. [PMID: 33298921 PMCID: PMC7686348 DOI: 10.1038/s41523-020-00204-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
Immunohistochemical (IHC) staining in breast cancer shows both gain and loss of COX2 expression with disease risk and progression. We investigated four common COX2 antibody clones and found high specificity for purified human COX2 for three clones; however, recognition of COX2 in cell lysates was clone dependent. Biochemical characterization revealed two distinct forms of COX2, with SP21 recognizing an S-nitrosylated form, and CX229 and CX294 recognizing non-nitrosylated COX2 antigen. We found S-nitrosylated and non-nitrosylated COX2 occupy different subcellular locations in normal and breast cancer tissue, implicating distinct synthetic/trafficking pathways and function. Dual stains of ~2000 breast cancer cases show early-onset breast cancer had increased expression of both forms of COX2 compared to postmenopausal cases. Our results highlight the strengths of using multiple, highly characterized antibody clones for COX2 IHC studies and raise the prospect that S-nitrosylation of COX2 may play a role in breast cancer biology.
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Affiliation(s)
- Sonali Jindal
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave., Mailing Code: KR-CDCB, Portland, OR, 97201, USA
- Knight Cancer Institute, Oregon Health & Science University, 2720 SW Moody Ave., Mailing Code: KR-ADM, Portland, OR, 97201, USA
| | - Nathan D Pennock
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave., Mailing Code: KR-CDCB, Portland, OR, 97201, USA
| | - Alex Klug
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave., Mailing Code: KR-CDCB, Portland, OR, 97201, USA
| | - Jayasri Narasimhan
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave., Mailing Code: KR-CDCB, Portland, OR, 97201, USA
| | - Andrea Calhoun
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave., Mailing Code: KR-CDCB, Portland, OR, 97201, USA
| | - Michelle R Roberts
- Department of Dermatology, Massachusetts General Hospital, 50 Staniford Street, Suite 200, Boston, MA, 02114, USA
| | - Rulla M Tamimi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02114, USA
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02114, USA
| | - Sheila Weinmann
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave., Portland, OR, 97227, USA
| | - Virginia F Borges
- School of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, MS8117, RC-1S, 8401K, 12801 E 17th Ave., Aurora, CO, 80045, USA
- Young Women's Breast Cancer Translational Program, School of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, MS8117, RC-1S, 8401K, 12801 E 17th Ave., Aurora, CO, 80045, USA
| | - Pepper Schedin
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave., Mailing Code: KR-CDCB, Portland, OR, 97201, USA.
- Knight Cancer Institute, Oregon Health & Science University, 2720 SW Moody Ave., Mailing Code: KR-ADM, Portland, OR, 97201, USA.
- School of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, MS8117, RC-1S, 8401K, 12801 E 17th Ave., Aurora, CO, 80045, USA.
- Young Women's Breast Cancer Translational Program, School of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, MS8117, RC-1S, 8401K, 12801 E 17th Ave., Aurora, CO, 80045, USA.
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