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Maymí VI, Zhu H, Jager M, Johnson S, Getchell R, Casey JW, Grenier JK, Wherry EJ, Smith NL, Grimson A, Rudd BD. Neonatal CD8+ T Cells Resist Exhaustion during Chronic Infection. J Immunol 2024; 212:834-843. [PMID: 38231127 DOI: 10.4049/jimmunol.2300396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024]
Abstract
Chronic viral infections, such as HIV and hepatitis C virus, represent a major public health problem. Although it is well understood that neonates and adults respond differently to chronic viral infections, the underlying mechanisms remain unknown. In this study, we transferred neonatal and adult CD8+ T cells into a mouse model of chronic infection (lymphocytic choriomeningitis virus clone 13) and dissected out the key cell-intrinsic differences that alter their ability to protect the host. Interestingly, we found that neonatal CD8+ T cells preferentially became effector cells early in chronic infection compared with adult CD8+ T cells and expressed higher levels of genes associated with cell migration and effector cell differentiation. During the chronic phase of infection, the neonatal cells retained more immune functionality and expressed lower levels of surface markers and genes related to exhaustion. Because the neonatal cells protect from viral replication early in chronic infection, the altered differentiation trajectories of neonatal and adult CD8+ T cells is functionally significant. Together, our work demonstrates how cell-intrinsic differences between neonatal and adult CD8+ T cells influence key cell fate decisions during chronic infection.
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Affiliation(s)
- Viviana I Maymí
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY
| | - Hongya Zhu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Mason Jager
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY
| | - Shawn Johnson
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY
| | - Rodman Getchell
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY
| | - James W Casey
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY
| | - Jennifer K Grenier
- Transcriptional Regulation and Expression Facility, Department of Biomedical Sciences, Cornell University, Ithaca, NY
| | - E John Wherry
- Institute for Immunology and Immune Health and Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Norah L Smith
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY
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2
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Watson NB, Patel RK, Kean C, Veazey J, Oyesola OO, Laniewski N, Grenier JK, Wang J, Tabilas C, Yee Mon KJ, McNairn AJ, Peng SA, Wesnak SP, Nzingha K, Davenport MP, Tait Wojno ED, Scheible KM, Smith NL, Grimson A, Rudd BD. The gene regulatory basis of bystander activation in CD8 + T cells. Sci Immunol 2024; 9:eadf8776. [PMID: 38394230 DOI: 10.1126/sciimmunol.adf8776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/26/2024] [Indexed: 02/25/2024]
Abstract
CD8+ T cells are classically recognized as adaptive lymphocytes based on their ability to recognize specific foreign antigens and mount memory responses. However, recent studies indicate that some antigen-inexperienced CD8+ T cells can respond to innate cytokines alone in the absence of cognate T cell receptor stimulation, a phenomenon referred to as bystander activation. Here, we demonstrate that neonatal CD8+ T cells undergo a robust and diverse program of bystander activation, which corresponds to enhanced innate-like protection against unrelated pathogens. Using a multi-omics approach, we found that the ability of neonatal CD8+ T cells to respond to innate cytokines derives from their capacity to undergo rapid chromatin remodeling, resulting in the usage of a distinct set of enhancers and transcription factors typically found in innate-like T cells. We observed that the switch between innate and adaptive functions in the CD8+ T cell compartment is mediated by changes in the abundance of distinct subsets of cells. The innate CD8+ T cell subset that predominates in early life was also present in adult mice and humans. Our findings provide support for the layered immune hypothesis and indicate that the CD8+ T cell compartment is more functionally diverse than previously thought.
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Affiliation(s)
- Neva B Watson
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Ravi K Patel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Connor Kean
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Janelle Veazey
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Oyebola O Oyesola
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Nathan Laniewski
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jennifer K Grenier
- Genomics Innovation Hub and TREx Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Jocelyn Wang
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Cybelle Tabilas
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Kristel J Yee Mon
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Adrian J McNairn
- Genomics Innovation Hub and TREx Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Seth A Peng
- Department of Clinical Science, Cornell University, Ithaca, NY 14853, USA
| | - Samantha P Wesnak
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Kito Nzingha
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Miles P Davenport
- Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, NSW 2052, Australia
| | - Elia D Tait Wojno
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Kristin M Scheible
- Department of Pediatrics, University of Rochester, Rochester, NY 14642, USA
| | - Norah L Smith
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
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3
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Vu LT, Ahmed F, Zhu H, Iu DSH, Fogarty EA, Kwak Y, Chen W, Franconi CJ, Munn PR, Tate AE, Levine SM, Stevens J, Mao X, Shungu DC, Moore GE, Keller BA, Hanson MR, Grenier JK, Grimson A. Single-cell transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation. Cell Rep Med 2024; 5:101373. [PMID: 38232699 PMCID: PMC10829790 DOI: 10.1016/j.xcrm.2023.101373] [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: 10/11/2022] [Revised: 08/10/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a serious and poorly understood disease. To understand immune dysregulation in ME/CFS, we use single-cell RNA sequencing (scRNA-seq) to examine immune cells in patient and control cohorts. Postexertional malaise (PEM), an exacerbation of symptoms following strenuous exercise, is a characteristic symptom of ME/CFS. To detect changes coincident with PEM, we applied scRNA-seq on the same cohorts following exercise. At baseline, ME/CFS patients display classical monocyte dysregulation suggestive of inappropriate differentiation and migration to tissue. We identify both diseased and more normal monocytes within patients, and the fraction of diseased cells correlates with disease severity. Comparing the transcriptome at baseline and postexercise challenge, we discover patterns indicative of improper platelet activation in patients, with minimal changes elsewhere in the immune system. Taken together, these data identify immunological defects present at baseline in patients and an additional layer of dysregulation in platelets.
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Affiliation(s)
- Luyen Tien Vu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Faraz Ahmed
- Genomics Innovation Hub and TREx Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Hongya Zhu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - David Shing Huk Iu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth A Fogarty
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Yeonui Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Weizhong Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Carl J Franconi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Paul R Munn
- Genomics Innovation Hub and TREx Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Ann E Tate
- Genomics Innovation Hub and TREx Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | | | | | - Xiangling Mao
- Department of Radiology, Weill Cornell Medicine, New York, NY, USA
| | - Dikoma C Shungu
- Department of Radiology, Weill Cornell Medicine, New York, NY, USA
| | - Geoffrey E Moore
- Department of Exercise Science and Athletic Training, Ithaca College, Ithaca, NY, USA
| | - Betsy A Keller
- Department of Exercise Science and Athletic Training, Ithaca College, Ithaca, NY, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jennifer K Grenier
- Genomics Innovation Hub and TREx Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA.
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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4
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Lê-Bury G, Chen Y, Rhen JM, Grenier JK, Singhal A, Russell DG, Boliar S. HIV-1 active and latent infections induce disparate chromatin reorganization and transcriptional regulation of mRNAs and lncRNAs in SupT1 cells. mBio 2023; 14:e0261923. [PMID: 38038477 PMCID: PMC10746154 DOI: 10.1128/mbio.02619-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 10/20/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE HIV-1 infection of T-lymphocytes depends on co-opting cellular transcriptional and translational machineries for viral replication. This requires significant changes in the cellular microenvironment. We have characterized and compared the changes in cellular chromatin structures as well as gene expression landscapes in T cells that are either actively or latently infected with HIV-1. Our results reveal that chromatin accessibility and expression of both protein-coding mRNAs and non-coding lncRNAs are uniquely regulated in HIV-1-infected T cells, depending on whether the virus is actively transcribing or remains in a transcriptionally silent, latent state. HIV-1 latent infection elicits more robust changes in the cellular chromatin organization than active viral infection. Our analysis also identifies the effects of such epigenomic changes on the cellular gene expression and subsequent biological pathways. This study comprehensively characterizes the cellular epigenomic and transcriptomic states that support active and latent HIV-1 infection in an in vitro model of SupT1 cells.
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Affiliation(s)
- Gabrielle Lê-Bury
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Yao Chen
- A*STAR Infectious Diseases Laboratories, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jordan M. Rhen
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Jennifer K. Grenier
- Transcription Regulation and Expression Facility, Cornell University, Ithaca, New York, USA
| | - Amit Singhal
- A*STAR Infectious Diseases Laboratories, Agency for Science, Technology and Research, Singapore, Singapore
| | - David G. Russell
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Saikat Boliar
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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5
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Olarte-Castillo XA, Plimpton L, McQueary H, Sun Y, Yu YT, Cover S, Richardson AN, Jin Y, Grenier JK, Cummings KJ, Bunting E, Diuk-Wasser M, Needle D, Schuler K, Stanhope MJ, Whittaker G, Goodman LB. Detection and characterization of novel luchacoviruses, genus Alphacoronavirus, in saliva and feces of meso-carnivores in the northeastern United States. J Virol 2023; 97:e0082923. [PMID: 37882520 PMCID: PMC10688340 DOI: 10.1128/jvi.00829-23] [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: 06/03/2023] [Accepted: 10/08/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Several coronaviruses (CoVs) have been detected in domesticated, farmed, and wild meso-carnivores, causing a wide range of diseases and infecting diverse species, highlighting their important but understudied role in the epidemiology of these viruses. Assessing the viral diversity hosted in wildlife species is essential to understand their significance in the cross-species transmission of CoVs. Our focus here was on CoV discovery in meso-carnivores in the Northeast United States as a potential "hotspot" area with high density of humans and urban wildlife. This study identifies novel alphacoronaviruses circulating in multiple free-ranging wild and domestic species in this area and explores their potential epidemiological importance based on regions of the Spike gene, which are relevant for virus-host interactions.
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Affiliation(s)
- Ximena A. Olarte-Castillo
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
| | - Laura Plimpton
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, USA
| | - Holly McQueary
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Yining Sun
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Y. Tina Yu
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Sarah Cover
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Amy N. Richardson
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Yuhan Jin
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Jennifer K. Grenier
- Transcriptional Regulation and Expression Facility, Biotechnology Resource Center, Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Kevin J. Cummings
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Elizabeth Bunting
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Maria Diuk-Wasser
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, USA
| | - David Needle
- New Hampshire Veterinary Diagnostic Laboratory, College of Life Sciences and Agriculture, University of New Hampshire, Durham, USA
| | - Krysten Schuler
- Cornell Wildlife Health Lab, Animal Health Diagnostic Center, Cornell College of Veterinary Medicine, Ithaca, New York, USA
| | - Michael J. Stanhope
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Gary Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Laura B. Goodman
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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6
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Shuster KA, Yang TS, Snyder KT, Creanza N, Mitchell PK, Goodman LB, Grenier JK, Tataryn NM, Himmel LE, Gibson-Corley KN. Polyomavirus-associated Disseminated T-cell Lymphoma in a Colony of Zebra Finches ( Taeniopygia guttata). Comp Med 2023; 73:383-390. [PMID: 38087403 PMCID: PMC10702165] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 12/18/2023]
Abstract
Four zebra finches in a closed research colony presented with variable clinical signs, including masses, skin lesions, shivering, and/or ruffled feathers. These birds were not responsive to treatment efforts; 3 died and one was euthanized. All 4 were submitted for necropsy to determine the cause of the clinical signs. Gross necropsy and histopathologic findings from all birds resulted in a diagnosis of round cell neoplasia in multiple organs, including the skin, liver, kidney, and reproductive tract, with intranuclear inclusion bodies in the neoplastic cells. In all 4 cases, immunohistochemical staining showed strong immunoreactivity for CD3 in 70% to 80% of the neoplastic round cells, with a relatively small subset that were immunopositive for Pax5. These findings supported a diagnosis of T-cell lymphoma. Frozen liver tissue from one case was submitted for next-generation sequencing (NGS), which revealed viral RNA with 100% sequence homology to canary polyomavirus strain 34639 that had originally been identified in a European goldfinch. Formalin-fixed paraffin-embedded scrolls from another case were also submitted for NGS, which revealed viral RNA with 97.2% sequence homology to canary polyomavirus strain 37273 that had originally been identified in a canary. To localize the virus in situ, RNAscope hybridization was performed using a probe designed to target the VP1 gene of the sequenced virus in frozen liver tissue. In all 4 cases, disseminated and robust hybridization signals were detected in neoplastic cells. These findings indicate that polyomaviruses have the potential to be oncogenic in zebra finches.
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Affiliation(s)
- Katherine A Shuster
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee;,
| | - Tzushan S Yang
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kate T Snyder
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | - Nicole Creanza
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | | | - Laura B Goodman
- Cornell University College of Veterinary Medicine, Ithaca, New York
| | - Jennifer K Grenier
- Cornell Institute of Biotechnology, Transcriptional Regulation and Expression Facility, Ithaca, New York
| | - Nicholas M Tataryn
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lauren E Himmel
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Katherine N Gibson-Corley
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
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7
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Olarte-Castillo XA, Plimpton L, McQueary H, Sun Y, Yu YT, Cover S, Richardson AN, Jin Y, Grenier JK, Cummings KJ, Bunting E, Diuk-Wasser M, Needle D, Schuler K, Stanhope MJ, Whittaker G, Goodman LB. Detection and characterization of novel luchacoviruses, genus Alphacoronavirus, shed in saliva and feces of meso-carnivores in the northeastern United States. bioRxiv 2023:2023.05.31.541188. [PMID: 37745528 PMCID: PMC10515766 DOI: 10.1101/2023.05.31.541188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Small to mid-sized carnivores, or meso-carnivores, comprise a group of diverse mammals, many of which can adapt to anthropogenically disturbed environments. Wild meso-carnivores living in urban areas may get exposed to or spread pathogens to other species, including stray/feral domestic animals. Several coronaviruses (CoVs) have been detected in domesticated and farmed meso-carnivores, but knowledge of CoVs circulating in free-ranging wild meso-carnivores remains limited. In this study, we analyzed 321 samples collected between 2016 and 2022 from 9 species of free-ranging wild meso-carnivores and stray/feral domestic cats in the northeastern United States. Using a pan-CoV PCR, we screened tissues, feces, and saliva, nasal, and rectal swabs. We detected CoV RNA in fecal and saliva samples of animals in four species: fisher (Pekania pennanti), bobcat (Lynx rufus), red fox (Vulpes vulpes), and domestic cat (Felis catus). Next-generation sequencing revealed that all these viruses belonged to the Luchacovirus subgenus (Alphacoronavirus genus), previously reported only in rodents and lagomorphs (i.e., rabbits). Genetic comparison of the 3'-end of the genome (~12,000bp) revealed that although the viruses detected group with, and have a genetic organization similar to other luchacoviruses, they are genetically distinct from those from rodents and lagomorphs. Genetic characterization of the spike protein revealed that the meso-carnivore luchacoviruses do not have an S1/S2 cleavage motif but do have highly variable structural loops containing cleavage motifs similar to those identified in certain pathogenic CoVs. This study highlights the importance of characterizing the spike protein of CoVs in wild species for further targeted epidemiologic monitoring.
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Affiliation(s)
- Ximena A. Olarte-Castillo
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Laura Plimpton
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Holly McQueary
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Yining Sun
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Y. Tina Yu
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Sarah Cover
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Amy N. Richardson
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Yuhan Jin
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Jennifer K. Grenier
- Transcriptional Regulation and Expression Facility, Biotechnology Resource Center, Institute of Biotechnology, Cornell University
| | - Kevin J. Cummings
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Elizabeth Bunting
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Maria Diuk-Wasser
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - David Needle
- New Hampshire Veterinary Diagnostic Laboratory, College of Life Sciences and Agriculture, University of New Hampshire
| | - Krysten Schuler
- Cornell Wildlife Health Lab, Animal Health Diagnostic Center, Cornell College of Veterinary Medicine, 240 Farrier Road, Ithaca, NY 14853
| | - Michael J. Stanhope
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gary Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Laura B. Goodman
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
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8
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Shuster KA, Yang TS, Snyder KT, Creanza N, Mitchell PK, Goodman LB, Grenier JK, Tataryn NM, Himmel LE, Gibson-Corley KN. Polyomavirus-associated Disseminated T-cell Lymphoma in a Colony of Zebra Finches (Taeniopygia guttata). Comp Med 2023. [PMID: 37696623 DOI: 10.30802/aalas-cm-23-000011] [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: 09/13/2023]
Abstract
Four zebra finches in a closed research colony presented with variable clinical signs, including masses, skin lesions,shivering, and/or ruffled feathers. These birds were not responsive to treatment efforts; 3 died and one was euthanized. All4 were submitted for necropsy to determine the cause of the clinical signs. Gross necropsy and histopathologic findings fromall birds resulted in a diagnosis of round cell neoplasia in multiple organs, including the skin, liver, kidney, and reproductivetract, with intranuclear inclusion bodies in the neoplastic cells. In all 4 cases, immunohistochemical staining showed strongimmunoreactivity for CD3 in 70% to 80% of the neoplastic round cells, with a relatively small subset that were immunopositivefor Pax5. These findings supported a diagnosis of T-cell lymphoma. Frozen liver tissue from one case was submittedfor next-generation sequencing (NGS), which revealed viral RNA with 100% sequence homology to canary polyomavirusstrain 34639 that had originally been identified in a European goldfinch. Formalin-fixed paraffin-embedded scrolls fromanother case were also submitted for NGS, which revealed viral RNA with 97.2% sequence homology to canary polyomavirusstrain 37273 that had originally been identified in a canary. To localize the virus in situ, RNAscope hybridizationwas performed using a probe designed to target the VP1 gene of the sequenced virus in frozen liver tissue. In all 4 cases,disseminated and robust hybridization signals were detected in neoplastic cells. These findings indicate that polyomaviruseshave the potential to be oncogenic in zebra finches.
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Affiliation(s)
- Katherine A Shuster
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Tzushan S Yang
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kate T Snyder
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | - Nicole Creanza
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | | | - Laura B Goodman
- Cornell University College of Veterinary Medicine, Ithaca, New York
| | - Jennifer K Grenier
- Cornell Institute of Biotechnology, Transcriptional Regulation and Expression Facility, Ithaca, New York
| | - Nicholas M Tataryn
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lauren E Himmel
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Katherine N Gibson-Corley
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
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9
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Peralta S, Grenier JK, Webb SM, Miller AD, Miranda IC, Parker JSL. Transcriptomic signatures of feline chronic gingivostomatitis are influenced by upregulated IL6. Sci Rep 2023; 13:13437. [PMID: 37596310 PMCID: PMC10439118 DOI: 10.1038/s41598-023-40679-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 08/16/2023] [Indexed: 08/20/2023] Open
Abstract
Feline chronic gingivostomatitis (FCGS) is a relatively common and debilitating disease characterized by bilateral inflammation and ulceration of the caudal oral mucosa, alveolar and buccal mucosa, and varying degrees of periodontal disease. The etiopathogenesis of FCGS remains unresolved. In this study, we performed bulk RNA-seq molecular profiling of affected tissues derived from a cohort of client-owned cats with FCGS compared to tissues from unaffected animals, to identify candidate genes and pathways that can help guide future exploration of novel clinical solutions. We complemented transcriptomic findings with immunohistochemistry and in situ hybridization assays to better understand the biological significance of the results and performed RNA-seq validation of biologically relevant differentially expressed genes using qPCR assays to demonstrate technical reproducibility. Transcriptomic profiles of oral mucosal tissues in cats with FCGS are enriched with immune- and inflammation-related genes and pathways that appear to be largely influenced by IL6, and include NFKB, JAK/STAT, IL-17 and IFN type I and II signaling, offering new opportunities to develop novel clinical applications based on a more rational understanding of the disease.
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Affiliation(s)
- Santiago Peralta
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
- Clinical Programs Center, College of Veterinary Medicine, Cornell University, Box 31, Ithaca, NY, 14853, USA.
| | - Jennifer K Grenier
- Transcriptional Regulation and Expression Facility, Biotechnology Resource Center, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Suzin M Webb
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew D Miller
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Ileana C Miranda
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, and The Rockefeller University, New York, NY, 10065, USA
| | - John S L Parker
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
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10
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Rodney AR, Skidmore ZL, Grenier JK, Griffith OL, Miller AD, Chu S, Ahmed F, Bryan JN, Peralta S, Warren WC. Genomic landscape and gene expression profiles of feline oral squamous cell carcinoma. Front Vet Sci 2023; 10:1079019. [PMID: 37266381 PMCID: PMC10229771 DOI: 10.3389/fvets.2023.1079019] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/29/2023] [Indexed: 06/03/2023] Open
Abstract
Feline oral squamous cell carcinoma (FOSCC) is a cancer of the squamous cell lining in the oral cavity and represents up to 80% of all oral cancers in cats, with a poor prognosis. We have used whole exome sequencing (WES) and RNA sequencing of the tumor to discover somatic mutations and gene expression changes that may be associated with FOSCC occurrence. FOSCC offers a potential comparative model to study human head and neck squamous cell carcinoma (HNSCC) due to its similar spontaneous formation, and morphological and histological features. In this first study using WES to identify somatic mutations in feline cancer, we have identified tumor-associated gene mutations in six cats with FOSCC and found some overlap with identified recurrently mutated genes observed in HNSCC. Four samples each had mutations in TP53, a common mutation in all cancers, but each was unique. Mutations in other cellular growth control genes were also found such as KAT2B and ARID1A. Enrichment analysis of FOSCC gene expression profiles suggests a molecular similarity to human OSCC as well, including alterations in epithelial to mesenchymal transition and IL6/JAK/STAT pathways. In this preliminary study, we present exome and transcriptome results that further our understanding of FOSCC.
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Affiliation(s)
- Alana R. Rodney
- Department of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Zachary L. Skidmore
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, United States
| | - Jennifer K. Grenier
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Obi L. Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, United States
| | - Andrew D. Miller
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Shirley Chu
- Department of Oncology, School of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Faraz Ahmed
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Jeffrey N. Bryan
- Department of Oncology, School of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Santiago Peralta
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Wesley C. Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO, United States
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11
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Peralta S, Grenier JK, Webb SM, Miller AD, Miranda IC, Parker JSL. Transcriptomic signatures of feline chronic gingivostomatitis are influenced by upregulated IL6. Res Sq 2023:rs.3.rs-2852140. [PMID: 37205490 PMCID: PMC10187381 DOI: 10.21203/rs.3.rs-2852140/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Feline chronic gingivostomatitis (FCGS) is a relatively common and debilitating disease characterized by bilateral inflammation and ulceration of the caudal oral mucosa, alveolar and buccal mucosa, and varying degrees of periodontal disease. The etiopathogenesis of FCGS remains unresolved. In this study, we performed bulk RNA-seq molecular profiling of affected tissues derived from a cohort of client-owned cats with FCGS compared to tissues from unaffected animals, to identify candidate genes and pathways that can help guide future exploration of novel clinical solutions. We complemented transcriptomic findings with immunohistochemistry and in situ hybridization assays to better understand the biological significance of the results and performed RNA-seq validation of selected differentially expressed genes using qPCR assays to demonstrate technical reproducibility. Transcriptomic profiles of oral mucosal tissues in cats with FCGS are enriched with immune- and inflammation-related genes and pathways that appear to be largely influenced by IL6 , and include NFKB, JAK/STAT, IL-17 and IFN type I and II signaling, offering new opportunities to develop novel clinical applications based on a more rational understanding of the disease.
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Affiliation(s)
| | | | | | | | - Ileana C Miranda
- Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, The Rockefeller University
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12
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Peralta S, Webb SM, Katt WP, Grenier JK, Duhamel GE. Cover Image. Vet Comp Oncol 2023. [DOI: 10.1111/vco.12883] [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: 02/17/2023]
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13
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Peralta S, Webb SM, Katt WP, Grenier JK, Duhamel GE. Highly recurrent BRAF p.V595E mutation in canine papillary oral squamous cell carcinoma. Vet Comp Oncol 2023; 21:138-144. [PMID: 36451536 DOI: 10.1111/vco.12869] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/20/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022]
Abstract
Oral squamous cell carcinoma (OSCC) is the most common oral epithelial malignancy in dogs. It exhibits locally aggressive biological behaviour with the potential to metastasize, and a reported 1-year survival rate of 0% when left untreated. Expression studies suggest that aberrant MAPK signalling plays a key role in canine OSCC tumorigenesis, which is consistent with BRAF and HRAS MAPK-activating mutations reported in some tumours. Several morphological subtypes of canine OSCC have been described, with papillary, conventional, and basaloid as the most common patterns. We hypothesized that mutational differences may underlie these phenotypic variations. In this study, targeted Sanger sequencing and restriction fragment length polymorphism assays demonstrate that up to 85.7% of canine papillary OSCC (n = 14) harbour a BRAF p.V595E mutation. Assessment of neoplastic epithelial cell proliferation using Ki67 immunolabelling (n = 10) confirmed a relatively high proliferation activity, consistent with their known aggressive clinical behaviour. These findings underscore a consistent genetic feature of canine papillary OSCC and provide a basis for the development of novel diagnostic and targeted therapeutic approaches that can improve the quality of veterinary care.
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Affiliation(s)
- Santiago Peralta
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Suzin M Webb
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - William P Katt
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Jennifer K Grenier
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Gerald E Duhamel
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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14
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Golshadi M, Claffey EF, Grenier JK, Miller A, Willand M, Edwards MG, Moore TP, Sledziona M, Gordon T, Borschel GH, Cheetham J. Delay modulates the immune response to nerve repair. NPJ Regen Med 2023; 8:12. [PMID: 36849720 PMCID: PMC9970988 DOI: 10.1038/s41536-023-00285-4] [Citation(s) in RCA: 1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/10/2023] [Indexed: 03/01/2023] Open
Abstract
Effective regeneration after peripheral nerve injury requires macrophage recruitment. We investigated the activation of remodeling pathways within the macrophage population when repair is delayed and identified alteration of key upstream regulators of the inflammatory response. We then targeted one of these regulators, using exogenous IL10 to manipulate the response to injury at the repair site. We demonstrate that this approach alters macrophage polarization, promotes macrophage recruitment, axon extension, neuromuscular junction formation, and increases the number of regenerating motor units reaching their target. We also demonstrate that this approach can rescue the effects of delayed nerve graft.
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Affiliation(s)
- Masoud Golshadi
- Cornell University College of Veterinary Medicine, 930 Campus Road, Ithaca, NY, 14853, USA
| | - Elaine F Claffey
- Cornell University College of Veterinary Medicine, 930 Campus Road, Ithaca, NY, 14853, USA
| | - Jennifer K Grenier
- Cornell University College of Veterinary Medicine, 930 Campus Road, Ithaca, NY, 14853, USA
| | - Andrew Miller
- Cornell University College of Veterinary Medicine, 930 Campus Road, Ithaca, NY, 14853, USA
| | - Michael Willand
- Epineuron Technologies Inc, 5100 Orbitor Dr., Mississauga, ON, L4W 5R8, Canada
| | | | - Tim P Moore
- Cornell University College of Veterinary Medicine, 930 Campus Road, Ithaca, NY, 14853, USA
| | - Michael Sledziona
- Cornell University College of Veterinary Medicine, 930 Campus Road, Ithaca, NY, 14853, USA
| | - Tessa Gordon
- Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1×8, Canada
| | | | - Jonathan Cheetham
- Cornell University College of Veterinary Medicine, 930 Campus Road, Ithaca, NY, 14853, USA.
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15
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Brieño-Enríquez MA, Faykoo-Martinez M, Goben M, Grenier JK, McGrath A, Prado AM, Sinopoli J, Wagner K, Walsh PT, Lopa SH, Laird DJ, Cohen PE, Wilson MD, Holmes MM, Place NJ. Postnatal oogenesis leads to an exceptionally large ovarian reserve in naked mole-rats. Nat Commun 2023; 14:670. [PMID: 36810851 PMCID: PMC9944903 DOI: 10.1038/s41467-023-36284-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 01/24/2023] [Indexed: 02/24/2023] Open
Abstract
In the long-lived naked mole-rat (NMR), the entire process of oogenesis occurs postnatally. Germ cell numbers increase significantly in NMRs between postnatal days 5 (P5) and P8, and germs cells positive for proliferation markers (Ki-67, pHH3) are present at least until P90. Using pluripotency markers (SOX2 and OCT4) and the primordial germ cell (PGC) marker BLIMP1, we show that PGCs persist up to P90 alongside germ cells in all stages of female differentiation and undergo mitosis both in vivo and in vitro. We identified VASA+ SOX2+ cells at 6 months and at 3-years in subordinate and reproductively activated females. Reproductive activation was associated with proliferation of VASA+ SOX2+ cells. Collectively, our results suggest that highly desynchronized germ cell development and the maintenance of a small population of PGCs that can expand upon reproductive activation are unique strategies that could help to maintain the NMR's ovarian reserve for its 30-year reproductive lifespan.
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Affiliation(s)
- Miguel Angel Brieño-Enríquez
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
- Aging Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Mariela Faykoo-Martinez
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Department of Psychology, University of Toronto, Mississauga, Mississauga, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Meagan Goben
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jennifer K Grenier
- RNA sequencing core and Center for Reproductive Genomics, College of Veterinary, Cornell University, Ithaca, NY, USA
| | - Ashley McGrath
- Department of Population Medicine & Diagnostic Sciences, Cornell University, Ithaca, NY, USA
| | - Alexandra M Prado
- Department of Population Medicine & Diagnostic Sciences, Cornell University, Ithaca, NY, USA
| | - Jacob Sinopoli
- Department of Population Medicine & Diagnostic Sciences, Cornell University, Ithaca, NY, USA
| | - Kate Wagner
- Department of Population Medicine & Diagnostic Sciences, Cornell University, Ithaca, NY, USA
| | - Patrick T Walsh
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Samia H Lopa
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Diana J Laird
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Paula E Cohen
- Center for Reproductive Genomics, Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Michael D Wilson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Melissa M Holmes
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Department of Psychology, University of Toronto, Mississauga, Mississauga, ON, Canada
| | - Ned J Place
- Department of Population Medicine & Diagnostic Sciences, Cornell University, Ithaca, NY, USA.
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16
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Sams KL, Mukai C, Marks BA, Mittal C, Demeter EA, Nelissen S, Grenier JK, Tate AE, Ahmed F, Coonrod SA. Delayed puberty, gonadotropin abnormalities and subfertility in male Padi2/Padi4 double knockout mice. Reprod Biol Endocrinol 2022; 20:150. [PMID: 36224627 PMCID: PMC9555066 DOI: 10.1186/s12958-022-01018-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Peptidylarginine deiminase enzymes (PADs) convert arginine residues to citrulline in a process called citrullination or deimination. Recently, two PADs, PAD2 and PAD4, have been linked to hormone signaling in vitro and the goal of this study was to test for links between PAD2/PAD4 and hormone signaling in vivo. METHODS Preliminary analysis of Padi2 and Padi4 single knockout (SKO) mice did not find any overt reproductive defects and we predicted that this was likely due to genetic compensation. To test this hypothesis, we created a Padi2/Padi4 double knockout (DKO) mouse model and tested these mice along with wild-type FVB/NJ (WT) and both strains of SKO mice for a range of reproductive defects. RESULTS Controlled breeding trials found that male DKO mice appeared to take longer to have their first litter than WT controls. This tendency was maintained when these mice were mated to either DKO or WT females. Additionally, unsexed 2-day old DKO pups and male DKO weanlings both weighed significantly less than their WT counterparts, took significantly longer than WT males to reach puberty, and had consistently lower serum testosterone levels. Furthermore, 90-day old adult DKO males had smaller testes than WT males with increased rates of germ cell apoptosis. CONCLUSIONS The Padi2/Padi4 DKO mouse model provides a new tool for investigating PAD function and outcomes from our studies provide the first in vivo evidence linking PADs with hormone signaling.
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Affiliation(s)
- Kelly L Sams
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Chinatsu Mukai
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Brooke A Marks
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Chitvan Mittal
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Elena Alina Demeter
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Sophie Nelissen
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Jennifer K Grenier
- Transcriptional Regulation and Expression Facility, Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Ann E Tate
- Transcriptional Regulation and Expression Facility, Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Faraz Ahmed
- Transcriptional Regulation and Expression Facility, Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Scott A Coonrod
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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17
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Francisco AB, Li J, Farghli AR, Kanke M, Shui B, Munn PR, Grenier JK, Soloway PD, Wang Z, Reid LM, Liu J, Sethupathy P. Chemical, Molecular, and Single-nucleus Analysis Reveal Chondroitin Sulfate Proteoglycan Aberrancy in Fibrolamellar Carcinoma. Cancer Res Commun 2022; 2:663-678. [PMID: 36923282 PMCID: PMC10010304 DOI: 10.1158/2767-9764.crc-21-0177] [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: 12/20/2021] [Revised: 03/21/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022]
Abstract
Fibrolamellar carcinoma (FLC) is an aggressive liver cancer with no effective therapeutic options. The extracellular environment of FLC tumors is poorly characterized and may contribute to cancer growth and/or metastasis. To bridge this knowledge gap, we assessed pathways relevant to proteoglycans, a major component of the extracellular matrix. We first analyzed gene expression data from FLC and nonmalignant liver tissue (n = 27) to identify changes in glycosaminoglycan (GAG) biosynthesis pathways and found that genes associated with production of chondroitin sulfate, but not other GAGs, are significantly increased by 8-fold. We then implemented a novel LC/MS-MS based method to quantify the abundance of different types of GAGs in patient tumors (n = 16) and found that chondroitin sulfate is significantly more abundant in FLC tumors by 6-fold. Upon further analysis of GAG-associated proteins, we found that versican (VCAN) expression is significantly upregulated at the mRNA and protein levels, the latter of which was validated by IHC. Finally, we performed single-cell assay for transposase-accessible chromatin sequencing on FLC tumors (n = 3), which revealed for the first time the different cell types in FLC tumors and also showed that VCAN is likely produced not only from FLC tumor epithelial cells but also activated stellate cells. Our results reveal a pathologic aberrancy in chondroitin (but not heparan) sulfate proteoglycans in FLC and highlight a potential role for activated stellate cells. Significance This study leverages a multi-disciplinary approach, including state-of-the-art chemical analyses and cutting-edge single-cell genomic technologies, to identify for the first time a marked chondroitin sulfate aberrancy in FLC that could open novel therapeutic avenues in the future.
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Affiliation(s)
- Adam B Francisco
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Jine Li
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina.,Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Alaa R Farghli
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Bo Shui
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Paul R Munn
- Genomics Innovation Hub, Biotechnology Resource Center, Cornell University, Ithaca, New York
| | - Jennifer K Grenier
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York.,Genomics Innovation Hub, Biotechnology Resource Center, Cornell University, Ithaca, New York
| | - Paul D Soloway
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Zhangjie Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P.R. China
| | - Lola M Reid
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
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18
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Peralta S, Duhamel GE, Katt WP, Heikinheimo K, Miller AD, Ahmed F, McCleary-Wheeler AL, Grenier JK. Comparative transcriptional profiling of canine acanthomatous ameloblastoma and homology with human ameloblastoma. Sci Rep 2021; 11:17792. [PMID: 34493785 PMCID: PMC8423744 DOI: 10.1038/s41598-021-97430-0] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/25/2021] [Indexed: 01/04/2023] Open
Abstract
Ameloblastomas are odontogenic tumors that are rare in people but have a relatively high prevalence in dogs. Because canine acanthomatous ameloblastomas (CAA) have clinicopathologic and molecular features in common with human ameloblastomas (AM), spontaneous CAA can serve as a useful translational model of disease. However, the molecular basis of CAA and how it compares to AM are incompletely understood. In this study, we compared the global genomic expression profile of CAA with AM and evaluated its dental origin by using a bulk RNA-seq approach. For these studies, healthy gingiva and canine oral squamous cell carcinoma served as controls. We found that aberrant RAS signaling, and activation of the epithelial-to-mesenchymal transition cellular program are involved in the pathogenesis of CAA, and that CAA is enriched with genes known to be upregulated in AM including those expressed during the early stages of tooth development, suggesting a high level of molecular homology. These results support the model that domestic dogs with spontaneous CAA have potential for pre-clinical assessment of targeted therapeutic modalities against AM.
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Affiliation(s)
- Santiago Peralta
- Department of Clinical Sciences, Clinical Programs Center, College of Veterinary Medicine, Cornell University, Box 31, Ithaca, NY, 14853, USA.
| | - Gerald E Duhamel
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - William P Katt
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Kristiina Heikinheimo
- Department of Oral and Maxillofacial Surgery, Institute of Dentistry, University of Turku and Turku University Hospital, Turku, Finland
| | - Andrew D Miller
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Faraz Ahmed
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Angela L McCleary-Wheeler
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Jennifer K Grenier
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
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19
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Herbert ZT, Thimmapuram J, Xie S, Kershner JP, Kolling FW, Ringelberg CS, LeClerc A, Alekseyev YO, Fan J, Podnar JW, Stevenson HS, Sommerville G, Gupta S, Berkeley M, Koeman J, Perera A, Scott AR, Grenier JK, Malik J, Ashton JM, Pivarski KL, Wang X, Kuffel G, Mesa TE, Smith AT, Shen J, Takata Y, Volkert TL, Love JA, Zhang Y, Wang J, Xuei X, Adams M, Levine SS. Multisite Evaluation of Next-Generation Methods for Small RNA Quantification. J Biomol Tech 2021; 31:47-56. [PMID: 31966025 DOI: 10.7171/jbt.20-3102-001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Small RNAs (smRNAs) are important regulators of many biologic processes and are now most frequently characterized using Illumina sequencing. However, although standard RNA sequencing library preparation has become routine in most sequencing facilities, smRNA sequencing library preparation has historically been challenging because of high input requirements, laborious protocols involving gel purifications, inability to automate, and a lack of benchmarking standards. Additionally, studies have suggested that many of these methods are nonlinear and do not accurately reflect the amounts of smRNAs in vivo. Recently, a number of new kits have become available that permit lower input amounts and less laborious, gel-free protocol options. Several of these new kits claim to reduce RNA ligase-dependent sequence bias through novel adapter modifications and to lessen adapter-dimer contamination in the resulting libraries. With the increasing number of smRNA kits available, understanding the relative strengths of each method is crucial for appropriate experimental design. In this study, we systematically compared 9 commercially available smRNA library preparation kits as well as NanoString probe hybridization across multiple study sites. Although several of the new methodologies do reduce the amount of artificially over- and underrepresented microRNAs (miRNAs), we observed that none of the methods was able to remove all of the bias in the library preparation. Identical samples prepared with different methods show highly varied levels of different miRNAs. Even so, many methods excelled in ease of use, lower input requirement, fraction of usable reads, and reproducibility across sites. These differences may help users select the most appropriate methods for their specific question of interest.
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Affiliation(s)
- Zachary T Herbert
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, Indiana, USA
| | | | - Fred W Kolling
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Carol S Ringelberg
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Ashley LeClerc
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, Massachusetts, USA
| | - Yuriy O Alekseyev
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, Massachusetts, USA.,Department of Pathology and Laboratory Medicine, Boston University, Boston, Massachusetts, USA
| | - Jun Fan
- Genomic Core Facility, Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, USA
| | - Jessica W Podnar
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Holly S Stevenson
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Gary Sommerville
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shipra Gupta
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Maura Berkeley
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Julie Koeman
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Allison R Scott
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Jennifer K Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | - Jeffrey Malik
- Genomics Research Center, University of Rochester, Rochester, New York, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester, Rochester, New York, USA
| | - Kara L Pivarski
- NUSeq Core Research Facility, Northwestern University, Chicago, Illinois, USA
| | - Xinkun Wang
- NUSeq Core Research Facility, Northwestern University, Chicago, Illinois, USA
| | - Gina Kuffel
- Loyola Genomics Facility, Loyola University Chicago, Maywood, Illinois, USA
| | - Tania E Mesa
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Andrew T Smith
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA
| | - Yoko Takata
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA
| | - Thomas L Volkert
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jennifer A Love
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Yanping Zhang
- Interdisciplinary Center for Biotechnology Research Gene Expression and Genotyping, University of Florida, Gainsville, Florida, USA
| | - Jun Wang
- Indiana University School of Medicine, Indianapolis, Indiana, USA; and
| | - Xiaoling Xuei
- Indiana University School of Medicine, Indianapolis, Indiana, USA; and
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Stuart S Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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20
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Pisu D, Huang L, Grenier JK, Russell DG. Dual RNA-Seq of Mtb-Infected Macrophages In Vivo Reveals Ontologically Distinct Host-Pathogen Interactions. Cell Rep 2021; 30:335-350.e4. [PMID: 31940480 PMCID: PMC7032562 DOI: 10.1016/j.celrep.2019.12.033] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/31/2019] [Accepted: 12/10/2019] [Indexed: 12/13/2022] Open
Abstract
Dissecting the in vivo host-pathogen interplay is crucial to understanding the molecular mechanisms governing control or progression of intracellular infections. In this work, we explore the in vivo molecular dynamics of Mtb infection by performing dual RNA-seq on Mycobacterium tuberculosis-infected, ontogenetically distinct macrophage lineages isolated directly from murine lungs. We first define an in vivo signature of 180 genes specifically upregulated by Mtb in mouse lung macrophages, then we uncover a divergent transcriptional response of the bacteria between alveolar macrophages that appear to sustain Mtb growth through increased access to iron and fatty acids and interstitial macrophages that restrict Mtb growth through iron sequestration and higher levels of nitric oxide. We use an enrichment protocol for bacterial transcripts, which enables us to probe Mtb physiology at the host cell level in an in vivo environment, with broader application in understanding the infection dynamics of intracellular pathogens in general. In this study Pisu et al. performed dual RNA-seq on Mycobacterium tuberculosis-infected, ontogenetically distinct macrophage lineages isolated directly from infected murine lungs. The transcriptional response of host and bacteria diverged between alveolar macrophages that sustain Mtb growth and interstitial macrophages that restrict Mtb growth.
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Affiliation(s)
- Davide Pisu
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Lu Huang
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Jennifer K Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - David G Russell
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
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21
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Abstract
Dual RNA-sequencing is a powerful technique to assess both bacterial and host transcriptomes in an unbiased way. We developed a protocol to perform Dual RNA-seq on in vivo-derived macrophage populations infected with Mycobacterium tuberculosis. Here, we provide a practical step-by-step guide to execute the protocol on Mtb-infected cells from a murine infection model. Our protocol can also be easily applied to perform Dual RNA-seq on in vitro-derived cells as well as different Mtb-infected host cell types. For complete details on the use and execution of this protocol, please refer to Pisu et al. (2020) Dual RNA-seq of M. tuberculosis-infected cells Simultaneous profiling of host and pathogen transcripts from an in vivo infection model Gain in-depth understanding of host-pathogen interactions at the molecular level
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Affiliation(s)
- Davide Pisu
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Lu Huang
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Bom Nae Rin Lee
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Jennifer K Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - David G Russell
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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22
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Singh P, Patel RK, Palmer N, Grenier JK, Paduch D, Kaldis P, Grimson A, Schimenti JC. CDK2 kinase activity is a regulator of male germ cell fate. Development 2019; 146:dev180273. [PMID: 31582414 PMCID: PMC6857589 DOI: 10.1242/dev.180273] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/21/2019] [Indexed: 12/27/2022]
Abstract
The ability of men to remain fertile throughout their lives depends upon establishment of a spermatogonial stem cell (SSC) pool from gonocyte progenitors, and thereafter balancing SSC renewal versus terminal differentiation. Here, we report that precise regulation of the cell cycle is crucial for this balance. Whereas cyclin-dependent kinase 2 (Cdk2) is not necessary for mouse viability or gametogenesis stages prior to meiotic prophase I, mice bearing a deregulated allele (Cdk2Y15S ) are severely deficient in spermatogonial differentiation. This allele disrupts an inhibitory phosphorylation site (Tyr15) for the kinase WEE1. Remarkably, Cdk2Y15S/Y15S mice possess abnormal clusters of mitotically active SSC-like cells, but these are eventually removed by apoptosis after failing to differentiate properly. Analyses of lineage markers, germ cell proliferation over time, and single cell RNA-seq data revealed delayed and defective differentiation of gonocytes into SSCs. Biochemical and genetic data demonstrated that Cdk2Y15S is a gain-of-function allele causing elevated kinase activity, which underlies these differentiation defects. Our results demonstrate that precise regulation of CDK2 kinase activity in male germ cell development is crucial for the gonocyte-to-spermatogonia transition and long-term spermatogenic homeostasis.
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Affiliation(s)
- Priti Singh
- Cornell University, College of Veterinary Medicine, Department of Biomedical Sciences, Ithaca, NY 14853, USA
| | - Ravi K Patel
- Cornell University, Department of Molecular Biology and Genetics, Ithaca, NY 14853, USA
| | - Nathan Palmer
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Singapore 138673
- Department of Biochemistry, National University of Singapore, Singapore 117599, Republic of Singapore
| | - Jennifer K Grenier
- Cornell University, College of Veterinary Medicine, Department of Biomedical Sciences, Ithaca, NY 14853, USA
| | - Darius Paduch
- Cornell University, Weill Cornell Medicine, Department of Urology, New York, NY 10065, USA
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Singapore 138673
- Department of Biochemistry, National University of Singapore, Singapore 117599, Republic of Singapore
| | - Andrew Grimson
- Cornell University, Department of Molecular Biology and Genetics, Ithaca, NY 14853, USA
| | - John C Schimenti
- Cornell University, College of Veterinary Medicine, Department of Biomedical Sciences, Ithaca, NY 14853, USA
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23
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Peralta S, McCleary‐Wheeler AL, Duhamel GE, Heikinheimo K, Grenier JK. Cover Image, Volume 17, Issue 3. Vet Comp Oncol 2019. [DOI: 10.1111/vco.12420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Santiago Peralta
- Department of Clinical Sciences, College of Veterinary MedicineCornell University Ithaca New York
| | - Angela L. McCleary‐Wheeler
- Department of Veterinary Medicine and Surgery, College of Veterinary MedicineUniversity of Missouri Columbia Missouri
- Department of Biomedical Sciences, College of Veterinary MedicineCornell University Ithaca New York
| | - Gerald E. Duhamel
- Department of Biomedical Sciences, College of Veterinary MedicineCornell University Ithaca New York
| | - Kristiina Heikinheimo
- Department of Oral and Maxillofacial Surgery, Institute of DentistryUniversity of Turku and Turku University Hospital Turku Finland
| | - Jennifer K. Grenier
- Department of Biomedical Sciences, College of Veterinary MedicineCornell University Ithaca New York
- RNA Sequencing CoreCornell University Ithaca New York
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24
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Peralta S, McCleary-Wheeler AL, Duhamel GE, Heikinheimo K, Grenier JK. Ultra-frequent HRAS p.Q61R somatic mutation in canine acanthomatous ameloblastoma reveals pathogenic similarities with human ameloblastoma. Vet Comp Oncol 2019; 17:439-445. [PMID: 31041834 DOI: 10.1111/vco.12487] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/11/2022]
Abstract
Ameloblastoma is a locally aggressive odontogenic tumour that occurs in humans and dogs. Most ameloblastomas (AM) in humans harbour mutually-exclusive driving mutations in BRAF, HRAS, KRAS, NRAS or FGFR2 that activate MAPK signalling, and in SMO that activates Hedgehog signalling. The remarkable clinical and histological similarities between canine acanthomatous ameloblastoma (CAA) and AM suggest they may harbour similar driving mutations. In this study, aimed at characterizing the mutational status of SMO, BRAF, HRAS, KRAS, NRAS and FGFR2 in CAA, we used RNA sequencing, Sanger sequencing and restriction fragment length polymorphism assays to demonstrate that 94% of CAA (n = 16) harbour a somatic HRAS p.Q61R mutation. The similarities in MAPK-activating mutational profiles between CAA and AM implicate conserved molecular mechanisms of tumorigenesis, thus, qualifying the dog as a potentially useful model of disease. Given the relevance of RAS mutations in the pathogenesis of odontogenic tumours and other types of cancer, the results of this study are of comparative, translational, and veterinary value.
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Affiliation(s)
- Santiago Peralta
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Angela L McCleary-Wheeler
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri.,Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Gerald E Duhamel
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Kristiina Heikinheimo
- Department of Oral and Maxillofacial Surgery, Institute of Dentistry, University of Turku and Turku University Hospital, Turku, Finland
| | - Jennifer K Grenier
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York.,RNA Sequencing Core, Cornell University, Ithaca, New York
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25
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Webb LM, Oyesola OO, Früh SP, Kamynina E, Still KM, Patel RK, Peng SA, Cubitt RL, Grimson A, Grenier JK, Harris TH, Danko CG, Tait Wojno ED. The Notch signaling pathway promotes basophil responses during helminth-induced type 2 inflammation. J Exp Med 2019; 216:1268-1279. [PMID: 30975892 PMCID: PMC6547860 DOI: 10.1084/jem.20180131] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 12/11/2018] [Accepted: 03/25/2019] [Indexed: 02/02/2023] Open
Abstract
Basophils promote type 2 inflammation that mediates worm clearance during murine infection with the gastrointestinal helminth parasite Trichuris muris. Webb et al. show for the first time that basophil–intrinsic Notch signaling is required for basophil gene expression and a functional program that support helminth expulsion. Type 2 inflammation drives the clearance of gastrointestinal helminth parasites, which infect over two billion people worldwide. Basophils are innate immune cells that support host-protective type 2 inflammation during murine infection with the helminth Trichuris muris. However, the mechanisms required for basophil function and gene expression regulation in this context remain unclear. We show that during T. muris infection, basophils localized to the intestine and up-regulated Notch receptor expression, rendering them sensitive to Notch signals that rapidly regulate gene expression programs. In vitro, Notch inhibition limited basophil cytokine production in response to cytokine stimulation. Basophil-intrinsic Notch signaling was required for T. muris–elicited changes in genome-wide basophil transcriptional programs. Mice lacking basophil-intrinsic functional Notch signaling had impaired worm clearance, decreased intestinal type 2 inflammation, altered basophil localization in the intestine, and decreased CD4+ T helper 2 cell responses following infection. These findings demonstrate that Notch is required for basophil gene expression and effector function associated with helminth expulsion during type 2 inflammation.
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Affiliation(s)
- Lauren M Webb
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Oyebola O Oyesola
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Simon P Früh
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Elena Kamynina
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Katherine M Still
- Center for Brain Immunology and Glia, Department of Neuroscience, University of Virginia, Charlottesville, VA
| | - Ravi K Patel
- Department of Molecular Biology and Genetics, College of Arts and Sciences, Cornell University, Ithaca, NY
| | - Seth A Peng
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Rebecca L Cubitt
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, College of Arts and Sciences, Cornell University, Ithaca, NY
| | - Jennifer K Grenier
- RNA Sequencing Core, Center for Reproductive Genomics, and Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Tajie H Harris
- Center for Brain Immunology and Glia, Department of Neuroscience, University of Virginia, Charlottesville, VA
| | - Charles G Danko
- Baker Institute for Animal Health and Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Elia D Tait Wojno
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY
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26
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Mann S, Sipka AS, Grenier JK. The degree of postpartum metabolic challenge in dairy cows is associated with peripheral blood mononuclear cell transcriptome changes of the innate immune system. Dev Comp Immunol 2019; 93:28-36. [PMID: 30500340 DOI: 10.1016/j.dci.2018.11.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
Dairy cows undergo a nutrient deficit immediately postpartum when lactational demands exceed nutrient intake. This occurs concurrently to an increased challenge due to bacterial and viral infections, yet ability for pathogen clearance is reduced despite a heightened and often host-damaging inflammatory response. We hypothesized that nutrient stress is associated with differences in the immune cell transcriptome. Our objective was therefore to investigate differentially expressed pathways (DEP) by RNA-seq in peripheral blood mononuclear cells harvested 3 weeks before and 1 week after calving from Holstein cows in low (L, n = 3) or high (H, n = 3) postpartum metabolic stress situations. Metabolic stress was defined by differences in circulating concentrations of glucose, fatty acids, and ketones postpartum. Cows in group H showed several upregulated DEP in relation to myeloid cell function and inflammatory response, as well as downregulation of the Th2 pathway. Principal components analysis showed that the transcriptome of group H postpartum samples was most different from all other samples. Differences in DE genes were noted even prepartum albeit fewer DE genes were identified and myeloid cell pathways in group H were generally downregulated at this time compared with group L. Samples within group L showed little difference between the two time points. We conclude that the metabolic phenotype of cows allowed us to identify differences in immune-regulatory pathways and that myeloid immune cells could play a dominant role in identifying these metabolically-associated differences that were demonstrated among a mixed mononuclear cell population.
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Affiliation(s)
- Sabine Mann
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Ithaca, NY, 14853, USA.
| | - Anja S Sipka
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Jennifer K Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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27
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Grive KJ, Hu Y, Shu E, Grimson A, Elemento O, Grenier JK, Cohen PE. Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing. PLoS Genet 2019; 15:e1007810. [PMID: 30893341 PMCID: PMC6443194 DOI: 10.1371/journal.pgen.1007810] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 04/01/2019] [Accepted: 02/18/2019] [Indexed: 12/22/2022] Open
Abstract
Spermatogenesis is the process by which male gametes are formed from a self-renewing population of spermatogonial stem cells (SSCs) residing in the testis. SSCs represent less than 1% of the total testicular cell population in adults, but must achieve a stable balance between self-renewal and differentiation. Once differentiation has occurred, the newly formed and highly proliferative spermatogonia must then enter the meiotic program in which DNA content is doubled, then halved twice to create haploid gametes. While much is known about the critical cellular processes that take place during the specialized cell division that is meiosis, much less is known about how the spermatocytes in the "first-wave" in juveniles compare to those that contribute to long-term, "steady-state" spermatogenesis in adults. Given the strictly-defined developmental process of spermatogenesis, this study explored the transcriptional profiles of developmental cell stages during testis maturation. Using a combination of comprehensive germ cell sampling with high-resolution, single-cell-mRNA-sequencing, we have generated a reference dataset of germ cell gene expression. We show that discrete developmental stages of spermatogenesis possess significant differences in the transcriptional profiles from neonates compared to juveniles and adults. Importantly, these gene expression dynamics are also reflected at the protein level in their respective cell types. We also show differential utilization of many biological pathways with age in both spermatogonia and spermatocytes, demonstrating significantly different underlying gene regulatory programs in these cell types over the course of testis development and spermatogenic waves. This dataset represents the first unbiased sampling of spermatogonia and spermatocytes during testis maturation, at high-resolution, single-cell depth. Not only does this analysis reveal previously unknown transcriptional dynamics of a highly transitional cell population, it has also begun to reveal critical differences in biological pathway utilization in developing spermatogonia and spermatocytes, including response to DNA damage and double-strand breaks.
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Affiliation(s)
- Kathryn J. Grive
- Center for Reproductive Genomics, Cornell University, Ithaca, NY, United States of America
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
| | - Yang Hu
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, United States of America
| | - Eileen Shu
- Center for Reproductive Genomics, Cornell University, Ithaca, NY, United States of America
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
| | - Andrew Grimson
- Center for Reproductive Genomics, Cornell University, Ithaca, NY, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, United States of America
| | - Jennifer K. Grenier
- Center for Reproductive Genomics, Cornell University, Ithaca, NY, United States of America
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
| | - Paula E. Cohen
- Center for Reproductive Genomics, Cornell University, Ithaca, NY, United States of America
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
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28
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Pennington MR, Grenier JK, Van de Walle GR. Transcriptome profiling of alphaherpesvirus-infected cells treated with the HIV-integrase inhibitor raltegravir reveals profound and specific alterations in host transcription. J Gen Virol 2018; 99:1115-1128. [PMID: 29916804 DOI: 10.1099/jgv.0.001090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Anti-microbial compounds typically exert their action by directly interfering with one or more stages of the pathogen's life cycle. However, some compounds also have secondary effects on the host that aid in pathogen clearance. Raltegravir is a human immunodeficiency virus (HIV)-integrase inhibitor that has been shown to alter the host immune response to HIV in addition to its direct antiviral effect. Interestingly, raltegravir can also directly inhibit the replication of various herpesviruses. However, the host-targeted effects of this drug in the context of a herpesvirus infection have not been explored. Here, we used felid alphaherpesvirus 1 (FHV-1), a close relative of human alphaherpesvirus 1 (HHV-1) that similarly causes ocular herpes, to characterize the host-targeted effects of raltegravir on corneal epithelial cells during an alphaherpesvirus infection. Using RNA deep sequencing, we found that raltegravir specifically boosts the expression of anti-angiogenic factors and promotes metabolic homeostasis in FHV-1-infected cells. In contrast, few changes in host gene transcription were found in uninfected cells. Importantly, we were able to demonstrate that these effects were specific to raltegravir and independent of the direct-acting antiviral effect of the drug, since treatment with the DNA polymerase inhibitor phosphonoacetic acid did not induce these host-targeted effects. Taken together, these results indicate that raltegravir has profound and specific effects on the host transcription profile of herpesvirus-infected cells that may contribute to the overall antiviral activity of the drug and could provide therapeutic benefits in vivo. Furthermore, this study provides a framework for future efforts evaluating the host-targeted effects of anti-microbial compounds.
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Affiliation(s)
- Matthew R Pennington
- 1Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Jennifer K Grenier
- 2Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Gerlinde R Van de Walle
- 1Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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29
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Tomlinson JE, Žygelytė E, Grenier JK, Edwards MG, Cheetham J. Temporal changes in macrophage phenotype after peripheral nerve injury. J Neuroinflammation 2018; 15:185. [PMID: 29907154 PMCID: PMC6003127 DOI: 10.1186/s12974-018-1219-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/29/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Macrophages play a key role in peripheral nerve repair and demonstrate complex phenotypes that are highly dependent on microenvironmental cues. METHODS We determined temporal changes in macrophage gene expression over time using RNA sequencing after fluorescence-activated cell sorting (FACS) macrophage populations from injured peripheral nerve. We identified key upstream regulators and dominant pathways using ingenuity pathway analysis and confirmed these changes with NanoString technology. We then investigate the effects of extreme polarizers of macrophage phenotype (IL4 and IFNγ) on nerve regeneration. We determined macrophage gene expression in vivo at the site of peripheral nerve injury with NanoString technology, and assessed recovery from sciatic nerve injury by cranial tibial muscle weights and retrograde labeling motor neurons in mice with deletion of IL4 or IFNγ receptors. RESULTS We demonstrate that IL4R and IFNγR deletions provide complementary responses to polarization, and alter expression of genes associated with angiogenesis and axonal extension, but do not influence recovery from peripheral nerve transection at 8 weeks after repair. CONCLUSIONS Overall, this study provides a framework to evaluate the phenotype of macrophages over time, and provides a broader and more precise assessment of gene expression changes than has previously been commonly used. This data suggests ways in which polarization may be modulated to improve repair.
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Affiliation(s)
- Joy E. Tomlinson
- Cornell University College of Veterinary Medicine, Ithaca, NY USA
| | - Emilija Žygelytė
- Cornell University College of Veterinary Medicine, Ithaca, NY USA
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30
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Smith NL, Patel RK, Reynaldi A, Grenier JK, Wang J, Watson NB, Nzingha K, Yee Mon KJ, Peng SA, Grimson A, Davenport MP, Rudd BD. Developmental Origin Governs CD8 + T Cell Fate Decisions during Infection. Cell 2018; 174:117-130.e14. [PMID: 29909981 DOI: 10.1016/j.cell.2018.05.029] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [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: 02/28/2018] [Revised: 04/03/2018] [Accepted: 05/11/2018] [Indexed: 12/22/2022]
Abstract
Heterogeneity is a hallmark feature of the adaptive immune system in vertebrates. Following infection, naive T cells differentiate into various subsets of effector and memory T cells, which help to eliminate pathogens and maintain long-term immunity. The current model suggests there is a single lineage of naive T cells that give rise to different populations of effector and memory T cells depending on the type and amounts of stimulation they encounter during infection. Here, we have discovered that multiple sub-populations of cells exist in the naive CD8+ T cell pool that are distinguished by their developmental origin, unique transcriptional profiles, distinct chromatin landscapes, and different kinetics and phenotypes after microbial challenge. These data demonstrate that the naive CD8+ T cell pool is not as homogeneous as previously thought and offers a new framework for explaining the remarkable heterogeneity in the effector and memory T cell subsets that arise after infection.
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Affiliation(s)
- Norah L Smith
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Ravi K Patel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Arnold Reynaldi
- Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, NSW 2052, Australia
| | - Jennifer K Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Jocelyn Wang
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Neva B Watson
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Kito Nzingha
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Kristel J Yee Mon
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Seth A Peng
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Miles P Davenport
- Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, NSW 2052, Australia
| | - Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA.
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31
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Kwan STC, King JH, Grenier JK, Yan J, Jiang X, Roberson MS, Caudill MA. Maternal Choline Supplementation during Normal Murine Pregnancy Alters the Placental Epigenome: Results of an Exploratory Study. Nutrients 2018; 10:nu10040417. [PMID: 29597262 PMCID: PMC5946202 DOI: 10.3390/nu10040417] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/23/2018] [Accepted: 03/26/2018] [Indexed: 12/14/2022] Open
Abstract
The placental epigenome regulates processes that affect placental and fetal development, and could be mediating some of the reported effects of maternal choline supplementation (MCS) on placental vascular development and nutrient delivery. As an extension of work previously conducted in pregnant mice, the current study sought to explore the effects of MCS on various epigenetic markers in the placenta. RNA and DNA were extracted from placentas collected on embryonic day 15.5 from pregnant mice fed a 1X or 4X choline diet, and were subjected to genome-wide sequencing procedures or mass-spectrometry-based assays to examine placental imprinted gene expression, DNA methylation patterns, and microRNA (miRNA) abundance. MCS yielded a higher (fold change = 1.63-2.25) expression of four imprinted genes (Ampd3, Tfpi2, Gatm and Aqp1) in the female placentas and a lower (fold change = 0.46-0.62) expression of three imprinted genes (Dcn, Qpct and Tnfrsf23) in the male placentas (false discovery rate (FDR) ≤ 0.05 for both sexes). Methylation in the promoter regions of these genes and global placental DNA methylation were also affected (p ≤ 0.05). Additionally, a lower (fold change = 0.3; Punadjusted = 2.05 × 10-4; FDR = 0.13) abundance of miR-2137 and a higher (fold change = 1.25-3.92; p < 0.05) expression of its target genes were detected in the 4X choline placentas. These data demonstrate that the placental epigenome is responsive to maternal choline intake during murine pregnancy and likely mediates some of the previously described choline-induced effects on placental and fetal outcomes.
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Affiliation(s)
| | - Julia H King
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA.
| | - Jennifer K Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA.
| | - Jian Yan
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA.
| | - Xinyin Jiang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA.
- Department of Health and Nutrition Sciences, Brooklyn College, Brooklyn, NY 11210, USA.
| | - Mark S Roberson
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA.
| | - Marie A Caudill
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA.
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Sones JL, Merriam AA, Seffens A, Brown-Grant DA, Butler SD, Zhao AM, Xu X, Shawber CJ, Grenier JK, Douglas NC. Angiogenic factor imbalance precedes complement deposition in placentae of the BPH/5 model of preeclampsia. FASEB J 2018; 32:2574-2586. [PMID: 29279353 DOI: 10.1096/fj.201701008r] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Preeclampsia (PE), a hypertensive disorder of pregnancy, is a leading cause of maternal and fetal morbidity and mortality. Although the etiology is unknown, PE is thought to be caused by defective implantation and decidualization in pregnancy. Pregnant blood pressure high (BPH)/5 mice spontaneously develop placentopathies and maternal features of human PE. We hypothesized that BPH/5 implantation sites have transcriptomic alterations. Next-generation RNA sequencing of implantation sites at peak decidualization, embryonic day (E)7.5, revealed complement gene up-regulation in BPH/5 vs. controls. In BPH/5, expression of complement factor 3 was increased around the decidual vasculature of E7.5 implantation sites and in the trophoblast giant cell layer of E10.5 placentae. Altered expression of VEGF pathway genes in E5.5 BPH/5 implantation sites preceded complement dysregulation, which correlated with abnormal vasculature and increased placental growth factor mRNA and VEGF164 expression at E7.5. By E10.5, proangiogenic genes were down-regulated, whereas antiangiogenic sFlt-1 was up-regulated in BPH/5 placentae. We found that early local misexpression of VEGF genes and abnormal decidual vasculature preceded sFlt-1 overexpression and increased complement deposition in BPH/5 placentae. Our findings suggest that abnormal decidual angiogenesis precedes complement activation, which in turn contributes to the aberrant trophoblast invasion and poor placentation that underlie PE.-Sones, J. L., Merriam, A. A., Seffens, A., Brown-Grant, D.-A., Butler, S. D., Zhao, A. M., Xu, X., Shawber, C. J., Grenier, J. K., Douglas, N. C. Angiogenic factor imbalance precedes complement deposition in placentae of the BPH/5 model of preeclampsia.
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Affiliation(s)
- Jennifer L Sones
- Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Audrey A Merriam
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Angelina Seffens
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Dex-Ann Brown-Grant
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Scott D Butler
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA; and
| | - Anna M Zhao
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Xinjing Xu
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Carrie J Shawber
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Jennifer K Grenier
- RNA Sequencing Core, Center for Reproductive Genomics, Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Nataki C Douglas
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York, USA
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Moon H, Donahue LR, Choi E, Scumpia PO, Lowry WE, Grenier JK, Zhu J, White AC. Melanocyte Stem Cell Activation and Translocation Initiate Cutaneous Melanoma in Response to UV Exposure. Cell Stem Cell 2017; 21:665-678.e6. [PMID: 29033353 PMCID: PMC9004284 DOI: 10.1016/j.stem.2017.09.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [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: 01/18/2017] [Revised: 06/20/2017] [Accepted: 08/31/2017] [Indexed: 12/20/2022]
Abstract
Melanoma is one of the deadliest cancers, yet the cells of origin and mechanisms of tumor initiation remain unclear. The majority of melanomas emerge from clear skin without a precursor lesion, but it is unknown whether these melanomas can arise from melanocyte stem cells (MCSCs). Here we employ mouse models to define the role of MCSCs as melanoma cells of origin, demonstrate that MCSC quiescence acts as a tumor suppressor, and identify the extrinsic environmental and molecular factors required for the critical early steps of melanoma initiation. Specifically, melanomas originate from melanoma-competent MCSCs upon stimulation by UVB, which induces MCSC activation and translocation via an inflammation-dependent process. Moreover, the chromatin-remodeling factor Hmga2 in the skin plays a critical role in UVB-mediated melanomagenesis. These findings delineate melanoma formation from melanoma-competent MCSCs following extrinsic stimuli, and they suggest that abrogation of Hmga2 function in the microenvironment can suppress MCSC-originating cutaneous melanomas.
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Affiliation(s)
- Hyeongsun Moon
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Leanne R Donahue
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Eunju Choi
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Philip O Scumpia
- Department of Medicine, Division of Dermatology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - William E Lowry
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jennifer K Grenier
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Jerry Zhu
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Andrew C White
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA.
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Grenier JK, Foureman PA, Sloma EA, Miller AD. RNA-seq transcriptome analysis of formalin fixed, paraffin-embedded canine meningioma. PLoS One 2017; 12:e0187150. [PMID: 29073243 PMCID: PMC5658167 DOI: 10.1371/journal.pone.0187150] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/14/2017] [Indexed: 12/21/2022] Open
Abstract
Meningiomas are the most commonly reported primary intracranial tumor in dogs and humans and between the two species there are similarities in histology and biologic behavior. Due to these similarities, dogs have been proposed as models for meningioma pathobiology. However, little is known about specific pathways and individual genes that are involved in the development and progression of canine meningioma. In addition, studies are lacking that utilize RNAseq to characterize gene expression in clinical cases of canine meningioma. The primary objective of this study was to develop a technique for which high quality RNA can be extracted from formalin-fixed, paraffin embedded tissue and then used for transcriptome analysis to determine patterns of gene expression. RNA was extracted from thirteen canine meningiomas-eleven from formalin fixed and two flash-frozen. These represented six grade I and seven grade II meningiomas based on the World Health Organization classification system for human meningioma. RNA was also extracted from fresh frozen leptomeninges from three control dogs for comparison. RNAseq libraries made from formalin fixed tissue were of sufficient quality to successfully identify 125 significantly differentially expressed genes, the majority of which were related to oncogenic processes. Twelve genes (AQP1, BMPER, FBLN2, FRZB, MEDAG, MYC, PAMR1, PDGFRL, PDPN, PECAM1, PERP, ZC2HC1C) were validated using qPCR. Among the differentially expressed genes were oncogenes, tumor suppressors, transcription factors, VEGF-related genes, and members of the WNT pathway. Our work demonstrates that RNA of sufficient quality can be extracted from FFPE canine meningioma samples to provide biologically relevant transcriptome analyses using a next-generation sequencing technique, such as RNA-seq.
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Affiliation(s)
- Jennifer K. Grenier
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, New York, United States of America
| | - Polly A. Foureman
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, New York, United States of America
- Division of Biological Sciences, Chandler-Gilbert Community College, Chandler, Arizona, United States of America
| | - Erica A. Sloma
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, New York, United States of America
| | - Andrew D. Miller
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, New York, United States of America
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35
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Meyers-Wallen VN, Boyko AR, Danko CG, Grenier JK, Mezey JG, Hayward JJ, Shannon LM, Gao C, Shafquat A, Rice EJ, Pujar S, Eggers S, Ohnesorg T, Sinclair AH. XX Disorder of Sex Development is associated with an insertion on chromosome 9 and downregulation of RSPO1 in dogs (Canis lupus familiaris). PLoS One 2017; 12:e0186331. [PMID: 29053721 PMCID: PMC5650465 DOI: 10.1371/journal.pone.0186331] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 09/28/2017] [Indexed: 12/15/2022] Open
Abstract
Remarkable progress has been achieved in understanding the mechanisms controlling sex determination, yet the cause for many Disorders of Sex Development (DSD) remains unknown. Of particular interest is a rare XX DSD subtype in which individuals are negative for SRY, the testis determining factor on the Y chromosome, yet develop testes or ovotestes, and both of these phenotypes occur in the same family. This is a naturally occurring disorder in humans (Homo sapiens) and dogs (C. familiaris). Phenotypes in the canine XX DSD model are strikingly similar to those of the human XX DSD subtype. The purposes of this study were to identify 1) a variant associated with XX DSD in the canine model and 2) gene expression alterations in canine embryonic gonads that could be informative to causation. Using a genome wide association study (GWAS) and whole genome sequencing (WGS), we identified a variant on C. familiaris autosome 9 (CFA9) that is associated with XX DSD in the canine model and in affected purebred dogs. This is the first marker identified for inherited canine XX DSD. It lies upstream of SOX9 within the canine ortholog for the human disorder, which resides on 17q24. Inheritance of this variant indicates that XX DSD is a complex trait in which breed genetic background affects penetrance. Furthermore, the homozygous variant genotype is associated with embryonic lethality in at least one breed. Our analysis of gene expression studies (RNA-seq and PRO-seq) in embryonic gonads at risk of XX DSD from the canine model identified significant RSPO1 downregulation in comparison to XX controls, without significant upregulation of SOX9 or other known testis pathway genes. Based on these data, a novel mechanism is proposed in which molecular lesions acting upstream of RSPO1 induce epigenomic gonadal mosaicism.
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Affiliation(s)
- Vicki N. Meyers-Wallen
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, United States of America
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
- * E-mail:
| | - Adam R. Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
| | - Charles G. Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, United States of America
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
| | - Jennifer K. Grenier
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
| | - Jason G. Mezey
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, United States of America
| | - Jessica J. Hayward
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
| | - Laura M. Shannon
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
| | - Chuan Gao
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
| | - Afrah Shafquat
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
| | - Edward J. Rice
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, United States of America
| | - Shashikant Pujar
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, United States of America
| | - Stefanie Eggers
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Thomas Ohnesorg
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Andrew H. Sinclair
- Murdoch Children’s Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
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36
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Watson NB, Peng S, Nzingha K, Wang J, Grenier JK, Smith NL, Patel RK, Grimson AW, Rudd BD. Neonatal CD8+ T cells provide innate immune protection against unrelated pathogens. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.151.3] [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] [Indexed: 01/02/2023]
Abstract
Abstract
We previously found that neonatal and adult CD8+ T cells adopt different fates after infection with specific pathogens because they are derived from a distinct progenitor cell that is distinguished by expression of Lin28b. In this report, we investigated if CD8+ T cells respond differently to unrelated pathogens in early life. To start, we compared gene expression profiles of neonatal and adult CD8+ T cells after stimulation with innate cytokines (IL-12 + IL-18). Interestingly, we found that neonatal CD8+ T cells are more responsive and express a distinct cytokine profile compared to their adult counterparts. To examine the biological significance of these age-related differences, we next adoptively transferred monoclonal populations of neonatal or adult CD8+ T cells into T cell-deficient recipients and compared their ability to mediate immune protection against an irrelevant strain of Listeria monocytogenes. Surprisingly, we found that neonatal donor cell displayed increased proliferation and effector functions, and the pathogen burden was significantly reduced when compared to recipients containing adult donor cells. We also found that Lin28b may be responsible for the enhanced responsiveness to innate cytokines in early life, as ectopic expression of Lin28b in adult cells enabled them to initiate a program of bystander activation that was analogous to neonates. Collectively, these findings indicate that neonatal CD8+ T cells possess innate-like functions during infections at the cost of generating memory, and these unique behaviors may be driven by high levels of Lin28b. We currently are employing ATAC-seq to determine whether Lin28b changes the program of bystander activation by altering the chromatin landscape.
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Abstract
Mammalian SIRT7 is a member of the sirtuin family that regulates multiple biological processes including genome stability, metabolic pathways, stress responses, and tumorigenesis. SIRT7 has been shown to be important for ribosome biogenesis and transcriptional regulation. SIRT7 knockout mice exhibit complications associated with fatty liver and increased aging in hematopoietic stem cells. However, the molecular basis for its biological function remains unclear, in part due to the lack of efficient enzymatic activity in vitro. Previously, we have demonstrated that double-stranded DNA could activate SIRT7's deacetylase activity in vitro, allowing it to deacetylate H3K18 in the context of chromatin. Here, we show that RNA can increase the catalytic efficiency of SIRT7 even better and that SIRT7 can remove long chain fatty acyl groups more efficiently than removing acetyl groups. Truncation and mutagenesis studies revealed residues at both the amino and carboxyl termini of SIRT7 that are involved in RNA-binding and important for activity. RNA immunoprecipitation-sequencing (RIP-seq) identified ribosomal RNA (rRNA) as the predominant RNA binding partner of SIRT7. The associated RNA was able to effectively activate the deacetylase and defatty-acylase activities of SIRT7. Knockdown of SIRT7 increased the lysine fatty acylation of several nuclear proteins based on metabolic labeling with an alkyne-tagged fatty acid analog, supporting that the defatty-acylase activity of SIRT7 is physiologically relevant. These findings provide important insights into the biological functions of SIRT7, as well as an improved platform to develop SIRT7 modulators.
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Affiliation(s)
- Zhen Tong
- Howard Hughes Medical
Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Miao Wang
- Howard Hughes Medical
Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yi Wang
- School
of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong, China
| | - David D. Kim
- Howard Hughes Medical
Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jennifer K. Grenier
- RNA Sequencing Core, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, United States
| | - Ji Cao
- Howard Hughes Medical
Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Sushabhan Sadhukhan
- Howard Hughes Medical
Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Quan Hao
- School
of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong, China
| | - Hening Lin
- Howard Hughes Medical
Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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38
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Arguello JR, Cardoso-Moreira M, Grenier JK, Gottipati S, Clark AG, Benton R. Extensive local adaptation within the chemosensory system following Drosophila melanogaster's global expansion. Nat Commun 2016; 7:ncomms11855. [PMID: 27292132 PMCID: PMC4910016 DOI: 10.1038/ncomms11855] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [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: 11/24/2015] [Accepted: 05/06/2016] [Indexed: 01/05/2023] Open
Abstract
How organisms adapt to new environments is of fundamental biological interest, but poorly understood at the genetic level. Chemosensory systems provide attractive models to address this problem, because they lie between external environmental signals and internal physiological responses. To investigate how selection has shaped the well-characterized chemosensory system of Drosophila melanogaster, we have analysed genome-wide data from five diverse populations. By couching population genomic analyses of chemosensory protein families within parallel analyses of other large families, we demonstrate that chemosensory proteins are not outliers for adaptive divergence between species. However, chemosensory families often display the strongest genome-wide signals of recent selection within D. melanogaster. We show that recent adaptation has operated almost exclusively on standing variation, and that patterns of adaptive mutations predict diverse effects on protein function. Finally, we provide evidence that chemosensory proteins have experienced relaxed constraint, and argue that this has been important for their rapid adaptation over short timescales. Fruit flies gain valuable information about their environment by sensing chemicals. Here, Arguello et al. show strong signals of recent selection on the chemosensory system of the fruit fly Drosophila melanogaster, consistent with the adaptation of populations to their local chemical environment.
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Affiliation(s)
- J Roman Arguello
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Margarida Cardoso-Moreira
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Jennifer K Grenier
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Srikanth Gottipati
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.,Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
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Guda S, Brendel C, Renella R, Du P, Bauer DE, Canver MC, Grenier JK, Grimson AW, Kamran SC, Thornton J, de Boer H, Root DE, Milsom MD, Orkin SH, Gregory RI, Williams DA. miRNA-embedded shRNAs for Lineage-specific BCL11A Knockdown and Hemoglobin F Induction. Mol Ther 2015; 23:1465-74. [PMID: 26080908 DOI: 10.1038/mt.2015.113] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 06/09/2015] [Indexed: 12/21/2022] Open
Abstract
RNA interference (RNAi) technology using short hairpin RNAs (shRNAs) expressed via RNA polymerase (pol) III promoters has been widely exploited to modulate gene expression in a variety of mammalian cell types. For certain applications, such as lineage-specific knockdown, embedding targeting sequences into pol II-driven microRNA (miRNA) architecture is required. Here, using the potential therapeutic target BCL11A, we demonstrate that pol III-driven shRNAs lead to significantly increased knockdown but also increased cytotoxcity in comparison to pol II-driven miRNA adapted shRNAs (shRNA(miR)) in multiple hematopoietic cell lines. We show that the two expression systems yield mature guide strand sequences that differ by a 4 bp shift. This results in alternate seed sequences and consequently influences the efficacy of target gene knockdown. Incorporating a corresponding 4 bp shift into the guide strand of shRNA(miR)s resulted in improved knockdown efficiency of BCL11A. This was associated with a significant de-repression of the hemoglobin target of BCL11A, human γ-globin or the murine homolog Hbb-y. Our results suggest the requirement for optimization of shRNA sequences upon incorporation into a miRNA backbone. These findings have important implications in future design of shRNA(miR)s for RNAi-based therapy in hemoglobinopathies and other diseases requiring lineage-specific expression of gene silencing sequences.
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Affiliation(s)
- Swaroopa Guda
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Christian Brendel
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Raffaele Renella
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Peng Du
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Stem Cell Program, Boston Children's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard Stem Cell Institute, Boston, Massachusetts, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Jennifer K Grenier
- Genetic Perturbation Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Andrew W Grimson
- Department of Molecular Biology & Genetics, College of Arts and Sciences, Cornell University, Ithaca, New York, USA
| | - Sophia C Kamran
- Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Boston, Massachusetts, USA
| | - James Thornton
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Stem Cell Program, Boston Children's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard Stem Cell Institute, Boston, Massachusetts, USA
| | - Helen de Boer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - David E Root
- Genetic Perturbation Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Michael D Milsom
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Boston, Massachusetts, USA
| | - Richard I Gregory
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Stem Cell Program, Boston Children's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard Stem Cell Institute, Boston, Massachusetts, USA
| | - David A Williams
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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Ayroles JF, Buchanan SM, O'Leary C, Skutt-Kakaria K, Grenier JK, Clark AG, Hartl DL, de Bivort BL. Behavioral idiosyncrasy reveals genetic control of phenotypic variability. Proc Natl Acad Sci U S A 2015; 112:6706-11. [PMID: 25953335 PMCID: PMC4450409 DOI: 10.1073/pnas.1503830112] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quantitative genetics has primarily focused on describing genetic effects on trait means and largely ignored the effect of alternative alleles on trait variability, potentially missing an important axis of genetic variation contributing to phenotypic differences among individuals. To study the genetic effects on individual-to-individual phenotypic variability (or intragenotypic variability), we used Drosophila inbred lines and measured the spontaneous locomotor behavior of flies walking individually in Y-shaped mazes, focusing on variability in locomotor handedness, an assay optimized to measure variability. We discovered that some lines had consistently high levels of intragenotypic variability among individuals, whereas lines with low variability behaved as although they tossed a coin at each left/right turn decision. We demonstrate that the degree of variability is itself heritable. Using a genome-wide association study (GWAS) for the degree of intragenotypic variability as the phenotype across lines, we identified several genes expressed in the brain that affect variability in handedness without affecting the mean. One of these genes, Ten-a, implicates a neuropil in the central complex of the fly brain as influencing the magnitude of behavioral variability, a brain region involved in sensory integration and locomotor coordination. We validated these results using genetic deficiencies, null alleles, and inducible RNAi transgenes. Our study reveals the constellation of phenotypes that can arise from a single genotype and shows that different genetic backgrounds differ dramatically in their propensity for phenotypic variabililty. Because traditional mean-focused GWASs ignore the contribution of variability to overall phenotypic variation, current methods may miss important links between genotype and phenotype.
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Affiliation(s)
- Julien F Ayroles
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; Harvard Society of Fellows, Harvard University, Cambridge, MA 02138; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853;
| | | | - Chelsea O'Leary
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; Rowland Institute at Harvard, Cambridge, MA 02142; and Center for Brain Science, Harvard University, Cambridge, MA 02138
| | - Kyobi Skutt-Kakaria
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; Center for Brain Science, Harvard University, Cambridge, MA 02138
| | - Jennifer K Grenier
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138;
| | - Benjamin L de Bivort
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; Rowland Institute at Harvard, Cambridge, MA 02142; and Center for Brain Science, Harvard University, Cambridge, MA 02138
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41
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Modzelewski AJ, Hilz S, Crate EA, Schweidenback CTH, Fogarty EA, Grenier JK, Freire R, Cohen PE, Grimson A. Dgcr8 and Dicer are essential for sex chromosome integrity during meiosis in males. J Cell Sci 2015; 128:2314-27. [PMID: 25934699 PMCID: PMC4487015 DOI: 10.1242/jcs.167148] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/21/2015] [Indexed: 12/22/2022] Open
Abstract
Small RNAs play crucial roles in regulating gene expression during mammalian meiosis. To investigate the function of microRNAs (miRNAs) and small interfering RNAs (siRNAs) during meiosis in males, we generated germ-cell-specific conditional deletions of Dgcr8 and Dicer in mice. Analysis of spermatocytes from both conditional knockout lines revealed that there were frequent chromosomal fusions during meiosis, always involving one or both sex chromosomes. RNA sequencing indicates upregulation of Atm in spermatocytes from miRNA-deficient mice, and immunofluorescence imaging demonstrates an increased abundance of activated ATM kinase and mislocalization of phosphorylated MDC1, an ATM phosphorylation substrate. The Atm 3′UTR contains many potential microRNA target sites, and, notably, target sites for several miRNAs depleted in both conditional knockout mice were highly effective at promoting repression. RNF8, a telomere-associated protein whose localization is controlled by the MDC1–ATM kinase cascade, normally associates with the sex chromosomes during pachytene, but in both conditional knockouts redistributed to the autosomes. Taken together, these results suggest that Atm dysregulation in microRNA-deficient germ lines contributes to the redistribution of proteins involved in chromosomal stability from the sex chromosomes to the autosomes, resulting in sex chromosome fusions during meiotic prophase I. Highlighted Article: miRNA-deficient spermatocytes display frequent sex chromosome fusions and fail to progress through meiosis in a process that is probably mediated by dysregulation of Atm.
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Affiliation(s)
| | - Stephanie Hilz
- Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth A Crate
- Departments of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | | | | | - Jennifer K Grenier
- Departments of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Raimundo Freire
- Unidad de Investigacion, Hospital Universitario de Canarias, Ofra s/n, La Cuesta, La Laguna, Tenerife 38320, Spain
| | - Paula E Cohen
- Departments of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Grimson
- Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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Wagner JP, Wolf-Yadlin A, Sevecka M, Grenier JK, Root DE, Lauffenburger DA, MacBeath G. Receptor tyrosine kinases fall into distinct classes based on their inferred signaling networks. Sci Signal 2013; 6:ra58. [PMID: 23861540 DOI: 10.1126/scisignal.2003994] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Although many anticancer drugs that target receptor tyrosine kinases (RTKs) provide clinical benefit, their long-term use is limited by resistance that is often attributed to increased abundance or activation of another RTK that compensates for the inhibited receptor. To uncover common and unique features in the signaling networks of RTKs, we measured time-dependent signaling in six isogenic cell lines, each expressing a different RTK as downstream proteins were systematically perturbed by RNA interference. Network models inferred from the data revealed a conserved set of signaling pathways and RTK-specific features that grouped the RTKs into three distinct classes: (i) an EGFR/FGFR1/c-Met class constituting epidermal growth factor receptor, fibroblast growth factor receptor 1, and the hepatocyte growth factor receptor c-Met; (ii) an IGF-1R/NTRK2 class constituting insulin-like growth factor 1 receptor and neurotrophic tyrosine receptor kinase 2; and (iii) a PDGFRβ class constituting platelet-derived growth factor receptor β. Analysis of cancer cell line data showed that many RTKs of the same class were coexpressed and that increased abundance of an RTK or its cognate ligand frequently correlated with resistance to a drug targeting another RTK of the same class. In contrast, abundance of an RTK or ligand of one class generally did not affect sensitivity to a drug targeting an RTK of a different class. Thus, classifying RTKs by their inferred networks and then therapeutically targeting multiple receptors within a class may delay or prevent the onset of resistance.
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Affiliation(s)
- Joel P Wagner
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Alejandro Wolf-Yadlin
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Mark Sevecka
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Jennifer K Grenier
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Gavin MacBeath
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.,Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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43
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Ketela T, Heisler LE, Brown KR, Ammar R, Kasimer D, Surendra A, Ericson E, Blakely K, Karamboulas D, Smith AM, Durbic T, Arnoldo A, Cheung-Ong K, Koh JLY, Gopal S, Cowley GS, Yang X, Grenier JK, Giaever G, Root DE, Moffat J, Nislow C. A comprehensive platform for highly multiplexed mammalian functional genetic screens. BMC Genomics 2011; 12:213. [PMID: 21548937 PMCID: PMC3115879 DOI: 10.1186/1471-2164-12-213] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [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: 11/04/2010] [Accepted: 05/06/2011] [Indexed: 11/15/2022] Open
Abstract
Background Genome-wide screening in human and mouse cells using RNA interference and open reading frame over-expression libraries is rapidly becoming a viable experimental approach for many research labs. There are a variety of gene expression modulation libraries commercially available, however, detailed and validated protocols as well as the reagents necessary for deconvolving genome-scale gene screens using these libraries are lacking. As a solution, we designed a comprehensive platform for highly multiplexed functional genetic screens in human, mouse and yeast cells using popular, commercially available gene modulation libraries. The Gene Modulation Array Platform (GMAP) is a single microarray-based detection solution for deconvolution of loss and gain-of-function pooled screens. Results Experiments with specially constructed lentiviral-based plasmid pools containing ~78,000 shRNAs demonstrated that the GMAP is capable of deconvolving genome-wide shRNA "dropout" screens. Further experiments with a larger, ~90,000 shRNA pool demonstrate that equivalent results are obtained from plasmid pools and from genomic DNA derived from lentivirus infected cells. Parallel testing of large shRNA pools using GMAP and next-generation sequencing methods revealed that the two methods provide valid and complementary approaches to deconvolution of genome-wide shRNA screens. Additional experiments demonstrated that GMAP is equivalent to similar microarray-based products when used for deconvolution of open reading frame over-expression screens. Conclusion Herein, we demonstrate four major applications for the GMAP resource, including deconvolution of pooled RNAi screens in cells with at least 90,000 distinct shRNAs. We also provide detailed methodologies for pooled shRNA screen readout using GMAP and compare next-generation sequencing to GMAP (i.e. microarray) based deconvolution methods.
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Affiliation(s)
- Troy Ketela
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
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44
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Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 2009; 326:257-63. [PMID: 19729616 PMCID: PMC2879337 DOI: 10.1126/science.1179050] [Citation(s) in RCA: 394] [Impact Index Per Article: 26.3] [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: 11/02/2022]
Abstract
Models of mammalian regulatory networks controlling gene expression have been inferred from genomic data but have largely not been validated. We present an unbiased strategy to systematically perturb candidate regulators and monitor cellular transcriptional responses. We applied this approach to derive regulatory networks that control the transcriptional response of mouse primary dendritic cells to pathogens. Our approach revealed the regulatory functions of 125 transcription factors, chromatin modifiers, and RNA binding proteins, which enabled the construction of a network model consisting of 24 core regulators and 76 fine-tuners that help to explain how pathogen-sensing pathways achieve specificity. This study establishes a broadly applicable, comprehensive, and unbiased approach to reveal the wiring and functions of a regulatory network controlling a major transcriptional response in primary mammalian cells.
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Affiliation(s)
- Ido Amit
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
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45
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Boehm JS, Zhao JJ, Yao J, Kim SY, Firestein R, Dunn IF, Sjostrom SK, Garraway LA, Weremowicz S, Richardson AL, Greulich H, Stewart CJ, Mulvey LA, Shen RR, Ambrogio L, Hirozane-Kishikawa T, Hill DE, Vidal M, Meyerson M, Grenier JK, Hinkle G, Root DE, Roberts TM, Lander ES, Polyak K, Hahn WC. Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell 2007; 129:1065-79. [PMID: 17574021 DOI: 10.1016/j.cell.2007.03.052] [Citation(s) in RCA: 476] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2006] [Revised: 01/16/2007] [Accepted: 03/22/2007] [Indexed: 01/12/2023]
Abstract
The karyotypic chaos exhibited by human epithelial cancers complicates efforts to identify mutations critical for malignant transformation. Here we integrate complementary genomic approaches to identify human oncogenes. We show that activation of the ERK and phosphatidylinositol 3-kinase (PI3K) signaling pathways cooperate to transform human cells. Using a library of activated kinases, we identify several kinases that replace PI3K signaling and render cells tumorigenic. Whole genome structural analyses reveal that one of these kinases, IKBKE (IKKepsilon), is amplified and overexpressed in breast cancer cell lines and patient-derived tumors. Suppression of IKKepsilon expression in breast cancer cell lines that harbor IKBKE amplifications induces cell death. IKKepsilon activates the nuclear factor-kappaB (NF-kappaB) pathway in both cell lines and breast cancers. These observations suggest a mechanism for NF-kappaB activation in breast cancer, implicate the NF-kappaB pathway as a downstream mediator of PI3K, and provide a framework for integrated genomic approaches in oncogene discovery.
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Affiliation(s)
- Jesse S Boehm
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
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46
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Moffat J, Grueneberg DA, Yang X, Kim SY, Kloepfer AM, Hinkle G, Piqani B, Eisenhaure TM, Luo B, Grenier JK, Carpenter AE, Foo SY, Stewart SA, Stockwell BR, Hacohen N, Hahn WC, Lander ES, Sabatini DM, Root DE. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 2006; 124:1283-98. [PMID: 16564017 DOI: 10.1016/j.cell.2006.01.040] [Citation(s) in RCA: 1377] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2005] [Revised: 11/29/2005] [Accepted: 01/04/2006] [Indexed: 11/23/2022]
Abstract
To enable arrayed or pooled loss-of-function screens in a wide range of mammalian cell types, including primary and nondividing cells, we are developing lentiviral short hairpin RNA (shRNA) libraries targeting the human and murine genomes. The libraries currently contain 104,000 vectors, targeting each of 22,000 human and mouse genes with multiple sequence-verified constructs. To test the utility of the library for arrayed screens, we developed a screen based on high-content imaging to identify genes required for mitotic progression in human cancer cells and applied it to an arrayed set of 5,000 unique shRNA-expressing lentiviruses that target 1,028 human genes. The screen identified several known and approximately 100 candidate regulators of mitotic progression and proliferation; the availability of multiple shRNAs targeting the same gene facilitated functional validation of putative hits. This work provides a widely applicable resource for loss-of-function screens, as well as a roadmap for its application to biological discovery.
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Affiliation(s)
- Jason Moffat
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
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47
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Moser MJ, Marshall DJ, Grenier JK, Kieffer CD, Killeen AA, Ptacin JL, Richmond CS, Roesch EB, Scherrer CW, Sherrill CB, Van Hout CV, Zanton SJ, Prudent JR. Exploiting the enzymatic recognition of an unnatural base pair to develop a universal genetic analysis system. Clin Chem 2003; 49:407-14. [PMID: 12600952 DOI: 10.1373/49.3.407] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND With the invention of the DNA chip, genome-wide analysis is now a reality. Unfortunately, solid-phase detection systems such as the DNA chip suffer from a narrow range in quantification and sensitivity. Today the best methodology for sensitive, wide dynamic range quantification and genotyping of nucleic acids is real-time PCR. However, multiplexed real-time PCR technologies require complicated and costly design and manufacturing of separate detection probes for each new target. METHODS We developed a novel real-time PCR technology that uses universal energy transfer probes constructed from An Expanded Genetic Information System (AEGIS) for both quantification and genotyping analyses. RESULTS RNA quantification by reverse transcription-PCR was linear over four orders of magnitude for the simultaneous analysis of beta-actin messenger RNA and 18S ribosomal RNA. A single trial validation study of 176 previously genotyped clinical specimens was performed by endpoint analysis for factor V Leiden and prothrombin 20210A mutation detection. There was concordance for 173 samples between the genotyping results from Invader tests and the AEGIS universal energy transfer probe system for both factor V Leiden and prothrombin G20210A. Two prothrombin and one factor V sample gave indeterminate results (no calls). CONCLUSION The AEGIS universal probe system allows for rapid development of PCR assays for nucleic acid quantification and genotyping.
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Affiliation(s)
- Michael J Moser
- Eragen Biosciences, Inc., 918 Deming Way, Madison, WI 53717-1944, USA
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48
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Abstract
The Hox genes have been implicated as central to the evolution of animal body plan diversity. Regulatory changes both in Hox expression domains and in Hox-regulated gene networks have arisen during the evolution of related taxa, but there is little knowledge of whether functional changes in Hox proteins have also contributed to morphological evolution. For example, the evolution of greater numbers of differentiated segments and body parts in insects, compared with the simpler body plans of arthropod ancestors, may have involved an increase in the spectrum of biochemical interactions of individual Hox proteins. Here, we compare the in vivo functions of orthologous Ultrabithorax (Ubx) proteins from the insect Drosophila melanogaster and from an onychophoran, a member of a sister phylum with a more primitive and homonomous body plan. These Ubx proteins, which have been diverging in sequence for over 540 million years, can generate many of the same gain-of-function tissue transformations and can activate and repress many of the same target genes when expressed during Drosophila development. However, the onychophora Ubx (OUbx) protein does not transform the segmental identity of the embryonic ectoderm or repress the Distal-less target gene. This functional divergence is due to sequence changes outside the conserved homeodomain region. The inability of OUbx to function like Drosophila Ubx (DUbx) in the embryonic ectoderm indicates that the Ubx protein may have acquired new cofactors or activity modifiers since the divergence of the onychophoran and insect lineages.
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Affiliation(s)
- J K Grenier
- Howard Hughes Medical Institute, Laboratory of Molecular Biology, University of Wisconsin, 1525 Linden Drive, Madison, WI 53706, USA
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49
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de Rosa R, Grenier JK, Andreeva T, Cook CE, Adoutte A, Akam M, Carroll SB, Balavoine G. Hox genes in brachiopods and priapulids and protostome evolution. Nature 1999; 399:772-6. [PMID: 10391241 DOI: 10.1038/21631] [Citation(s) in RCA: 435] [Impact Index Per Article: 17.4] [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: 11/09/2022]
Abstract
Understanding the early evolution of animal body plans requires knowledge both of metazoan phylogeny and of the genetic and developmental changes involved in the emergence of particular forms. Recent 18S ribosomal RNA phylogenies suggest a three-branched tree for the Bilateria comprising the deuterostomes and two great protostome clades, the lophotrochozoans and ecdysozoans. Here, we show that the complement of Hox genes in critical protostome phyla reflects these phylogenetic relationships and reveals the early evolution of developmental regulatory potential in bilaterians. We have identified Hox genes that are shared by subsets of protostome phyla. These include a diverged pair of posterior (Abdominal-B-like) genes in both a brachiopod and a polychaete annelid, which supports the lophotrochozoan assemblage, and a distinct posterior Hox gene shared by a priapulid, a nematode and the arthropods, which supports the ecdysozoan clade. The ancestors of each of these two major protostome lineages had a minimum of eight to ten Hox genes. The major period of Hox gene expansion and diversification thus occurred before the radiation of each of the three great bilaterian clades.
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Affiliation(s)
- R de Rosa
- Laboratoire de Biologie Cellulaire 4, CNRS UPRESA Q8080, Université Paris-Sud, Orsay, France
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50
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Grenier JK, Garber TL, Warren R, Whitington PM, Carroll S. Evolution of the entire arthropod Hox gene set predated the origin and radiation of the onychophoran/arthropod clade. Curr Biol 1997; 7:547-53. [PMID: 9259556 DOI: 10.1016/s0960-9822(06)00253-3] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Dramatic changes in body size and pattern occurred during the radiation of many taxa in the Cambrian, and these changes are best documented for the arthropods. The sudden appearance of such diverse body plans raises the fundamental question of when the genes and the developmental control systems that regulate these designs evolved. As Hox genes regulate arthropod body patterns, the evolution of these genes may have played a role in the origin and diversification of the arthropod body plan from a homonomous ancestor. To trace the origin of arthropod Hox genes, we examined their distribution in a myriapod and in the Onychophora, a sister group to the arthropods. RESULTS Despite the limited segmental diversity within myriapods and Onychophora, all insect Hox genes are present in both taxa, including the trunk Hox genes Ultrabithorax and abdominal-A as well as an ortholog of the fushi tarazu gene. Comparative analysis of Hox gene deployment revealed that the anterior boundary of expression of trunk Hox genes has shifted dramatically along the anteroposterior axis between Onychophora and different arthropod classes. Furthermore, we found that repression of expression of the Hox target gene Distal-less is unique to the insect lineage. CONCLUSIONS A complete arthropod Hox gene family existed in the ancestor of the onychophoran/arthropod clade. No new Hox genes were therefore required to catalyze the arthropod radiation; instead, arthropod body-plan diversity arose through changes in the regulation of Hox genes and their downstream targets.
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Affiliation(s)
- J K Grenier
- Howard Hughes Medical Institute, University of Wisconsin, Madison 53708, USA
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