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Creekmore BC, Kixmoeller K, Black BE, Lee EB, Chang YW. Ultrastructure of human brain tissue vitrified from autopsy revealed by cryo-ET with cryo-plasma FIB milling. Nat Commun 2024; 15:2660. [PMID: 38531877 PMCID: PMC10965902 DOI: 10.1038/s41467-024-47066-1] [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: 09/27/2023] [Accepted: 03/19/2024] [Indexed: 03/28/2024] Open
Abstract
Ultrastructure of human brain tissue has traditionally been examined using electron microscopy (EM) following fixation, staining, and sectioning, which limit resolution and introduce artifacts. Alternatively, cryo-electron tomography (cryo-ET) allows higher resolution imaging of unfixed cellular samples while preserving architecture, but it requires samples to be vitreous and thin enough for transmission EM. Due to these requirements, cryo-ET has yet to be employed to investigate unfixed, never previously frozen human brain tissue. Here we present a method for generating lamellae in human brain tissue obtained at time of autopsy that can be imaged via cryo-ET. We vitrify the tissue via plunge-freezing and use xenon plasma focused ion beam (FIB) milling to generate lamellae directly on-grid at variable depth inside the tissue. Lamellae generated in Alzheimer's disease brain tissue reveal intact subcellular structures including components of autophagy and potential pathologic tau fibrils. Furthermore, we reveal intact compact myelin and functional cytoplasmic expansions. These images indicate that plasma FIB milling with cryo-ET may be used to elucidate nanoscale structures within the human brain.
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Affiliation(s)
- Benjamin C Creekmore
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn Kixmoeller
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Dos Santos Pacheco N, Tell I Puig A, Guérin A, Martinez M, Maco B, Tosetti N, Delgado-Betancourt E, Lunghi M, Striepen B, Chang YW, Soldati-Favre D. Sustained rhoptry docking and discharge requires Toxoplasma gondii intraconoidal microtubule-associated proteins. Nat Commun 2024; 15:379. [PMID: 38191574 PMCID: PMC10774369 DOI: 10.1038/s41467-023-44631-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024] Open
Abstract
In Apicomplexa, rhoptry discharge is essential for invasion and involves an apical vesicle (AV) docking one or two rhoptries to a macromolecular secretory apparatus. Toxoplasma gondii is armed with 10-12 rhoptries and 5-6 microtubule-associated vesicles (MVs) presumably for iterative rhoptry discharge. Here, we have addressed the localization and functional significance of two intraconoidal microtubule (ICMT)-associated proteins instrumental for invasion. Mechanistically, depletion of ICMAP2 leads to a dissociation of the ICMTs, their detachment from the conoid and dispersion of MVs and rhoptries. ICMAP3 exists in two isoforms that contribute to the control of the ICMTs length and the docking of the two rhoptries at the AV, respectively. This study illuminates the central role ICMTs play in scaffolding the discharge of multiple rhoptries. This process is instrumental for virulence in the mouse model of infection and in addition promotes sterile protection against T. gondii via the release of key effectors inducing immunity.
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Affiliation(s)
- Nicolas Dos Santos Pacheco
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Albert Tell I Puig
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Amandine Guérin
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew Martinez
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bohumil Maco
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Nicolò Tosetti
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Estefanía Delgado-Betancourt
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Matteo Lunghi
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Boris Striepen
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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3
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Trombley S, Powell J, Guttipatti P, Matamoros A, Lin X, O'Harrow T, Steinschaden T, Miles L, Wang Q, Wang S, Qiu J, Li Q, Li F, Song Y. Glia instruct axon regeneration via a ternary modulation of neuronal calcium channels in Drosophila. Nat Commun 2023; 14:6490. [PMID: 37838791 PMCID: PMC10576831 DOI: 10.1038/s41467-023-42306-2] [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: 08/13/2021] [Accepted: 10/04/2023] [Indexed: 10/16/2023] Open
Abstract
A neuron's regenerative capacity is governed by its intrinsic and extrinsic environment. Both peripheral and central neurons exhibit cell-type-dependent axon regeneration, but the underlying mechanism is unclear. Glia provide a milieu essential for regeneration. However, the routes of glia-neuron signaling remain underexplored. Here, we show that regeneration specificity is determined by the axotomy-induced Ca2+ transients only in the fly regenerative neurons, which is mediated by L-type calcium channels, constituting the core intrinsic machinery. Peripheral glia regulate axon regeneration via a three-layered and balanced modulation. Glia-derived tumor necrosis factor acts through its neuronal receptor to maintain calcium channel expression after injury. Glia sustain calcium channel opening by enhancing membrane hyperpolarization via the inwardly-rectifying potassium channel (Irk1). Glia also release adenosine which signals through neuronal adenosine receptor (AdoR) to activate HCN channels (Ih) and dampen Ca2+ transients. Together, we identify a multifaceted glia-neuron coupling which can be hijacked to promote neural repair.
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Affiliation(s)
- Shannon Trombley
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Jackson Powell
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Pavithran Guttipatti
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Andrew Matamoros
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xiaohui Lin
- Department of Neurosurgery, Zhongshan Hospital, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Fudan University, 200032, Shanghai, China
| | - Tristan O'Harrow
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Tobias Steinschaden
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Leann Miles
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Qin Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shuchao Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Jingyun Qiu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Qingyang Li
- Department of Neurosurgery, Zhongshan Hospital, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Fudan University, 200032, Shanghai, China
| | - Feng Li
- Department of Neurosurgery, Zhongshan Hospital, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Fudan University, 200032, Shanghai, China.
| | - Yuanquan Song
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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4
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Chamberlin LA, Yang SS, McEachern EP, Lucas JTM, McLeod Ii OW, Rolland CA, Mack NR, Ferguson BR, Gao WJ. Pharmacogenetic activation of parvalbumin interneurons in the prefrontal cortex rescues cognitive deficits induced by adolescent MK801 administration. Neuropsychopharmacology 2023:10.1038/s41386-023-01576-6. [PMID: 37041206 DOI: 10.1038/s41386-023-01576-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 03/23/2023] [Accepted: 03/26/2023] [Indexed: 04/13/2023]
Abstract
The cognitive symptoms of schizophrenia (SZ) present a significant clinical burden. They are treatment resistant and are the primary predictor of functional outcomes. Although the neural mechanisms underlying these deficits remain unclear, pathological GABAergic signaling likely plays an essential role. Perturbations with parvalbumin (PV)-expressing fast-spiking (FS) interneurons in the prefrontal cortex (PFC) are consistently found in post-mortem studies of patients with SZ, as well as in animal models. Our studies have shown decreased prefrontal synaptic inhibition and PV immunostaining, along with working memory and cognitive flexibility deficits in the MK801 model. To test the hypothesized association between PV cell perturbations and impaired cognition in SZ, we activated prefrontal PV cells by using an excitatory DREADD viral vector with a PV promoter to rescue the cognitive deficits induced by adolescent MK801 administration in female rats. We found that targeted pharmacogenetic upregulation of prefrontal PV interneuron activity can restore E/I balance and improve cognition in the MK801 model. Our findings support the hypothesis that the reduced PV cell activity levels disrupt GABA transmission, resulting in the disinhibition of excitatory pyramidal cells. This disinhibition leads to an elevated prefrontal excitation/inhibition (E/I) balance that could be causal for cognitive impairments. Our study provides novel insights into the causal role of PV cells in cognitive function and has clinical implications for understanding the pathophysiology and management of SZ.
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Affiliation(s)
- Linda A Chamberlin
- Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA
- MD/PhD program, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Sha-Sha Yang
- Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA
- Institute for Translational Brain Research, Department of Neurology, Fudan University, Shanghai, 200032, China
| | - Erin P McEachern
- Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Joshua T M Lucas
- MD program, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Owen W McLeod Ii
- Interdisciplinary Health Sciences Program, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Claire A Rolland
- Interdisciplinary Health Sciences Program, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Nancy R Mack
- Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Brielle R Ferguson
- Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA.
- 2 Blackfan circle, Cetern for Life Science, Boston, MA, 02115, USA.
| | - Wen-Jun Gao
- Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA.
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5
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Abstract
Cellular signaling systems play a vital role in maintaining homeostasis when a cell is exposed to different perturbations. Components of the systems are organized as hierarchical networks, and perturbing different components often leads to transcriptomic profiles that exhibit compositional statistical patterns. Mining such patterns to investigate how cellular signals are encoded is an important problem in systems biology, where artificial intelligence techniques can be of great assistance. Here, we investigated the capability of deep generative models (DGMs) to modeling signaling systems and learn representations of cellular states underlying transcriptomic responses to diverse perturbations. Specifically, we show that the variational autoencoder and the supervised vector-quantized variational autoencoder can accurately regenerate gene expression data in response to perturbagen treatments. The models can learn representations that reveal the relationships between different classes of perturbagens and enable mappings between drugs and their target genes. In summary, DGMs can adequately learn and depict how cellular signals are encoded. The resulting representations have broad applications, demonstrating the power of artificial intelligence in systems biology and precision medicine.
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Affiliation(s)
- Yifan Xue
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15206, USA
| | - Michael Q Ding
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15206, USA
| | - Xinghua Lu
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15206, USA.
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15206, USA.
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6
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Kumar R, Cruz L, Sandhu PK, Buchkovich NJ. UL88 Mediates the Incorporation of a Subset of Proteins into the Virion Tegument. J Virol 2020; 94:e00474-20. [PMID: 32376624 PMCID: PMC7343191 DOI: 10.1128/jvi.00474-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/30/2020] [Indexed: 12/11/2022] Open
Abstract
Little is known about the human cytomegalovirus (HCMV) tegument protein UL88. Large-scale genomic studies have reported disparate results for UL88-null viruses, reporting both no phenotype and a >1-log decrease in virus titers. UL88 has also been reported to interact with UL69 and UL48, but the functional relevance of this interaction is unknown. Here, we report that UL88, which is conserved among different viral strains, is dispensable for production of infectious HCMV virions in multiple HCMV strains and cell types. However, the specific infectivity of HCMV virions suffers in the absence of UL88, as more genomes are required per PFU. This may be a result of altered virion tegument protein composition, as Western blot analysis shows a significant reduction in the tegument levels of pp71, UL47, and UL48 in viruses lacking UL88. While an interaction between UL88 and UL48 has previously been reported, we show that UL88 can interact with UL47; however, UL88 does not appear to be part of a stable complex consisting of UL47 and UL48. These findings identify an important role for UL88 in incorporating the viral proteins UL47 and UL48 into the virion tegument layer.IMPORTANCE A better understanding of the role and functions of tegument proteins in HCMV, many of which remain uncharacterized, will contribute to our understanding of the biology of HCMV. The virus has a large genome, greater than 230 kb, and functional annotation of these genes is important for identifying novel targets for improving therapeutic intervention. This study identifies a role for a viral tegument protein with unknown function, UL88, in maintaining the proper tegument composition of HCMV virions. Virions produced in the absence of UL88 exhibit decreased fitness and require more genomes per infectious unit.
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Affiliation(s)
- Rinki Kumar
- Department of Microbiology & Immunology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Linda Cruz
- Department of Microbiology & Immunology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Praneet K Sandhu
- Department of Microbiology & Immunology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Nicholas J Buchkovich
- Department of Microbiology & Immunology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
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7
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Newmaster KT, Nolan ZT, Chon U, Vanselow DJ, Weit AR, Tabbaa M, Hidema S, Nishimori K, Hammock EAD, Kim Y. Quantitative cellular-resolution map of the oxytocin receptor in postnatally developing mouse brains. Nat Commun 2020; 11:1885. [PMID: 32313029 PMCID: PMC7171089 DOI: 10.1038/s41467-020-15659-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 03/19/2020] [Indexed: 12/17/2022] Open
Abstract
The oxytocin receptor (OTR) plays critical roles in social behavior development. Despite its significance, brain-wide quantitative understanding of OTR expression remains limited in postnatally developing brains. Here, we develop postnatal 3D template brains to register whole brain images with cellular resolution to systematically quantify OTR cell densities. We utilize fluorescent reporter mice (Otrvenus/+) and find that cortical regions show temporally and spatially heterogeneous patterns with transient postnatal OTR expression without cell death. Cortical OTR cells are largely glutamatergic neurons with the exception of cells in layer 6b. Subcortical regions show similar temporal regulation except the hypothalamus and two hypothalamic nuclei display sexually dimorphic OTR expression. Lack of OTR expression correlates with reduced dendritic spine densities in selected cortical regions of developing brains. Lastly, we create a website to visualize our high-resolution imaging data. In summary, our research provides a comprehensive resource for postnatal OTR expression in the mouse brain.
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Affiliation(s)
- Kyra T Newmaster
- Department of Neural and Behavioral Sciences, Penn State University, Hershey, PA, USA
| | - Zachary T Nolan
- Department of Neural and Behavioral Sciences, Penn State University, Hershey, PA, USA
| | - Uree Chon
- Department of Neural and Behavioral Sciences, Penn State University, Hershey, PA, USA
| | - Daniel J Vanselow
- Department of Neural and Behavioral Sciences, Penn State University, Hershey, PA, USA
- Department of Pathology, College of Medicine, Penn State University, Hershey, PA, USA
| | - Abigael R Weit
- Department of Neural and Behavioral Sciences, Penn State University, Hershey, PA, USA
| | - Manal Tabbaa
- Department of Psychology and Program in Neuroscience, Florida State University, Tallahassee, FL, USA
| | - Shizu Hidema
- Tohoku University Graduate School of Agricultural Science, Miyagi, Japan
- Department of Bioregulation and Pharmacological Medicine, Fukushima Medical University, Hikarigaoka 1, Fukushima City, Fukushima Prefecture, Japan
| | - Katsuhiko Nishimori
- Tohoku University Graduate School of Agricultural Science, Miyagi, Japan
- Department of Obesity and Internal Inflammation, Fukushima Medical University, Hikarigaoka 1, Fukushima City, Fukushima Prefecture, Japan
| | - Elizabeth A D Hammock
- Department of Psychology and Program in Neuroscience, Florida State University, Tallahassee, FL, USA
| | - Yongsoo Kim
- Department of Neural and Behavioral Sciences, Penn State University, Hershey, PA, USA.
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8
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Maldonado RJK, Rice B, Chen EC, Tuffy KM, Chiari EF, Fahrbach KM, Hope TJ, Parent LJ. Visualizing Association of the Retroviral Gag Protein with Unspliced Viral RNA in the Nucleus. mBio 2020; 11:e00524-20. [PMID: 32265329 PMCID: PMC7157774 DOI: 10.1128/mbio.00524-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 03/12/2020] [Indexed: 11/20/2022] Open
Abstract
Packaging of genomic RNA (gRNA) by retroviruses is essential for infectivity, yet the subcellular site of the initial interaction between the Gag polyprotein and gRNA remains poorly defined. Because retroviral particles are released from the plasma membrane, it was previously thought that Gag proteins initially bound to gRNA in the cytoplasm or at the plasma membrane. However, the Gag protein of the avian retrovirus Rous sarcoma virus (RSV) undergoes active nuclear trafficking, which is required for efficient gRNA encapsidation (L. Z. Scheifele, R. A. Garbitt, J. D. Rhoads, and L. J. Parent, Proc Natl Acad Sci U S A 99:3944-3949, 2002, https://doi.org/10.1073/pnas.062652199; R. Garbitt-Hirst, S. P. Kenney, and L. J. Parent, J Virol 83:6790-6797, 2009, https://doi.org/10.1128/JVI.00101-09). These results raise the intriguing possibility that the primary contact between Gag and gRNA might occur in the nucleus. To examine this possibility, we created a RSV proviral construct that includes 24 tandem repeats of MS2 RNA stem-loops, making it possible to track RSV viral RNA (vRNA) in live cells in which a fluorophore-conjugated MS2 coat protein is coexpressed. Using confocal microscopy, we observed that both wild-type Gag and a nuclear export mutant (Gag.L219A) colocalized with vRNA in the nucleus. In live-cell time-lapse images, the wild-type Gag protein trafficked together with vRNA as a single ribonucleoprotein (RNP) complex in the nucleoplasm near the nuclear periphery, appearing to traverse the nuclear envelope into the cytoplasm. Furthermore, biophysical imaging methods suggest that Gag and the unspliced vRNA physically interact in the nucleus. Taken together, these data suggest that RSV Gag binds unspliced vRNA to export it from the nucleus, possibly for packaging into virions as the viral genome.IMPORTANCE Retroviruses cause severe diseases in animals and humans, including cancer and acquired immunodeficiency syndromes. To propagate infection, retroviruses assemble new virus particles that contain viral proteins and unspliced vRNA to use as gRNA. Despite the critical requirement for gRNA packaging, the molecular mechanisms governing the identification and selection of gRNA by the Gag protein remain poorly understood. In this report, we demonstrate that the Rous sarcoma virus (RSV) Gag protein colocalizes with unspliced vRNA in the nucleus in the interchromatin space. Using live-cell confocal imaging, RSV Gag and unspliced vRNA were observed to move together from inside the nucleus across the nuclear envelope, suggesting that the Gag-gRNA complex initially forms in the nucleus and undergoes nuclear export into the cytoplasm as a viral ribonucleoprotein (vRNP) complex.
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Affiliation(s)
| | - Breanna Rice
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Eunice C Chen
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Kevin M Tuffy
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Estelle F Chiari
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Kelly M Fahrbach
- Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois, USA
| | - Thomas J Hope
- Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois, USA
| | - Leslie J Parent
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, Pennsylvania, USA
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9
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Abstract
Anatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context. However, the two most-used mouse brain atlases, the Franklin-Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute for Brain Science, have accumulated inconsistencies in anatomical delineations and nomenclature, creating confusion among neuroscientists. To overcome these issues, we adopt here the FP labels into the CCF to merge the labels in the single atlas framework. We use cell type-specific transgenic mice and an MRI atlas to adjust and further segment our labels. Moreover, detailed segmentations are added to the dorsal striatum using cortico-striatal connectivity data. Lastly, we digitize our anatomical labels based on the Allen ontology, create a web-interface for visualization, and provide tools for comprehensive comparisons between the CCF and FP labels. Our open-source labels signify a key step towards a unified mouse brain atlas.
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Affiliation(s)
- Uree Chon
- Department of Neural and Behavioral Sciences, College of Medicine, Penn State University, Hershey, PA, USA
| | - Daniel J Vanselow
- Department of Pathology, College of Medicine, Penn State University, Hershey, PA, USA
| | - Keith C Cheng
- Department of Pathology, College of Medicine, Penn State University, Hershey, PA, USA
| | - Yongsoo Kim
- Department of Neural and Behavioral Sciences, College of Medicine, Penn State University, Hershey, PA, USA.
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10
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Abstract
Endometrial cancer (EMCA) is a clinically heterogeneous disease. Previously, we tested the efficacy of Verteporfin (VP) in EMCA cells and observed cytotoxic and anti-proliferative effects. In this study, we analyzed RNA sequencing data to investigate the comprehensive transcriptomic landscape of VP treated Type 1 EMCA cell lines, including HEC-1-A and HEC-1-B. There were 549 genes with differential expression of two-fold or greater and P < 0.05 after false discovery rate correction for the HEC-1-B cell line. Positive regulation of TGFβ1 production, regulation of lipoprotein metabolic process, cell adhesion, endodermal cell differentiation, formation and development, and integrin mediated signaling pathway were among the significantly associated terms. A functional enrichment analysis of differentially expressed genes after VP treatment revealed extracellular matrix organization Gene Ontology as the most significant. CDC23 and BUB1B, two genes crucially involved in mitotic checkpoint progression, were found to be the pair with the best association from STRING among differentially expressed genes in VP treated HEC-1-B cells. Our in vivo results indicate that subcutaneous tumors in mice were regressed after VP treatment by inhibiting cell cycle pathway proteins. The present study revealed multiple key genes of pathological significance in EMCA, thereby improving our understanding of molecular profiles of EMCA cells.
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Affiliation(s)
- Lisa Gahyun Bang
- Biomedical and Translational Informatics Institute, Geisinger, Danville, PA, USA
| | | | - Dokyoon Kim
- Biomedical and Translational Informatics Institute, Geisinger, Danville, PA, USA
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Radhika P Gogoi
- Weis Center for Research, Geisinger Clinic, Danville, PA, USA.
- Geisinger Medical Center, Danville, PA, USA.
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11
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Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative condition marked by a decline in cognitive functions with no validated disease modifying treatment. It is critical for timely treatment to detect AD in its earlier stage before clinical manifestation. Mild cognitive impairment (MCI) is an intermediate stage between cognitively normal older adults and AD. To predict conversion from MCI to probable AD, we applied a deep learning approach, multimodal recurrent neural network. We developed an integrative framework that combines not only cross-sectional neuroimaging biomarkers at baseline but also longitudinal cerebrospinal fluid (CSF) and cognitive performance biomarkers obtained from the Alzheimer's Disease Neuroimaging Initiative cohort (ADNI). The proposed framework integrated longitudinal multi-domain data. Our results showed that 1) our prediction model for MCI conversion to AD yielded up to 75% accuracy (area under the curve (AUC) = 0.83) when using only single modality of data separately; and 2) our prediction model achieved the best performance with 81% accuracy (AUC = 0.86) when incorporating longitudinal multi-domain data. A multi-modal deep learning approach has potential to identify persons at risk of developing AD who might benefit most from a clinical trial or as a stratification approach within clinical trials.
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Affiliation(s)
- Garam Lee
- Department of Software and Computer Engineering, Ajou University, Suwon, South Korea
- Biomedical & Translational Informatics Institute, Geisinger, Danville, USA
| | - Kwangsik Nho
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Byungkon Kang
- Department of Software and Computer Engineering, Ajou University, Suwon, South Korea
| | - Kyung-Ah Sohn
- Department of Software and Computer Engineering, Ajou University, Suwon, South Korea.
| | - Dokyoon Kim
- Biomedical & Translational Informatics Institute, Geisinger, Danville, USA.
- The Huck Institute of the Life Sciences, Pennsylvania State University, University Park, USA.
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Cai J, Nichols RG, Koo I, Kalikow ZA, Zhang L, Tian Y, Zhang J, Smith PB, Patterson AD. Multiplatform Physiologic and Metabolic Phenotyping Reveals Microbial Toxicity. mSystems 2018; 3:e00123-18. [PMID: 30417115 PMCID: PMC6222046 DOI: 10.1128/msystems.00123-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/11/2018] [Indexed: 02/06/2023] Open
Abstract
The gut microbiota is susceptible to modulation by environmental stimuli and therefore can serve as a biological sensor. Recent evidence suggests that xenobiotics can disrupt the interaction between the microbiota and host. Here, we describe an approach that combines in vitro microbial incubation (isolated cecal contents from mice), flow cytometry, and mass spectrometry- and 1H nuclear magnetic resonance (NMR)-based metabolomics to evaluate xenobiotic-induced microbial toxicity. Tempol, a stabilized free radical scavenger known to remodel the microbial community structure and function in vivo, was studied to assess its direct effect on the gut microbiota. The microbiota was isolated from mouse cecum and was exposed to tempol for 4 h under strict anaerobic conditions. The flow cytometry data suggested that short-term tempol exposure to the microbiota is associated with disrupted membrane physiology as well as compromised metabolic activity. Mass spectrometry and NMR metabolomics revealed that tempol exposure significantly disrupted microbial metabolic activity, specifically indicated by changes in short-chain fatty acids, branched-chain amino acids, amino acids, nucleotides, glucose, and oligosaccharides. In addition, a mouse study with tempol (5 days gavage) showed similar microbial physiologic and metabolic changes, indicating that the in vitro approach reflected in vivo conditions. Our results, through evaluation of microbial viability, physiology, and metabolism and a comparison of in vitro and in vivo exposures with tempol, suggest that physiologic and metabolic phenotyping can provide unique insight into gut microbiota toxicity. IMPORTANCE The gut microbiota is modulated physiologically, compositionally, and metabolically by xenobiotics, potentially causing metabolic consequences to the host. We recently reported that tempol, a stabilized free radical nitroxide, can exert beneficial effects on the host through modulation of the microbiome community structure and function. Here, we investigated a multiplatform phenotyping approach that combines high-throughput global metabolomics with flow cytometry to evaluate the direct effect of tempol on the microbiota. This approach may be useful in deciphering how other xenobiotics directly influence the microbiota.
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Affiliation(s)
- Jingwei Cai
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Robert G. Nichols
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Imhoi Koo
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Zachary A. Kalikow
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Limin Zhang
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS), Wuhan, China
| | - Yuan Tian
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS), Wuhan, China
| | - Jingtao Zhang
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Philip B. Smith
- Metabolomics Facility, Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew D. Patterson
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
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