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Rufenacht KE, Asson AJ, Hossain K, Santoro SW. The influence of olfactory experience on the birthrates of olfactory sensory neurons with specific odorant receptor identities. Genesis 2024; 62:e23611. [PMID: 38888221 PMCID: PMC11189617 DOI: 10.1002/dvg.23611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/20/2024]
Abstract
Olfactory sensory neurons (OSNs) are one of a few neuron types that are generated continuously throughout life in mammals. The persistence of olfactory sensory neurogenesis beyond early development has long been thought to function simply to replace neurons that are lost or damaged through exposure to environmental insults. The possibility that olfactory sensory neurogenesis may also serve an adaptive function has received relatively little consideration, largely due to the assumption that the generation of new OSNs is stochastic with respect to OSN subtype, as defined by the single odorant receptor gene that each neural precursor stochastically chooses for expression out of hundreds of possibilities. Accordingly, the relative birthrates of different OSN subtypes are predicted to be constant and impervious to olfactory experience. This assumption has been called into question, however, by evidence that the birthrates of specific OSN subtypes can be selectively altered by manipulating olfactory experience through olfactory deprivation, enrichment, and conditioning paradigms. Moreover, studies of recovery of the OSN population following injury provide further evidence that olfactory sensory neurogenesis may not be strictly stochastic with respect to subtype. Here we review this evidence and consider mechanistic and functional implications of the prospect that specific olfactory experiences can regulate olfactory sensory neurogenesis rates in a subtype-selective manner.
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Affiliation(s)
- Karlin E Rufenacht
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Alexa J Asson
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kawsar Hossain
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Stephen W Santoro
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado, USA
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2
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Azzopardi SA, Lu HY, Monette S, Rabinowitsch AI, Salmon JE, Matsunami H, Blobel CP. Role of iRhom2 in Olfaction: Implications for Odorant Receptor Regulation and Activity-Dependent Adaptation. Int J Mol Sci 2024; 25:6079. [PMID: 38892263 PMCID: PMC11173328 DOI: 10.3390/ijms25116079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
The cell surface metalloprotease ADAM17 (a disintegrin and metalloprotease 17) and its binding partners iRhom2 and iRhom1 (inactive Rhomboid-like proteins 1 and 2) modulate cell-cell interactions by mediating the release of membrane proteins such as TNFα (Tumor necrosis factor α) and EGFR (Epidermal growth factor receptor) ligands from the cell surface. Most cell types express both iRhoms, though myeloid cells exclusively express iRhom2, and iRhom1 is the main iRhom in the mouse brain. Here, we report that iRhom2 is uniquely expressed in olfactory sensory neurons (OSNs), highly specialized cells expressing one olfactory receptor (OR) from a repertoire of more than a thousand OR genes in mice. iRhom2-/- mice had no evident morphological defects in the olfactory epithelium (OE), yet RNAseq analysis revealed differential expression of a small subset of ORs. Notably, while the majority of ORs remain unaffected in iRhom2-/- OE, OSNs expressing ORs that are enriched in iRhom2-/- OE showed fewer gene expression changes upon odor environmental changes than the majority of OSNs. Moreover, we discovered an inverse correlation between the expression of iRhom2 compared to OSN activity genes and that odor exposure negatively regulates iRhom2 expression. Given that ORs are specialized G-protein coupled receptors (GPCRs) and many GPCRs activate iRhom2/ADAM17, we investigated if ORs could activate iRhom2/ADAM17. Activation of an olfactory receptor that is ectopically expressed in keratinocytes (OR2AT4) by its agonist Sandalore leads to ERK1/2 phosphorylation, likely via an iRhom2/ADAM17-dependent pathway. Taken together, these findings point to a mechanism by which odor stimulation of OSNs activates iRhom2/ADAM17 catalytic activity, resulting in downstream transcriptional changes to the OR repertoire and activity genes, and driving a negative feedback loop to downregulate iRhom2 expression.
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Affiliation(s)
- Stephanie A. Azzopardi
- Weill Cornell Medicine/Rockefeller University/Memorial Sloan-Kettering Cancer Center, Tri-Institutional MD-PhD Program, New York, NY 10021, USA; (S.A.A.); (A.I.R.)
- Physiology, Biophysics and Systems Biology Program, Weill Cornell Medicine, New York, NY 10021, USA
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY 10021, USA
| | - Hsiu-Yi Lu
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA;
| | - Sebastien Monette
- Tri-Institutional Laboratory of Comparative Pathology, Hospital for Special Surgery, Memorial Sloan Kettering Cancer Center, The Rockefeller University, Weill Cornell Medicine, New York, NY 10021, USA;
| | - Ariana I. Rabinowitsch
- Weill Cornell Medicine/Rockefeller University/Memorial Sloan-Kettering Cancer Center, Tri-Institutional MD-PhD Program, New York, NY 10021, USA; (S.A.A.); (A.I.R.)
- Department of Biochemistry, Cellular and Molecular Biology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jane E. Salmon
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA;
- Department of Neurobiology, Duke Institute for Brain Sciences, Duke University, Durham, NC 27710, USA
| | - Carl P. Blobel
- Weill Cornell Medicine/Rockefeller University/Memorial Sloan-Kettering Cancer Center, Tri-Institutional MD-PhD Program, New York, NY 10021, USA; (S.A.A.); (A.I.R.)
- Physiology, Biophysics and Systems Biology Program, Weill Cornell Medicine, New York, NY 10021, USA
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY 10021, USA
- Department of Biochemistry, Cellular and Molecular Biology, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
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Hossain K, Smith M, Santoro SW. In mice, discrete odors can selectively promote the neurogenesis of sensory neuron subtypes that they stimulate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579748. [PMID: 38405728 PMCID: PMC10888860 DOI: 10.1101/2024.02.10.579748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
In mammals, olfactory sensory neurons (OSNs) are born throughout life, presumably solely to replace neurons lost via turnover or injury. This assumption follows from the hypothesis that olfactory neurogenesis is strictly stochastic with respect to neuron subtype, as defined by the single odorant receptor allele that each neural precursor stochastically chooses out of hundreds of possibilities. This hypothesis is challenged by recent findings that the birthrates of a fraction of subtypes are selectively diminished by olfactory deprivation. These findings raise questions about how, and why, olfactory stimuli are required to promote the neurogenesis of some OSN subtypes, including whether the stimuli are generic (e.g., broadly activating odors or mechanical stimuli) or specific (e.g., discrete odorants). Based on RNA-seq and scRNA-seq analyses, we hypothesized that the neurogenic stimuli are specific odorants that selectively activate the same OSN subtypes whose birthrates are accelerated. In support of this, we have found, using subtype-specific OSN birthdating, that exposure to male and musk odors can accelerate the birthrates of responsive OSNs. Collectively, our findings reveal that certain odor experiences can selectively "amplify" specific OSN subtypes, and that persistent OSN neurogenesis may serve, in part, an adaptive function.
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Affiliation(s)
- Kawsar Hossain
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Madeline Smith
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Stephen W Santoro
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Aurora, CO, USA
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4
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Fang A, Yu CR. Activity-dependent formation of the topographic map and the critical period in the development of mammalian olfactory system. Genesis 2024; 62:e23586. [PMID: 38593162 PMCID: PMC11003738 DOI: 10.1002/dvg.23586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 04/11/2024]
Abstract
Neural activity influences every aspect of nervous system development. In olfactory systems, sensory neurons expressing the same odorant receptor project their axons to stereotypically positioned glomeruli, forming a spatial map of odorant receptors in the olfactory bulb. As individual odors activate unique combinations of glomeruli, this map forms the basis for encoding olfactory information. The establishment of this stereotypical olfactory map requires coordinated regulation of axon guidance molecules instructed by spontaneous activity. Recent studies show that sensory experiences also modify innervation patterns in the olfactory bulb, especially during a critical period of the olfactory system development. This review examines evidence in the field to suggest potential mechanisms by which various aspects of neural activity regulate axon targeting. We also discuss the precise functions served by neural plasticity during the critical period.
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Affiliation(s)
- Ai Fang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - C. Ron Yu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Cell Biology and Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
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5
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Yang S, Zhou X. SRT-Server: powering the analysis of spatial transcriptomic data. Genome Med 2024; 16:18. [PMID: 38279156 PMCID: PMC10811909 DOI: 10.1186/s13073-024-01288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND Spatial resolved transcriptomics (SRT) encompasses a rapidly developing set of technologies that enable the measurement of gene expression in tissue while retaining spatial localization information. SRT technologies and the enabled SRT studies have provided unprecedent insights into the structural and functional underpinnings of complex tissues. As SRT technologies have advanced and an increasing number of SRT studies have emerged, numerous sophisticated statistical and computational methods have been developed to facilitate the analysis and interpretation of SRT data. However, despite the growing popularity of SRT studies and the widespread availability of SRT analysis methods, analysis of large-scale and complex SRT datasets remains challenging and not easily accessible to researchers with limited statistical and computational backgrounds. RESULTS Here, we present SRT-Server, the first webserver designed to carry out comprehensive SRT analyses for a wide variety of SRT technologies while requiring minimal prior computational knowledge. Implemented with cutting-edge web development technologies, SRT-Server is user-friendly and features multiple analytic modules that can perform a range of SRT analyses. With a flowchart-style interface, these different analytic modules on the SRT-Server can be dragged into the main panel and connected to each other to create custom analytic pipelines. SRT-Server then automatically executes the desired analyses, generates corresponding figures, and outputs results-all without requiring prior programming knowledge. We demonstrate the advantages of SRT-Server through three case studies utilizing SRT data collected from two common platforms, highlighting its versatility and values to researchers with varying analytic expertise. CONCLUSIONS Overall, SRT-Server presents a user-friendly, efficient, effective, secure, and expandable solution for SRT data analysis, opening new doors for researchers in the field. SRT-Server is freely available at https://spatialtranscriptomicsanalysis.com/ .
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Affiliation(s)
- Sheng Yang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, China.
| | - Xiang Zhou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA.
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
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Mussalo L, Avesani S, Shahbaz MA, Závodná T, Saveleva L, Järvinen A, Lampinen R, Belaya I, Krejčík Z, Ivanova M, Hakkarainen H, Kalapudas J, Penttilä E, Löppönen H, Koivisto AM, Malm T, Topinka J, Giugno R, Aakko-Saksa P, Chew S, Rönkkö T, Jalava P, Kanninen KM. Emissions from modern engines induce distinct effects in human olfactory mucosa cells, depending on fuel and aftertreatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167038. [PMID: 37709087 DOI: 10.1016/j.scitotenv.2023.167038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/30/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Ultrafine particles (UFP) with a diameter of ≤0.1 μm, are contributors to ambient air pollution and derived mainly from traffic emissions, yet their health effects remain poorly characterized. The olfactory mucosa (OM) is located at the rooftop of the nasal cavity and directly exposed to both the environment and the brain. Mounting evidence suggests that pollutant particles affect the brain through the olfactory tract, however, the exact cellular mechanisms of how the OM responds to air pollutants remain poorly known. Here we show that the responses of primary human OM cells are altered upon exposure to UFPs and that different fuels and engines elicit different adverse effects. We used UFPs collected from exhausts of a heavy-duty-engine run with renewable diesel (A0) and fossil diesel (A20), and from a modern diesel vehicle run with renewable diesel (Euro6) and compared their health effects on the OM cells by assessing cellular processes on the functional and transcriptomic levels. Quantification revealed all samples as UFPs with the majority of particles being ≤0.1 μm by an aerodynamic diameter. Exposure to A0 and A20 induced substantial alterations in processes associated with inflammatory response, xenobiotic metabolism, olfactory signaling, and epithelial integrity. Euro6 caused only negligible changes, demonstrating the efficacy of aftertreatment devices. Furthermore, when compared to A20, A0 elicited less pronounced effects on OM cells, suggesting renewable diesel induces less adverse effects in OM cells. Prior studies and these results suggest that PAHs may disturb the inflammatory process and xenobiotic metabolism in the OM and that UFPs might mediate harmful effects on the brain through the olfactory route. This study provides important information on the adverse effects of UFPs in a human-based in vitro model, therefore providing new insight to form the basis for mitigation and preventive actions against the possible toxicological impairments caused by UFP exposure.
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Affiliation(s)
- Laura Mussalo
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Simone Avesani
- Department of Computer Science, University of Verona, 37134 Verona, Italy
| | - Muhammad Ali Shahbaz
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Táňa Závodná
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Liudmila Saveleva
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Anssi Järvinen
- VTT Technical Research Centre of Finland, VTT, 02044 Espoo, Finland
| | - Riikka Lampinen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Irina Belaya
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Zdeněk Krejčík
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Mariia Ivanova
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Henri Hakkarainen
- Inhalation Toxicology Laboratory, Department of Environmental and Biological Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Juho Kalapudas
- Department of Neurology, Neuro Centre, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Elina Penttilä
- Department of Otorhinolaryngology, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Heikki Löppönen
- Department of Otorhinolaryngology, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Anne M Koivisto
- Department of Neurology, Neuro Centre, Kuopio University Hospital, 70210 Kuopio, Finland; Brain Research Unit, Department of Neurology, School of Medicine, University of Eastern Finland, 70210 Kuopio, Finland; Department of Neurology and Geriatrics, Helsinki University Hospital and Neurosciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Tarja Malm
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, 37134 Verona, Italy
| | | | - Sweelin Chew
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Topi Rönkkö
- Aerosol Physics Laboratory, Physics Unit, Tampere University, 33014 Tampere, Finland
| | - Pasi Jalava
- Inhalation Toxicology Laboratory, Department of Environmental and Biological Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Katja M Kanninen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70210 Kuopio, Finland.
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7
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Massri AJ, Fitzpatrick M, Cunny H, Li JL, Harry GJ. Differential gene expression profiling implicates altered network development in rat postnatal day 4 cortex following 4-Methylimidazole (4-MeI) induced maternal seizures. Neurotoxicol Teratol 2023; 100:107301. [PMID: 37783441 PMCID: PMC10843020 DOI: 10.1016/j.ntt.2023.107301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/31/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023]
Abstract
Compromised maternal health leading to maternal seizures can have adverse effects on the healthy development of offspring. This may be the result of inflammation, hypoxia-ischemia, and altered GABA signaling. The current study examined cortical tissue from F2b (2nd litter of the 2nd generation) postnatal day 4 (PND4) offspring of female Harlan SD rats chronically exposed to the seizuregenic compound, 4-Methylimidazole (0, 750, or 2500 ppm 4-MeI). Maternal seizures were evident only at 2500 ppm 4-MeI. GABA related gene expression as examined by qRT-PCR and whole genome microarray showed no indication of disrupted GABA or glutamatergic signaling. Canonical pathway hierarchical clustering and multi-omics combinatory genomic (CNet) plots of differentially expressed genes (DEG) showed alterations in genes associated with regulatory processes of cell development including neuronal differentiation and synaptogenesis. Functional enrichment analysis showed a similarity of cellular processes across the two exposure groups however, the genes comprising each cluster were primarily unique rather than shared and often showed different directionality. A dose-related induction of cytokine signaling was indicated however, pathways associated with individual cytokine signaling were not elevated, suggesting an alternative involvement of cytokine signaling. Pathways related to growth process and cell signaling showed a negative activation supporting an interpretation of disruption or delay in developmental processes at the 2500 ppm 4-MeI exposure level with maternal seizures. Thus, while GABA signaling was not altered as has been observed with maternal seizures, the pattern of DEG suggested a potential for alteration in neuronal network formation.
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Affiliation(s)
- Abdull J Massri
- Integrative Bioinformatics, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mackenzie Fitzpatrick
- Mechanistic Toxicology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Helen Cunny
- Office of the Scientific Director, Division of Translational Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jian-Liang Li
- Integrative Bioinformatics, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - G Jean Harry
- Mechanistic Toxicology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA.
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8
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Hossain K, Smith M, Santoro SW. A histological protocol for quantifying the birthrates of specific subtypes of olfactory sensory neurons in mice. STAR Protoc 2023; 4:102432. [PMID: 37436902 PMCID: PMC10511921 DOI: 10.1016/j.xpro.2023.102432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/16/2023] [Accepted: 06/12/2023] [Indexed: 07/14/2023] Open
Abstract
Mammals typically have hundreds of distinct olfactory sensory neuron subtypes, each defined by expression of a specific odorant receptor gene, which undergo neurogenesis throughout life at rates that can depend on olfactory experience. Here, we present a protocol to quantify the birthrates of specific neuron subtypes via the simultaneous detection of corresponding receptor mRNAs and 5-ethynyl-2'-deoxyuridine. For preparation prior to beginning the protocol, we detail procedures for generating odorant receptor-specific riboprobes and experimental mouse olfactory epithelial tissue sections. For complete details on the use and execution of this protocol, please refer to van der Linden et al. (2020).1.
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Affiliation(s)
- Kawsar Hossain
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Molecular and Cellular Life Sciences Program, University of Wyoming, Laramie, WY 82071, USA
| | - Madeline Smith
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Stephen W Santoro
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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9
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Transcriptional adaptation of olfactory sensory neurons to GPCR identity and activity. Nat Commun 2022; 13:2929. [PMID: 35614043 PMCID: PMC9132991 DOI: 10.1038/s41467-022-30511-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/04/2022] [Indexed: 01/02/2023] Open
Abstract
In mammals, chemoperception relies on a diverse set of neuronal sensors able to detect chemicals present in the environment, and to adapt to various levels of stimulation. The contribution of endogenous and external factors to these neuronal identities remains to be determined. Taking advantage of the parallel coding lines present in the olfactory system, we explored the potential variations of neuronal identities before and after olfactory experience. We found that at rest, the transcriptomic profiles of mouse olfactory sensory neuron populations are already divergent, specific to the olfactory receptor they express, and are associated with the sequence of these latter. These divergent profiles further evolve in response to the environment, as odorant exposure leads to reprogramming via the modulation of transcription. These findings highlight a broad range of sensory neuron identities that are present at rest and that adapt to the experience of the individual, thus adding to the complexity and flexibility of sensory coding.
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10
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Spatially informed cell-type deconvolution for spatial transcriptomics. Nat Biotechnol 2022; 40:1349-1359. [PMID: 35501392 PMCID: PMC9464662 DOI: 10.1038/s41587-022-01273-7] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/07/2022] [Indexed: 12/16/2022]
Abstract
Many spatially resolved transcriptomic technologies do not have single-cell resolution but measure the average gene expression for each spot from a mixture of cells of potentially heterogeneous cell types. Here, we introduce a deconvolution method, conditional autoregressive deconvolution (CARD), that combines cell type–specific expression information from single-cell RNA sequencing (scRNA-seq) with correlation in cell type composition across tissue locations. Modeling spatial correlation allows us to borrow the cell-type composition information across locations, improving accuracy of deconvolution even with a mismatched scRNA-seq reference. CARD can also impute cell type compositions and gene expression levels at unmeasured tissue locations, enable the construction of a refined spatial tissue map with a resolution arbitrarily higher than that measured in the original study, and perform deconvolution without a scRNA-seq reference. Applications to four datasets including a pancreatic cancer dataset identified multiple cell types and molecular markers with distinct spatial localization that define the progression, heterogeneity, and compartmentalization of pancreatic cancer.
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11
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Tsukahara T, Brann DH, Pashkovski SL, Guitchounts G, Bozza T, Datta SR. A transcriptional rheostat couples past activity to future sensory responses. Cell 2021; 184:6326-6343.e32. [PMID: 34879231 PMCID: PMC8758202 DOI: 10.1016/j.cell.2021.11.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/07/2021] [Accepted: 11/11/2021] [Indexed: 10/19/2022]
Abstract
Animals traversing different environments encounter both stable background stimuli and novel cues, which are thought to be detected by primary sensory neurons and then distinguished by downstream brain circuits. Here, we show that each of the ∼1,000 olfactory sensory neuron (OSN) subtypes in the mouse harbors a distinct transcriptome whose content is precisely determined by interactions between its odorant receptor and the environment. This transcriptional variation is systematically organized to support sensory adaptation: expression levels of more than 70 genes relevant to transforming odors into spikes continuously vary across OSN subtypes, dynamically adjust to new environments over hours, and accurately predict acute OSN-specific odor responses. The sensory periphery therefore separates salient signals from predictable background via a transcriptional rheostat whose moment-to-moment state reflects the past and constrains the future; these findings suggest a general model in which structured transcriptional variation within a cell type reflects individual experience.
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Affiliation(s)
- Tatsuya Tsukahara
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - David H Brann
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Stan L Pashkovski
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Thomas Bozza
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
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12
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Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors. Cell Rep 2021; 33:108210. [PMID: 33027656 PMCID: PMC7569022 DOI: 10.1016/j.celrep.2020.108210] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 07/03/2020] [Accepted: 09/09/2020] [Indexed: 12/18/2022] Open
Abstract
In mammals, olfactory sensory neurons (OSNs) are born throughout life, ostensibly solely to replace damaged OSNs. During differentiation, each OSN precursor “chooses,” out of hundreds of possibilities, a single odorant receptor (OR) gene, which defines the identity of the mature OSN. The relative neurogenesis rates of the hundreds of distinct OSN “subtypes” are thought to be constant, as they are determined by a stochastic process in which each OR is chosen with a fixed probability. Here, using histological, single-cell, and targeted affinity purification approaches, we show that closing one nostril in mice selectively reduces the number of newly generated OSNs of specific subtypes. Moreover, these reductions depend on an animal’s age and/or environment. Stimulation-dependent changes in the number of new OSNs are not attributable to altered rates of cell survival but rather production. Our findings indicate that the relative birth rates of distinct OSN subtypes depend on olfactory experience. In mammals, the odorant receptor identities of newly generated olfactory sensory neurons are thought to be determined by each progenitor cell’s random choice of a single receptor. Here, van der Linden et al. show that, in mice, the birth rates of neurons expressing a subset of receptors depend on olfactory stimulation.
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13
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Abstract
There is increasing appreciation that G-protein-coupled receptors (GPCRs) can initiate diverse cellular responses by activating multiple G proteins, arrestins, and other biochemical effectors. Structurally different ligands targeting the same receptor are thought to stabilize the receptor in multiple distinct active conformations such that specific subsets of signaling effectors are engaged at the exclusion of others, creating a bias toward a particular outcome, which has been referred to as ligand-induced selective signaling, biased agonism, ligand-directed signaling, and functional selectivity, among others. The potential involvement of functional selectivity in mammalian olfactory signal transduction has received little attention, notwithstanding the fact that mammalian olfactory receptors comprise the largest family of mammalian GPCRs. This position review considers the possibility that, although such complexity in G-protein function may have been lost in the specialization of olfactory receptors to serve as sensory receptors, the ability of olfactory receptor neurons (ORNs) to function as signal integrators and growing appreciation that this functionality is widespread in the receptor population suggest otherwise. We pose that functional selectivity driving 2 opponent inputs have the potential to generate an output that reflects the balance of ligand-dependent signaling, the direction of which could be either suppressive or synergistic and, as such, needs to be considered as a mechanistic basis for signal integration in mammalian ORNs.
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Affiliation(s)
- Barry W Ache
- Whitney Laboratory, Departments of Biology and Neuroscience, and Center for Smell and Taste, University of Florida, Gainesville, FL, USA
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14
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Baxter BD, Larson ED, Merle L, Feinstein P, Polese AG, Bubak AN, Niemeyer CS, Hassell J, Shepherd D, Ramakrishnan VR, Nagel MA, Restrepo D. Transcriptional profiling reveals potential involvement of microvillous TRPM5-expressing cells in viral infection of the olfactory epithelium. BMC Genomics 2021; 22:224. [PMID: 33781205 PMCID: PMC8007386 DOI: 10.1186/s12864-021-07528-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 03/12/2021] [Indexed: 02/07/2023] Open
Abstract
Background Understanding viral infection of the olfactory epithelium is essential because the olfactory nerve is an important route of entry for viruses to the central nervous system. Specialized chemosensory epithelial cells that express the transient receptor potential cation channel subfamily M member 5 (TRPM5) are found throughout the airways and intestinal epithelium and are involved in responses to viral infection. Results Herein we performed deep transcriptional profiling of olfactory epithelial cells sorted by flow cytometry based on the expression of mCherry as a marker for olfactory sensory neurons and for eGFP in OMP-H2B::mCherry/TRPM5-eGFP transgenic mice (Mus musculus). We find profuse expression of transcripts involved in inflammation, immunity and viral infection in TRPM5-expressing microvillous cells compared to olfactory sensory neurons. Conclusion Our study provides new insights into a potential role for TRPM5-expressing microvillous cells in viral infection of the olfactory epithelium. We find that, as found for solitary chemosensory cells (SCCs) and brush cells in the airway epithelium, and for tuft cells in the intestine, the transcriptome of TRPM5-expressing microvillous cells indicates that they are likely involved in the inflammatory response elicited by viral infection of the olfactory epithelium. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07528-y.
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Affiliation(s)
- B Dnate' Baxter
- Neuroscience Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Eric D Larson
- Department of Otolaryngology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Laetitia Merle
- Neuroscience Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Paul Feinstein
- The Graduate Center Biochemistry, Biology and CUNY-Neuroscience-Collaborative Programs and Biological Sciences Department, Hunter College, City University of New York, New York, NY, 10065, USA
| | - Arianna Gentile Polese
- Neuroscience Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.,Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Andrew N Bubak
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Christy S Niemeyer
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - James Hassell
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Doug Shepherd
- Department of Pharmacology, University of Colorado Anschutz Medical Campus and Center for Biological Physics and Department of Physics, Arizona State University, Tempe, USA
| | - Vijay R Ramakrishnan
- Department of Otolaryngology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Maria A Nagel
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Diego Restrepo
- Neuroscience Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA. .,Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
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15
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Maddala R, Gao J, Mathias RT, Lewis TR, Arshavsky VY, Levine A, Backer JM, Bresnick AR, Rao PV. Absence of S100A4 in the mouse lens induces an aberrant retina-specific differentiation program and cataract. Sci Rep 2021; 11:2203. [PMID: 33500475 PMCID: PMC7838418 DOI: 10.1038/s41598-021-81611-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/05/2021] [Indexed: 11/21/2022] Open
Abstract
S100A4, a member of the S100 family of multifunctional calcium-binding proteins, participates in several physiological and pathological processes. In this study, we demonstrate that S100A4 expression is robustly induced in differentiating fiber cells of the ocular lens and that S100A4 (-/-) knockout mice develop late-onset cortical cataracts. Transcriptome profiling of lenses from S100A4 (-/-) mice revealed a robust increase in the expression of multiple photoreceptor- and Müller glia-specific genes, as well as the olfactory sensory neuron-specific gene, S100A5. This aberrant transcriptional profile is characterized by corresponding increases in the levels of proteins encoded by the aberrantly upregulated genes. Ingenuity pathway network and curated pathway analyses of differentially expressed genes in S100A4 (-/-) lenses identified Crx and Nrl transcription factors as the most significant upstream regulators, and revealed that many of the upregulated genes possess promoters containing a high-density of CpG islands bearing trimethylation marks at histone H3K27 and/or H3K4, respectively. In support of this finding, we further documented that S100A4 (-/-) knockout lenses have altered levels of trimethylated H3K27 and H3K4. Taken together, our findings suggest that S100A4 suppresses the expression of retinal genes during lens differentiation plausibly via a mechanism involving changes in histone methylation.
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Affiliation(s)
- Rupalatha Maddala
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA.
| | - Junyuan Gao
- Department of Physiology and Biophysics, Stony Brook University, Stony-Brook, NY, USA
| | - Richard T Mathias
- Department of Physiology and Biophysics, Stony Brook University, Stony-Brook, NY, USA
| | - Tylor R Lewis
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Adriana Levine
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jonathan M Backer
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Anne R Bresnick
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ponugoti V Rao
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA.
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
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16
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Baxter BD, Larson ED, Merle L, Feinstein P, Polese AG, Bubak AN, Niemeyer CS, Hassell J, Shepherd D, Ramakrishnan VR, Nagel MA, Restrepo D. Transcriptional profiling reveals potential involvement of microvillous TRPM5-expressing cells in viral infection of the olfactory epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32511400 DOI: 10.1101/2020.05.14.096016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background Understanding viral infection of the olfactory epithelium is essential because the olfactory nerve is an important route of entry for viruses to the central nervous system. Specialized chemosensory epithelial cells that express the transient receptor potential cation channel subfamily M member 5 (TRPM5) are found throughout the airways and intestinal epithelium and are involved in responses to viral infection. Results Herein we performed deep transcriptional profiling of olfactory epithelial cells sorted by flow cytometry based on the expression of mCherry as a marker for olfactory sensory neurons and for eGFP in OMP-H2B::mCherry/TRPM5-eGFP transgenic mice ( Mus musculus ). We find profuse expression of transcripts involved in inflammation, immunity and viral infection in TRPM5-expressing microvillous cells. Conclusion Our study provides new insights into a potential role for TRPM5-expressing microvillous cells in viral infection of the olfactory epithelium. We find that, as found for solitary chemosensory cells (SCCs) and brush cells in the airway epithelium, and for tuft cells in the intestine, the transcriptome of TRPM5-expressing microvillous cells indicates that they are likely involved in the inflammatory response elicited by viral infection of the olfactory epithelium.
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17
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McClintock TS, Khan N, Alimova Y, Aulisio M, Han DY, Breheny P. Encoding the Odor of Cigarette Smoke. J Neurosci 2020; 40:7043-7053. [PMID: 32801155 PMCID: PMC7480249 DOI: 10.1523/jneurosci.1144-20.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/23/2020] [Accepted: 08/09/2020] [Indexed: 11/21/2022] Open
Abstract
The encoding of odors is believed to begin as a combinatorial code consisting of distinct patterns of responses from odorant receptors (ORs), trace-amine associated receptors (TAARs), or both. To determine how specific response patterns arise requires detecting patterns in vivo and understanding how the components of an odor, which are nearly always mixtures of odorants, give rise to parts of the pattern. Cigarette smoke, a common and clinically relevant odor consisting of >400 odorants, evokes responses from 144 ORs and 3 TAARs in freely behaving male and female mice, the first example of in vivo responses of both ORs and TAARs to an odor. As expected, a simplified artificial mimic of cigarette smoke odor tested at low concentration to identify highly sensitive receptors evokes responses from four ORs, all also responsive to cigarette smoke. Human subjects of either sex identify 1-pentanethiol as the odorant most critical for perception of the artificial mimic; and in mice the OR response patterns to these two odors are significantly similar. Fifty-eight ORs respond to the headspace above 25% 1-pentanethiol, including 9 ORs responsive to cigarette smoke. The response patterns to both cigarette smoke and 1-pentanethiol have strongly responsive ORs spread widely across OR sequence diversity, consistent with most other combinatorial codes previously measured in vivo The encoding of cigarette smoke is accomplished by a broad receptor response pattern, and 1-pentanethiol is responsible for a small subset of the responsive ORs in this combinatorial code.SIGNIFICANCE STATEMENT Complex odors are usually perceived as distinct odor objects. Cigarette smoke is the first complex odor whose in vivo receptor response pattern has been measured. It is also the first pattern shown to include responses from both odorant receptors and trace-amine associated receptors, confirming that the encoding of complex odors can be enriched by signals coming through both families of receptors. Measures of human perception and mouse receptor physiology agree that 1-pentanethiol is a critical component of a simplified odorant mixture designed to mimic cigarette smoke odor. Its receptor response pattern helps to link those of the artificial mimic and real cigarette smoke, consistent with expectations about perceptual similarity arising from shared elements in receptor response patterns.
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Affiliation(s)
| | - Naazneen Khan
- Department of Physiology, University of Kentucky, Lexington, Kentucky 40536
| | - Yelena Alimova
- Department of Physiology, University of Kentucky, Lexington, Kentucky 40536
| | - Madeline Aulisio
- College of Public Health, University of Kentucky, Lexington, Kentucky 40536
| | - Dong Y Han
- Department of Neurology, University of Kentucky, Lexington, Kentucky 40536
| | - Patrick Breheny
- Department of Biostatistics, University of Iowa, Iowa City, Iowa 52242
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18
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Abstract
The encoding of odors is believed to begin as a combinatorial code consisting of distinct patterns of responses from odorant receptors (ORs), trace-amine associated receptors (TAARs), or both. To determine how specific response patterns arise requires detecting patterns in vivo and understanding how the components of an odor, which are nearly always mixtures of odorants, give rise to parts of the pattern. Cigarette smoke, a common and clinically relevant odor consisting of >400 odorants, evokes responses from 144 ORs and 3 TAARs in freely behaving male and female mice, the first example of in vivo responses of both ORs and TAARs to an odor. As expected, a simplified artificial mimic of cigarette smoke odor tested at low concentration to identify highly sensitive receptors evokes responses from four ORs, all also responsive to cigarette smoke. Human subjects of either sex identify 1-pentanethiol as the odorant most critical for perception of the artificial mimic; and in mice the OR response patterns to these two odors are significantly similar. Fifty-eight ORs respond to the headspace above 25% 1-pentanethiol, including 9 ORs responsive to cigarette smoke. The response patterns to both cigarette smoke and 1-pentanethiol have strongly responsive ORs spread widely across OR sequence diversity, consistent with most other combinatorial codes previously measured in vivo The encoding of cigarette smoke is accomplished by a broad receptor response pattern, and 1-pentanethiol is responsible for a small subset of the responsive ORs in this combinatorial code.SIGNIFICANCE STATEMENT Complex odors are usually perceived as distinct odor objects. Cigarette smoke is the first complex odor whose in vivo receptor response pattern has been measured. It is also the first pattern shown to include responses from both odorant receptors and trace-amine associated receptors, confirming that the encoding of complex odors can be enriched by signals coming through both families of receptors. Measures of human perception and mouse receptor physiology agree that 1-pentanethiol is a critical component of a simplified odorant mixture designed to mimic cigarette smoke odor. Its receptor response pattern helps to link those of the artificial mimic and real cigarette smoke, consistent with expectations about perceptual similarity arising from shared elements in receptor response patterns.
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19
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Aljaibeji H, Mohammed AK, Alkayyali S, Hachim MY, Hasswan H, El-Huneidi W, Taneera J, Sulaiman N. Genetic Variants of the PLCXD3 Gene Are Associated with Risk of Metabolic Syndrome in the Emirati Population. Genes (Basel) 2020; 11:genes11060665. [PMID: 32570874 PMCID: PMC7349663 DOI: 10.3390/genes11060665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/13/2020] [Accepted: 06/16/2020] [Indexed: 11/16/2022] Open
Abstract
Phosphatidylinositol-specific phospholipase C X domain 3 (PLCXD3) has been shown to influence pancreatic β-cell function by disrupting insulin signaling. Herein, we investigated two genetic variants in the PLCXD3 gene in relation to type 2 diabetes (T2D) or metabolic syndrome (MetS) in the Emirati population. In total, 556 adult Emirati individuals (306 T2D and 256 controls) were genotyped for two PLCXD3 variants (rs319013 and rs9292806) using TaqMan genotyping assays. The frequency distribution of minor homozygous CC genotype of rs9292806 and GG genotype of rs319013 were significantly higher in subjects with MetS compared to Non-MetS (p < 0.01). The minor homozygous rs9292806-CC and rs319013-GG genotypes were significantly associated with increased risk of MetS (adj. OR 2.92; 95% CI 1.61–5.3; p < 0.001) (adj. OR 2.62; 95% CI 1.42–4.83; p = 0.002), respectively. However, no associations were detected with T2D. In healthy participants, the homozygous minor genotypes of both rs9292806 and rs319013 were significantly higher fasting glucose (adj. p < 0.005), HbA1c (adj. p < 0.005) and lower HDL-cholesterol (adj. p < 0.05) levels. Data from T2D Knowledge Portal database disclosed a nominal association of rs319013 and rs9292806 with T2D and components of MetS. Bioinformatics prediction analysis showed a deleterious effect of rs9292806 on the regulatory regions of PLCXD3. In conclusion, this study identifies rs319013 and rs9292806 variants of PLCXD3 as additional risk factors for MetS in the Emirati population.
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Affiliation(s)
- Hayat Aljaibeji
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, UAE; (H.A.); (A.K.M.); (H.H.)
| | - Abdul Khader Mohammed
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, UAE; (H.A.); (A.K.M.); (H.H.)
| | - Sami Alkayyali
- Laboratory of Clinical Chemistry and Transfusion Medicine, Central Hospital of Växjö, Växjö 35188, Sweden;
| | - Mahmood Yaseen Hachim
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, UAE;
| | - Hind Hasswan
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, UAE; (H.A.); (A.K.M.); (H.H.)
| | - Waseem El-Huneidi
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, UAE;
| | - Jalal Taneera
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, UAE; (H.A.); (A.K.M.); (H.H.)
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, UAE;
- Correspondence: (J.T.); (N.S.); Tel.: +971-65057743 (J.T.); +971-65057206 (N.S.); Fax: +971-65585879 (J.T. or N.S.)
| | - Nabil Sulaiman
- Department of Family Medicine, College of Medicine, University of Sharjah, Sharjah 27272, UAE
- Baker IDI Heart and Diabetes Institute, Melbourne 3004, Australia
- Correspondence: (J.T.); (N.S.); Tel.: +971-65057743 (J.T.); +971-65057206 (N.S.); Fax: +971-65585879 (J.T. or N.S.)
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20
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Aljaibeji H, Mukhopadhyay D, Mohammed AK, Dhaiban S, Hachim MY, Elemam NM, Sulaiman N, Salehi A, Taneera J. Reduced Expression of PLCXD3 Associates With Disruption of Glucose Sensing and Insulin Signaling in Pancreatic β-Cells. Front Endocrinol (Lausanne) 2019; 10:735. [PMID: 31781030 PMCID: PMC6851018 DOI: 10.3389/fendo.2019.00735] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/10/2019] [Indexed: 01/17/2023] Open
Abstract
Previous work has shown that reduced expression of PLCXD3, a member of the phosphoinositide-specific phospholipases (PI-PLC) family, impaired insulin secretion with an unclear mechanism. In the current study, we aim to investigate the mechanism underlying this effect using human islets and rat INS-1 (832/13) cells. Microarray and RNA sequencing data showed that PLCXD3 is among the highly expressed PI-PLCs in human islets and INS-1 (832/13) cells. Expression of PLCXD3 was reduced in human diabetic islets, correlated positively with Insulin and GLP1R expression and inversely with the donor's body mass index (BMI) and glycated hemoglobin (HbA1c). Expression silencing of PLCXD3 in INS-1 (832/13) cells was found to reduce glucose-stimulated insulin secretion (GSIS) and insulin content. In addition, the expression of Insulin, NEUROD1, GLUT2, GCK, INSR, IRS2, and AKT was downregulated. Cell viability and apoptosis rate were unaffected. In conclusion, our data suggest that low expression of PLCXD3 in pancreatic β-cells associates with downregulation of the key insulin signaling and insulin biosynthesis genes as well as reduction in glucose sensing.
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Affiliation(s)
- Hayat Aljaibeji
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Debasmita Mukhopadhyay
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Abdul Khader Mohammed
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Sarah Dhaiban
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Mahmood Y. Hachim
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Noha M. Elemam
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Nabil Sulaiman
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Albert Salehi
- Department of Clinical Sciences, Lund University Diabetes Centre (LUDC), Lund University, Malmö, Sweden
| | - Jalal Taneera
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- *Correspondence: Jalal Taneera
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Breheny P, Stromberg A, Lambert J. p-Value Histograms: Inference and Diagnostics. High Throughput 2018; 7:ht7030023. [PMID: 30200313 PMCID: PMC6164648 DOI: 10.3390/ht7030023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/26/2018] [Accepted: 08/30/2018] [Indexed: 11/16/2022] Open
Abstract
It is increasingly common for experiments in biology and medicine to involve large numbers of hypothesis tests. A natural graphical method for visualizing these tests is to construct a histogram from the p-values of these tests. In this article, we examine the shapes, both regular and irregular, that these histograms can take on, as well as present simple inferential procedures that help to interpret the shapes in terms of diagnosing potential problems with the experiment. We examine potential causes of these problems in detail, and discuss potential remedies. Throughout, examples of irregular-looking p-value histograms are provided and based on case studies involving real biological experiments.
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Affiliation(s)
- Patrick Breheny
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA.
| | - Arnold Stromberg
- Department of Statistics, University of Kentucky, Lexington, KY 40508, USA.
| | - Joshua Lambert
- Department of Statistics, University of Kentucky, Lexington, KY 40508, USA.
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22
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Wang Q, Titlow WB, McClintock DA, Stromberg AJ, McClintock TS. Activity-Dependent Gene Expression in the Mammalian Olfactory Epithelium. Chem Senses 2018; 42:611-624. [PMID: 28525560 DOI: 10.1093/chemse/bjx028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Activity-dependent processes are important to olfactory sensory neurons (OSNs) in several ways, such as cell survival and the specificity of axonal convergence. The identification of activity-dependent mRNAs has contributed to our understanding of OSN axon convergence, but has revealed surprisingly little about other processes. Published studies of activity-dependent mRNAs in olfactory mucosae overlap poorly, but by combining these agreements with meta-analysis of existing data we identify 443 mRNAs that respond to methods that alter OSN activity. Three hundred and fifty of them are expressed in mature OSNs, consistent with the expectation that activity-dependent responses are cell autonomous and driven by odor stimulation. Many of these mRNAs encode proteins that function at presynaptic terminals or support electrical activity, consistent with hypotheses linking activity dependence to synaptic plasticity and energy conservation. The lack of agreement between studies is due largely to underpowered experiments. In addition, methods used to alter OSN activity are susceptible to indirect or off-target effects. These effects deserve greater attention, not only to rigorously identify OSN mRNAs that respond to altered OSN activity, but also because these effects are of significant interest in their own right. For example, the mRNAs of some sustentacular cell enzymes believed to function in odorant clearance (Cyp2a4 and Cyp2g1) are sensitive to unilateral naris occlusion used to reduce odorant stimulation of the ipsilateral olfactory epithelium. Also problematic are odorant receptor mRNAs, which show little agreement across studies and are susceptible to differences in frequency of expression that masquerade as activity-dependent changes in mRNA abundance.
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Affiliation(s)
- Qiang Wang
- Department of Physiology, University of Kentucky, 800 Rose St., Lexington, KY 40536-0298, USA
| | - William B Titlow
- Department of Physiology, University of Kentucky, 800 Rose St., Lexington, KY 40536-0298, USA
| | - Declan A McClintock
- Department of Physiology, University of Kentucky, 800 Rose St., Lexington, KY 40536-0298, USA
| | - Arnold J Stromberg
- Department of Statistics, University of Kentucky, 725 Rose St., Lexington, KY 40536-0082, USA
| | - Timothy S McClintock
- Department of Physiology, University of Kentucky, 800 Rose St., Lexington, KY 40536-0298, USA
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23
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Wheeler LC, Harms MJ. Human S100A5 binds Ca 2+ and Cu 2+ independently. BMC BIOPHYSICS 2017; 10:8. [PMID: 29201357 PMCID: PMC5700546 DOI: 10.1186/s13628-017-0040-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/08/2017] [Indexed: 12/21/2022]
Abstract
Background S100A5 is a calcium binding protein found in a small subset of amniote tissues. Little is known about the biological roles of S100A5, but it may be involved in inflammation and olfactory signaling. Previous work indicated that S100A5 displays antagonism between binding of Ca2+ and Cu2+ ions-one of the most commonly cited features of the protein. We set out to characterize the interplay between Ca2+ and Cu2+ binding by S100A5 using isothermal titration calorimetry (ITC), circular dichroism spectroscopy (CD), and analytical ultracentrifugation (AUC). Results We found that human S100A5 is capable of binding both Cu2+ and Ca2+ ions simultaneously. The wildtype protein was extremely aggregation-prone in the presence of Cu2+ and Ca2+. A Cys-free version of S100A5, however, was not prone to precipitation or oligomerization. Mutation of the cysteines does not disrupt the binding of either Ca2+ or Cu2+ to S100A5. In the Cys-free background, we measured Ca2+ and Cu2+ binding in the presence and absence of the other metal using ITC. Saturating concentrations of Ca2+ or Cu2+ do not disrupt the binding of one another. Ca2+ and Cu2+ binding induce structural changes in S100A5, which are measurable using CD spectroscopy. We show via sedimentation velocity AUC that the wildtype protein is prone to the formation of soluble oligomers, which are not present in Cys-free samples. Conclusions S100A5 can bind Ca2+ and Cu2+ ions simultaneously and independently. This observation is in direct contrast to previously-reported antagonism between binding of Cu2+ and Ca2+ ions. The previous result is likely due to metal-dependent aggregation. Little is known about the biology of S100A5, so an accurate understanding of the biochemistry is necessary to make informed biological hypotheses. Our observations suggest the possibility of independent biological functions for Cu2+ and Ca2+ binding by S100A5.
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Affiliation(s)
- Lucas C Wheeler
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, 97403 OR USA.,Insitute of Molecular Biology, University of Oregon, Eugene, 97403 OR USA
| | - Michael J Harms
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, 97403 OR USA.,Insitute of Molecular Biology, University of Oregon, Eugene, 97403 OR USA
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Gene Expression Profiles of Main Olfactory Epithelium in Adenylyl Cyclase 3 Knockout Mice. Int J Mol Sci 2015; 16:28320-33. [PMID: 26633363 PMCID: PMC4691054 DOI: 10.3390/ijms161226107] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 01/03/2023] Open
Abstract
Adenylyl Cyclase 3 (AC3) plays an important role in the olfactory sensation-signaling pathway in mice. AC3 deficiency leads to defects in olfaction. However, it is still unknown whether AC3 deficiency affects gene expression or olfactory signal transduction pathways within the main olfactory epithelium (MOE). In this study, gene microarrays were used to screen differentially expressed genes in MOE from AC3 knockout (AC3−/−) and wild-type (AC3+/+) mice. The differentially expressed genes identified were subjected to bioinformatic analysis and verified by qRT-PCR. Gene expression in the MOE from AC3−/− mice was significantly altered, compared to AC3+/+ mice. Of the 41266 gene probes, 3379 had greater than 2-fold fold change in expression levels between AC3−/− and AC3+/+ mice, accounting for 8% of the total gene probes. Of these genes, 1391 were up regulated, and 1988 were down regulated, including 425 olfactory receptor genes, 99 genes that are specifically expressed in the immature olfactory neurons, 305 genes that are specifically expressed in the mature olfactory neurons, and 155 genes that are involved in epigenetic regulation. Quantitative RT-PCR verification of the differentially expressed epigenetic regulation related genes, olfactory receptors, ion transporter related genes, neuron development and differentiation related genes, lipid metabolism and membrane protein transport etc. related genes showed that P75NTR, Hinfp, Gadd45b, and Tet3 were significantly up-regulated, while Olfr370, Olfr1414, Olfr1208, Golf, Faim2, Tsg101, Mapk10, Actl6b, H2BE, ATF5, Kirrrel2, OMP, Drd2etc. were significantly down-regulated. In summary, AC3 may play a role in proximal olfactory signaling and play a role in the regulation of differentially expressed genes in mouse MOE.
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Saleh M, Jürchott K, Oberland S, Neuhaus EM, Kramer A, Abraham U. Genome-Wide Screen Reveals Rhythmic Regulation of Genes Involved in Odor Processing in the Olfactory Epithelium. J Biol Rhythms 2015; 30:506-18. [PMID: 26482709 DOI: 10.1177/0748730415610197] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Odor discrimination behavior displays circadian fluctuations in mice, indicating that mammalian olfactory function is under control of the circadian system. This is further supported by the facts that odor discrimination rhythms depend on the presence of clock genes and that olfactory tissues contain autonomous circadian clocks. However, the molecular link between circadian function and olfactory processing is still unknown. To elucidate the molecular mechanisms underlying this link, we focused on the olfactory epithelium (OE), the primary target of odors and the site of the initial events in olfactory processing. We asked whether olfactory sensory neurons (OSNs) within the OE possess an autonomous circadian clock and whether olfactory pathways are under circadian control. Employing clock gene-driven bioluminescence reporter assays and time-dependent immunohistochemistry on OE samples, we found robust circadian rhythms of core clock genes and their proteins in OSNs, suggesting that the OE indeed contains an autonomous circadian clock. Furthermore, we performed a circadian transcriptome analysis and identified several OSN-specific components that are under circadian control, including those with putative roles in circadian olfactory processing, such as KIRREL2-an established factor involved in short-term OSN activation. The spatiotemporal expression patterns of our candidate proteins suggest that they are involved in short-term anabolic processes to rhythmically prepare the cell for peak performances and to promote circadian function of OSNs.
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Affiliation(s)
- Manjana Saleh
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Karsten Jürchott
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sonja Oberland
- Cluster of Excellence NeuroCure, Charité-Universtitätsmedizin Berlin, Berlin, Germany Department of Pharmacology and Toxicology, University Hospital Jena, Jena, Germany
| | - Eva M Neuhaus
- Department of Pharmacology and Toxicology, University Hospital Jena, Jena, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ute Abraham
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
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Abstract
Our understanding of mammalian olfactory coding has been impeded by the paucity of information about the odorant receptors (ORs) that respond to a given odorant ligand in awake, freely behaving animals. Identifying the ORs that respond in vivo to a given odorant ligand from among the ∼1100 ORs in mice is intrinsically challenging but critical for our understanding of olfactory coding at the periphery. Here, we report an in vivo assay that is based on a novel gene-targeted mouse strain, S100a5-tauGFP, in which a fluorescent reporter selectively marks olfactory sensory neurons that have been activated recently in vivo. Because each olfactory sensory neuron expresses a single OR gene, multiple ORs responding to a given odorant ligand can be identified simultaneously by capturing the population of activated olfactory sensory neurons and using expression profiling methods to screen the repertoire of mouse OR genes. We used this in vivo assay to re-identify known eugenol- and muscone-responsive mouse ORs. We identified additional ORs responsive to eugenol or muscone. Heterologous expression assays confirmed nine eugenol-responsive ORs (Olfr73, Olfr178, Olfr432, Olfr610, Olfr958, Olfr960, Olfr961, Olfr913, and Olfr1234) and four muscone-responsive ORs (Olfr74, Olfr235, Olfr816, and Olfr1440). We found that the human ortholog of Olfr235 and Olfr1440 responds to macrocyclic ketone and lactone musk odorants but not to polycyclic musk odorants or a macrocyclic diester musk odorant. This novel assay, called the Kentucky in vivo odorant ligand-receptor assay, should facilitate the in vivo identification of mouse ORs for a given odorant ligand of interest.
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Abstract
Our understanding of mammalian olfactory coding has been impeded by the paucity of information about the odorant receptors (ORs) that respond to a given odorant ligand in awake, freely behaving animals. Identifying the ORs that respond in vivo to a given odorant ligand from among the ∼1100 ORs in mice is intrinsically challenging but critical for our understanding of olfactory coding at the periphery. Here, we report an in vivo assay that is based on a novel gene-targeted mouse strain, S100a5-tauGFP, in which a fluorescent reporter selectively marks olfactory sensory neurons that have been activated recently in vivo. Because each olfactory sensory neuron expresses a single OR gene, multiple ORs responding to a given odorant ligand can be identified simultaneously by capturing the population of activated olfactory sensory neurons and using expression profiling methods to screen the repertoire of mouse OR genes. We used this in vivo assay to re-identify known eugenol- and muscone-responsive mouse ORs. We identified additional ORs responsive to eugenol or muscone. Heterologous expression assays confirmed nine eugenol-responsive ORs (Olfr73, Olfr178, Olfr432, Olfr610, Olfr958, Olfr960, Olfr961, Olfr913, and Olfr1234) and four muscone-responsive ORs (Olfr74, Olfr235, Olfr816, and Olfr1440). We found that the human ortholog of Olfr235 and Olfr1440 responds to macrocyclic ketone and lactone musk odorants but not to polycyclic musk odorants or a macrocyclic diester musk odorant. This novel assay, called the Kentucky in vivo odorant ligand-receptor assay, should facilitate the in vivo identification of mouse ORs for a given odorant ligand of interest.
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