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Nakashima A, Takeuchi H. Roles of odorant receptors during olfactory glomerular map formation. Genesis 2024; 62:e23610. [PMID: 38874301 DOI: 10.1002/dvg.23610] [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: 01/03/2024] [Revised: 04/11/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024]
Abstract
The organization of the olfactory glomerular map involves the convergence of olfactory sensory neurons (OSNs) expressing the same odorant receptor (OR) into glomeruli in the olfactory bulb (OB). A remarkable feature of the olfactory glomerular map formation is that the identity of OR instructs the topography of the bulb, resulting in thousands of discrete glomeruli in mice. Several lines of evidence indicate that ORs control the expression levels of various kinds of transmembrane proteins to form glomeruli at appropriate regions of the OB. In this review, we will discuss how the OR identity is decoded by OSNs into gene expression through intracellular regulatory mechanisms.
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Affiliation(s)
- Ai Nakashima
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Haruki Takeuchi
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Brewer KK, Brewer KM, Terry TT, Caspary T, Vaisse C, Berbari NF. Postnatal Dynamic Ciliary ARL13B and ADCY3 Localization in the Mouse Brain. Cells 2024; 13:259. [PMID: 38334651 PMCID: PMC10854790 DOI: 10.3390/cells13030259] [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: 01/16/2024] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/10/2024] Open
Abstract
Primary cilia are hair-like structures found on nearly all mammalian cell types, including cells in the developing and adult brain. A diverse set of receptors and signaling proteins localize within cilia to regulate many physiological and developmental pathways, including the Hedgehog (Hh) pathway. Defects in cilia structure, protein localization, and function lead to genetic disorders called ciliopathies, which present with various clinical features that include several neurodevelopmental phenotypes and hyperphagia-associated obesity. Despite their dysfunction being implicated in several disease states, understanding their roles in central nervous system (CNS) development and signaling has proven challenging. We hypothesize that dynamic changes to ciliary protein composition contribute to this challenge and may reflect unrecognized diversity of CNS cilia. The proteins ARL13B and ADCY3 are established markers of cilia in the brain. ARL13B is a regulatory GTPase important for regulating cilia structure, protein trafficking, and Hh signaling, and ADCY3 is a ciliary adenylyl cyclase. Here, we examine the ciliary localization of ARL13B and ADCY3 in the perinatal and adult mouse brain. We define changes in the proportion of cilia enriched for ARL13B and ADCY3 depending on brain region and age. Furthermore, we identify distinct lengths of cilia within specific brain regions of male and female mice. ARL13B+ cilia become relatively rare with age in many brain regions, including the hypothalamic feeding centers, while ADCY3 becomes a prominent cilia marker in the mature adult brain. It is important to understand the endogenous localization patterns of these proteins throughout development and under different physiological conditions as these common cilia markers may be more dynamic than initially expected. Understanding regional- and developmental-associated cilia protein composition signatures and physiological condition cilia dynamic changes in the CNS may reveal the molecular mechanisms associated with the features commonly observed in ciliopathy models and ciliopathies, like obesity and diabetes.
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Affiliation(s)
- Katlyn K. Brewer
- Department of Biology, Indiana University-Indianapolis, 723 W. Michigan St., Indianapolis, IN 46202, USA; (K.K.B.); (K.M.B.)
| | - Kathryn M. Brewer
- Department of Biology, Indiana University-Indianapolis, 723 W. Michigan St., Indianapolis, IN 46202, USA; (K.K.B.); (K.M.B.)
| | - Tiffany T. Terry
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; (T.T.T.); (T.C.)
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; (T.T.T.); (T.C.)
| | - Christian Vaisse
- Diabetes Center and Department of Medicine, University of California San Francisco, San Francisco, CA 92697, USA;
| | - Nicolas F. Berbari
- Department of Biology, Indiana University-Indianapolis, 723 W. Michigan St., Indianapolis, IN 46202, USA; (K.K.B.); (K.M.B.)
- Stark Neurosciences Research Institute, Indiana University-Indianapolis, Indianapolis, IN 46202, USA
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Lyu P, Li Y, Wen X, Cao H. JUMP: replicability analysis of high-throughput experiments with applications to spatial transcriptomic studies. Bioinformatics 2023; 39:btad366. [PMID: 37279733 PMCID: PMC10279524 DOI: 10.1093/bioinformatics/btad366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/26/2023] [Accepted: 06/02/2023] [Indexed: 06/08/2023] Open
Abstract
MOTIVATION Replicability is the cornerstone of scientific research. The current statistical method for high-dimensional replicability analysis either cannot control the false discovery rate (FDR) or is too conservative. RESULTS We propose a statistical method, JUMP, for the high-dimensional replicability analysis of two studies. The input is a high-dimensional paired sequence of p-values from two studies and the test statistic is the maximum of p-values of the pair. JUMP uses four states of the p-value pairs to indicate whether they are null or non-null. Conditional on the hidden states, JUMP computes the cumulative distribution function of the maximum of p-values for each state to conservatively approximate the probability of rejection under the composite null of replicability. JUMP estimates unknown parameters and uses a step-up procedure to control FDR. By incorporating different states of composite null, JUMP achieves a substantial power gain over existing methods while controlling the FDR. Analyzing two pairs of spatially resolved transcriptomic datasets, JUMP makes biological discoveries that otherwise cannot be obtained by using existing methods. AVAILABILITY AND IMPLEMENTATION An R package JUMP implementing the JUMP method is available on CRAN (https://CRAN.R-project.org/package=JUMP).
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Affiliation(s)
- Pengfei Lyu
- Department of Statistics, Florida State University, 600 W College AVE, Tallahassee, FL 32306, United States
| | - Yan Li
- School of Mathematics, Jilin University, 2699 Qianjin ST, Changchun, Jilin 130012, China
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Hongyuan Cao
- Department of Statistics, Florida State University, 600 W College AVE, Tallahassee, FL 32306, United States
- School of Mathematics, Jilin University, 2699 Qianjin ST, Changchun, Jilin 130012, China
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Shayya HJ, Kahiapo JK, Duffié R, Lehmann KS, Bashkirova L, Monahan K, Dalton RP, Gao J, Jiao S, Schieren I, Belluscio L, Lomvardas S. ER stress transforms random olfactory receptor choice into axon targeting precision. Cell 2022; 185:3896-3912.e22. [PMID: 36167070 PMCID: PMC9588687 DOI: 10.1016/j.cell.2022.08.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 01/26/2023]
Abstract
Olfactory sensory neurons (OSNs) convert the stochastic choice of one of >1,000 olfactory receptor (OR) genes into precise and stereotyped axon targeting of OR-specific glomeruli in the olfactory bulb. Here, we show that the PERK arm of the unfolded protein response (UPR) regulates both the glomerular coalescence of like axons and the specificity of their projections. Subtle differences in OR protein sequences lead to distinct patterns of endoplasmic reticulum (ER) stress during OSN development, converting OR identity into distinct gene expression signatures. We identify the transcription factor Ddit3 as a key effector of PERK signaling that maps OR-dependent ER stress patterns to the transcriptional regulation of axon guidance and cell-adhesion genes, instructing targeting precision. Our results extend the known functions of the UPR from a quality-control pathway that protects cells from misfolded proteins to a sensor of cellular identity that interprets physiological states to direct axon wiring.
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Affiliation(s)
- Hani J Shayya
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Medical Scientist Training Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Jerome K Kahiapo
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Rachel Duffié
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Katherine S Lehmann
- Developmental Neural Plasticity Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lisa Bashkirova
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Kevin Monahan
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Ryan P Dalton
- The Miller Institute for Basic Research in Science, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joanna Gao
- Barnard College, New York, NY 10025, USA
| | - Song Jiao
- Developmental Neural Plasticity Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ira Schieren
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Leonardo Belluscio
- Developmental Neural Plasticity Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stavros Lomvardas
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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Gao F, Gao K, Zhang P, Fu Y, Liu X, Bai S, Li W, Qian Z. A biomimetic sensor using neurotransmitter detection to decode odor perception by an olfactory network. Biosens Bioelectron 2022; 211:114391. [DOI: 10.1016/j.bios.2022.114391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/08/2022] [Accepted: 05/15/2022] [Indexed: 11/02/2022]
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The role of GPCRs in bone diseases and dysfunctions. Bone Res 2019; 7:19. [PMID: 31646011 PMCID: PMC6804689 DOI: 10.1038/s41413-019-0059-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 12/13/2022] Open
Abstract
The superfamily of G protein-coupled receptors (GPCRs) contains immense structural and functional diversity and mediates a myriad of biological processes upon activation by various extracellular signals. Critical roles of GPCRs have been established in bone development, remodeling, and disease. Multiple human GPCR mutations impair bone development or metabolism, resulting in osteopathologies. Here we summarize the disease phenotypes and dysfunctions caused by GPCR gene mutations in humans as well as by deletion in animals. To date, 92 receptors (5 glutamate family, 67 rhodopsin family, 5 adhesion, 4 frizzled/taste2 family, 5 secretin family, and 6 other 7TM receptors) have been associated with bone diseases and dysfunctions (36 in humans and 72 in animals). By analyzing data from these 92 GPCRs, we found that mutation or deletion of different individual GPCRs could induce similar bone diseases or dysfunctions, and the same individual GPCR mutation or deletion could induce different bone diseases or dysfunctions in different populations or animal models. Data from human diseases or dysfunctions identified 19 genes whose mutation was associated with human BMD: 9 genes each for human height and osteoporosis; 4 genes each for human osteoarthritis (OA) and fracture risk; and 2 genes each for adolescent idiopathic scoliosis (AIS), periodontitis, osteosarcoma growth, and tooth development. Reports from gene knockout animals found 40 GPCRs whose deficiency reduced bone mass, while deficiency of 22 GPCRs increased bone mass and BMD; deficiency of 8 GPCRs reduced body length, while 5 mice had reduced femur size upon GPCR deletion. Furthermore, deficiency in 6 GPCRs induced osteoporosis; 4 induced osteoarthritis; 3 delayed fracture healing; 3 reduced arthritis severity; and reduced bone strength, increased bone strength, and increased cortical thickness were each observed in 2 GPCR-deficiency models. The ever-expanding number of GPCR mutation-associated diseases warrants accelerated molecular analysis, population studies, and investigation of phenotype correlation with SNPs to elucidate GPCR function in human diseases.
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