1
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Gui Y, Thomas MH, Garcia P, Karout M, Halder R, Michelucci A, Kollmus H, Zhou C, Melmed S, Schughart K, Balling R, Mittelbronn M, Nadeau JH, Williams RW, Sauter T, Buttini M, Sinkkonen L. Pituitary Tumor Transforming Gene 1 Orchestrates Gene Regulatory Variation in Mouse Ventral Midbrain During Aging. Front Genet 2020; 11:566734. [PMID: 33173537 PMCID: PMC7538689 DOI: 10.3389/fgene.2020.566734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/27/2020] [Indexed: 01/07/2023] Open
Abstract
Dopaminergic neurons in the midbrain are of particular interest due to their role in diseases such as Parkinson’s disease and schizophrenia. Genetic variation between individuals can affect the integrity and function of dopaminergic neurons but the DNA variants and molecular cascades modulating dopaminergic neurons and other cells types of ventral midbrain remain poorly defined. Three genetically diverse inbred mouse strains – C57BL/6J, A/J, and DBA/2J – differ significantly in their genomes (∼7 million variants), motor and cognitive behavior, and susceptibility to neurotoxins. To further dissect the underlying molecular networks responsible for these variable phenotypes, we generated RNA-seq and ChIP-seq data from ventral midbrains of the 3 mouse strains. We defined 1000–1200 transcripts that are differentially expressed among them. These widespread differences may be due to altered activity or expression of upstream transcription factors. Interestingly, transcription factors were significantly underrepresented among the differentially expressed genes, and only one transcription factor, Pttg1, showed significant differences between all three strains. The changes in Pttg1 expression were accompanied by consistent alterations in histone H3 lysine 4 trimethylation at Pttg1 transcription start site. The ventral midbrain transcriptome of 3-month-old C57BL/6J congenic Pttg1–/– mutants was only modestly altered, but shifted toward that of A/J and DBA/2J in 9-month-old mice. Principle component analysis (PCA) identified the genes underlying the transcriptome shift and deconvolution of these bulk RNA-seq changes using midbrain single cell RNA-seq data suggested that the changes were occurring in several different cell types, including neurons, oligodendrocytes, and astrocytes. Taken together, our results show that Pttg1 contributes to gene regulatory variation between mouse strains and influences mouse midbrain transcriptome during aging.
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Affiliation(s)
- Yujuan Gui
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Mélanie H Thomas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Pierre Garcia
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.,National Center of Pathology, Laboratoire National de Santé, Dudelange, Luxembourg.,Luxembourg Centre of Neuropathology, Dudelange, Luxembourg
| | - Mona Karout
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Alessandro Michelucci
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.,Department of Oncology, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Heike Kollmus
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Cuiqi Zhou
- Cedars Sinai Medical Centre, Los Angeles, CA, United States
| | - Shlomo Melmed
- Cedars Sinai Medical Centre, Los Angeles, CA, United States
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Department of Infection Genetics, University of Veterinary Medicine Hannover, Hanover, Germany.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Michel Mittelbronn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.,National Center of Pathology, Laboratoire National de Santé, Dudelange, Luxembourg.,Luxembourg Centre of Neuropathology, Dudelange, Luxembourg.,Department of Oncology, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Joseph H Nadeau
- Pacific Northwest Research Institute, Seattle, WA, United States.,Maine Medical Center Research Institute, Scarborough, ME, United States
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Thomas Sauter
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
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2
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Egervari G, Ciccocioppo R, Jentsch JD, Hurd YL. Shaping vulnerability to addiction - the contribution of behavior, neural circuits and molecular mechanisms. Neurosci Biobehav Rev 2018; 85:117-125. [PMID: 28571877 PMCID: PMC5708151 DOI: 10.1016/j.neubiorev.2017.05.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 05/11/2017] [Accepted: 05/22/2017] [Indexed: 12/11/2022]
Abstract
Substance use disorders continue to impose increasing medical, financial and emotional burdens on society in the form of morbidity and overdose, family disintegration, loss of employment and crime, while advances in prevention and treatment options remain limited. Importantly, not all individuals exposed to abused substances effectively develop the disease. Genetic factors play a significant role in determining addiction vulnerability and interactions between innate predisposition, environmental factors and personal experiences are also critical. Thus, understanding individual differences that contribute to the initiation of substance use as well as on long-term maladaptations driving compulsive drug use and relapse propensity is of critical importance to reduce this devastating disorder. In this paper, we discuss current topics in the field of addiction regarding individual vulnerability related to behavioral endophenotypes, neural circuits, as well as genetics and epigenetic mechanisms. Expanded knowledge of these factors is of importance to improve and personalize prevention and treatment interventions in the future.
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Affiliation(s)
- Gabor Egervari
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 10029 New York, NY, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 10029 New York, NY, USA
| | - Roberto Ciccocioppo
- School of Pharmacy, Pharmacology Unit, University of Camerino, 62032 Camerino, Italy
| | - J David Jentsch
- Department of Psychology, Binghamton University, 13902 Binghamton, NY, USA
| | - Yasmin L Hurd
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 10029 New York, NY, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 10029 New York, NY, USA.
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3
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Bryant DT, Landles C, Papadopoulou AS, Benjamin AC, Duckworth JK, Rosahl T, Benn CL, Bates GP. Disruption to schizophrenia-associated gene Fez1 in the hippocampus of HDAC11 knockout mice. Sci Rep 2017; 7:11900. [PMID: 28928414 PMCID: PMC5605701 DOI: 10.1038/s41598-017-11630-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 08/25/2017] [Indexed: 12/18/2022] Open
Abstract
Histone Deacetylase 11 (HDAC11) is highly expressed in the central nervous system where it has been reported to have roles in neural differentiation. In contrast with previous studies showing nuclear and cytoplasmic localisation, we observed synaptic enrichment of HDAC11. Knockout mouse models for HDACs 1-9 have been important for guiding the development of isoform specific HDAC inhibitors as effective therapeutics. Given the close relationship between HDAC11 and neural cells in vitro, we examined neural tissue in a previously uncharacterised Hdac11 knockout mouse (Hdac11 KO/KO). Loss of HDAC11 had no obvious impact on brain morphology and neural stem/precursor cells isolated from Hdac11 KO/KO mice had comparable proliferation and differentiation characteristics. However, in differentiating neural cells we observed decreased expression of schizophrenia-associated gene Fez1 (fasciculation and elongation protein zeta 1), a gene previously reported to be regulated by HDAC11 activity. FEZ1 has been associated with the dendritic growth of neurons and risk of schizophrenia via its interaction with DISC1 (disrupted in schizophrenia 1). Examination of cortical, cerebellar and hippocampal tissue reveal decreased Fez1 expression specifically in the hippocampus of adult mice. The results of this study demonstrate that loss of HDAC11 has age dependent and brain-region specific consequences.
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Affiliation(s)
- Dale T Bryant
- UCL Huntington's Disease Centre, Sobell Department of Motor Neuroscience, UCL Institute of Neurology, University College London, London, United Kingdom.,Neusentis, Pfizer Ltd, The Portway, Granta Park, Abington, Cambridge, United Kingdom
| | - Christian Landles
- UCL Huntington's Disease Centre, Sobell Department of Motor Neuroscience, UCL Institute of Neurology, University College London, London, United Kingdom
| | - Aikaterini S Papadopoulou
- UCL Huntington's Disease Centre, Sobell Department of Motor Neuroscience, UCL Institute of Neurology, University College London, London, United Kingdom
| | - Agnesska C Benjamin
- UCL Huntington's Disease Centre, Sobell Department of Motor Neuroscience, UCL Institute of Neurology, University College London, London, United Kingdom
| | - Joshua K Duckworth
- Neusentis, Pfizer Ltd, The Portway, Granta Park, Abington, Cambridge, United Kingdom
| | | | - Caroline L Benn
- Neusentis, Pfizer Ltd, The Portway, Granta Park, Abington, Cambridge, United Kingdom
| | - Gillian P Bates
- UCL Huntington's Disease Centre, Sobell Department of Motor Neuroscience, UCL Institute of Neurology, University College London, London, United Kingdom.
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4
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Chintalapudi SR, Jablonski MM. Systems Genetics Analysis to Identify the Genetic Modulation of a Glaucoma-Associated Gene. Methods Mol Biol 2017; 1488:391-417. [PMID: 27933535 DOI: 10.1007/978-1-4939-6427-7_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Recently, γ-synuclein (SNCG) was shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the regulation of Sncg in RGCs, we used a systems genetics approach to identify a gene that modulates the expression of Sncg, followed by confirmatory studies in both healthy and diseased retinas. We found that chromosome 1 harbors an eQTL that modulates the expression of Sncg in the mouse retina and identified Pfdn2 as the candidate upstream modulator of Sncg expression. Downregulation of Pfdn2 in enriched RGCs causes a concomitant reduction in Sncg. In this chapter, we describe our strategy and methods for identifying and confirming a genetic modulation of a glaucoma-associated gene. A similar method can be applied to other genes expressed in other tissues.
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Affiliation(s)
- Sumana R Chintalapudi
- Department of Anatomy and Neurobiology, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA
| | - Monica M Jablonski
- Department of Ophthalmology, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA. .,Department of Anatomy and Neurobiology, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA. .,Department of Pharmaceutical Sciences, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA.
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5
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Kadiyala SB, Ferland RJ. Dissociation of spontaneous seizures and brainstem seizure thresholds in mice exposed to eight flurothyl-induced generalized seizures. Epilepsia Open 2016; 2:48-58. [PMID: 28825051 PMCID: PMC5560332 DOI: 10.1002/epi4.12031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Objective C57BL/6J mice exposed to eight flurothyl‐induced generalized clonic seizures exhibit a change in seizure phenotype following a 28‐day incubation period and subsequent flurothyl rechallenge. Mice now develop a complex seizure semiology originating in the forebrain and propagating into the brainstem seizure network (a forebrain→brainstem seizure). In contrast, this phenotype change does not occur in seizure‐sensitive DBA/2J mice. The underlying mechanism was the focus of this study. Methods DBA/2J mice were exposed to eight flurothyl‐induced seizures (1/day) followed by 24‐h video‐electroencephalographic recordings for 28 days. Forebrain and brainstem seizure thresholds were determined in C57BL/6J and DBA/2J mice following one or eight flurothyl‐induced seizures, or after eight flurothyl‐induced seizures, a 28‐day incubation period, and final flurothyl rechallenge. Results Similar to C57BL/6J mice, DBA/2J mice expressed spontaneous seizures. However, unlike C57BL/6J mice, DBA/2J mice continued to have spontaneous seizures without remission. Because DBA/2J mice did not express forebrain→brainstem seizures following flurothyl rechallenge after a 28‐day incubation period, this indicated that spontaneous seizures were not sufficient for the evolution of forebrain→brainstem seizures. Therefore, we determined whether brainstem seizure thresholds were changing during this repeated‐flurothyl model and whether this could account for the expression of forebrain→brainstem seizures. Brainstem seizure thresholds were not different between C57BL/6J and DBA/2J mice on day 1 or on the last induction seizure trial (day 8). However, brainstem seizure thresholds did differ significantly on flurothyl rechallenge (day 28), with DBA/2J mice showing no lowering of their brainstem seizure thresholds. Significance These results demonstrate that DBA/2J mice exposed to the repeated‐flurothyl model develop spontaneous seizures without evidence of seizure remission and provide a new model of epileptogenesis. Moreover, these findings indicated that the transition of forebrain ictal discharge into the brainstem seizure network occurs as a result of changes in brainstem seizure thresholds that are independent of spontaneous seizure expression.
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Affiliation(s)
- Sridhar B Kadiyala
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208, USA
| | - Russell J Ferland
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208, USA.,Department of Neurology, Albany Medical College, Albany, NY 12208, USA
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6
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Variability of brain anatomy for three common mouse strains. Neuroimage 2016; 142:656-662. [DOI: 10.1016/j.neuroimage.2016.03.069] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 03/24/2016] [Accepted: 03/26/2016] [Indexed: 11/23/2022] Open
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7
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Wang L, Jiao Y, Wang Y, Zhang M, Gu W. Self-Confirmation and Ascertainment of the Candidate Genomic Regions of Complex Trait Loci - A None-Experimental Solution. PLoS One 2016; 11:e0153676. [PMID: 27203862 PMCID: PMC4874692 DOI: 10.1371/journal.pone.0153676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 04/01/2016] [Indexed: 01/24/2023] Open
Abstract
Over the past half century, thousands of quantitative trait loci (QTL) have been identified by using animal models and plant populations. However, the none-reliability and imprecision of the genomic regions of these loci have remained the major hurdle for the identification of the causal genes for the correspondent traits. We used a none-experimental strategy of strain number reduction for testing accuracy and ascertainment of the candidate region for QTL. We tested the strategy in over 400 analyses with data from 47 studies. These studies include: 1) studies with recombinant inbred (RI) strains of mice. We first tested two previously mapped QTL with well-defined genomic regions; We then tested additional four studies with known QTL regions; and finally we examined the reliability of QTL in 38 sets of data which are produced from relatively large numbers of RI strains, derived from C57BL/6J (B6) X DBA/2J (D2), known as BXD RI mouse strains; 2) studies with RI strains of rats and plants; and 3) studies using F2 populations in mice, rats and plants. In these cases, our method identified the reliability of mapped QTL and localized the candidate genes into the defined genomic regions. Our data also suggests that LRS score produced by permutation tests does not necessarily confirm the reliability of the QTL. Number of strains are not the reliable indicators for the accuracy of QTL either. Our strategy determines the reliability and accuracy of the genomic region of a QTL without any additional experimental study such as congenic breeding.
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Affiliation(s)
- Lishi Wang
- Department of Orthopedic Surgery & BME, -Campbell-Clinic, University of Tennessee Health Science Center, Memphis, TN, 38163, United States of America
- Department of Basic Research, Inner Mongolia Medical University, Inner Mongolia, 010110, PR China
| | - Yan Jiao
- Department of Orthopedic Surgery & BME, -Campbell-Clinic, University of Tennessee Health Science Center, Memphis, TN, 38163, United States of America
- Mudanjiang Medical College, Mudanjiang, Heilongjiang, 157001, PR China
| | - Yongjun Wang
- Department. of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, PR China
| | - Mengchen Zhang
- National Center of Soybean Research, Institute of Hebei Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, 050011, PR China
| | - Weikuan Gu
- Department of Orthopedic Surgery & BME, -Campbell-Clinic, University of Tennessee Health Science Center, Memphis, TN, 38163, United States of America
- Research Service, Veterans Affairs Medical Center, 1030 Jefferson Avenue, Memphis, TN, 38104, United States of America
- * E-mail:
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8
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Babcock AA, Ilkjær L, Clausen BH, Villadsen B, Dissing-Olesen L, Bendixen ATM, Lyck L, Lambertsen KL, Finsen B. Cytokine-producing microglia have an altered beta-amyloid load in aged APP/PS1 Tg mice. Brain Behav Immun 2015; 48:86-101. [PMID: 25774009 DOI: 10.1016/j.bbi.2015.03.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/21/2015] [Accepted: 03/06/2015] [Indexed: 12/17/2022] Open
Abstract
Beta-amyloid (Aβ) plaques and chronic neuroinflammation are significant neuropathological features of Alzheimer's disease. Microglial cells in aged brains have potential to produce cytokines such as TNF and IL-1 family members (IL-1α, IL-1β, and IL-1Ra) and to phagocytose Aβ in Alzheimer's disease, however the inter-relationship between these processes is poorly understood. Here we show that % Aβ plaque load followed a sigmoidal trajectory with age in the neocortex of APPswe/PS1ΔE9 Tg mice, and correlated positively with soluble Aβ40 and Aβ42. Aβ measures were moderately correlated with mRNA levels of CD11b, TNF, and IL-1Ra. Cytokine production and Aβ load were assessed in neocortical CD11b(+)(CD45(+)) microglia by flow cytometry. Whereas most microglia in aged mice produced IL-1Ra, relatively low proportions of microglia produced TNF, IL-1α, and IL-1β. However, microglial production of these latter cytokines was generally increased in APP/PS1 Tg mice. Microglia that phagocytosed endogenously-produced Aβ were only observed in APP/PS1 Tg mice. Differences in phagocytic index and total Aβ load were observed in microglia with specific cytokine profiles. Both phagocytic index and total Aβ load were higher in IL-1α(+) and IL-1Ra(+) microglia, than microglia that did not produce these cytokines. In contrast, total Aβ load was lower in IL-1β(+) and TNF(+) microglia, compared to IL-1β(-) and TNF(-) microglia, and TNF(+) microglia also had a lower phagocytic index. Using GFP bone marrow chimeric mice, we confirmed that the majority of neocortical CD11b(+)(CD45(+)) microglia were resident cells (GFP(-)) in APP/PS1 Tg mice, even after selectively analysing CD11b(+)CD45(high) cells, which are typically considered to be infiltrating cells. Together, our data demonstrate that cytokine expression is selectively correlated with age and Aβ pathology, and is associated with an altered Aβ load in phagocytic microglia from APP/PS1 Tg mice. These findings have implications for understanding the regulation of microglial cytokine production and phagocytosis of Aβ in Alzheimer's disease.
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Affiliation(s)
- Alicia A Babcock
- Institute of Molecular Medicine, University of Southern Denmark, JB Winsløws Vej 25, 2, 5000 Odense C, Denmark.
| | - Laura Ilkjær
- Institute of Molecular Medicine, University of Southern Denmark, JB Winsløws Vej 25, 2, 5000 Odense C, Denmark.
| | - Bettina H Clausen
- Institute of Molecular Medicine, University of Southern Denmark, JB Winsløws Vej 25, 2, 5000 Odense C, Denmark.
| | - Birgitte Villadsen
- Institute of Molecular Medicine, University of Southern Denmark, JB Winsløws Vej 25, 2, 5000 Odense C, Denmark.
| | - Lasse Dissing-Olesen
- Institute of Molecular Medicine, University of Southern Denmark, JB Winsløws Vej 25, 2, 5000 Odense C, Denmark.
| | - Anita T M Bendixen
- Institute of Molecular Medicine, University of Southern Denmark, JB Winsløws Vej 25, 2, 5000 Odense C, Denmark.
| | - Lise Lyck
- Institute of Molecular Medicine, University of Southern Denmark, JB Winsløws Vej 25, 2, 5000 Odense C, Denmark.
| | - Kate L Lambertsen
- Institute of Molecular Medicine, University of Southern Denmark, JB Winsløws Vej 25, 2, 5000 Odense C, Denmark.
| | - Bente Finsen
- Institute of Molecular Medicine, University of Southern Denmark, JB Winsløws Vej 25, 2, 5000 Odense C, Denmark.
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9
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Massé IO, Guillemette S, Laramée ME, Bronchti G, Boire D. Strain differences of the effect of enucleation and anophthalmia on the size and growth of sensory cortices in mice. Brain Res 2014; 1588:113-26. [PMID: 25242615 DOI: 10.1016/j.brainres.2014.09.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 09/05/2014] [Accepted: 09/10/2014] [Indexed: 11/27/2022]
Abstract
Anophthalmia is a condition in which the eye does not develop from the early embryonic period. Early blindness induces cross-modal plastic modifications in the brain such as auditory and haptic activations of the visual cortex and also leads to a greater solicitation of the somatosensory and auditory cortices. The visual cortex is activated by auditory stimuli in anophthalmic mice and activity is known to alter the growth pattern of the cerebral cortex. The size of the primary visual, auditory and somatosensory cortices and of the corresponding specific sensory thalamic nuclei were measured in intact and enucleated C57Bl/6J mice and in ZRDCT anophthalmic mice (ZRDCT/An) to evaluate the contribution of cross-modal activity on the growth of the cerebral cortex. In addition, the size of these structures were compared in intact, enucleated and anophthalmic fourth generation backcrossed hybrid C57Bl/6J×ZRDCT/An mice to parse out the effects of mouse strains and of the different visual deprivations. The visual cortex was smaller in the anophthalmic ZRDCT/An than in the intact and enucleated C57Bl/6J mice. Also the auditory cortex was larger and the somatosensory cortex smaller in the ZRDCT/An than in the intact and enucleated C57Bl/6J mice. The size differences of sensory cortices between the enucleated and anophthalmic mice were no longer present in the hybrid mice, showing specific genetic differences between C57Bl/6J and ZRDCT mice. The post natal size increase of the visual cortex was less in the enucleated than in the anophthalmic and intact hybrid mice. This suggests differences in the activity of the visual cortex between enucleated and anophthalmic mice and that early in-utero spontaneous neural activity in the visual system contributes to the shaping of functional properties of cortical networks.
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Affiliation(s)
- Ian O Massé
- Département d׳anatomie, Université du Québec à Trois-Rivières, Québec, Canada G9A 5H7.
| | - Sonia Guillemette
- Département d׳anatomie, Université du Québec à Trois-Rivières, Québec, Canada G9A 5H7.
| | - Marie-Eve Laramée
- Département d׳anatomie, Université du Québec à Trois-Rivières, Québec, Canada G9A 5H7.
| | - Gilles Bronchti
- Département d׳anatomie, Université du Québec à Trois-Rivières, Québec, Canada G9A 5H7.
| | - Denis Boire
- Département d׳anatomie, Université du Québec à Trois-Rivières, Québec, Canada G9A 5H7; École d׳optométrie, Université de Montréal, Québec, Canada H3C 3J7.
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10
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Wang L, Jiao Y, Cao Y, Liu G, Wang Y, Gu W. Limitation of number of strains and persistence of false positive loci in QTL mapping using recombinant inbred strains. PLoS One 2014; 9:e102307. [PMID: 25032693 PMCID: PMC4102522 DOI: 10.1371/journal.pone.0102307] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 06/17/2014] [Indexed: 01/21/2023] Open
Abstract
While the identification of causal genes of quantitative trait loci (QTL) remains a difficult problem in the post-genome era, the number of QTL continues to accumulate, mainly identified using the recombinant inbred (RI) strains. Over the last decade, hundreds of publications have reported nearly a thousand QTL identified from RI strains. We hypothesized that the inaccuracy of most of these QTL makes it difficult to identify causal genes. Using data from RI strains derived from C57BL/6J (B6) X DBA/2J (D2), we tested the possibility of detection of reliable QTL with different numbers of strains in the same trait in five different traits. Our results indicated that studies using RI strains of less than 30 in general have a higher probability of failing to detect reliable QTL. Errors in many studies could include false positive loci, switches between QTL with small and major effects, and missing the real major loci. The similar data was obtained from a RI strain population derived from a different pair of parents and a RI strain population of rat. Thus, thousands of reported QTL from studies of RI strains may need to be double-checked for accuracy before proceeding to causal gene identification.
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Affiliation(s)
- Lishi Wang
- Department of Orthopedic Surgery and BME, Campbell-Clinic, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Department of Basic Medical Research, Inner Mongolia Medical University, Inner Mongolia, China
| | - Yan Jiao
- Department of Orthopedic Surgery and BME, Campbell-Clinic, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Mudanjiang Medical College, Mudanjiang, PR China
| | - Yanhong Cao
- Department of Orthopedic Surgery and BME, Campbell-Clinic, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Institute of Kaschin-Beck Disease, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University; Key Laboratory of Etiologic Epidemiology, Education Bureau of Heilongjiang Province and Ministry of Health (23618104), Harbin, China
| | - Gaifen Liu
- Department. of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yongjun Wang
- Department. of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Weikuan Gu
- Department of Orthopedic Surgery and BME, Campbell-Clinic, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- * E-mail:
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11
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Abstract
Transcriptome studies have revealed a surprisingly high level of variation among individuals in expression of key genes in the CNS under both normal and experimental conditions. Ten-fold variation is common, yet the specific causes and consequences of this variation are largely unknown. By combining classic gene mapping methods-family linkage studies and genomewide association-with high-throughput genomics, it is now possible to define quantitative trait loci (QTLs), single-gene variants, and even single SNPs and indels that control gene expression in different brain regions and cells. This review considers some of the major technical and conceptual challenges in analyzing variation in expression in the CNS with a focus on mRNAs, rather than noncoding RNAs or proteins. At one level of analysis, this work has been highly successful, and we finally have techniques that can be used to track down small numbers of loci that control expression in the CNS. But at a higher level of analysis, we still do not understand the genetic architecture of gene expression in brain, the consequences of expression QTLs on protein levels or on cell function, or the combined impact of expression differences on behavior and disease risk. These important gaps are likely to be bridged over the next several decades using (1) much larger sample sizes, (2) more powerful RNA sequencing and proteomic methods, and (3) novel statistical and computational models to predict genome-to-phenome relations.
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Affiliation(s)
- Ashutosh K Pandey
- Department of Genetics, Genomics and Informatics, Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, Tennessee, USA.
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12
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Ullmann JFP, Watson C, Janke AL, Kurniawan ND, Reutens DC. A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex. Neuroimage 2013; 78:196-203. [PMID: 23587687 DOI: 10.1016/j.neuroimage.2013.04.008] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 03/26/2013] [Accepted: 04/05/2013] [Indexed: 10/27/2022] Open
Abstract
The neocortex is the largest component of the mammalian cerebral cortex. It integrates sensory inputs with experiences and memory to produce sophisticated responses to an organism's internal and external environment. While areal patterning of the mouse neocortex has been mapped using histological techniques, the neocortex has not been comprehensively segmented in magnetic resonance images. This study presents a method for systematic segmentation of the C57BL/6J mouse neocortex. We created a minimum deformation atlas, which was hierarchically segmented into 74 neocortical and cortical-related regions, making it the most detailed atlas of the mouse neocortex currently available. In addition, we provide mean volumes and relative intensities for each structure as well as a nomenclature comparison between the two most cited histological atlases of the mouse brain. This MR atlas is available for download, and it should enable researchers to perform automated segmentation in genetic models of cortical disorders.
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Affiliation(s)
- Jeremy F P Ullmann
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia.
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13
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Gat-Viks I, Chevrier N, Wilentzik R, Eisenhaure T, Raychowdhury R, Steuerman Y, Shalek A, Hacohen N, Amit I, Regev A. Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli. Nat Biotechnol 2013; 31:342-9. [PMID: 23503680 PMCID: PMC3622156 DOI: 10.1038/nbt.2519] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 02/04/2013] [Indexed: 01/24/2023]
Abstract
Individual genetic variation affects gene responsiveness to stimuli, often by influencing complex molecular circuits. Here we combine genomic and intermediate-scale transcriptional profiling with computational methods to identify variants that affect the responsiveness of genes to stimuli (responsiveness quantitative trait loci or reQTLs) and to position these variants in molecular circuit diagrams. We apply this approach to study variation in transcriptional responsiveness to pathogen components in dendritic cells from recombinant inbred mouse strains. We identify reQTLs that correlate with particular stimuli and position them in known pathways. For example, in response to a virus-like stimulus, a trans-acting variant responds as an activator of the antiviral response; using RNA interference, we identify Rgs16 as the likely causal gene. Our approach charts an experimental and analytic path to decipher the mechanisms underlying genetic variation in circuits that control responses to stimuli.
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Affiliation(s)
- Irit Gat-Viks
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nicolas Chevrier
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- Graduate Program in Immunology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Roni Wilentzik
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Thomas Eisenhaure
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Raktima Raychowdhury
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Yael Steuerman
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Alex Shalek
- Departments of Chemistry and Chemical Biology and of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA, and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ido Amit
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Aviv Regev
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
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14
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Hager R, Lu L, Rosen GD, Williams RW. Genetic architecture supports mosaic brain evolution and independent brain-body size regulation. Nat Commun 2013; 3:1079. [PMID: 23011133 PMCID: PMC4267555 DOI: 10.1038/ncomms2086] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 08/23/2012] [Indexed: 01/13/2023] Open
Abstract
The mammalian brain consists of distinct parts that fulfil different functions. Finlay and Darlington have argued that evolution of the mammalian brain is constrained by developmental programs, suggesting that different brain parts are not free to respond individually to selection and evolve independent of other parts or overall brain size. However, comparisons among mammals with matched brain weights often reveal greater differences in brain part size, arguing against strong developmental constraints. Here, we test these hypotheses using a quantitative genetic approach involving over 10,000 mice. We identify independent loci for size variation in seven key parts of the brain, and observe that brain parts show low or no phenotypic correlation, as is predicted by a mosaic scenario. We also demonstrate that variation in brain size is independently regulated from body size. The allometric relations seen at higher phylogenetic levels are thus unlikely to be the product of strong developmental constraints.
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Affiliation(s)
- Reinmar Hager
- Computational and Evolutionary Biology Group, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Lu Lu
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA.,Jiangsu Key Laboratory of Neuroregeneration, Nantong University, China
| | - Glenn D Rosen
- Department of Neurology, Beth Isreal Deaconess Medical Center, 330 Brookline Ave., Boston, MA 02215, USA
| | - Robert W Williams
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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15
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Talishinsky A, Rosen GD. Systems genetics of the lateral septal nucleus in mouse: heritability, genetic control, and covariation with behavioral and morphological traits. PLoS One 2012; 7:e44236. [PMID: 22952935 PMCID: PMC3432065 DOI: 10.1371/journal.pone.0044236] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 07/30/2012] [Indexed: 11/19/2022] Open
Abstract
The lateral septum has strong efferent projections to hypothalamic and midbrain regions, and has been associated with modulation of social behavior, anxiety, fear conditioning, memory-related behaviors, and the mesolimbic reward pathways. Understanding natural variation of lateral septal anatomy and function, as well as its genetic modulation, may provide important insights into individual differences in these evolutionarily important functions. Here we address these issues by using efficient and unbiased stereological probes to estimate the volume of the lateral septum in the BXD line of recombinant inbred mice. Lateral septum volume is a highly variable trait, with a 2.5-fold difference among animals. We find that this trait covaries with a number of behavioral and physiological phenotypes, many of which have already been associated with behaviors modulated by the lateral septum, such as spatial learning, anxiety, and reward-seeking. Heritability of lateral septal volume is moderate (h(2) = 0.52), and much of the heritable variation is caused by a locus on the distal portion of chromosome (Chr) 1. Composite interval analysis identified a secondary interval on Chr 2 that works additively with the Chr 1 locus to increase lateral septum volume. Using bioinformatic resources, we identified plausible candidate genes in both intervals that may influence the volume of this key nucleus, as well as associated behaviors.
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Affiliation(s)
- Alexander Talishinsky
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Glenn D. Rosen
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
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16
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Andreux PA, Williams EG, Koutnikova H, Houtkooper RH, Champy MF, Henry H, Schoonjans K, Williams RW, Auwerx J. Systems genetics of metabolism: the use of the BXD murine reference panel for multiscalar integration of traits. Cell 2012; 150:1287-99. [PMID: 22939713 DOI: 10.1016/j.cell.2012.08.012] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 06/06/2012] [Accepted: 08/03/2012] [Indexed: 01/22/2023]
Abstract
Metabolic homeostasis is achieved by complex molecular and cellular networks that differ significantly among individuals and are difficult to model with genetically engineered lines of mice optimized to study single gene function. Here, we systematically acquired metabolic phenotypes by using the EUMODIC EMPReSS protocols across a large panel of isogenic but diverse strains of mice (BXD type) to study the genetic control of metabolism. We generated and analyzed 140 classical phenotypes and deposited these in an open-access web service for systems genetics (www.genenetwork.org). Heritability, influence of sex, and genetic modifiers of traits were examined singly and jointly by using quantitative-trait locus (QTL) and expression QTL-mapping methods. Traits and networks were linked to loci encompassing both known variants and novel candidate genes, including alkaline phosphatase (ALPL), here linked to hypophosphatasia. The assembled and curated phenotypes provide key resources and exemplars that can be used to dissect complex metabolic traits and disorders.
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Affiliation(s)
- Pénélope A Andreux
- Laboratory of Integrative and Systems Physiology, School of Life Sciences, École Polytechnique Fédérale de Lausanne 1015, Switzerland
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17
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Newbury AJ, Rosen GD. Genetic, morphometric, and behavioral factors linked to the midsagittal area of the corpus callosum. Front Genet 2012; 3:91. [PMID: 22666227 PMCID: PMC3364465 DOI: 10.3389/fgene.2012.00091] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 05/07/2012] [Indexed: 12/23/2022] Open
Abstract
The corpus callosum is the main commissure connecting left and right cerebral hemispheres, and varies widely in size. Differences in the midsagittal area of the corpus callosum (MSACC) have been associated with a number of cognitive and behavioral phenotypes, including obsessive-compulsive disorders, psychopathy, suicidal tendencies, bipolar disorder, schizophrenia, autism, and attention deficit hyperactivity disorder. Although there is evidence to suggest that MSACC is heritable in normal human populations, there is surprisingly little evidence concerning the genetic modulation of this variation. Mice provide a potentially ideal tool to dissect the genetic modulation of MSACC. Here, we use a large genetic reference panel – the BXD recombinant inbred line – to dissect the natural variation of the MSACC. We estimated the MSACC in over 300 individuals from nearly 80 strains. We found a 4-fold difference in MSACC between individual mice, and a 2.5-fold difference among strains. MSACC is a highly heritable trait (h2 = 0.60), and we mapped a suggestive QTL to the distal portion of Chr 14. Using sequence data and neocortical expression databases, we were able to identify eight positional and plausible biological candidate genes within this interval. Finally, we found that MSACC correlated with behavioral traits associated with anxiety and attention.
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Affiliation(s)
- Alex J Newbury
- Department of Neurology, Beth Israel Deaconess Medical Center Boston, MA, USA
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18
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Rietman ML, Sommeijer JP, Levelt CN, Heimel JA. Candidate genes in ocular dominance plasticity. Front Neurosci 2012; 6:11. [PMID: 22347157 PMCID: PMC3269753 DOI: 10.3389/fnins.2012.00011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 01/16/2012] [Indexed: 11/16/2022] Open
Abstract
Many studies have been devoted to the identification of genes involved in experience-dependent plasticity in the visual cortex. To discover new candidate genes, we have reexamined data from one such study on ocular dominance (OD) plasticity in recombinant inbred BXD mouse strains. We have correlated the level of plasticity with the gene expression data in the neocortex that have become available for these same strains. We propose that genes with a high correlation are likely to play a role in OD plasticity. We have tested this hypothesis for genes whose inactivation is known to affect OD plasticity. The expression levels of these genes indeed correlated with OD plasticity if their levels showed strong differences between the BXD strains. To narrow down our candidate list of correlated genes, we have selected only those genes that were previously found to be regulated by visual experience and associated with pathways implicated in OD plasticity. This resulted in a list of 32 candidate genes. The list contained unproven, but not unexpected candidates such as the genes for IGF-1, NCAM1, NOGO-A, the gamma2 subunit of the GABA(A) receptor, acetylcholine esterase, and the catalytic subunit of cAMP-dependent protein kinase A. This demonstrates the viability of our approach. More interestingly, the following novel candidate genes were identified: Akap7, Akt1, Camk2d, Cckbr, Cd44, Crim1, Ctdsp2, Dnajc5, Gnai1, Itpka, Mapk8, Nbea, Nfatc3, Nlk, Npy5r, Phf21a, Phip, Ppm1l, Ppp1r1b, Rbbp4, Slc1a3, Slit2, Socs2, Spock3, St8sia1, Zfp207. Whether all these novel candidates indeed function in OD plasticity remains to be established, but possible roles of some of them are discussed in the article.
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Affiliation(s)
- M Liset Rietman
- Department of Molecular Visual Plasticity, Netherlands Institute for Neuroscience, An Institute of the Royal Netherlands Academy of Arts and Sciences Amsterdam, Netherlands
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19
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Wang X, Mozhui K, Li Z, Mulligan MK, Ingels JF, Zhou X, Hori RT, Chen H, Cook MN, Williams RW, Lu L. A promoter polymorphism in the Per3 gene is associated with alcohol and stress response. Transl Psychiatry 2012; 2:e73. [PMID: 22832735 PMCID: PMC3309544 DOI: 10.1038/tp.2011.71] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The period homolog genes Per1, Per2 and Per3 are important components of the circadian clock system. In addition to their role in maintaining circadian rhythm, these genes have been linked to mood disorders, stress response and vulnerability to addiction and alcoholism. In this study, we combined high-resolution sequence analysis and quantitative trait locus (QTL) mapping of gene expression and behavioral traits to identify Per3 as a compelling candidate for the interaction between circadian rhythm, alcohol and stress response. In the BXD family of mouse strains, sequence variants in Per3 have marked effects on steady-state mRNA and protein levels. As a result, the transcript maps as a cis-acting expression QTL (eQTL). We found that an insertion/deletion (indel) variant in a putative stress response element in the promoter region of Per3 causes local control of transcript abundance. This indel results in differences in protein binding affinities between the two alleles through the Nrf2 transcriptional activator. Variation in Per3 is also associated with downstream differences in the expression of genes involved in circadian rhythm, alcohol, stress response and schizophrenia. We found that the Per3 locus is linked to stress/anxiety traits, and that the basal expression of Per3 is also correlated with several anxiety and addiction-related phenotypes. Treatment with alcohol results in increased expression of Per3 in the hippocampus, and this effect interacts with acute restraint stress. Our data provide strong evidence that variation in the Per3 transcript is causally associated with and also responsive to stress and alcohol.
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Affiliation(s)
- X Wang
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - K Mozhui
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Z Li
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - M K Mulligan
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - J F Ingels
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - X Zhou
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - R T Hori
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - H Chen
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - M N Cook
- Department of Psychology, University of Memphis, Memphis, TN, USA
| | - R W Williams
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - L Lu
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA,Jiangsu Ley Laboratory of Neuroregeneration, Nantong University, Nantong, China,Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, 855 Monroe Avenue, Memphis, TN 38163, USA. E-mail:
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20
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Novel candidate genes associated with hippocampal oscillations. PLoS One 2011; 6:e26586. [PMID: 22066001 PMCID: PMC3204991 DOI: 10.1371/journal.pone.0026586] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 09/29/2011] [Indexed: 12/14/2022] Open
Abstract
The hippocampus is critical for a wide range of emotional and cognitive behaviors. Here, we performed the first genome-wide search for genes influencing hippocampal oscillations. We measured local field potentials (LFPs) using 64-channel multi-electrode arrays in acute hippocampal slices of 29 BXD recombinant inbred mouse strains. Spontaneous activity and carbachol-induced fast network oscillations were analyzed with spectral and cross-correlation methods and the resulting traits were used for mapping quantitative trait loci (QTLs), i.e., regions on the genome that may influence hippocampal function. Using genome-wide hippocampal gene expression data, we narrowed the QTLs to eight candidate genes, including Plcb1, a phospholipase that is known to influence hippocampal oscillations. We also identified two genes coding for calcium channels, Cacna1b and Cacna1e, which mediate presynaptic transmitter release and have not been shown to regulate hippocampal network activity previously. Furthermore, we showed that the amplitude of the hippocampal oscillations is genetically correlated with hippocampal volume and several measures of novel environment exploration.
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21
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Herculano-Houzel S, Ribeiro P, Campos L, Valotta da Silva A, Torres LB, Catania KC, Kaas JH. Updated neuronal scaling rules for the brains of Glires (rodents/lagomorphs). BRAIN, BEHAVIOR AND EVOLUTION 2011; 78:302-14. [PMID: 21985803 DOI: 10.1159/000330825] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 07/07/2011] [Indexed: 11/19/2022]
Abstract
Brain size scales as different functions of its number of neurons across mammalian orders such as rodents, primates, and insectivores. In rodents, we have previously shown that, across a sample of 6 species, from mouse to capybara, the cerebral cortex, cerebellum and the remaining brain structures increase in size faster than they gain neurons, with an accompanying decrease in neuronal density in these structures [Herculano-Houzel et al.: Proc Natl Acad Sci USA 2006;103:12138-12143]. Important remaining questions are whether such neuronal scaling rules within an order apply equally to all pertaining species, and whether they extend to closely related taxa. Here, we examine whether 4 other species of Rodentia, as well as the closely related rabbit (Lagomorpha), conform to the scaling rules identified previously for rodents. We report the updated neuronal scaling rules obtained for the average values of each species in a way that is directly comparable to the scaling rules that apply to primates [Gabi et al.: Brain Behav Evol 2010;76:32-44], and examine whether the scaling relationships are affected when phylogenetic relatedness in the dataset is accounted for. We have found that the brains of the spiny rat, squirrel, prairie dog and rabbit conform to the neuronal scaling rules that apply to the previous sample of rodents. The conformity to the previous rules of the new set of species, which includes the rabbit, suggests that the cellular scaling rules we have identified apply to rodents in general, and probably to Glires as a whole (rodents/lagomorphs), with one notable exception: the naked mole-rat brain is apparently an outlier, with only about half of the neurons expected from its brain size in its cerebral cortex and cerebellum.
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Affiliation(s)
- Suzana Herculano-Houzel
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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22
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Natural and engineered coding variation in antidepressant-sensitive serotonin transporters. Neuroscience 2011; 197:28-36. [PMID: 21893166 DOI: 10.1016/j.neuroscience.2011.08.056] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 08/23/2011] [Accepted: 08/24/2011] [Indexed: 12/17/2022]
Abstract
The presynaptic serotonin (5-HT) transporter (SERT) is a key regulator of 5-HT signaling and is a major target for antidepressant medications and psychostimulants. In recent years, studies of natural and engineered genetic variation in SERT have provided new opportunities to understand structural dimensions of drug interactions and regulation of the transporter, to explore 5-HT contributions to antidepressant action, and to assess the impact of SERT-mediated 5-HT contributions to neuropsychiatric disorders. Here we review three examples from our recent studies where genetic changes in SERT, identified or engineered, have led to new models, findings, and theories that cast light on new dimensions of 5-HT action in the CNS and periphery. First, we review our work to identify specific residues through which SERT recognizes antagonists, and the conversion of this knowledge to the creation of mice lacking high-affinity antidepressant and cocaine sensitivity. Second, we discuss our studies of functional coding variation in SERT that exists in commonly used strains of inbred mice, and how this variation is beginning to reveal novel 5-HT-associated phenotypes. Third, we review our identification and functional characterization of multiple, hyperactive SERT coding variants in subjects with autism. Each of these activities has driven the development of new model systems that can be further exploited to understand the contribution of 5-HT signaling to risk for neuropsychiatric disorders and their treatment.
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23
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Genetic dissection of behavioral flexibility: reversal learning in mice. Biol Psychiatry 2011; 69:1109-16. [PMID: 21392734 PMCID: PMC3090526 DOI: 10.1016/j.biopsych.2011.01.014] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 12/30/2010] [Accepted: 01/06/2011] [Indexed: 12/20/2022]
Abstract
BACKGROUND Behavioral inflexibility is a feature of schizophrenia, attention-deficit/hyperactivity disorder, and behavior addictions that likely results from heritable deficits in the inhibitory control over behavior. Here, we investigate the genetic basis of individual differences in flexibility, measured using an operant reversal learning task. METHODS We quantified discrimination acquisition and subsequent reversal learning in a cohort of 51 BXD strains of mice (2-5 mice/strain, n = 176) for which we have matched data on sequence, gene expression in key central nervous system regions, and neuroreceptor levels. RESULTS Strain variation in trials to criterion on acquisition and reversal was high, with moderate heritability (∼.3). Acquisition and reversal learning phenotypes did not covary at the strain level, suggesting that these traits are effectively under independent genetic control. Reversal performance did covary with dopamine D2 receptor levels in the ventral midbrain, consistent with a similar observed relationship between impulsivity and D2 receptors in humans. Reversal, but not acquisition, is linked to a locus on mouse chromosome 10 with a peak likelihood ratio statistic at 86.2 megabase (p < .05 genome-wide). Variance in messenger RNA levels of select transcripts expressed in neocortex, hippocampus, and striatum correlated with the reversal learning phenotype, including Syn3, Nt5dc3, and Hcfc2. CONCLUSIONS This work demonstrates the clear trait independence between, and genetic control of, discrimination acquisition and reversal and illustrates how globally coherent data sets for a single panel of highly related strains can be interrogated and integrated to uncover genetic sources and molecular and neuropharmacological candidates of complex behavioral traits relevant to human psychopathology.
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24
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Alberts R, Lu L, Williams RW, Schughart K. Genome-wide analysis of the mouse lung transcriptome reveals novel molecular gene interaction networks and cell-specific expression signatures. Respir Res 2011; 12:61. [PMID: 21535883 PMCID: PMC3105947 DOI: 10.1186/1465-9921-12-61] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 05/02/2011] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The lung is critical in surveillance and initial defense against pathogens. In humans, as in mice, individual genetic differences strongly modulate pulmonary responses to infectious agents, severity of lung disease, and potential allergic reactions. In a first step towards understanding genetic predisposition and pulmonary molecular networks that underlie individual differences in disease vulnerability, we performed a global analysis of normative lung gene expression levels in inbred mouse strains and a large family of BXD strains that are widely used for systems genetics. Our goal is to provide a key community resource on the genetics of the normative lung transcriptome that can serve as a foundation for experimental analysis and allow predicting genetic predisposition and response to pathogens, allergens, and xenobiotics. METHODS Steady-state polyA+ mRNA levels were assayed across a diverse and fully genotyped panel of 57 isogenic strains using the Affymetrix M430 2.0 array. Correlations of expression levels between genes were determined. Global expression QTL (eQTL) analysis and network covariance analysis was performed using tools and resources in GeneNetwork http://www.genenetwork.org. RESULTS Expression values were highly variable across strains and in many cases exhibited a high heritability factor. Several genes which showed a restricted expression to lung tissue were identified. Using correlations between gene expression values across all strains, we defined and extended memberships of several important molecular networks in the lung. Furthermore, we were able to extract signatures of immune cell subpopulations and characterize co-variation and shared genetic modulation. Known QTL regions for respiratory infection susceptibility were investigated and several cis-eQTL genes were identified. Numerous cis- and trans-regulated transcripts and chromosomal intervals with strong regulatory activity were mapped. The Cyp1a1 P450 transcript had a strong trans-acting eQTL (LOD 11.8) on Chr 12 at 36 ± 1 Mb. This interval contains the transcription factor Ahr that has a critical mis-sense allele in the DBA/2J haplotype and evidently modulates transcriptional activation by AhR. CONCLUSIONS Large-scale gene expression analyses in genetic reference populations revealed lung-specific and immune-cell gene expression profiles and suggested specific gene regulatory interactions.
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Affiliation(s)
- Rudi Alberts
- Department of Infection Genetics, University of Veterinary Medicine Hannover, Inhoffenstr, Braunschweig, Germany
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25
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Reinius B, Shi C, Hengshuo L, Sandhu KS, Radomska KJ, Rosen GD, Lu L, Kullander K, Williams RW, Jazin E. Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse. BMC Genomics 2010; 11:614. [PMID: 21047393 PMCID: PMC3091755 DOI: 10.1186/1471-2164-11-614] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 11/03/2010] [Indexed: 02/01/2023] Open
Abstract
Background Sexual dimorphism in brain gene expression has been recognized in several animal species. However, the relevant regulatory mechanisms remain poorly understood. To investigate whether sex-biased gene expression in mammalian brain is globally regulated or locally regulated in diverse brain structures, and to study the genomic organisation of brain-expressed sex-biased genes, we performed a large scale gene expression analysis of distinct brain regions in adult male and female mice. Results This study revealed spatial specificity in sex-biased transcription in the mouse brain, and identified 173 sex-biased genes in the striatum; 19 in the neocortex; 12 in the hippocampus and 31 in the eye. Genes located on sex chromosomes were consistently over-represented in all brain regions. Analysis on a subset of genes with sex-bias in more than one tissue revealed Y-encoded male-biased transcripts and X-encoded female-biased transcripts known to escape X-inactivation. In addition, we identified novel coding and non-coding X-linked genes with female-biased expression in multiple tissues. Interestingly, the chromosomal positions of all of the female-biased non-coding genes are in close proximity to protein-coding genes that escape X-inactivation. This defines X-chromosome domains each of which contains a coding and a non-coding female-biased gene. Lack of repressive chromatin marks in non-coding transcribed loci supports the possibility that they escape X-inactivation. Moreover, RNA-DNA combined FISH experiments confirmed the biallelic expression of one such novel domain. Conclusion This study demonstrated that the amount of genes with sex-biased expression varies between individual brain regions in mouse. The sex-biased genes identified are localized on many chromosomes. At the same time, sexually dimorphic gene expression that is common to several parts of the brain is mostly restricted to the sex chromosomes. Moreover, the study uncovered multiple female-biased non-coding genes that are non-randomly co-localized on the X-chromosome with protein-coding genes that escape X-inactivation. This raises the possibility that expression of long non-coding RNAs may play a role in modulating gene expression in domains that escape X-inactivation in mouse.
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Affiliation(s)
- Björn Reinius
- Department of Evolution and Development, EBC, Uppsala University, Sweden.
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Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ. High-throughput behavioral phenotyping in the expanded panel of BXD recombinant inbred strains. GENES, BRAIN, AND BEHAVIOR 2010; 9:129-59. [PMID: 19958391 PMCID: PMC2855868 DOI: 10.1111/j.1601-183x.2009.00540.x] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 08/14/2009] [Accepted: 09/09/2009] [Indexed: 01/10/2023]
Abstract
Genetic reference populations, particularly the BXD recombinant inbred (BXD RI) strains derived from C57BL/6J and DBA/2J mice, are a valuable resource for the discovery of the bio-molecular substrates and genetic drivers responsible for trait variation and covariation. This approach can be profitably applied in the analysis of susceptibility and mechanisms of drug and alcohol use disorders for which many predisposing behaviors may predict the occurrence and manifestation of increased preference for these substances. Many of these traits are modeled by common mouse behavioral assays, facilitating the detection of patterns and sources of genetic coregulation of predisposing phenotypes and substance consumption. Members of the Tennessee Mouse Genome Consortium (TMGC) have obtained phenotype data from over 250 measures related to multiple behavioral assays across several batteries: response to, and withdrawal from cocaine, 3,4-methylenedioxymethamphetamine; "ecstasy" (MDMA), morphine and alcohol; novelty seeking; behavioral despair and related neurological phenomena; pain sensitivity; stress sensitivity; anxiety; hyperactivity and sleep/wake cycles. All traits have been measured in both sexes in approximately 70 strains of the recently expanded panel of BXD RI strains. Sex differences and heritability estimates were obtained for each trait, and a comparison of early (N = 32) and recent (N = 37) BXD RI lines was performed. Primary data are publicly available for heritability, sex difference and genetic analyses using the MouseTrack database, and are also available in GeneNetwork.org for quantitative trait locus (QTL) detection and genetic analysis of gene expression. Together with the results of related studies, these data form a public resource for integrative systems genetic analysis of neurobehavioral traits.
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Affiliation(s)
- V M Philip
- Systems Genetics Group, Biosciences Division, Oak Ridge National LaboratoryOak Ridge TN
| | - S Duvvuru
- Systems Genetics Group, Biosciences Division, Oak Ridge National LaboratoryOak Ridge TN
| | - B Gomero
- Systems Genetics Group, Biosciences Division, Oak Ridge National LaboratoryOak Ridge TN
| | - T A Ansah
- Department of Neurobiology and Neurotoxicology, Meharry Medical CollegeNashville, TN
| | - C D Blaha
- Department of Psychology, The University of MemphisMemphis, TN
| | - M N Cook
- Department of Psychology, The University of MemphisMemphis, TN
| | - K M Hamre
- Departments of Anatomy and Neurobiology, University of Tennessee Health Science CenterMemphis, TN
| | - W R Lariviere
- Departments of Anesthesiology and Neurobiology, University of Pittsburgh School of MedicinePittsburgh, PA
| | - D B Matthews
- Departments of Psychology and Neuroscience, Baylor UniversityWaco, TX, USA
- Present address: Department of Psychology, Nanyang Technological UniversitySingapore
| | - G Mittleman
- Department of Psychology, The University of MemphisMemphis, TN
| | - D Goldowitz
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British ColumbiaVancouver, BC, Canada
| | - E J Chesler
- Systems Genetics Group, Biosciences Division, Oak Ridge National LaboratoryOak Ridge TN
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