1
|
Ham LM, Staunton H, Schulz JM, Tillmann J, Volz D, Murtagh L, Chatham C, O'Connor EC, Chamberlain S, Schoenenberger P, Pandina G, Wang P, Kas MJH, Arango C, Murphy D. Points to consider when initiating clinical investigations in autistic paediatric populations-A White Paper. Eur Neuropsychopharmacol 2024; 86:35-42. [PMID: 38917772 DOI: 10.1016/j.euroneuro.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/27/2024]
Abstract
Many individuals with autism spectrum disorder (ASD) experience various degrees of impairment in social interaction and communication, restricted, repetitive behaviours, interests/activities. These impairments make a significant contribution to poorer everyday adaptive functioning. Yet, there are no pharmacological therapies to effectively treat the core symptoms of ASD. Since symptoms of ASD likely emerge from a complex interplay of vulnerabilities, environmental factors and compensatory mechanisms during the early developmental period, pharmacological interventions arguably would have the greatest impact to improve long-term outcomes when implemented at a young age. It is essential therefore, that clinical development programmes of investigational drugs in ASD include the paediatric population early on in clinical trials. Such trials need to offer the prospect of direct benefit (PDB) for participants. In most cases in drug development this prospect is supported by evidence of efficacy in adults. However, the effectiveness of treatment approaches may be age-dependent, so that clinical trials in adults may not provide sufficient evidence for a PDB in children. In this white paper, we consolidate recommendations from regulatory guidelines, as well as advice from the Food and Drug Administration, USA (FDA) and the Committee for Human Medicinal Products (CHMP) consultations on various development programmes on: 1) elements to support a PDB to participants in early paediatric clinical trials in ASD, including single-gene neurodevelopment disorders, 2) aspects of study design to allow for a PDB. This white paper is intended to be complementary to existing regulatory guidelines in guiding industry and academic sponsors in their conduct of early paediatric clinical trials in ASD.
Collapse
Affiliation(s)
| | | | - Jan Michael Schulz
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Julian Tillmann
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | - Lorraine Murtagh
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | - Eoin C O'Connor
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Stormy Chamberlain
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Philipp Schoenenberger
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | - Paul Wang
- Clinical Research Associates LLC, Simons Foundation, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Martien J H Kas
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh, Groningen, the Netherlands
| | - Celso Arango
- Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, CIBERSAM, IiSGM, Universidad Complutense, School of Medicine, Madrid, Spain
| | - Declan Murphy
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| |
Collapse
|
2
|
Kautt AF, Chen J, Lewarch CL, Hu C, Turner K, Lassance JM, Baier F, Bedford NL, Bendesky A, Hoekstra HE. Evolution of gene expression across brain regions in behaviourally divergent deer mice. Mol Ecol 2024:e17270. [PMID: 38263608 DOI: 10.1111/mec.17270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/25/2024]
Abstract
The evolution of innate behaviours is ultimately due to genetic variation likely acting in the nervous system. Gene regulation may be particularly important because it can evolve in a modular brain-region specific fashion through the concerted action of cis- and trans-regulatory changes. Here, to investigate transcriptional variation and its regulatory basis across the brain, we perform RNA sequencing (RNA-Seq) on ten brain subregions in two sister species of deer mice (Peromyscus maniculatus and P. polionotus)-which differ in a range of innate behaviours, including their social system-and their F1 hybrids. We find that most of the variation in gene expression distinguishes subregions, followed by species. Interspecific differential expression (DE) is pervasive (52-59% of expressed genes), whereas the number of DE genes between sexes is modest overall (~3%). Interestingly, the identity of DE genes varies considerably across brain regions. Much of this modularity is due to cis-regulatory divergence, and while 43% of genes were consistently assigned to the same gene regulatory class across subregions (e.g. conserved, cis- or trans-regulatory divergence), a similar number were assigned to two or more different gene regulatory classes. Together, these results highlight the modularity of gene expression differences and divergence in the brain, which may be key to explain how the evolution of brain gene expression can contribute to the astonishing diversity of animal behaviours.
Collapse
Affiliation(s)
- Andreas F Kautt
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Jenny Chen
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Caitlin L Lewarch
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Caroline Hu
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Kyle Turner
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Jean-Marc Lassance
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Felix Baier
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Nicole L Bedford
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Andres Bendesky
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Hopi E Hoekstra
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| |
Collapse
|
3
|
Wang S, Pan C, Sheng H, Yang M, Yang C, Feng X, Hu C, Ma Y. Construction of a molecular regulatory network related to fat deposition by multi-tissue transcriptome sequencing of Jiaxian red cattle. iScience 2023; 26:108346. [PMID: 38026203 PMCID: PMC10665818 DOI: 10.1016/j.isci.2023.108346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/26/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Intramuscular fat (IMF) refers to the fat that accumulates between muscle bundles or within muscle cells, whose content significantly impacts the taste, tenderness, and flavor of meat products, making it a crucial economic characteristic in livestock production. However, the intricate mechanisms governing IMF deposition, involving non-coding RNAs (ncRNAs), genes, and complex regulatory networks, remain largely enigmatic. Identifying adipose tissue-specific genes and ncRNAs is paramount to unravel these molecular mysteries. This study, conducted on Jiaxian red cattle, harnessed whole transcriptome sequencing to unearth the nuances of circRNAs and miRNAs across seven distinct tissues. The interplay of these ncRNAs was assessed through differential expression analysis and network analysis. These findings are not only pivotal in unveiling the intricacies of fat deposition mechanisms but also lay a robust foundation for future research, setting the stage for enhancing IMF content in Jiaxian red cattle breeding.
Collapse
Affiliation(s)
- Shuzhe Wang
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Cuili Pan
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Hui Sheng
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Mengli Yang
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Chaoyun Yang
- Xichang College, Liangshan Prefecture, Sichuan Province, China
| | - Xue Feng
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Chunli Hu
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| |
Collapse
|
4
|
Voelker P, Weible AP, Niell CM, Rothbart MK, Posner MI. Molecular Mechanisms for Changing Brain Connectivity in Mice and Humans. Int J Mol Sci 2023; 24:15840. [PMID: 37958822 PMCID: PMC10648558 DOI: 10.3390/ijms242115840] [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: 09/29/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
The goal of this study was to examine commonalities in the molecular basis of learning in mice and humans. In previous work we have demonstrated that the anterior cingulate cortex (ACC) and hippocampus (HC) are involved in learning a two-choice visuospatial discrimination task. Here, we began by looking for candidate genes upregulated in mouse ACC and HC with learning. We then determined which of these were also upregulated in mouse blood. Finally, we used RT-PCR to compare candidate gene expression in mouse blood with that from humans following one of two forms of learning: a working memory task (network training) or meditation (a generalized training shown to change many networks). Two genes were upregulated in mice following learning: caspase recruitment domain-containing protein 6 (Card6) and inosine monophosphate dehydrogenase 2 (Impdh2). The Impdh2 gene product catalyzes the first committed step of guanine nucleotide synthesis and is tightly linked to cell proliferation. The Card6 gene product positively modulates signal transduction. In humans, Card6 was significantly upregulated, and Impdh2 trended toward upregulation with training. These genes have been shown to regulate pathways that influence nuclear factor kappa B (NF-κB), a factor previously found to be related to enhanced synaptic function and learning.
Collapse
Affiliation(s)
- Pascale Voelker
- Department of Psychology, University of Oregon, Eugene, OR 97403, USA (M.I.P.)
| | - Aldis P. Weible
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA; (A.P.W.); (C.M.N.)
| | - Cristopher M. Niell
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA; (A.P.W.); (C.M.N.)
- Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Mary K. Rothbart
- Department of Psychology, University of Oregon, Eugene, OR 97403, USA (M.I.P.)
| | - Michael I. Posner
- Department of Psychology, University of Oregon, Eugene, OR 97403, USA (M.I.P.)
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA; (A.P.W.); (C.M.N.)
| |
Collapse
|
5
|
Lalonde C, Sreetharan S, Murray A, Stoa L, Cybulski ME, Kennedy A, Landry N, Stillar A, Khurana S, Tharmalingam S, Wilson J, Khaper N, Lees SJ, Boreham D, Tai TC. Absence of Depressive and Anxious Behavior with Genetic Dysregulation in Adult C57Bl/6J Mice after Prenatal Exposure to Ionizing Radiation. Int J Mol Sci 2023; 24:ijms24108466. [PMID: 37239811 DOI: 10.3390/ijms24108466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023] Open
Abstract
The exposure of ionizing radiation during early gestation often leads to deleterious and even lethal effects; however, few extensive studies have been conducted on late gestational exposures. This research examined the behavior al effects of C57Bl/6J mouse offspring exposed to low dose ionizing gamma irradiation during the equivalent third trimester. Pregnant dams were randomly assigned to sham or exposed groups to either low dose or sublethal dose radiation (50, 300, or 1000 mGy) at gestational day 15. Adult offspring underwent a behavioral and genetic analysis after being raised under normal murine housing conditions. Our results indicate very little change in the behavioral tasks measuring general anxiety, social anxiety, and stress-management in animals exposed prenatally across the low dose radiation conditions. Quantitative real-time polymerase chain reactions were conducted on the cerebral cortex, hippocampus, and cerebellum of each animal; results indicate some dysregulation in markers of DNA damage, synaptic activity, reactive oxygen species (ROS) regulation, and methylation pathways in the offspring. Together, our results provide evidence in the C57Bl/6J strain, that exposure to sublethal dose radiation (<1000 mGy) during the last period of gestation leads to no observable changes in behaviour when assessed as adults, although some changes in gene expression were observed for specific brain regions. These results indicate that the level of oxidative stress occurring during late gestation for this mouse strain is not sufficient for a change in the assessed behavioral phenotype, but results in some modest dysregulation of the genetic profile of the brain.
Collapse
Affiliation(s)
- Christine Lalonde
- Biomolecular Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - Shayenthiran Sreetharan
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
- Department of Biology, McMaster University, Hamilton, ON L8S4L8, Canada
| | - Alyssa Murray
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - Lisa Stoa
- Department of Biology, McMaster University, Hamilton, ON L8S4L8, Canada
| | | | - Allison Kennedy
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - Nicholas Landry
- Department of Psychology, Nipissing University, North Bay, ON P1B8L7, Canada
| | - Amy Stillar
- Department of Psychology, Nipissing University, North Bay, ON P1B8L7, Canada
| | - Sandhya Khurana
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - Sujeenthar Tharmalingam
- Biomolecular Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - Joanna Wilson
- Department of Biology, McMaster University, Hamilton, ON L8S4L8, Canada
| | - Neelam Khaper
- Biomolecular Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - Simon J Lees
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - Douglas Boreham
- Biomolecular Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - T C Tai
- Biomolecular Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| |
Collapse
|
6
|
Sanford LD, Wellman LL, Adkins AM, Guo ML, Zhang Y, Ren R, Yang L, Tang X. Modeling integrated stress, sleep, fear and neuroimmune responses: Relevance for understanding trauma and stress-related disorders. Neurobiol Stress 2023; 23:100517. [PMID: 36793998 PMCID: PMC9923229 DOI: 10.1016/j.ynstr.2023.100517] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 12/30/2022] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Sleep and stress have complex interactions that are implicated in both physical diseases and psychiatric disorders. These interactions can be modulated by learning and memory, and involve additional interactions with the neuroimmune system. In this paper, we propose that stressful challenges induce integrated responses across multiple systems that can vary depending on situational variables in which the initial stress was experienced, and with the ability of the individual to cope with stress- and fear-inducing challenges. Differences in coping may involve differences in resilience and vulnerability and/or whether the stressful context allows adaptive learning and responses. We provide data demonstrating both common (corticosterone, SIH and fear behaviors) and distinguishing (sleep and neuroimmune) responses that are associated with an individual's ability to respond and relative resilience and vulnerability. We discuss neurocircuitry regulating integrated stress, sleep, neuroimmune and fear responses, and show that responses can be modulated at the neural level. Finally, we discuss factors that need to be considered in models of integrated stress responses and their relevance for understanding stress-related disorders in humans.
Collapse
Affiliation(s)
- Larry D. Sanford
- Sleep Research Laboratory, Center for Integrative Neuroscience and Inflammatory Diseases, Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Laurie L. Wellman
- Sleep Research Laboratory, Center for Integrative Neuroscience and Inflammatory Diseases, Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Austin M. Adkins
- Sleep Research Laboratory, Center for Integrative Neuroscience and Inflammatory Diseases, Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Ming-Lei Guo
- Drug Addiction Laboratory, Center for Integrative Neuroscience and Inflammatory Diseases, Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Ye Zhang
- Sleep Medicine Center, Department of Respiratory and Critical Care Medicine, Mental Health Center, Translational Neuroscience Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Rong Ren
- Sleep Medicine Center, Department of Respiratory and Critical Care Medicine, Mental Health Center, Translational Neuroscience Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Linghui Yang
- Sleep Medicine Center, Department of Respiratory and Critical Care Medicine, Mental Health Center, Translational Neuroscience Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xiangdong Tang
- Sleep Medicine Center, Department of Respiratory and Critical Care Medicine, Mental Health Center, Translational Neuroscience Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
7
|
Tabbaa M, Knoll A, Levitt P. Mouse population genetics phenocopies heterogeneity of human Chd8 haploinsufficiency. Neuron 2023; 111:539-556.e5. [PMID: 36738737 PMCID: PMC9960295 DOI: 10.1016/j.neuron.2023.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/13/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
Preclinical models of neurodevelopmental disorders typically use single inbred mouse strains, which fail to capture the genetic diversity and symptom heterogeneity that is common clinically. We tested whether modeling genetic background diversity in mouse genetic reference panels would recapitulate population and individual differences in responses to a syndromic mutation in the high-confidence autism risk gene, CHD8. We measured clinically relevant phenotypes in >1,000 mice from 33 strains, including brain and body weights and cognition, activity, anxiety, and social behaviors, using 5 behavioral assays: cued fear conditioning, open field tests in dark and bright light, direct social interaction, and social dominance. Trait disruptions mimicked those seen clinically, with robust strain and sex differences. Some strains exhibited large effect-size trait disruptions, sometimes in opposite directions, and-remarkably-others expressed resilience. Therefore, systematically introducing genetic diversity into models of neurodevelopmental disorders provides a better framework for discovering individual differences in symptom etiologies.
Collapse
Affiliation(s)
- Manal Tabbaa
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Allison Knoll
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Pat Levitt
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA.
| |
Collapse
|
8
|
Yagound B, West AJ, Richardson MF, Gruber J, Reid JG, Whiting MJ, Rollins LA. Captivity induces large and population-dependent brain transcriptomic changes in wild-caught cane toads (Rhinella marina). Mol Ecol 2022; 31:4949-4961. [PMID: 35894800 PMCID: PMC9804778 DOI: 10.1111/mec.16633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/14/2022] [Accepted: 07/25/2022] [Indexed: 01/09/2023]
Abstract
Gene expression levels are key molecular phenotypes at the interplay between genotype and environment. Mounting evidence suggests that short-term changes in environmental conditions, such as those encountered in captivity, can substantially affect gene expression levels. Yet, the exact magnitude of this effect, how general it is, and whether it results in parallel changes across populations are not well understood. Here, we take advantage of the well-studied cane toad, Rhinella marina, to examine the effect of short-term captivity on brain gene expression levels, and determine whether effects of captivity differ between long-colonized and vanguard populations of the cane toad's Australian invasion range. We compared the transcriptomes of wild-caught toads immediately assayed with those from toads captured from the same populations but maintained in captivity for seven months. We found large differences in gene expression levels between captive and wild-caught toads from the same population, with an over-representation of processes related to behaviour and the response to stress. Captivity had a much larger effect on both gene expression levels and gene expression variability in toads from vanguard populations compared to toads from long-colonized areas, potentially indicating an increased plasticity in toads at the leading edge of the invasion. Overall, our findings indicate that short-term captivity can induce large and population-specific transcriptomic changes, which has significant implications for studies comparing phenotypic traits of wild-caught organisms from different populations that have been held in captivity.
Collapse
Affiliation(s)
- Boris Yagound
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Andrea J. West
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| | - Mark F. Richardson
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia,Deakin Genomics Centre, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| | - Jodie Gruber
- College of Life and Environmental SciencesUniversity of ExeterPenrynUK,School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | - Jack G. Reid
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| | - Martin J. Whiting
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Lee A. Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia,Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| |
Collapse
|
9
|
Vijaya Shankara J, Horsley KG, Cheng N, Rho JM, Antle MC. Circadian Responses to Light in the BTBR Mouse. J Biol Rhythms 2022; 37:498-515. [PMID: 35722987 PMCID: PMC9452857 DOI: 10.1177/07487304221102279] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Animals with altered freerunning periods are valuable in understanding properties of the circadian clock. Understanding the relationship between endogenous clock properties, entrainment, and influence of light in terms of parametric and non-parametric models can help us better understand how different populations adapt to external light cycles. Many clinical populations often show significant changes in circadian properties that in turn cause sleep and circadian problems, possibly exacerbating their underlying clinical condition. BTBR T+Itpr3tf/J (BTBR) mice are a model commonly used for the study of autism spectrum disorders (ASD). Adults and adolescents with ASD frequently exhibit profound sleep and circadian disruptions, including increased latency to sleep, insomnia, advanced and delayed sleep phase disorders, and sleep fragmentation. Here, we investigated the circadian phenotype of BTBR mice in freerunning and light-entrained conditions and found that this strain of mice showed noticeably short freerunning periods (~22.75 h). In addition, when compared to C57BL/6J controls, BTBR mice also showed higher levels of activity even though this activity was compressed into a shorter active phase. Phase delays and phase advances to light were significantly larger in BTBR mice. Despite the short freerunning period, BTBR mice exhibited normal entrainment in light-dark cycles and accelerated entrainment to both advanced and delayed light cycles. Their ability to entrain to skeleton photoperiods of 1 min suggests that this entrainment cannot be attributed to masking. Period differences were also correlated with differences in the number of vasoactive intestinal polypeptide–expressing cells in the suprachiasmatic nucleus (SCN). Overall, the BTBR model, with their unique freerunning and entrainment properties, makes an interesting model to understand the underlying circadian clock.
Collapse
Affiliation(s)
- Jhenkruthi Vijaya Shankara
- Department of Psychology, University of Calgary, Calgary, AB, Canada.,Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Katelyn G Horsley
- Department of Psychology, University of Calgary, Calgary, AB, Canada.,Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ning Cheng
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Jong M Rho
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Departments of Neurosciences and Pediatrics, University of California, San Diego and Rady Children's Hospital, San Diego, California, USA
| | - Michael C Antle
- Department of Psychology, University of Calgary, Calgary, AB, Canada.,Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
10
|
Yagound B, West AJ, Richardson MF, Selechnik D, Shine R, Rollins LA. Brain transcriptome analysis reveals gene expression differences associated with dispersal behaviour between range-front and range-core populations of invasive cane toads in Australia. Mol Ecol 2022; 31:1700-1715. [PMID: 35028988 PMCID: PMC9303232 DOI: 10.1111/mec.16347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/19/2021] [Accepted: 01/07/2022] [Indexed: 11/27/2022]
Abstract
Understanding the mechanisms allowing invasive species to adapt to novel environments is a challenge in invasion biology. Many invaders demonstrate rapid evolution of behavioural traits involved in range expansion such as locomotor activity, exploration and risk‐taking. However, the molecular mechanisms that underpin these changes are poorly understood. In 86 years, invasive cane toads (Rhinella marina) in Australia have drastically expanded their geographic range westward from coastal Queensland to Western Australia. During their range expansion, toads have undergone extensive phenotypic changes, particularly in behaviours that enhance the toads’ dispersal ability. Common‐garden experiments have shown that some changes in behavioural traits related to dispersal are heritable. At the molecular level, it is currently unknown whether these changes in dispersal‐related behaviour are underlain by small or large differences in gene expression, nor is known the biological function of genes showing differential expression. Here, we used RNA‐seq to gain a better understanding of the molecular mechanisms underlying dispersal‐related behavioural changes. We compared the brain transcriptomes of toads from the Hawai'ian source population, as well as three distinct populations from across the Australian invasive range. We found markedly different gene expression profiles between the source population and Australian toads. By contrast, toads from across the Australian invasive range had very similar transcriptomic profiles. Yet, key genes with functions putatively related to dispersal behaviour showed differential expression between populations located at each end of the invasive range. These genes could play an important role in the behavioural changes characteristic of range expansion in Australian cane toads.
Collapse
Affiliation(s)
- Boris Yagound
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Andrea J West
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Mark F Richardson
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Daniel Selechnik
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Richard Shine
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Lee A Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| |
Collapse
|
11
|
Lin Y, Yerukala Sathipati S, Ho SY. Predicting the Risk Genes of Autism Spectrum Disorders. Front Genet 2021; 12:665469. [PMID: 34194469 PMCID: PMC8236850 DOI: 10.3389/fgene.2021.665469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022] Open
Abstract
Autism spectrum disorder (ASD) refers to a wide spectrum of neurodevelopmental disorders that emerge during infancy and continue throughout a lifespan. Although substantial efforts have been made to develop therapeutic approaches, core symptoms persist lifelong in ASD patients. Identifying the brain temporospatial regions where the risk genes are expressed in ASD patients may help to improve the therapeutic strategies. Accordingly, this work aims to predict the risk genes of ASD and identify the temporospatial regions of the brain structures at different developmental time points for exploring the specificity of ASD gene expression in the brain that would help in possible ASD detection in the future. A dataset consisting of 13 developmental stages ranging from 8 weeks post-conception to 8 years from 26 brain structures was retrieved from the BrainSpan atlas. This work proposes a support vector machine–based risk gene prediction method ASD-Risk to distinguish the risk genes of ASD and non-ASD genes. ASD-Risk used an optimal feature selection algorithm called inheritable bi-objective combinatorial genetic algorithm to identify the brain temporospatial regions for prediction of the risk genes of ASD. ASD-Risk achieved a 10-fold cross-validation accuracy, sensitivity, specificity, area under a receiver operating characteristic curve, and a test accuracy of 81.83%, 0.84, 0.79, 0.84, and 72.27%, respectively. We prioritized the temporospatial features according to their contribution to the prediction accuracy. The top identified temporospatial regions of the brain for risk gene prediction included the posteroventral parietal cortex at 13 post-conception weeks feature. The identified temporospatial features would help to explore the risk genes that are specifically expressed in different brain regions of ASD patients.
Collapse
Affiliation(s)
- Yenching Lin
- Interdisciplinary Neuroscience Ph.D. Program, National Chiao Tung University, Hsinchu, Taiwan
| | - Srinivasulu Yerukala Sathipati
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, United States.,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Shinn-Ying Ho
- Interdisciplinary Neuroscience Ph.D. Program, National Chiao Tung University, Hsinchu, Taiwan.,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Center For Intelligent Drug Systems and Smart Bio-Devices (IDS2B), National Chiao Tung University, Hsinchu, Taiwan
| |
Collapse
|
12
|
Slc1a3-2A-CreERT2 mice reveal unique features of Bergmann glia and augment a growing collection of Cre drivers and effectors in the 129S4 genetic background. Sci Rep 2021; 11:5412. [PMID: 33686166 PMCID: PMC7940647 DOI: 10.1038/s41598-021-84887-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 02/22/2021] [Indexed: 12/26/2022] Open
Abstract
Genetic variation is a primary determinant of phenotypic diversity. In laboratory mice, genetic variation can be a serious experimental confounder, and thus minimized through inbreeding. However, generalizations of results obtained with inbred strains must be made with caution, especially when working with complex phenotypes and disease models. Here we compared behavioral characteristics of C57Bl/6—the strain most widely used in biomedical research—with those of 129S4. In contrast to 129S4, C57Bl/6 demonstrated high within-strain and intra-litter behavioral hyperactivity. Although high consistency would be advantageous, the majority of disease models and transgenic tools are in C57Bl/6. We recently established six Cre driver lines and two Cre effector lines in 129S4. To augment this collection, we genetically engineered a Cre line to study astrocytes in 129S4. It was validated with two Cre effector lines: calcium indicator gCaMP5g-tdTomato and RiboTag—a tool widely used to study cell type-specific translatomes. These reporters are in different genomic loci, and in both the Cre was functional and astrocyte-specific. We found that calcium signals lasted longer and had a higher amplitude in cortical compared to hippocampal astrocytes, genes linked to a single neurodegenerative disease have highly divergent expression patterns, and that ribosome proteins are non-uniformly expressed across brain regions and cell types.
Collapse
|
13
|
Emami-Khoyi A, Parbhu SP, Ross JG, Murphy EC, Bothwell J, Monsanto DM, Vuuren BJV, Teske PR, Paterson AM. De Novo Transcriptome Assembly and Annotation of Liver and Brain Tissues of Common Brushtail Possums ( Trichosurus vulpecula) in New Zealand: Transcriptome Diversity after Decades of Population Control. Genes (Basel) 2020; 11:genes11040436. [PMID: 32316496 PMCID: PMC7230921 DOI: 10.3390/genes11040436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022] Open
Abstract
The common brushtail possum (Trichosurus vulpecula), introduced from Australia in the mid-nineteenth century, is an invasive species in New Zealand where it is widespread and forms the largest self-sustained reservoir of bovine tuberculosis (Mycobacterium bovis) among wild populations. Conservation and agricultural authorities regularly apply a series of population control measures to suppress brushtail possum populations. The evolutionary consequence of more than half a century of intensive population control operations on the species’ genomic diversity and population structure is hindered by a paucity of available genomic resources. This study is the first to characterise the functional content and diversity of brushtail possum liver and brain cerebral cortex transcriptomes. Raw sequences from hepatic cells and cerebral cortex were assembled into 58,001 and 64,735 transcripts respectively. Functional annotation and polymorphism assignment of the assembled transcripts demonstrated a considerable level of variation in the core metabolic pathways that represent potential targets for selection pressure exerted by chemical toxicants. This study suggests that the brushtail possum population in New Zealand harbours considerable variation in metabolic pathways that could potentially promote the development of tolerance against chemical toxicants.
Collapse
Affiliation(s)
- Arsalan Emami-Khoyi
- Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Shilpa Pradeep Parbhu
- Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa
| | - James G Ross
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Elaine C Murphy
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Jennifer Bothwell
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Daniela M Monsanto
- Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa
| | - Bettine Jansen van Vuuren
- Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa
| | - Peter R Teske
- Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa
| | - Adrian M Paterson
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| |
Collapse
|
14
|
Colter BT, Garber HF, Fleming SM, Fowler JP, Harding GD, Hooven MK, Howes AA, Infante SK, Lang AL, MacDougall MC, Stegman M, Taylor KR, Curran CP. Ahr and Cyp1a2 genotypes both affect susceptibility to motor deficits following gestational and lactational exposure to polychlorinated biphenyls. Neurotoxicology 2019; 65:125-134. [PMID: 29409959 DOI: 10.1016/j.neuro.2018.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/16/2018] [Accepted: 01/21/2018] [Indexed: 02/04/2023]
Abstract
Polychlorinated biphenyls (PCBs) are persistent organic pollutants known to cause adverse health effects and linked to neurological deficits in both human and animal studies. Children born to exposed mothers are at highest risk of learning and memory and motor deficits. We developed a mouse model that mimics human variation in the aryl hydrocarbon receptor and cytochrome P450 1A2 (CYP1A2) to determine if genetic variation increases susceptibility to developmental PCB exposure. In our previous studies, we found that high-affinity AhrbCyp1a2(-/-) and poor-affinity AhrdCyp1a2(-/-) knockout mice were most susceptible to learning and memory deficits following developmental PCB exposure compared with AhrbCyp1a2(+/+) wild type mice (C57BL/6J strain). Our follow-up studies focused on motor deficits, because human studies have identified PCBs as a potential risk factor for Parkinson's disease. Dams were treated with an environmentally relevant PCB mixture at gestational day 10 and postnatal day 5. We used a motor battery that included tests of nigrostriatal function as well as cerebellar function, because PCBs deplete thyroid hormone, which is essential to normal cerebellar development. There was a significant effect of PCB treatment in the rotarod test with impaired performance in all three genotypes, but decreased motor learning as well in the two Cyp1a2(-/-) knockout lines. Interestingly, we found a main effect of genotype with corn oil-treated control Cyp1a2(-/-) mice performing significantly worse than Cyp1a2(+/+) wild type mice. In contrast, we found that PCB-treated high-affinity Ahrb mice were most susceptible to disruption of nigrostriatal function with the greatest deficits in AhrbCyp1a2(-/-) mice. We conclude that differences in AHR affinity combined with the absence of CYP1A2 protein affect susceptibility to motor deficits following developmental PCB exposure.
Collapse
Affiliation(s)
- Breann T Colter
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, 41076, USA
| | - Helen Frances Garber
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, 41076, USA
| | - Sheila M Fleming
- Department of Psychology and Neurology, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Jocelyn Phillips Fowler
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, 41076, USA
| | - Gregory D Harding
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, 41076, USA
| | - Molly Kromme Hooven
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, 41076, USA
| | - Amy Ashworth Howes
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, 41076, USA
| | - Smitha Krishnan Infante
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, 41076, USA
| | - Anna L Lang
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, 41076, USA
| | | | - Melinda Stegman
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, 41076, USA
| | - Kelsey Rae Taylor
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, 41076, USA
| | - Christine Perdan Curran
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, 41076, USA.
| |
Collapse
|
15
|
Driessen TM, Lee PJ, Lim J. Molecular pathway analysis towards understanding tissue vulnerability in spinocerebellar ataxia type 1. eLife 2018; 7:39981. [PMID: 30507379 PMCID: PMC6292693 DOI: 10.7554/elife.39981] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/02/2018] [Indexed: 12/13/2022] Open
Abstract
The neurodegenerative disorder spinocerebellar ataxia type 1 (SCA1) affects the cerebellum and inferior olive, though previous research has focused primarily on the cerebellum. As a result, it is unknown what molecular alterations are present in the inferior olive, and whether these changes are found in other affected tissues. This study addresses these questions for the first time using two different SCA1 mouse models. We found that differentially regulated genes in the inferior olive segregated into several biological pathways. Comparison of the inferior olive and cerebellum demonstrates that vulnerable tissues in SCA1 are not uniform in their gene expression changes, and express largely discrete but some commonly enriched biological pathways. Importantly, we also found that brain-region-specific differences occur early in disease initiation and progression, and they are shared across the two mouse models of SCA1. This suggests different mechanisms of degeneration at work in the inferior olive and cerebellum.
Collapse
Affiliation(s)
- Terri M Driessen
- Department of Genetics, Yale School of Medicine, New Haven, Unites States
| | - Paul J Lee
- Department of Genetics, Yale School of Medicine, New Haven, Unites States
| | - Janghoo Lim
- Department of Genetics, Yale School of Medicine, New Haven, Unites States.,Department of Neuroscience, Yale School of Medicine, New Haven, Unites States.,Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, Unites States
| |
Collapse
|
16
|
Abstract
The MAPK pathway is a prominent intracellular signaling pathway regulating various intracellular functions. Components of this pathway are mutated in a related collection of congenital syndromes collectively referred to as neuro-cardio-facio-cutaneous syndromes (NCFC) or Rasopathies. Recently, it has been appreciated that these disorders are associated with autism spectrum disorders (ASD). In addition, idiopathic ASD has also implicated the MAPK signaling cascade as a common pathway that is affected by many of the genetic variants that have been found to be linked to ASDs. This chapter describes the components of the MAPK pathway and how it is regulated. Furthermore, this chapter will highlight the various functions of the MAPK pathway during both embryonic development of the central nervous system (CNS) and its roles in neuronal physiology and ultimately, behavior. Finally, we will summarize the perturbations to MAPK signaling in various models of autism spectrum disorders and Rasopathies to highlight how dysregulation of this pivotal pathway may contribute to the pathogenesis of autism.
Collapse
|
17
|
Khan AM, Grant AH, Martinez A, Burns GAPC, Thatcher BS, Anekonda VT, Thompson BW, Roberts ZS, Moralejo DH, Blevins JE. Mapping Molecular Datasets Back to the Brain Regions They are Extracted from: Remembering the Native Countries of Hypothalamic Expatriates and Refugees. ADVANCES IN NEUROBIOLOGY 2018; 21:101-193. [PMID: 30334222 PMCID: PMC6310046 DOI: 10.1007/978-3-319-94593-4_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This article focuses on approaches to link transcriptomic, proteomic, and peptidomic datasets mined from brain tissue to the original locations within the brain that they are derived from using digital atlas mapping techniques. We use, as an example, the transcriptomic, proteomic and peptidomic analyses conducted in the mammalian hypothalamus. Following a brief historical overview, we highlight studies that have mined biochemical and molecular information from the hypothalamus and then lay out a strategy for how these data can be linked spatially to the mapped locations in a canonical brain atlas where the data come from, thereby allowing researchers to integrate these data with other datasets across multiple scales. A key methodology that enables atlas-based mapping of extracted datasets-laser-capture microdissection-is discussed in detail, with a view of how this technology is a bridge between systems biology and systems neuroscience.
Collapse
Affiliation(s)
- Arshad M Khan
- UTEP Systems Neuroscience Laboratory, University of Texas at El Paso, El Paso, TX, USA.
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA.
- Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, USA.
| | - Alice H Grant
- UTEP Systems Neuroscience Laboratory, University of Texas at El Paso, El Paso, TX, USA
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
- Graduate Program in Pathobiology, University of Texas at El Paso, El Paso, TX, USA
| | - Anais Martinez
- UTEP Systems Neuroscience Laboratory, University of Texas at El Paso, El Paso, TX, USA
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
- Graduate Program in Pathobiology, University of Texas at El Paso, El Paso, TX, USA
| | - Gully A P C Burns
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA, USA
| | - Brendan S Thatcher
- VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Vishwanath T Anekonda
- VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Benjamin W Thompson
- VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Zachary S Roberts
- VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Daniel H Moralejo
- Division of Neonatology, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - James E Blevins
- VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical Center, Seattle, WA, USA
- Division of Metabolism, Endocrinology, and Nutrition, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| |
Collapse
|
18
|
Lee HJ, Schneider RF, Manousaki T, Kang JH, Lein E, Franchini P, Meyer A. Lateralized Feeding Behavior is Associated with Asymmetrical Neuroanatomy and Lateralized Gene Expressions in the Brain in Scale-Eating Cichlid Fish. Genome Biol Evol 2017; 9:3122-3136. [PMID: 29069363 PMCID: PMC5737854 DOI: 10.1093/gbe/evx218] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2017] [Indexed: 12/20/2022] Open
Abstract
Lateralized behavior ("handedness") is unusual, but consistently found across diverse animal lineages, including humans. It is thought to reflect brain anatomical and/or functional asymmetries, but its neuro-molecular mechanisms remain largely unknown. Lake Tanganyika scale-eating cichlid fish, Perissodus microlepis show pronounced asymmetry in their jaw morphology as well as handedness in feeding behavior-biting scales preferentially only from one or the other side of their victims. This makes them an ideal model in which to investigate potential laterality in neuroanatomy and transcription in the brain in relation to behavioral handedness. After determining behavioral handedness in P. microlepis (preferred attack side), we estimated the volume of the hemispheres of brain regions and captured their gene expression profiles. Our analyses revealed that the degree of behavioral handedness is mirrored at the level of neuroanatomical asymmetry, particularly in the tectum opticum. Transcriptome analyses showed that different brain regions (tectum opticum, telencephalon, hypothalamus, and cerebellum) display distinct expression patterns, potentially reflecting their developmental interrelationships. For numerous genes in each brain region, their extent of expression differences between hemispheres was found to be correlated with the degree of behavioral lateralization. Interestingly, the tectum opticum and telencephalon showed divergent biases on the direction of up- or down-regulation of the laterality candidate genes (e.g., grm2) in the hemispheres, highlighting the connection of handedness with gene expression profiles and the different roles of these brain regions. Hence, handedness in predation behavior may be caused by asymmetric size of brain hemispheres and also by lateralized gene expressions in the brain.
Collapse
Affiliation(s)
- Hyuk Je Lee
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, Germany
- Present address: Molecular Ecology and Evolution Laboratory, Department of Biological Science, Sangji University, Wonju, Korea
| | - Ralf F Schneider
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, Germany
| | - Tereza Manousaki
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, Germany
- Present address: Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology, and Aquaculture (IMBBC), Heraklion, Greece
| | - Ji Hyoun Kang
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, Germany
- Present address: Korean Entomological Institute, Korea University, Seoul, Korea
| | - Etienne Lein
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, Germany
- Present address: Department of Collective Behaviour, Max Planck Institute for Ornithology and University of Konstanz, Konstanz, Germany
| | - Paolo Franchini
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, Germany
| |
Collapse
|
19
|
Pacheco NL, Heaven MR, Holt LM, Crossman DK, Boggio KJ, Shaffer SA, Flint DL, Olsen ML. RNA sequencing and proteomics approaches reveal novel deficits in the cortex of Mecp2-deficient mice, a model for Rett syndrome. Mol Autism 2017; 8:56. [PMID: 29090078 PMCID: PMC5655833 DOI: 10.1186/s13229-017-0174-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/02/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by mutations in the transcriptional regulator MeCP2. Much of our understanding of MeCP2 function is derived from transcriptomic studies with the general assumption that alterations in the transcriptome correlate with proteomic changes. Advances in mass spectrometry-based proteomics have facilitated recent interest in the examination of global protein expression to better understand the biology between transcriptional and translational regulation. METHODS We therefore performed the first comprehensive transcriptome-proteome comparison in a RTT mouse model to elucidate RTT pathophysiology, identify potential therapeutic targets, and further our understanding of MeCP2 function. The whole cortex of wild-type and symptomatic RTT male littermates (n = 4 per genotype) were analyzed using RNA-sequencing and data-independent acquisition liquid chromatography tandem mass spectrometry. Ingenuity® Pathway Analysis was used to identify significantly affected pathways in the transcriptomic and proteomic data sets. RESULTS Our results indicate these two "omics" data sets supplement one another. In addition to confirming previous works regarding mRNA expression in Mecp2-deficient animals, the current study identified hundreds of novel protein targets. Several selected protein targets were validated by Western blot analysis. These data indicate RNA metabolism, proteostasis, monoamine metabolism, and cholesterol synthesis are disrupted in the RTT proteome. Hits common to both data sets indicate disrupted cellular metabolism, calcium signaling, protein stability, DNA binding, and cytoskeletal cell structure. Finally, in addition to confirming disrupted pathways and identifying novel hits in neuronal structure and synaptic transmission, our data indicate aberrant myelination, inflammation, and vascular disruption. Intriguingly, there is no evidence of reactive gliosis, but instead, gene, protein, and pathway analysis suggest astrocytic maturation and morphological deficits. CONCLUSIONS This comparative omics analysis supports previous works indicating widespread CNS dysfunction and may serve as a valuable resource for those interested in cellular dysfunction in RTT.
Collapse
Affiliation(s)
- Natasha L. Pacheco
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd, Birmingham, AL 35294 USA
| | - Michael R. Heaven
- Vulcan Analytical, LLC, 1500 1st Ave. North, Birmingham, AL 35203 USA
| | - Leanne M. Holt
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd, Birmingham, AL 35294 USA
- School of Neuroscience, Virginia Polytechnic and State University, Life Sciences Building Room 213, 970 Washington St. SW, Blacksburg, VA 24061 USA
| | - David K. Crossman
- UAB Heflin Center for Genomic Science, Department of Genetics, University of Alabama at Birmingham, Kaul 424A, 1720 2nd Ave. South, Birmingham, AL 35294 USA
| | - Kristin J. Boggio
- Proteomics and Mass Spectrometry Facility, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 222 Maple Ave., Fuller Building, Shrewsbury, MA 01545 USA
| | - Scott A. Shaffer
- Proteomics and Mass Spectrometry Facility, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 222 Maple Ave., Fuller Building, Shrewsbury, MA 01545 USA
| | - Daniel L. Flint
- Luxumbra Strategic Research, LLC, 1331 South Eads St, Arlington, VA 22202 USA
| | - Michelle L. Olsen
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd, Birmingham, AL 35294 USA
- School of Neuroscience, Virginia Polytechnic and State University, Life Sciences Building Room 213, 970 Washington St. SW, Blacksburg, VA 24061 USA
| |
Collapse
|
20
|
Napoli E, Song G, Liu S, Espejo A, Perez CJ, Benavides F, Giulivi C. Zdhhc13-dependent Drp1 S-palmitoylation impacts brain bioenergetics, anxiety, coordination and motor skills. Sci Rep 2017; 7:12796. [PMID: 29038583 PMCID: PMC5643561 DOI: 10.1038/s41598-017-12889-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/14/2017] [Indexed: 01/14/2023] Open
Abstract
Protein S-palmitoylation is a reversible post-translational modification mediated by palmitoyl acyltransferase enzymes, a group of Zn2+-finger DHHC-domain-containing proteins (ZDHHC). Here, for the first time, we show that Zdhhc13 plays a key role in anxiety-related behaviors and motor function, as well as brain bioenergetics, in a mouse model (luc) carrying a spontaneous Zdhhc13 recessive mutation. At 3 m of age, mutant mice displayed increased sensorimotor gating, anxiety, hypoactivity, and decreased motor coordination, compared to littermate controls. Loss of Zdhhc13 in cortex and cerebellum from 3- and 24 m old hetero- and homozygous male mutant mice resulted in lower levels of Drp1 S-palmitoylation accompanied by altered mitochondrial dynamics, increased glycolysis, glutaminolysis and lactic acidosis, and neurotransmitter imbalances. Employing in vivo and in vitro models, we identified that Zdhhc13-dependent Drp1 S-palmitoylation, which acting alone or in concert, enables the normal occurrence of the fission-fusion process. In vitro and in vivo direct Zdhhc13-Drp1 protein interaction was observed, confirming Drp1 as a substrate of Zdhhc13. Abnormal fission-fusion processes result in disrupted mitochondria morphology and distribution affecting not only mitochondrial ATP output but neurotransmission and integrity of synaptic structures in the brain, setting the basis for the behavioral abnormalities described in the Zdhhc13-deficient mice.
Collapse
Affiliation(s)
- Eleonora Napoli
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Gyu Song
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Siming Liu
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Alexsandra Espejo
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, and The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, 77030, USA
| | - Carlos J Perez
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, and The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, 77030, USA
| | - Fernando Benavides
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, and The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, 77030, USA
| | - Cecilia Giulivi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, 95616, USA. .,Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, Davis, CA, 95817, USA.
| |
Collapse
|
21
|
Meyza KZ, Blanchard DC. The BTBR mouse model of idiopathic autism - Current view on mechanisms. Neurosci Biobehav Rev 2017; 76:99-110. [PMID: 28167097 DOI: 10.1016/j.neubiorev.2016.12.037] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/17/2016] [Accepted: 12/19/2016] [Indexed: 02/07/2023]
Abstract
Autism spectrum disorder (ASD) is the most commonly diagnosed neurodevelopmental disorder, with current estimates of more than 1% of affected children across nations. The patients form a highly heterogeneous group with only the behavioral phenotype in common. The genetic heterogeneity is reflected in a plethora of animal models representing multiple mutations found in families of affected children. Despite many years of scientific effort, for the majority of cases the genetic cause remains elusive. It is therefore crucial to include well-validated models of idiopathic autism in studies searching for potential therapeutic agents. One of these models is the BTBR T+Itpr3tf/J mouse. The current review summarizes data gathered in recent research on potential molecular mechanisms responsible for the autism-like behavioral phenotype of this strain.
Collapse
Affiliation(s)
- K Z Meyza
- Laboratory of Emotions' Neurobiology, Nencki Institute of Experimental Biology, 3 Pasteur Street, Warsaw, 02-093, Poland.
| | - D C Blanchard
- Department of Psychology, University of Hawaii at Manoa,1993 East-West Road, Honolulu, HI 96822, USA
| |
Collapse
|
22
|
Bruinenberg VM, van der Goot E, van Vliet D, de Groot MJ, Mazzola PN, Heiner-Fokkema MR, van Faassen M, van Spronsen FJ, van der Zee EA. The Behavioral Consequence of Phenylketonuria in Mice Depends on the Genetic Background. Front Behav Neurosci 2016; 10:233. [PMID: 28066199 PMCID: PMC5167755 DOI: 10.3389/fnbeh.2016.00233] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 11/28/2016] [Indexed: 12/31/2022] Open
Abstract
To unravel the role of gene mutations in the healthy and the diseased state, countless studies have tried to link genotype with phenotype. However, over the years, it became clear that the strain of mice can influence these results. Nevertheless, identical gene mutations in different strains are often still considered equals. An example of this, is the research done in phenylketonuria (PKU), an inheritable metabolic disorder. In this field, a PKU mouse model (either on a BTBR or C57Bl/6 background) is often used to examine underlying mechanisms of the disease and/or new treatment strategies. Both strains have a point mutation in the gene coding for the enzyme phenylalanine hydroxylase which causes toxic concentrations of the amino acid phenylalanine in blood and brain, as found in PKU patients. Although the mutation is identical and therefore assumed to equally affect physiology and behavior in both strains, no studies directly compared the two genetic backgrounds to test this assumption. Therefore, this study compared the BTBR and C57Bl/6 wild-type and PKU mice on PKU-relevant amino acid- and neurotransmitter-levels and at a behavioral level. The behavioral paradigms were selected from previous literature on the PKU mouse model and address four domains, namely (1) activity levels, (2) motor performance, (3) anxiety and/or depression-like behavior, and (4) learning and memory. The results of this study showed comparable biochemical changes in phenylalanine and neurotransmitter concentrations. In contrast, clear differences in behavioral outcome between the strains in all four above-mentioned domains were found, most notably in the learning and memory domain. The outcome in this domain seem to be primarily due to factors inherent to the genetic background of the mouse and much less by differences in PKU-specific biochemical parameters in blood and brain. The difference in behavioral outcome between PKU of both strains emphasizes that the consequence of the PAH mutation is influenced by other factors than Phe levels alone. Therefore, future research should consider these differences when choosing one of the genetic strains to investigate the pathophysiological mechanism underlying PKU-related behavior, especially when combined with new treatment strategies.
Collapse
Affiliation(s)
- Vibeke M Bruinenberg
- Molecular Neurobiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
| | - Els van der Goot
- Molecular Neurobiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
| | - Danique van Vliet
- Department of Pediatrics, Beatrix Children's Hospital, University Medical Center Groningen Groningen, Netherlands
| | - Martijn J de Groot
- Department of Pediatrics, Beatrix Children's Hospital, University Medical Center Groningen Groningen, Netherlands
| | - Priscila N Mazzola
- Molecular Neurobiology, Groningen Institute for Evolutionary Life Sciences, University of GroningenGroningen, Netherlands; Department of Pediatrics, Beatrix Children's Hospital, University Medical Center GroningenGroningen, Netherlands
| | | | - Martijn van Faassen
- Laboratory Medicine, University of Groningen, University Medical Center Groningen, Netherlands
| | - Francjan J van Spronsen
- Department of Pediatrics, Beatrix Children's Hospital, University Medical Center Groningen Groningen, Netherlands
| | - Eddy A van der Zee
- Molecular Neurobiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
| |
Collapse
|
23
|
Ficek J, Zygmunt M, Piechota M, Hoinkis D, Rodriguez Parkitna J, Przewlocki R, Korostynski M. Molecular profile of dissociative drug ketamine in relation to its rapid antidepressant action. BMC Genomics 2016; 17:362. [PMID: 27188165 PMCID: PMC4869301 DOI: 10.1186/s12864-016-2713-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 05/06/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The NMDA receptor antagonist ketamine was found to act as a fast-acting antidepressant. The effects of single treatment were reported to persist for days to weeks, even in otherwise treatment-refractory cases. Identification of the mechanisms underlying ketamine's antidepressant action may permit development of novel drugs, with similar clinical properties but lacking psychotomimetic, sedative and other side effects. METHODS We applied whole-genome microarray profiling to analyze detailed time-course (1, 2, 4 and 8 h) of transcriptome alterations in the striatum and hippocampus following acute administration of ketamine, memantine and phencyclidine in C57BL/6 J mice. The transcriptional effects of ketamine were further analyzed using next-generation sequencing and quantitative PCR. Gene expression alterations induced by the NMDA antagonists were compared to the molecular profiles of psychotropic drugs: antidepressants, antipsychotics, anxiolytics, psychostimulants and opioids. RESULTS We identified 52 transcripts (e.g. Dusp1, Per1 and Fkbp5) with altered expression (FDR < 1 %) in response to treatment with NMDA receptor antagonists. Functional links that connect expression of the regulated genes to the MAPK, IL-6 and insulin signaling pathways were indicated. Moreover, ketamine-regulated expression of specific gene isoforms was detected (e.g. Tsc22d3, Sgk1 and Hif3a). The comparison with other psychotropic drugs revealed that the molecular effects of ketamine are most similar to memantine and phencyclidine. Clustering based on expression profiles placed the NMDA antagonists among fluoxetine, tianeptine, as well as opioids and ethanol. CONCLUSIONS The identified patterns of gene expression alteration in the brain provided novel molecular classification of ketamine. The transcriptional profile of ketamine reflects its multi-target pharmacological nature. The results reveal similarities between the effects of ketamine and monoaminergic antidepressants that may explain the mechanisms of its rapid antidepressant action.
Collapse
Affiliation(s)
- Joanna Ficek
- Department of Molecular Neuropharmacology, Institute of Pharmacology PAS, Smetna 12, Krakow, 31-343, Poland
| | - Magdalena Zygmunt
- Department of Molecular Neuropharmacology, Institute of Pharmacology PAS, Smetna 12, Krakow, 31-343, Poland
| | - Marcin Piechota
- Department of Molecular Neuropharmacology, Institute of Pharmacology PAS, Smetna 12, Krakow, 31-343, Poland
| | - Dzesika Hoinkis
- Department of Molecular Neuropharmacology, Institute of Pharmacology PAS, Smetna 12, Krakow, 31-343, Poland
| | - Jan Rodriguez Parkitna
- Department of Molecular Neuropharmacology, Institute of Pharmacology PAS, Smetna 12, Krakow, 31-343, Poland
| | - Ryszard Przewlocki
- Department of Molecular Neuropharmacology, Institute of Pharmacology PAS, Smetna 12, Krakow, 31-343, Poland
| | - Michal Korostynski
- Department of Molecular Neuropharmacology, Institute of Pharmacology PAS, Smetna 12, Krakow, 31-343, Poland.
| |
Collapse
|
24
|
Loos M, Li KW, van der Schors R, Gouwenberg Y, van der Loo R, Williams RW, Smit AB, Spijker S. Impact of genetic variation on synaptic protein levels in genetically diverse mice. Proteomics 2016; 16:1123-30. [DOI: 10.1002/pmic.201500154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 12/07/2015] [Accepted: 01/13/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Maarten Loos
- Department of Molecular and Cellular Neurobiology; Center for Neurogenomics and Cognitive Research; Neuroscience Campus Amsterdam; VU University Amsterdam; Amsterdam The Netherlands
- Sylics (Synaptologics BV); Amsterdam The Netherlands
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology; Center for Neurogenomics and Cognitive Research; Neuroscience Campus Amsterdam; VU University Amsterdam; Amsterdam The Netherlands
| | - Roel van der Schors
- Department of Molecular and Cellular Neurobiology; Center for Neurogenomics and Cognitive Research; Neuroscience Campus Amsterdam; VU University Amsterdam; Amsterdam The Netherlands
| | - Yvonne Gouwenberg
- Department of Molecular and Cellular Neurobiology; Center for Neurogenomics and Cognitive Research; Neuroscience Campus Amsterdam; VU University Amsterdam; Amsterdam The Netherlands
| | - Rolinka van der Loo
- Department of Molecular and Cellular Neurobiology; Center for Neurogenomics and Cognitive Research; Neuroscience Campus Amsterdam; VU University Amsterdam; Amsterdam The Netherlands
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics; University of Tennessee Health Science Center; Memphis TN USA
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology; Center for Neurogenomics and Cognitive Research; Neuroscience Campus Amsterdam; VU University Amsterdam; Amsterdam The Netherlands
| | - Sabine Spijker
- Department of Molecular and Cellular Neurobiology; Center for Neurogenomics and Cognitive Research; Neuroscience Campus Amsterdam; VU University Amsterdam; Amsterdam The Netherlands
| |
Collapse
|
25
|
Daimon CM, Jasien JM, Wood WH, Zhang Y, Becker KG, Silverman JL, Crawley JN, Martin B, Maudsley S. Hippocampal Transcriptomic and Proteomic Alterations in the BTBR Mouse Model of Autism Spectrum Disorder. Front Physiol 2015; 6:324. [PMID: 26635614 PMCID: PMC4656818 DOI: 10.3389/fphys.2015.00324] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/27/2015] [Indexed: 12/25/2022] Open
Abstract
Autism spectrum disorders (ASD) are complex heterogeneous neurodevelopmental disorders of an unclear etiology, and no cure currently exists. Prior studies have demonstrated that the black and tan, brachyury (BTBR) T+ Itpr3tf/J mouse strain displays a behavioral phenotype with ASD-like features. BTBR T+ Itpr3tf/J mice (referred to simply as BTBR) display deficits in social functioning, lack of communication ability, and engagement in stereotyped behavior. Despite extensive behavioral phenotypic characterization, little is known about the genes and proteins responsible for the presentation of the ASD-like phenotype in the BTBR mouse model. In this study, we employed bioinformatics techniques to gain a wide-scale understanding of the transcriptomic and proteomic changes associated with the ASD-like phenotype in BTBR mice. We found a number of genes and proteins to be significantly altered in BTBR mice compared to C57BL/6J (B6) control mice controls such as BDNF, Shank3, and ERK1, which are highly relevant to prior investigations of ASD. Furthermore, we identified distinct functional pathways altered in BTBR mice compared to B6 controls that have been previously shown to be altered in both mouse models of ASD, some human clinical populations, and have been suggested as a possible etiological mechanism of ASD, including “axon guidance” and “regulation of actin cytoskeleton.” In addition, our wide-scale bioinformatics approach also discovered several previously unidentified genes and proteins associated with the ASD phenotype in BTBR mice, such as Caskin1, suggesting that bioinformatics could be an avenue by which novel therapeutic targets for ASD are uncovered. As a result, we believe that informed use of synergistic bioinformatics applications represents an invaluable tool for elucidating the etiology of complex disorders like ASD.
Collapse
Affiliation(s)
- Caitlin M Daimon
- Metabolism Unit, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - Joan M Jasien
- Metabolism Unit, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - William H Wood
- Gene Expression and Genomics Unit, National Institutes of Health Baltimore, MD, USA
| | - Yongqing Zhang
- Gene Expression and Genomics Unit, National Institutes of Health Baltimore, MD, USA
| | - Kevin G Becker
- Gene Expression and Genomics Unit, National Institutes of Health Baltimore, MD, USA
| | - Jill L Silverman
- Laboratory of Behavioral Neuroscience, Intramural Research Program, National Institute of Mental Health Bethesda, MD, USA ; MIND Institute, University of California Davis School of Medicine Sacramento, CA, USA
| | - Jacqueline N Crawley
- Laboratory of Behavioral Neuroscience, Intramural Research Program, National Institute of Mental Health Bethesda, MD, USA ; MIND Institute, University of California Davis School of Medicine Sacramento, CA, USA
| | - Bronwen Martin
- Metabolism Unit, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - Stuart Maudsley
- Receptor Pharmacology Unit, National Institute on Aging, National Institutes of Health Baltimore, MD, USA ; Translational Neurobiology Group, VIB Department of Molecular Genetics, University of Antwerp Antwerp, Belgium ; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp Antwerpen, Belgium
| |
Collapse
|
26
|
Ziats MN, Grosvenor LP, Rennert OM. Functional genomics of human brain development and implications for autism spectrum disorders. Transl Psychiatry 2015; 5:e665. [PMID: 26506051 PMCID: PMC4930130 DOI: 10.1038/tp.2015.153] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 09/03/2015] [Accepted: 09/06/2015] [Indexed: 12/13/2022] Open
Abstract
Transcription of the inherited DNA sequence into copies of messenger RNA is the most fundamental process by which the genome functions to guide development. Encoded sequence information, inherited epigenetic marks and environmental influences all converge at the level of mRNA gene expression to allow for cell-type-specific, tissue-specific, spatial and temporal patterns of expression. Thus, the transcriptome represents a complex interplay between inherited genomic structure, dynamic experiential demands and external signals. This property makes transcriptome studies uniquely positioned to provide insight into complex genetic-epigenetic-environmental processes such as human brain development, and disorders with non-Mendelian genetic etiologies such as autism spectrum disorders. In this review, we describe recent studies exploring the unique functional genomics profile of the human brain during neurodevelopment. We then highlight two emerging areas of research with great potential to increase our understanding of functional neurogenomics-non-coding RNA expression and gene interaction networks. Finally, we review previous functional genomics studies of autism spectrum disorder in this context, and discuss how investigations at the level of functional genomics are beginning to identify convergent molecular mechanisms underlying this genetically heterogeneous disorder.
Collapse
Affiliation(s)
- M N Ziats
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA,University of Cambridge, Robinson College, Cambridgeshire, UK,Baylor College of Medicine MSTP, One Baylor Plaza, Houston, TX, USA,Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Drive, Building 49, Room 2C08, Bethesda, MD 20814, USA. E-mail:
| | - L P Grosvenor
- Pediatrics and Developmental Neuroscience Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - O M Rennert
- Laboratory of Clinical and Developmental Genomics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
27
|
Jaeger C, Glaab E, Michelucci A, Binz TM, Koeglsberger S, Garcia P, Trezzi JP, Ghelfi J, Balling R, Buttini M. The mouse brain metabolome: region-specific signatures and response to excitotoxic neuronal injury. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:1699-712. [PMID: 25934215 DOI: 10.1016/j.ajpath.2015.02.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 02/04/2015] [Accepted: 02/10/2015] [Indexed: 11/26/2022]
Abstract
Neurodegeneration is a multistep process characterized by a multitude of molecular entities and their interactions. Systems analyses, or omics approaches, have become an important tool in characterizing this process. Although RNA and protein profiling made their entry into this field a couple of decades ago, metabolite profiling is a more recent addition. The metabolome represents a large part or all metabolites in a tissue, and gives a snapshot of its physiology. By using gas chromatography coupled to mass spectrometry, we analyzed the metabolic profile of brain regions of the mouse, and found that each region is characterized by its own metabolic signature. We then analyzed the metabolic profile of the mouse brain after excitotoxic injury, a mechanism of neurodegeneration implicated in numerous neurological diseases. More important, we validated our findings by measuring, histologically and molecularly, actual neurodegeneration and glial response. We found that a specific global metabolic signature, best revealed by machine learning algorithms, rather than individual metabolites, was the most robust correlate of neuronal injury and the accompanying gliosis, and this signature could serve as a global biomarker for neurodegeneration. We also observed that brain lesioning induced several metabolites with neuroprotective properties. Our results deepen the understanding of metabolic changes accompanying neurodegeneration in disease models, and could help rapidly evaluate these changes in preclinical drug studies.
Collapse
Affiliation(s)
- Christian Jaeger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alessandro Michelucci
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Tina M Binz
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sandra Koeglsberger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Pierre Garcia
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jean-Pierre Trezzi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jenny Ghelfi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| |
Collapse
|
28
|
Myers EM, Bartlett CW, Machiraju R, Bohland JW. An integrative analysis of regional gene expression profiles in the human brain. Methods 2015; 73:54-70. [DOI: 10.1016/j.ymeth.2014.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/27/2014] [Accepted: 12/06/2014] [Indexed: 10/24/2022] Open
|
29
|
Jasien JM, Daimon CM, Wang R, Shapiro BK, Martin B, Maudsley S. The effects of aging on the BTBR mouse model of autism spectrum disorder. Front Aging Neurosci 2014; 6:225. [PMID: 25225482 PMCID: PMC4150363 DOI: 10.3389/fnagi.2014.00225] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/08/2014] [Indexed: 01/11/2023] Open
Abstract
Autism spectrum disorder (ASD) is a complex heterogeneous neurodevelopmental disorder characterized by alterations in social functioning, communicative abilities, and engagement in repetitive or restrictive behaviors. The process of aging in individuals with autism and related neurodevelopmental disorders is not well understood, despite the fact that the number of individuals with ASD aged 65 and older is projected to increase by over half a million individuals in the next 20 years. To elucidate the effects of aging in the context of a modified central nervous system, we investigated the effects of age on the BTBR T + tf/j mouse, a well characterized and widely used mouse model that displays an ASD-like phenotype. We found that a reduction in social behavior persists into old age in male BTBR T + tf/j mice. We employed quantitative proteomics to discover potential alterations in signaling systems that could regulate aging in the BTBR mice. Unbiased proteomic analysis of hippocampal and cortical tissue of BTBR mice compared to age-matched wild-type controls revealed a significant decrease in brain derived neurotrophic factor and significant increases in multiple synaptic markers (spinophilin, Synapsin I, PSD 95, NeuN), as well as distinct changes in functional pathways related to these proteins, including “Neural synaptic plasticity regulation” and “Neurotransmitter secretion regulation.” Taken together, these results contribute to our understanding of the effects of aging on an ASD-like mouse model in regards to both behavior and protein alterations, though additional studies are needed to fully understand the complex interplay underlying aging in mouse models displaying an ASD-like phenotype.
Collapse
Affiliation(s)
- Joan M Jasien
- Metabolism Unit, Laboratory of Clinical Investigation, National Institutes of Health, National Institute on Aging Baltimore, MD, USA ; Department of Neurology, Johns Hopkins University School of Medicine, Kennedy Krieger Institute Baltimore, MD, USA
| | - Caitlin M Daimon
- Metabolism Unit, Laboratory of Clinical Investigation, National Institutes of Health, National Institute on Aging Baltimore, MD, USA
| | - Rui Wang
- Metabolism Unit, Laboratory of Clinical Investigation, National Institutes of Health, National Institute on Aging Baltimore, MD, USA
| | - Bruce K Shapiro
- Department of Neurology, Johns Hopkins University School of Medicine, Kennedy Krieger Institute Baltimore, MD, USA
| | - Bronwen Martin
- Metabolism Unit, Laboratory of Clinical Investigation, National Institutes of Health, National Institute on Aging Baltimore, MD, USA
| | - Stuart Maudsley
- Receptor Pharmacology Unit, Laboratory of Neurosciences, National Institute on Aging Baltimore, MD, USA ; VIB-Department of Molecular Genetics, University of Antwerp Antwerp, Belgium
| |
Collapse
|
30
|
Cendelin J, Tuma J, Korelusova I, Vozeh F. The effect of genetic background on behavioral manifestation of Grid2Lc mutation. Behav Brain Res 2014; 271:218-27. [DOI: 10.1016/j.bbr.2014.06.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 06/06/2014] [Accepted: 06/10/2014] [Indexed: 11/26/2022]
|
31
|
Martins EP, Bhat A. Population-level personalities in zebrafish: aggression-boldness across but not within populations. Behav Ecol 2014. [DOI: 10.1093/beheco/aru007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
|
32
|
Gene and MicroRNA transcriptome analysis of Parkinson's related LRRK2 mouse models. PLoS One 2014; 9:e85510. [PMID: 24427314 PMCID: PMC3888428 DOI: 10.1371/journal.pone.0085510] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/28/2013] [Indexed: 12/12/2022] Open
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most frequent cause of genetic Parkinson’s disease (PD). The biological function of LRRK2 and how mutations lead to disease remain poorly defined. It has been proposed that LRRK2 could function in gene transcription regulation; however, this issue remains controversial. Here, we investigated in parallel gene and microRNA (miRNA) transcriptome profiles of three different LRRK2 mouse models. Striatal tissue was isolated from adult LRRK2 knockout (KO) mice, as well as mice expressing human LRRK2 wildtype (hLRRK2-WT) or the PD-associated R1441G mutation (hLRRK2-R1441G). We identified a total of 761 genes and 24 miRNAs that were misregulated in the absence of LRRK2 when a false discovery rate of 0.2 was applied. Notably, most changes in gene expression were modest (i.e., <2 fold). By real-time quantitative RT-PCR, we confirmed the variations of selected genes (e.g., adra2, syt2, opalin) and miRNAs (e.g., miR-16, miR-25). Surprisingly, little or no changes in gene expression were observed in mice expressing hLRRK2-WT or hLRRK2-R1441G when compared to non-transgenic controls. Nevertheless, a number of miRNAs were misexpressed in these models. Bioinformatics analysis identified several miRNA-dependent and independent networks dysregulated in LRRK2-deficient mice, including PD-related pathways. These results suggest that brain LRRK2 plays an overall modest role in gene transcription regulation in mammals; however, these effects seem context and RNA type-dependent. Our data thus set the stage for future investigations regarding LRRK2 function in PD development.
Collapse
|
33
|
Abstract
Across animals, there is remarkable diversity in behavior. Modern genomic approaches have made it possible to identify the molecular underpinnings of varied behavioral phenotypes. By examining species with plastic phenotypes we have begun to understand the dynamic and flexible nature of neural transcriptomes and identified gene modules associated with variation in social and reproductive behaviors in diverse species. Importantly, it is becoming increasingly clear that some candidate genes and gene networks are involved in complex social behaviors across even divergent species, yet few comparative transcriptomics studies have been conducted that examine a specific behavior across species. We discuss the implications of a range of important and insightful studies that have increased our understanding of the neurogenomics of behavioral plasticity. Despite its successes, behavioral genomics has been criticized for its lack of hypotheses and causative insights. We propose here a novel avenue to overcome some of these short-comings by complementing "forward genomics" studies (i.e., from phenotype to behaviorally relevant gene modules) with a "reverse genomics" approach (i.e., manipulating novel gene modules to examine effects on behavior, hormones, and the genome itself) to examine the functional causes and consequences of differential gene expression patterns. We discuss how several established approaches (such as pharmacological manipulations of a novel candidate pathway, fine scale mapping of novel candidate gene expression in the brain, or identifying direct targets of a novel transcription factor of interest) can be used in combination with the analysis of the accompanying neurogenomic responses to reveal unexpected biological processes. The integration of forward and reverse genomics will move the field beyond statistical associations and yield great insights into the neural and molecular control of social behavior and its evolution.
Collapse
|
34
|
Callejón R, Nadler S, De Rojas M, Zurita A, Petrášová J, Cutillas C. Molecular characterization and phylogeny of whipworm nematodes inferred from DNA sequences of cox1 mtDNA and 18S rDNA. Parasitol Res 2013; 112:3933-49. [PMID: 24018707 DOI: 10.1007/s00436-013-3584-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 08/21/2013] [Indexed: 01/15/2023]
Abstract
A molecular phylogenetic hypothesis is presented for the genus Trichuris based on sequence data from the mitochondrial cytochrome c oxidase 1 (cox1) and ribosomal 18S genes. The taxa consisted of different described species and several host-associated isolates (undescribed taxa) of Trichuris collected from hosts from Spain. Sequence data from mitochondrial cox1 (partial gene) and nuclear 18S near-complete gene were analyzed by maximum likelihood and Bayesian inference methods, as separate and combined datasets, to evaluate phylogenetic relationships among taxa. Phylogenetic results based on 18S ribosomal DNA (rDNA) were robust for relationships among species; cox1 sequences delimited species and revealed phylogeographic variation, but most relationships among Trichuris species were poorly resolved by mitochondrial sequences. The phylogenetic hypotheses for both genes strongly supported monophyly of Trichuris, and distinct genetic lineages corresponding to described species or nematodes associated with certain hosts were recognized based on cox1 sequences. Phylogenetic reconstructions based on concatenated sequences of the two loci, cox1 (mitochondrial DNA (mtDNA)) and 18S rDNA, were congruent with the overall topology inferred from 18S and previously published results based on internal transcribed spacer sequences. Our results demonstrate that the 18S rDNA and cox1 mtDNA genes provide resolution at different levels, but together resolve relationships among geographic populations and species in the genus Trichuris.
Collapse
Affiliation(s)
- Rocío Callejón
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012, Seville, Spain
| | | | | | | | | | | |
Collapse
|
35
|
Qian Y, Chen M, Forssberg H, Diaz Heijtz R. Genetic variation in dopamine-related gene expression influences motor skill learning in mice. GENES BRAIN AND BEHAVIOR 2013; 12:604-14. [PMID: 23819855 DOI: 10.1111/gbb.12062] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 05/06/2013] [Accepted: 06/24/2013] [Indexed: 11/30/2022]
Abstract
Several neurodevelopmental disorders with a strong genetic basis, including attention-deficit/hyperactivity disorder, autism spectrum disorders and developmental coordination disorder, involve deficits in fine motor skills. This phenotype may depend on heritable variation in components of the dopamine (DA) system, which is known to play a critical role in motor skill learning. In this study, we took advantage of two inbred strains of mice (BALB/c and C57BL/6) that differ markedly in the number of midbrain DA neurons in order to investigate the influence of such naturally occurring genetic variation on the acquisition and performance of fine motor skills. Gene expression analysis of midbrain, frontal cortex and striatum showed significant differences in the expression of presynaptic and postsynaptic dopaminergic (DAergic) markers (e.g. tyrosine hydroxylase, DA transporter, DA D4 receptor, DA D5 receptor and DARPP-32) between these two strains. BALB/c mice had lower learning rate and performance scores in a complex skilled reaching task when compared with C57BL/6 mice. A negative correlation was found between the motor learning rate and level of DARPP-32 mRNA expression in the frontal cortex contralateral to the trained forelimb. The rate of motor learning was also negatively correlated with the levels of DARPP-32 and DA D1 receptor mRNAs in the striatum. Our results suggest that genetically driven variation in frontostriatal DAergic neurotransmission is a major contributor to individual differences in motor skill learning. Moreover, these findings implicate the D1R/cAMP/DARPP-32 signaling pathway in those neurodevelopmental disorders that are associated with fine motor skill deficits.
Collapse
Affiliation(s)
- Y Qian
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | | | | | | |
Collapse
|
36
|
Age-related changes of gene expression in the neocortex: preliminary data on RNA-Seq of the transcriptome in three functionally distinct cortical areas. Dev Psychopathol 2013; 24:1427-42. [PMID: 23062308 DOI: 10.1017/s0954579412000818] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The study of gene expression (i.e., the study of the transcriptome) in different cells and tissues allows us to understand the molecular mechanisms of their differentiation, development and functioning. In this article, we describe some studies of gene-expression profiling for the purposes of understanding developmental (age-related) changes in the brain using different technologies (e.g., DNA-Microarray) and the new and increasingly popular RNA-Seq. We focus on advancements in studies of gene expression in the human brain, which have provided data on the structure and age-related variability of the transcriptome in the brain. We present data on RNA-Seq of the transcriptome in three distinct areas of the neocortex from different ages: mature and elderly individuals. We report that most age-related transcriptional changes affect cellular signaling systems, and, as a result, the transmission of nerve impulses. In general, the results demonstrate the high potential of RNA-Seq for the study of distinctive features of gene expression among cortical areas and the changes in expression through normal and atypical development of the central nervous system.
Collapse
|
37
|
Matagne V, Budden S, Ojeda SR, Raber J. Correcting deregulated Fxyd1 expression ameliorates a behavioral impairment in a mouse model of Rett syndrome. Brain Res 2012; 1496:104-14. [PMID: 23246925 DOI: 10.1016/j.brainres.2012.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 11/12/2012] [Accepted: 12/08/2012] [Indexed: 12/29/2022]
Abstract
Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by mutations in the MECP2. Several genes have been shown to be MECP2 targets. We previously identified FXYD1 (encoding phospholemman; a protein containing the motif phenylalanine-X-tyrosine-aspartate), a gene encoding a transmembrane modulator of the Na, K-ATPase (NKA) enzyme, as one of them. In the absence of MECP2, FXYD1 expression is increased in the frontal cortex (FC) of both RTT patients and Mecp2(Bird) null mice. Here, we show that Fxyd1 mRNA levels are also increased in the FC and hippocampus (HC) of male mice carrying a truncating mutation of the Mecp2 gene (Mecp2(308)). To test the hypothesis that some of the behavioral phenotypes seen in these Mecp2 mutants could be ameliorated by genetically preventing the Fxyd1 response to MECP2 deficiency, we crossed Fxyd1 null male mice with Mecp2(308) heterozygous females and behaviorally tested the adult male offspring. Mecp2(308) mice had impaired HC-dependent novel location recognition, and this impairment was rescued by deletion of both Fxyd1 alleles. No other behavioral or sensorimotor impairments were rescued. These results indicate that reducing FXYD1 levels improves a specific cognitive impairment in MECP2-deficient mice.
Collapse
Affiliation(s)
- Valerie Matagne
- Division of Neuroscience, Oregon National Primate Research Center/Oregon Health & Science University, Beaverton, OR 97006, USA.
| | | | | | | |
Collapse
|
38
|
Naumova OY, Lee M, Rychkov SY, Vlasova NV, Grigorenko EL. Gene expression in the human brain: the current state of the study of specificity and spatiotemporal dynamics. Child Dev 2012; 84:76-88. [PMID: 23145569 DOI: 10.1111/cdev.12014] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Gene expression is one of the main molecular processes regulating the differentiation, development, and functioning of cells and tissues. In this review a handful of relevant terms and concepts are introduced and the most common techniques used in studies of gene expression/expression profiling (also referred to as studies of the transcriptome or transcriptomics) are described. The main foci of this review are the advancements in studies of the transcriptome in the human brain, the transcriptome's variability across different brain structures, and the systematic changes that occur through different developmental stages across the life span in general and childhood in particular. Finally, the question of how the accumulating data on the spatial and temporal dynamics of the transcriptome may shed light on the molecular mechanisms of the typical and atypical development of the central nervous system is addressed.
Collapse
|
39
|
Impact of experience-dependent and -independent factors on gene expression in songbird brain. Proc Natl Acad Sci U S A 2012; 109 Suppl 2:17245-52. [PMID: 23045667 DOI: 10.1073/pnas.1200655109] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Songbirds provide rich natural models for studying the relationships between brain anatomy, behavior, environmental signals, and gene expression. Under the Songbird Neurogenomics Initiative, investigators from 11 laboratories collected brain samples from six species of songbird under a range of experimental conditions, and 488 of these samples were analyzed systematically for gene expression by microarray. ANOVA was used to test 32 planned contrasts in the data, revealing the relative impact of different factors. The brain region from which tissue was taken had the greatest influence on gene expression profile, affecting the majority of signals measured by 18,848 cDNA spots on the microarray. Social and environmental manipulations had a highly variable impact, interpreted here as a manifestation of paradoxical "constitutive plasticity" (fewer inducible genes) during periods of enhanced behavioral responsiveness. Several specific genes were identified that may be important in the evolution of linkages between environmental signals and behavior. The data were also analyzed using weighted gene coexpression network analysis, followed by gene ontology analysis. This revealed modules of coexpressed genes that are also enriched for specific functional annotations, such as "ribosome" (expressed more highly in juvenile brain) and "dopamine metabolic process" (expressed more highly in striatal song control nucleus area X). These results underscore the complexity of influences on neural gene expression and provide a resource for studying how these influences are integrated during natural experience.
Collapse
|
40
|
Jeong J, Kim Y, Kyung Seong J, Lee KJ. Comprehensive identification of novel post-translational modifications in cellular peroxiredoxin 6. Proteomics 2012; 12:1452-62. [PMID: 22589192 DOI: 10.1002/pmic.201100558] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peroxiredoxin 6 (PRDX6), a 1-Cys peroxiredoxin, is a bifunctional enzyme acting both as a glutathione peroxidase and a phospholipase A2. However, the underlying mechanisms and their regulation mechanisms are not well understood. Because post-translational modifications (PTMs) have been shown to play important roles in the function of many proteins, we undertook, in this study, to identify the PTMs in PRDX6 utilizing proteomic tools including nanoUPLC-ESI-q-TOF MS/MS employing selectively excluded mass screening analysis (SEMSA) in conjunction with MOD(i) and MODmap algorithm. We chose PRDX6 obtained from liver tissues from two inbred mouse strains, C57BL/6J and C3H/HeJ, which vary in their susceptibility to high-fat diet-induced obesity and atherosclerosis, and a B16F10 melanoma cell line for this study. When PRDX6 protein samples were separated on 2D-PAGE based on pI, several PRDX6 spots appeared. They were purified and the low abundant PTMs in each PRDX6 spot were analyzed. Unexpected mass shifts (Δm = -34, +25, +64, +87, +103, +134, +150, +284 Da) observed at active site cysteine residue (Cys47) were quantified using precursor ion intensities. Mass differences of -34, +25, and +64 Da are presumed to reflect the conversion of cysteine to dehydroalanine, cyano, and Cys-SO(2) -SH, respectively. We also detected acrylamide adducts of sulfenic and sulfinic acids (+87 and +103 Da) as well as unknown modifications (+134, +150, +284 Da). Comprehensive analysis of these PTMs revealed that the PRDX6 exists as a heterogeneous mixture of molecules containing a multitude of PTMs. Several of these modifications occur at cysteine residue in the enzyme active site. Other modifications observed, in PRDX6 from mouse liver tissues included, among others, mono- and dioxidation at Trp and Met, acetylation at Lys, and deamidation at Asn and Gln. Comprehensive identification of the diverse PTMs occurring in this bifunctional PRDX6 enzyme should help understand how PRDX6 plays key roles in oxidative stresses.
Collapse
Affiliation(s)
- Jaeho Jeong
- The Center for Cell Signaling & Drug Discovery Research, College of Pharmacy, Division of Life & Pharmaceutical Sciences, Department of Bioinspired Science, Ewha Womans University, Seoul, Korea
| | | | | | | |
Collapse
|
41
|
Meyza KZ, Defensor EB, Jensen AL, Corley MJ, Pearson BL, Pobbe RLH, Bolivar VJ, Blanchard DC, Blanchard RJ. The BTBR T+ tf/J mouse model for autism spectrum disorders-in search of biomarkers. Behav Brain Res 2012; 251:25-34. [PMID: 22958973 DOI: 10.1016/j.bbr.2012.07.021] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/11/2012] [Accepted: 07/12/2012] [Indexed: 12/28/2022]
Abstract
Autism spectrum disorders (ASD) form a common group of neurodevelopmental disorders appearing to be under polygenic control, but also strongly influenced by multiple environmental factors. The brain mechanisms responsible for ASD are not understood and animal models paralleling related emotional and cognitive impairments may prove helpful in unraveling them. BTBR T+ tf/J (BTBR) mice display behaviors consistent with the three diagnostic categories for ASD. They show impaired social interaction and communication as well as increased repetitive behaviors. This review covers much of the data available to date on BTBR behavior, neuroanatomy and physiology in search for candidate biomarkers, which could both serve as diagnostic tools and help to design effective treatments for the behavioral symptoms of ASD.
Collapse
Affiliation(s)
- Ksenia Z Meyza
- Pacific Biosciences Research Center, University of Hawaii, 1993 East-west Road, Honolulu, HI 96822, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Transcriptome atlases of mouse brain reveals differential expression across brain regions and genetic backgrounds. G3-GENES GENOMES GENETICS 2012; 2:203-11. [PMID: 22384399 PMCID: PMC3284328 DOI: 10.1534/g3.111.001602] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 11/13/2011] [Indexed: 11/27/2022]
Abstract
Mouse models play a crucial role in the study of human behavioral traits and diseases. Variation of gene expression in brain may play a critical role in behavioral phenotypes, and thus it is of great importance to understand regulation of transcription in mouse brain. In this study, we analyzed the role of two important factors influencing steady-state transcriptional variation in mouse brain. First we considered the effect of assessing whole brain vs. discrete regions of the brain. Second, we investigated the genetic basis of strain effects on gene expression. We examined the transcriptome of three brain regions using Affymetrix expression arrays: whole brain, forebrain, and hindbrain in adult mice from two common inbred strains (C57BL/6J vs. NOD/ShiLtJ) with eight replicates for each brain region and strain combination. We observed significant differences between the transcriptomes of forebrain and hindbrain. In contrast, the transcriptomes of whole brain and forebrain were very similar. Using 4.3 million single-nucleotide polymorphisms identified through whole-genome sequencing of C57BL/6J and NOD/ShiLtJ strains, we investigated the relationship between strain effect in gene expression and DNA sequence similarity. We found that cis-regulatory effects play an important role in gene expression differences between strains and that the cis-regulatory elements are more often located in 5′ and/or 3′ transcript boundaries, with no apparent preference on either 5′ or 3′ ends.
Collapse
|
43
|
Hunsaker MR. Comprehensive neurocognitive endophenotyping strategies for mouse models of genetic disorders. Prog Neurobiol 2012; 96:220-41. [PMID: 22266125 PMCID: PMC3289520 DOI: 10.1016/j.pneurobio.2011.12.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 12/06/2011] [Accepted: 12/20/2011] [Indexed: 01/21/2023]
Abstract
There is a need for refinement of the current behavioral phenotyping methods for mouse models of genetic disorders. The current approach is to perform a behavioral screen using standardized tasks to define a broad phenotype of the model. This phenotype is then compared to what is known concerning the disorder being modeled. The weakness inherent in this approach is twofold: First, the tasks that make up these standard behavioral screens do not model specific behaviors associated with a given genetic mutation but rather phenotypes affected in various genetic disorders; secondly, these behavioral tasks are insufficiently sensitive to identify subtle phenotypes. An alternate phenotyping strategy is to determine the core behavioral phenotypes of the genetic disorder being studied and develop behavioral tasks to evaluate specific hypotheses concerning the behavioral consequences of the genetic mutation. This approach emphasizes direct comparisons between the mouse and human that facilitate the development of neurobehavioral biomarkers or quantitative outcome measures for studies of genetic disorders across species.
Collapse
Affiliation(s)
- Michael R Hunsaker
- Department of Neurological Surgery, University of California, Davis, Davis, CA 95616, USA.
| |
Collapse
|
44
|
Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2012. [PMID: 23195313 DOI: 10.1016/b978-0-12-398323-7.00005-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Postgenomic studies of the function of genes and their role in disease have now become an area of intense study since efforts to define the raw sequence material of the genome have largely been completed. The use of whole-genome approaches such as microarray expression profiling and, more recently, RNA-sequence analysis of transcript abundance has allowed an unprecedented look at the workings of the genome. However, the accurate derivation of such high-throughput data and their analysis in terms of biological function has been critical to truly leveraging the postgenomic revolution. This chapter will describe an approach that focuses on the use of gene networks to both organize and interpret genomic expression data. Such networks, derived from statistical analysis of large genomic datasets and the application of multiple bioinformatics data resources, potentially allow the identification of key control elements for networks associated with human disease, and thus may lead to derivation of novel therapeutic approaches. However, as discussed in this chapter, the leveraging of such networks cannot occur without a thorough understanding of the technical and statistical factors influencing the derivation of genomic expression data. Thus, while the catch phrase may be "it's the network … stupid," the understanding of factors extending from RNA isolation to genomic profiling technique, multivariate statistics, and bioinformatics are all critical to defining fully useful gene networks for study of complex biology.
Collapse
|
45
|
Barabas P, Huang W, Chen H, Koehler CL, Howell G, John SWM, Tian N, Rentería RC, Krizaj D. Missing optomotor head-turning reflex in the DBA/2J mouse. Invest Ophthalmol Vis Sci 2011; 52:6766-73. [PMID: 21757588 DOI: 10.1167/iovs.10-7147] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
PURPOSE The optomotor reflex of DBA/2J (D2), DBA/2J-Gpnmb+ (D2-Gpnmb+), and C57BL/6J (B6) mouse strains was assayed, and the retinal ganglion cell (RGC) firing patterns, direction selectivity, vestibulomotor function and central vision was compared between the D2 and B6 mouse lines. METHODS Intraocular pressure (IOP) measurements, real-time PCR, and immunohistochemical analysis were used to assess the time course of glaucomatous changes in D2 retinas. Behavioral analyses of optomotor head-turning reflex, visible platform Morris water maze and Rotarod measurements were conducted to test vision and vestibulomotor function. Electroretinogram (ERG) measurements were used to assay outer retinal function. The multielectrode array (MEA) technique was used to characterize RGC spiking and direction selectivity in D2 and B6 retinas. RESULTS Progressive increase in IOP and loss of Brn3a signals in D2 animals were consistent with glaucoma progression starting after 6 months of age. D2 mice showed no response to visual stimulation that evoked robust optomotor responses in B6 mice at any age after eye opening. Spatial frequency threshold was also not measurable in the D2-Gpnmb+ strain control. ERG a- and b-waves, central vision, vestibulomotor function, the spiking properties of ON, OFF, ON-OFF, and direction-selective RGCs were normal in young D2 mice. CONCLUSIONS The D2 strain is characterized by a lack of optomotor reflex before IOP elevation and RGC degeneration are observed. This behavioral deficit is D2 strain-specific, but is independent of retinal function and glaucoma. Caution is advised when using the optomotor reflex to follow glaucoma progression in D2 mice.
Collapse
Affiliation(s)
- Peter Barabas
- Department of Ophthalmology and Visual Sciences, John Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Kasukawa T, Masumoto KH, Nikaido I, Nagano M, Uno KD, Tsujino K, Hanashima C, Shigeyoshi Y, Ueda HR. Quantitative expression profile of distinct functional regions in the adult mouse brain. PLoS One 2011; 6:e23228. [PMID: 21858037 PMCID: PMC3155528 DOI: 10.1371/journal.pone.0023228] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 07/12/2011] [Indexed: 11/18/2022] Open
Abstract
The adult mammalian brain is composed of distinct regions with specialized roles including regulation of circadian clocks, feeding, sleep/awake, and seasonal rhythms. To find quantitative differences of expression among such various brain regions, we conducted the BrainStars (B*) project, in which we profiled the genome-wide expression of ∼50 small brain regions, including sensory centers, and centers for motion, time, memory, fear, and feeding. To avoid confounds from temporal differences in gene expression, we sampled each region every 4 hours for 24 hours, and pooled the samples for DNA-microarray assays. Therefore, we focused on spatial differences in gene expression. We used informatics to identify candidate genes with expression changes showing high or low expression in specific regions. We also identified candidate genes with stable expression across brain regions that can be used as new internal control genes, and ligand-receptor interactions of neurohormones and neurotransmitters. Through these analyses, we found 8,159 multi-state genes, 2,212 regional marker gene candidates for 44 small brain regions, 915 internal control gene candidates, and 23,864 inferred ligand-receptor interactions. We also found that these sets include well-known genes as well as novel candidate genes that might be related to specific functions in brain regions. We used our findings to develop an integrated database (http://brainstars.org/) for exploring genome-wide expression in the adult mouse brain, and have made this database openly accessible. These new resources will help accelerate the functional analysis of the mammalian brain and the elucidation of its regulatory network systems.
Collapse
Affiliation(s)
- Takeya Kasukawa
- Functional Genomics Unit, RIKEN Center for Developmental Biology, Kobe, Hyogo, Japan
| | - Koh-hei Masumoto
- Laboratory for Systems Biology, RIKEN Center for Developmental Biology, Kobe, Hyogo, Japan
- Department of Anatomy and Neurobiology, Kinki University School of Medicine, Osaka, Japan
| | - Itoshi Nikaido
- Functional Genomics Unit, RIKEN Center for Developmental Biology, Kobe, Hyogo, Japan
- Laboratory for Systems Biology, RIKEN Center for Developmental Biology, Kobe, Hyogo, Japan
| | - Mamoru Nagano
- Department of Anatomy and Neurobiology, Kinki University School of Medicine, Osaka, Japan
| | - Kenichiro D. Uno
- Functional Genomics Unit, RIKEN Center for Developmental Biology, Kobe, Hyogo, Japan
| | - Kaori Tsujino
- Laboratory for Systems Biology, RIKEN Center for Developmental Biology, Kobe, Hyogo, Japan
- Graduate School of Science, Osaka University, Osaka, Japan
| | - Carina Hanashima
- Laboratory for Neocortical Development, RIKEN Center for Developmental Biology, Hyogo, Japan
| | - Yasufumi Shigeyoshi
- Department of Anatomy and Neurobiology, Kinki University School of Medicine, Osaka, Japan
- * E-mail: (HRU); (YS)
| | - Hiroki R. Ueda
- Functional Genomics Unit, RIKEN Center for Developmental Biology, Kobe, Hyogo, Japan
- Laboratory for Systems Biology, RIKEN Center for Developmental Biology, Kobe, Hyogo, Japan
- Graduate School of Science, Osaka University, Osaka, Japan
- Department of Mathematics, Graduate School of Science, Kyoto University, Kyoto, Japan
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Kobe, Hyogo, Japan
- * E-mail: (HRU); (YS)
| |
Collapse
|
47
|
Bissonette GB, Powell EM. Reversal learning and attentional set-shifting in mice. Neuropharmacology 2011; 62:1168-74. [PMID: 21439304 DOI: 10.1016/j.neuropharm.2011.03.011] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 03/08/2011] [Accepted: 03/09/2011] [Indexed: 11/16/2022]
Abstract
Schizophrenia is a complex developmental disorder that presents challenges to modern neuroscience in terms of discovering etiology and aiding in effective treatment of afflicted humans. One approach is to divide the constellation of symptoms of human neuropsychiatric disorders into discrete units for study. Multiple animal models are used to study brain ontogeny, response to psychoactive compounds, substrates of defined behaviors. Frontal cortical areas have been found to have abnormal anatomy and neurotransmitter levels in postmortem brains from schizophrenic patients. The mouse model has the advantage of rather straightforward genetic manipulation and offers numerous genetic variations within the same species. However, until recently, the behavioral analyses in the mice lagged behind the primate and rat, especially with respect to testing of frontal cortical regions. Current reports of mouse prefrontal anatomy and function advocate the mouse as a feasible animal model to study prefrontal cortical function. This review highlights the most recent developments from behavioral paradigms for testing orbital and medial prefrontal cortical function in pharmacological and genetic models of human schizophrenia.
Collapse
Affiliation(s)
- Gregory B Bissonette
- Department of Anatomy & Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | |
Collapse
|
48
|
CNS animal fMRI in pain and analgesia. Neurosci Biobehav Rev 2010; 35:1125-43. [PMID: 21126534 DOI: 10.1016/j.neubiorev.2010.11.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 11/22/2010] [Accepted: 11/23/2010] [Indexed: 11/22/2022]
Abstract
Animal imaging of brain systems offers exciting opportunities to better understand the neurobiology of pain and analgesia. Overall functional studies have lagged behind human studies as a result of technical issues including the use of anesthesia. Now that many of these issues have been overcome including the possibility of imaging awake animals, there are new opportunities to study whole brain systems neurobiology of acute and chronic pain as well as analgesic effects on brain systems de novo (using pharmacological MRI) or testing in animal models of pain. Understanding brain networks in these areas may provide new insights into translational science, and use neural networks as a "language of translation" between preclinical to clinical models. In this review we evaluate the role of functional and anatomical imaging in furthering our understanding in pain and analgesia.
Collapse
|
49
|
Integrated genomics of susceptibility to alkylator-induced leukemia in mice. BMC Genomics 2010; 11:638. [PMID: 21080971 PMCID: PMC3018144 DOI: 10.1186/1471-2164-11-638] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 11/17/2010] [Indexed: 11/10/2022] Open
Abstract
Background Therapy-related acute myeloid leukemia (t-AML) is a secondary, generally incurable, malignancy attributable to chemotherapy exposure. Although there is a genetic component to t-AML susceptibility in mice, the relevant loci and the mechanism(s) by which they contribute to t-AML are largely unknown. An improved understanding of susceptibility factors and the biological processes in which they act may lead to the development of t-AML prevention strategies. Results In this work we applied an integrated genomics strategy in inbred strains of mice to find novel factors that might contribute to susceptibility. We found that the pre-exposure transcriptional state of hematopoietic stem/progenitor cells predicts susceptibility status. More than 900 genes were differentially expressed between susceptible and resistant strains and were highly enriched in the apoptotic program, but it remained unclear which genes, if any, contribute directly to t-AML susceptibility. To address this issue, we integrated gene expression data with genetic information, including single nucleotide polymorphisms (SNPs) and DNA copy number variants (CNVs), to identify genetic networks underlying t-AML susceptibility. The 30 t-AML susceptibility networks we found are robust: they were validated in independent, previously published expression data, and different analytical methods converge on them. Further, the networks are enriched in genes involved in cell cycle and DNA repair (pathways not discovered in traditional differential expression analysis), suggesting that these processes contribute to t-AML susceptibility. Within these networks, the putative regulators (e.g., Parp2, Casp9, Polr1b) are the most likely to have a non-redundant role in the pathogenesis of t-AML. While identifying these networks, we found that current CNVR and SNP-based haplotype maps in mice represented distinct sources of genetic variation contributing to expression variation, implying that mapping studies utilizing either source alone will have reduced sensitivity. Conclusion The identification and prioritization of genes and networks not previously implicated in t-AML generates novel hypotheses on the biology and treatment of this disease that will be the focus of future research.
Collapse
|
50
|
June HL, Tzeng Yang ARS, Bryant JL, Jones O, Royal W. Vitamin A deficiency and behavioral and motor deficits in the human immunodeficiency virus type 1 transgenic rat. J Neurovirol 2010; 15:380-9. [PMID: 19995129 DOI: 10.3109/13550280903350200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The human immunodeficiency virus type 1 (HIV-1) transgenic (Tg) rat model incorporates a noninfectious viral genome that is under similar regulatory control mechanisms in vivo as those that exist with natural infection in humans. Vitamin A (VA) deficiency in humans has been associated with progressive systemic HIV disease and with impaired cognition in rodent models. The effects on of VA deficiency on the development of behavioral abnormalities with HIV infection have not been previously described. In these studies, wild-type (Wt) and Tg rats maintained on either a normal (VA+) or a VA-deficient (VA-) diet were examined for activity in an open field (horizontal activity, total distance, vertical activity, and rearing) and on rotarod testing. On both open field and rotarod testing, the Tg rats performed worse than the Wt rats, with the most severe deficits noted in the TgVA- animals. Analysis of the specific effects of the presence of the HIV transgene and the diet on the performance on the open field tests showed a dominant effect from the transgene on all of the tests, with an effect from the diet on only the number of rearings. On rotarod testing, effects form both the diet and the transgene were observed at lower speeds, at the highest speeds, and on the accelerating rotarod. These studies therefore demonstrate that behavioral and motor abnormalities can be detected in this model and are likely due to similar mechanisms by which humans infected with HIV might develop cognitive-motor impairment in association with VA deficiency.
Collapse
Affiliation(s)
- Harry L June
- Department of Neurology, The University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | |
Collapse
|