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Thakur A, Yue G, Ahire D, Mettu VS, Al Maghribi A, Ford K, Peixoto L, Leeder JS, Prasad B. Sex and the Kidney Drug-Metabolizing Enzymes and Transporters: Are Preclinical Drug Disposition Data Translatable to Humans? Clin Pharmacol Ther 2024. [PMID: 38711199 DOI: 10.1002/cpt.3277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/06/2024] [Indexed: 05/08/2024]
Abstract
Cross-species differences in drug transport and metabolism are linked to poor translation of preclinical pharmacokinetic and toxicology data to humans, often resulting in the failure of new chemical entities (NCEs) during clinical drug development. Specifically, inaccurate prediction of renal clearance and renal accumulation of NCEs due to differential abundance of enzymes and transporters in kidneys can lead to differences in pharmacokinetics and toxicity between experimental animals and humans. We carried out liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based protein quantification of 78 membrane drug-metabolizing enzymes and transporters (DMETs) in the kidney membrane fractions of humans, rats, and mice for characterization of cross-species and sex-dependent differences. In general, majority of DMET proteins were higher in rodents than in humans. Significant cross-species differences were observed in 30 out of 33 membrane DMET proteins quantified in all three species. Although no significant sex-dependent differences were observed in humans, the abundance of 28 and 46 membrane proteins showed significant sex dependence in rats and mice, respectively. These cross-species and sex-dependent quantitative abundance data are valuable for gaining a mechanistic understanding of drug renal disposition and accumulation. Further, these data can also be integrated into systems pharmacology tools, such as physiologically based pharmacokinetic models, to enhance the interpretation of preclinical pharmacokinetic and toxicological data.
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Affiliation(s)
- Aarzoo Thakur
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington, USA
| | - Guihua Yue
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington, USA
| | - Deepak Ahire
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington, USA
| | - Vijaya S Mettu
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington, USA
| | - Abrar Al Maghribi
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA
| | - Kaitlyn Ford
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA
| | - Lucia Peixoto
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA
| | | | - Bhagwat Prasad
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington, USA
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2
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Ford K, Zuin E, Righelli D, Medina E, Schoch H, Singletary K, Muheim C, Frank MG, Hicks SC, Risso D, Peixoto L. A Global Transcriptional Atlas of the Effect of Sleep Deprivation in the Mouse Frontal Cortex. bioRxiv 2023:2023.11.28.569011. [PMID: 38076891 PMCID: PMC10705260 DOI: 10.1101/2023.11.28.569011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Sleep deprivation (SD) has negative effects on brain function. Sleep problems are prevalent in neurodevelopmental, neurodegenerative and psychiatric disorders. Thus, understanding the molecular consequences of SD is of fundamental importance in neuroscience. In this study, we present the first simultaneous bulk and single-nuclear (sn)RNA sequencing characterization of the effects of SD in the mouse frontal cortex. We show that SD predominantly affects glutamatergic neurons, specifically in layers 4 and 5, and produces isoform switching of thousands of transcripts. At both the global and cell-type specific level, SD has a large repressive effect on transcription, down-regulating thousands of genes and transcripts; underscoring the importance of accounting for the effects of sleep loss in transcriptome studies of brain function. As a resource we provide extensive characterizations of cell types, genes, transcripts and pathways affected by SD; as well as tutorials for data analysis.
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Affiliation(s)
- Kaitlyn Ford
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Elena Zuin
- Department of Biology, University of Padova, Italy
- Department of Statistical Sciences, University of Padova, Italy
| | - Dario Righelli
- Department of Statistical Sciences, University of Padova, Italy
| | - Elizabeth Medina
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Hannah Schoch
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Kristan Singletary
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Christine Muheim
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Marcos G Frank
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, MD, USA
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, Italy
| | - Lucia Peixoto
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center. Elson S. Floyd College of Medicine. Washington State University, Spokane, WA
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3
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Medina E, Peterson S, Ford K, Singletary K, Peixoto L. Critical periods and Autism Spectrum Disorders, a role for sleep. Neurobiol Sleep Circadian Rhythms 2023; 14:100088. [PMID: 36632570 PMCID: PMC9826922 DOI: 10.1016/j.nbscr.2022.100088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Brain development relies on both experience and genetically defined programs. Time windows where certain brain circuits are particularly receptive to external stimuli, resulting in heightened plasticity, are referred to as "critical periods". Sleep is thought to be essential for normal brain development. Importantly, studies have shown that sleep enhances critical period plasticity and promotes experience-dependent synaptic pruning in the developing mammalian brain. Therefore, normal plasticity during critical periods depends on sleep. Problems falling and staying asleep occur at a higher rate in Autism Spectrum Disorder (ASD) relative to typical development. In this review, we explore the potential link between sleep, critical period plasticity, and ASD. First, we review the importance of critical period plasticity in typical development and the role of sleep in this process. Next, we summarize the evidence linking ASD with deficits in synaptic plasticity in rodent models of high-confidence ASD gene candidates. We then show that the high-confidence rodent models of ASD that show sleep deficits also display plasticity deficits. Given how important sleep is for critical period plasticity, it is essential to understand the connections between synaptic plasticity, sleep, and brain development in ASD. However, studies investigating sleep or plasticity during critical periods in ASD mouse models are lacking. Therefore, we highlight an urgent need to consider developmental trajectory in studies of sleep and plasticity in neurodevelopmental disorders.
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Affiliation(s)
- Elizabeth Medina
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Sarah Peterson
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Kaitlyn Ford
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Kristan Singletary
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Lucia Peixoto
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
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4
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Muheim CM, Ford K, Medina E, Singletary K, Peixoto L, Frank MG. Ontogenesis of the molecular response to sleep loss. Neurobiol Sleep Circadian Rhythms 2023; 14:100092. [PMID: 37020466 PMCID: PMC10068260 DOI: 10.1016/j.nbscr.2023.100092] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
Sleep deprivation (SD) results in profound cellular and molecular changes in the adult mammalian brain. Some of these changes may result in, or aggravate, brain disease. However, little is known about how SD impacts gene expression in developing animals. We examined the transcriptional response in the prefrontal cortex (PFC) to SD across postnatal development in male mice. We used RNA sequencing to identify functional gene categories that were specifically impacted by SD. We find that SD has dramatically different effects on PFC genes depending on developmental age. Gene expression differences after SD fall into 3 categories: present at all ages (conserved), present when mature sleep homeostasis is first emerging, and those unique to certain ages. Developmentally conserved gene expression was limited to a few functional categories, including Wnt-signaling which suggests that this pathway is a core mechanism regulated by sleep. In younger ages, genes primarily related to growth and development are affected while changes in genes related to metabolism are specific to the effect of SD in adults.
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Muheim CM, Ford K, Medina E, Singletary K, Peixoto L, Frank MG. Ontogenesis of the molecular response to sleep loss. bioRxiv 2023:2023.01.16.524266. [PMID: 36712085 PMCID: PMC9882159 DOI: 10.1101/2023.01.16.524266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Sleep deprivation (SD) results in profound cellular and molecular changes in the adult mammalian brain. Some of these changes may result in, or aggravate, brain disease. However, little is known about how SD impacts gene expression in developing animals. We examined the transcriptional response in the prefrontal cortex (PFC) to SD across postnatal development in male mice. We used RNA sequencing to identify functional gene categories that were specifically impacted by SD. We find that SD has dramatically different effects on PFC genes depending on developmental age. Gene expression differences after SD fall into 3 categories: present at all ages (conserved), present when mature sleep homeostasis is first emerging, and those unique to certain ages in adults. Developmentally conserved gene expression was limited to a few functional categories, including Wnt-signaling which suggests that this pathway is a core mechanism regulated by sleep. In younger ages, genes primarily related to growth and development are affected while changes in genes related to metabolism are specific to the effect of SD in adults.
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Affiliation(s)
- Christine M. Muheim
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,WSU Health Sciences Spokane, Steve Gleason Institute for Neuroscience, 412 E. Spokane Falls Blvd., Spokane, WA 99202, USA
| | - Kaitlyn Ford
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA
| | - Elizabeth Medina
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA
| | - Kristan Singletary
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,WSU Health Sciences Spokane, Steve Gleason Institute for Neuroscience, 412 E. Spokane Falls Blvd., Spokane, WA 99202, USA
| | - Lucia Peixoto
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,Correspondence: & , Tel.: +01-509 368 6747
| | - Marcos G. Frank
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,WSU Health Sciences Spokane, Steve Gleason Institute for Neuroscience, 412 E. Spokane Falls Blvd., Spokane, WA 99202, USA,Correspondence: & , Tel.: +01-509 368 6747
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6
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Medina E, Schoch H, Ford K, Wintler T, Singletary KG, Peixoto L. Shank3 influences mammalian sleep development. J Neurosci Res 2022; 100:2174-2186. [PMID: 36056598 PMCID: PMC9588578 DOI: 10.1002/jnr.25119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 08/05/2022] [Accepted: 08/14/2022] [Indexed: 01/11/2023]
Abstract
Sleep problems are prevalent in autism spectrum disorder (ASD), can be observed before diagnosis, and are associated with increased restricted and repetitive behaviors. Therefore, sleep abnormalities may be a core feature of the disorder, but the developmental trajectory remains unknown. Animal models provide a unique opportunity to understand sleep ontogenesis in ASD. Previously we showed that adult mice with a truncation in the high-confidence ASD gene Shank3 (Shank3∆C ) recapitulate the clinical sleep phenotype. In this study we used longitudinal electro-encephalographic (EEG) recordings to define, for the first time, changes in sleep from weaning to young adulthood in an ASD mouse model. We show that Shank3∆C male mice sleep less overall throughout their lifespan, have increased rapid eye movement (REM) sleep early in life despite significantly reduced non-rapid eye movement (NREM) sleep, and have abnormal responses to increased sleep pressure that emerge during a specific developmental period. We demonstrate that the ability to fall asleep quickly in response to sleep loss develops normally between 24 and 30 days in mice. However, mutants are unable to reduce sleep latency after periods of prolonged waking and maintain the same response to sleep loss regardless of age. This phenomenon seems independent of homeostatic NREM sleep slow-wave dynamics. Overall, our study recapitulates both preclinical models and clinical studies showing that reduced sleep is consistently associated with ASD and suggests that problems falling asleep may reflect abnormal development of sleep and arousal mechanisms.
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Affiliation(s)
- Elizabeth Medina
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of MedicineWashington State UniversitySpokaneWashingtonUSA
| | - Hannah Schoch
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of MedicineWashington State UniversitySpokaneWashingtonUSA
| | - Kaitlyn Ford
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of MedicineWashington State UniversitySpokaneWashingtonUSA
| | - Taylor Wintler
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of MedicineWashington State UniversitySpokaneWashingtonUSA
| | - Kristan G. Singletary
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of MedicineWashington State UniversitySpokaneWashingtonUSA
| | - Lucia Peixoto
- Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of MedicineWashington State UniversitySpokaneWashingtonUSA
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7
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Wintler T, Schoch H, Frank M, Peixoto L. Sleep, brain development, and autism spectrum disorders: Insights from animal models. J Neurosci Res 2020; 98:1137-1149. [PMID: 32215963 PMCID: PMC7199437 DOI: 10.1002/jnr.24619] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/07/2020] [Accepted: 02/29/2020] [Indexed: 01/28/2023]
Abstract
Sleep is an evolutionarily conserved and powerful drive, although its complete functions are still unknown. One possible function of sleep is that it promotes brain development. The amount of sleep is greatest during ages when the brain is rapidly developing, and sleep has been shown to influence critical period plasticity. This supports a role for sleep in brain development and suggests that abnormal sleep in early life may lead to abnormal development. Autism spectrum disorder (ASD) is the most prevalent neurodevelopmental disorder in the United States. It is estimated that insomnia affects 44%-86% of the ASD population, predicting the severity of ASD core symptoms and associated behavioral problems. Sleep problems impact the quality of life of both ASD individuals and their caregivers, thus it is important to understand why they are so prevalent. In this review, we explore the role of sleep in early life as a causal factor in ASD. First, we review fundamental steps in mammalian sleep ontogeny and regulation and how sleep influences brain development. Next, we summarize current knowledge gained from studying sleep in animal models of ASD. Ultimately, our goal is to highlight the importance of understanding the role of sleep in brain development and the use of animal models to provide mechanistic insight into the origin of sleep problems in ASD.
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Affiliation(s)
- Taylor Wintler
- Washington State University Elson S Floyd College of Medicine, Biomedical Sciences Spokane, WA, 99202USA
| | - Hannah Schoch
- Washington State University Elson S Floyd College of Medicine, Biomedical Sciences Spokane, WA, 99202USA
| | - Marcos Frank
- Washington State University Elson S Floyd College of Medicine, Biomedical Sciences Spokane, WA, 99202USA
| | - Lucia Peixoto
- Washington State University Elson S Floyd College of Medicine, Biomedical Sciences Spokane, WA, 99202USA
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8
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Ingiosi AM, Schoch H, Wintler T, Singletary KG, Righelli D, Roser LG, Medina E, Risso D, Frank MG, Peixoto L. Shank3 modulates sleep and expression of circadian transcription factors. eLife 2019; 8:e42819. [PMID: 30973326 PMCID: PMC6488297 DOI: 10.7554/elife.42819] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 04/10/2019] [Indexed: 12/30/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is the most prevalent neurodevelopmental disorder in the United States and often co-presents with sleep problems. Sleep problems in ASD predict the severity of ASD core diagnostic symptoms and have a considerable impact on the quality of life of caregivers. Little is known, however, about the underlying molecular mechanisms of sleep problems in ASD. We investigated the role of Shank3, a high confidence ASD gene candidate, in sleep architecture and regulation. We show that mice lacking exon 21 of Shank3 have problems falling asleep even when sleepy. Using RNA-seq we show that sleep deprivation increases the differences in prefrontal cortex gene expression between mutants and wild types, downregulating circadian transcription factors Per3, Bhlhe41, Hlf, Tef, and Nr1d1. Shank3 mutants also have trouble regulating wheel-running activity in constant darkness. Overall, our study shows that Shank3 is an important modulator of sleep and clock gene expression.
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Affiliation(s)
- Ashley M Ingiosi
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Hannah Schoch
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Taylor Wintler
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Kristan G Singletary
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Dario Righelli
- Istituto per le Applicazioni del Calcolo “M. Picone”Consiglio Nazionale della RicercheNapoliItaly
- Dipartimento di Scienze Aziendali Management & Innovation SystemsUniversity of FuscianoFiscianoItaly
| | - Leandro G Roser
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Elizabeth Medina
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Davide Risso
- Department of Statistical SciencesUniversity of PadovaPadovaItaly
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and ResearchWeill Cornell MedicineNew YorkUnited States
| | - Marcos G Frank
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
| | - Lucia Peixoto
- Department of Biomedical Sciences, Elson S. Floyd College of MedicineWashington State UniversitySpokaneUnited States
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9
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Koberstein JN, Poplawski SG, Wimmer ME, Porcari G, Kao C, Gomes B, Risso D, Hakonarson H, Zhang NR, Schultz RT, Abel T, Peixoto L. Learning-dependent chromatin remodeling highlights noncoding regulatory regions linked to autism. Sci Signal 2018; 11:11/513/eaan6500. [PMID: 29339533 DOI: 10.1126/scisignal.aan6500] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Autism spectrum disorder (ASD) is a prevalent neurodevelopmental disorder that is associated with genetic risk factors. Most human disease-associated single-nucleotide polymorphisms (SNPs) are not located in genes but rather are in regulatory regions that control gene expression. The function of regulatory regions is determined through epigenetic mechanisms. Parallels between the cellular basis of development and the formation of long-term memory have long been recognized, particularly the role of epigenetic mechanisms in both processes. We analyzed how learning alters chromatin accessibility in the mouse hippocampus using a new high-throughput sequencing bioinformatics strategy we call DEScan (differential enrichment scan). DEScan, which enabled the analysis of data from epigenomic experiments containing multiple replicates, revealed changes in chromatin accessibility at 2365 regulatory regions-most of which were promoters. Learning-regulated promoters were active during forebrain development in mice and were enriched in epigenetic modifications indicative of bivalent promoters. These promoters were disproportionally intronic, showed a complex relationship with gene expression and alternative splicing during memory consolidation and retrieval, and were enriched in the data set relative to known ASD risk genes. Genotyping in a clinical cohort within one of these promoters (SHANK3 promoter 6) revealed that the SNP rs6010065 was associated with ASD. Our data support the idea that learning recapitulates development at the epigenetic level and demonstrate that behaviorally induced epigenetic changes in mice can highlight regulatory regions relevant to brain disorders in patients.
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Affiliation(s)
- John N Koberstein
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine. Washington State University, Spokane, WA 99202, USA
| | | | - Mathieu E Wimmer
- Department of Psychology and Program in Neuroscience, College of Liberal Arts, Temple University, Philadelphia, PA 19122, USA
| | - Giulia Porcari
- Vanderbilt University Medical School, Nashville, TN 37232, USA
| | - Charlly Kao
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medicine, New York, NY 10065, USA
| | - Bruce Gomes
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine. Washington State University, Spokane, WA 99202, USA
| | - Davide Risso
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medicine, New York, NY 10065, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nancy R Zhang
- Department of Statistics, Wharton School, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert T Schultz
- Center for Autism Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ted Abel
- Iowa Neuroscience Institute, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Lucia Peixoto
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine. Washington State University, Spokane, WA 99202, USA.
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10
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Park AJ, Havekes R, Fu X, Hansen R, Tudor JC, Peixoto L, Li Z, Wu YC, Poplawski SG, Baraban JM, Abel T. Learning induces the translin/trax RNase complex to express activin receptors for persistent memory. eLife 2017; 6. [PMID: 28927503 PMCID: PMC5606845 DOI: 10.7554/elife.27872] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/01/2017] [Indexed: 12/16/2022] Open
Abstract
Long-lasting forms of synaptic plasticity and memory require de novo protein synthesis. Yet, how learning triggers this process to form memory is unclear. Translin/trax is a candidate to drive this learning-induced memory mechanism by suppressing microRNA-mediated translational silencing at activated synapses. We find that mice lacking translin/trax display defects in synaptic tagging, which requires protein synthesis at activated synapses, and long-term memory. Hippocampal samples harvested from these mice following learning show increases in several disease-related microRNAs targeting the activin A receptor type 1C (ACVR1C), a component of the transforming growth factor-β receptor superfamily. Furthermore, the absence of translin/trax abolishes synaptic upregulation of ACVR1C protein after learning. Finally, synaptic tagging and long-term memory deficits in mice lacking translin/trax are mimicked by ACVR1C inhibition. Thus, we define a new memory mechanism by which learning reverses microRNA-mediated silencing of the novel plasticity protein ACVR1C via translin/trax.
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Affiliation(s)
- Alan Jung Park
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Robbert Havekes
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Xiuping Fu
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, United States
| | - Rolf Hansen
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Jennifer C Tudor
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Lucia Peixoto
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Zhi Li
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, United States
| | - Yen-Ching Wu
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, United States
| | - Shane G Poplawski
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Jay M Baraban
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, United States
| | - Ted Abel
- Department of Biology, University of Pennsylvania, Philadelphia, United States.,Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
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11
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Gerstner JR, Koberstein JN, Watson AJ, Zapero N, Risso D, Speed TP, Frank MG, Peixoto L. Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex. BMC Genomics 2016; 17:727. [PMID: 27801296 PMCID: PMC5088519 DOI: 10.1186/s12864-016-3065-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Why we sleep is still one of the most perplexing mysteries in biology. Strong evidence indicates that sleep is necessary for normal brain function and that sleep need is a tightly regulated process. Surprisingly, molecular mechanisms that determine sleep need are incompletely described. Moreover, very little is known about transcriptional changes that specifically accompany the accumulation and discharge of sleep need. Several studies have characterized differential gene expression changes following sleep deprivation. Much less is known, however, about changes in gene expression during the compensatory response to sleep deprivation (i.e. recovery sleep). RESULTS In this study we present a comprehensive analysis of the effects of sleep deprivation and subsequent recovery sleep on gene expression in the mouse cortex. We used a non-traditional analytical method for normalization of genome-wide gene expression data, Removal of Unwanted Variation (RUV). RUV improves detection of differential gene expression following sleep deprivation. We also show that RUV normalization is crucial to the discovery of differentially expressed genes associated with recovery sleep. Our analysis indicates that the majority of transcripts upregulated by sleep deprivation require 6 h of recovery sleep to return to baseline levels, while the majority of downregulated transcripts return to baseline levels within 1-3 h. We also find that transcripts that change rapidly during recovery (i.e. within 3 h) do so on average with a time constant that is similar to the time constant for the discharge of sleep need. CONCLUSIONS We demonstrate that proper data normalization is essential to identify changes in gene expression that are specifically linked to sleep deprivation and recovery sleep. Our results provide the first evidence that recovery sleep is comprised of two waves of transcriptional regulation that occur at different times and affect functionally distinct classes of genes.
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Affiliation(s)
- Jason R Gerstner
- Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA
| | - John N Koberstein
- Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA
| | - Adam J Watson
- Department of Neuroscience, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nikolai Zapero
- Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA
| | - Davide Risso
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Terence P Speed
- Department of Statistics, University of California, Berkeley, CA, USA.,Department of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Marcos G Frank
- Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA.
| | - Lucia Peixoto
- Washington State University, Elson S. Floyd College of Medicine, Spokane, WA, 99202, USA.
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12
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Poplawski SG, Peixoto L, Porcari GS, Wimmer ME, McNally AG, Mizuno K, Giese KP, Chatterjee S, Koberstein JN, Risso D, Speed TP, Abel T. Contextual fear conditioning induces differential alternative splicing. Neurobiol Learn Mem 2016; 134 Pt B:221-35. [PMID: 27451143 DOI: 10.1016/j.nlm.2016.07.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 07/16/2016] [Accepted: 07/19/2016] [Indexed: 12/20/2022]
Abstract
The process of memory consolidation requires transcription and translation to form long-term memories. Significant effort has been dedicated to understanding changes in hippocampal gene expression after contextual fear conditioning. However, alternative splicing by differential transcript regulation during this time period has received less attention. Here, we use RNA-seq to determine exon-level changes in expression after contextual fear conditioning and retrieval. Our work reveals that a short variant of Homer1, Ania-3, is regulated by contextual fear conditioning. The ribosome biogenesis regulator Las1l, small nucleolar RNA Snord14e, and the RNA-binding protein Rbm3 also change specific transcript usage after fear conditioning. The changes in Ania-3 and Las1l are specific to either the new context or the context-shock association, while the changes in Rbm3 occur after context or shock only. Our analysis revealed novel transcript regulation of previously undetected changes after learning, revealing the importance of high throughput sequencing approaches in the study of gene expression changes after learning.
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Affiliation(s)
- Shane G Poplawski
- Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Lucia Peixoto
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA; Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Giulia S Porcari
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Mathieu E Wimmer
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Anna G McNally
- Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Keiko Mizuno
- Centre for the Cellular Basis of Behaviour, King's College London, London, UK
| | - K Peter Giese
- Centre for the Cellular Basis of Behaviour, King's College London, London, UK
| | | | - John N Koberstein
- Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Davide Risso
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
| | - Terence P Speed
- Department of Statistics, University of California, Berkeley, CA, USA; Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Mathematics and Statistics, The University of Melbourne, Victoria, Australia
| | - Ted Abel
- Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
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13
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Tudor JC, Davis EJ, Peixoto L, Wimmer ME, van Tilborg E, Park AJ, Poplawski SG, Chung CW, Havekes R, Huang J, Gatti E, Pierre P, Abel T. Sleep deprivation impairs memory by attenuating mTORC1-dependent protein synthesis. Sci Signal 2016; 9:ra41. [PMID: 27117251 DOI: 10.1126/scisignal.aad4949] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Sleep deprivation is a public health epidemic that causes wide-ranging deleterious consequences, including impaired memory and cognition. Protein synthesis in hippocampal neurons promotes memory and cognition. The kinase complex mammalian target of rapamycin complex 1 (mTORC1) stimulates protein synthesis by phosphorylating and inhibiting the eukaryotic translation initiation factor 4E-binding protein 2 (4EBP2). We investigated the involvement of the mTORC1-4EBP2 axis in the molecular mechanisms mediating the cognitive deficits caused by sleep deprivation in mice. Using an in vivo protein translation assay, we found that loss of sleep impaired protein synthesis in the hippocampus. Five hours of sleep loss attenuated both mTORC1-mediated phosphorylation of 4EBP2 and the interaction between eukaryotic initiation factor 4E (eIF4E) and eIF4G in the hippocampi of sleep-deprived mice. Increasing the abundance of 4EBP2 in hippocampal excitatory neurons before sleep deprivation increased the abundance of phosphorylated 4EBP2, restored the amount of eIF4E-eIF4G interaction and hippocampal protein synthesis to that seen in mice that were not sleep-deprived, and prevented the hippocampus-dependent memory deficits associated with sleep loss. These findings collectively demonstrate that 4EBP2-regulated protein synthesis is a critical mediator of the memory deficits caused by sleep deprivation.
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Affiliation(s)
- Jennifer C Tudor
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emily J Davis
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lucia Peixoto
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mathieu E Wimmer
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erik van Tilborg
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alan J Park
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shane G Poplawski
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Caroline W Chung
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robbert Havekes
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jiayan Huang
- Global Statistical Science, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Evelina Gatti
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, INSERM U1104, CNRS UMR7280, 13288 Marseille, France. Institute for Research in Biomedicine (iBiMED) and Aveiro Health Sciences Program, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Philippe Pierre
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, INSERM U1104, CNRS UMR7280, 13288 Marseille, France. Institute for Research in Biomedicine (iBiMED) and Aveiro Health Sciences Program, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ted Abel
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA.
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14
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Chen RJ, Kelly G, Sengupta A, Heydendael W, Nicholas B, Beltrami S, Luz S, Peixoto L, Abel T, Bhatnagar S. MicroRNAs as biomarkers of resilience or vulnerability to stress. Neuroscience 2015. [PMID: 26208845 DOI: 10.1016/j.neuroscience.2015.07.045] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Identifying novel biomarkers of resilience or vulnerability to stress could provide valuable information for the prevention and treatment of stress-related psychiatric disorders. To investigate the utility of blood microRNAs as biomarkers of resilience or vulnerability to stress, microRNAs were assessed before and after 7days of chronic social defeat in rats. Additionally, microRNA profiles of two important stress-regulatory brain regions, the medial prefrontal cortex (mPFC) and basolateral amygdala (BLA), were assessed. Rats that displayed vulnerability to subsequent chronic stress exhibited reductions in circulating miR-24-2-5p, miR-27a-3p, miR-30e-5p, miR-3590-3p, miR-362-3p, and miR-532-5p levels. In contrast, rats that became resilient to stress displayed reduced levels of miR-139-5p, miR-28-3p, miR-326-3p, and miR-99b-5p compared to controls. In the mPFC, miR-126a-3p and miR-708-5p levels were higher in vulnerability compared to resilient rats. In the BLA, 77 microRNAs were significantly altered by stress but none were significantly different between resilient and vulnerable animals. These results provide proof-of-principle that assessment of circulating microRNAs is useful in identifying individuals who are vulnerable to the effects of future stress or individuals who have become resilient to the effects of stress. Furthermore, these data suggest that microRNAs in the mPFC but not in the BLA are regulators of resilience/vulnerability to stress.
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Affiliation(s)
- R J Chen
- Department of Anesthesiology, Children's Hospital of Philadelphia, United States
| | - G Kelly
- Department of Anesthesiology, Children's Hospital of Philadelphia, United States
| | - A Sengupta
- Department of Anesthesiology, Children's Hospital of Philadelphia, United States
| | - W Heydendael
- Department of Anesthesiology, Children's Hospital of Philadelphia, United States
| | - B Nicholas
- Department of Anesthesiology, Children's Hospital of Philadelphia, United States
| | - S Beltrami
- Department of Anesthesiology, Children's Hospital of Philadelphia, United States
| | - S Luz
- Department of Anesthesiology, Children's Hospital of Philadelphia, United States
| | - L Peixoto
- Department of Biology, University of Pennsylvania, United States
| | - T Abel
- Department of Biology, University of Pennsylvania, United States
| | - S Bhatnagar
- Department of Anesthesiology, Children's Hospital of Philadelphia, United States; Department of Anesthesiology, University of Pennsylvania, Perelman School of Medicine, United States.
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15
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Peixoto L, Risso D, Poplawski SG, Wimmer ME, Speed TP, Wood MA, Abel T. How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets. Nucleic Acids Res 2015. [PMID: 26202970 PMCID: PMC4652761 DOI: 10.1093/nar/gkv736] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The sequencing of the full transcriptome (RNA-seq) has become the preferred choice for the measurement of genome-wide gene expression. Despite its widespread use, challenges remain in RNA-seq data analysis. One often-overlooked aspect is normalization. Despite the fact that a variety of factors or ‘batch effects’ can contribute unwanted variation to the data, commonly used RNA-seq normalization methods only correct for sequencing depth. The study of gene expression is particularly problematic when it is influenced simultaneously by a variety of biological factors in addition to the one of interest. Using examples from experimental neuroscience, we show that batch effects can dominate the signal of interest; and that the choice of normalization method affects the power and reproducibility of the results. While commonly used global normalization methods are not able to adequately normalize the data, more recently developed RNA-seq normalization can. We focus on one particular method, RUVSeq and show that it is able to increase power and biological insight of the results. Finally, we provide a tutorial outlining the implementation of RUVSeq normalization that is applicable to a broad range of studies as well as meta-analysis of publicly available data.
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Affiliation(s)
- Lucia Peixoto
- Department of Biology, University of Pennsylvania, Smilow Center for Translational Research, Room 10-170, Building 421, 3400 Civic Center Boulevard, Philadelphia, PA 19104-6168, USA
| | - Davide Risso
- Division of Biostatistics, School of Public Health, University of California, Berkeley, 344 Li Ka Shing Center, #3370, Berkeley, CA 94720-3370, USA
| | - Shane G Poplawski
- Department of Biology, University of Pennsylvania, Smilow Center for Translational Research, Room 10-170, Building 421, 3400 Civic Center Boulevard, Philadelphia, PA 19104-6168, USA
| | - Mathieu E Wimmer
- Department of Biology, University of Pennsylvania, Smilow Center for Translational Research, Room 10-170, Building 421, 3400 Civic Center Boulevard, Philadelphia, PA 19104-6168, USA
| | - Terence P Speed
- Department of Statistics, University of California, Berkeley, Department of Mathematics and Statistics, The University of Melbourne, Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Australia
| | - Marcelo A Wood
- University of California, Irvine, Department of Neurobiology and Behavior, USA
| | - Ted Abel
- Department of Biology, University of Pennsylvania, Smilow Center for Translational Research, Room 10-170, Building 421, 3400 Civic Center Boulevard, Philadelphia, PA 19104-6168, USA
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16
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Beiting DP, Peixoto L, Akopyants NS, Beverley SM, Wherry EJ, Christian DA, Hunter CA, Brodsky IE, Roos DS. Differential induction of TLR3-dependent innate immune signaling by closely related parasite species. PLoS One 2014; 9:e88398. [PMID: 24505488 PMCID: PMC3914978 DOI: 10.1371/journal.pone.0088398] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 12/31/2013] [Indexed: 12/20/2022] Open
Abstract
The closely related protozoan parasites Toxoplasma gondii and Neospora caninum display similar life cycles, subcellular ultrastructure, invasion mechanisms, metabolic pathways, and genome organization, but differ in their host range and disease pathogenesis. Type II (γ) interferon has long been known to be the major mediator of innate and adaptive immunity to Toxoplasma infection, but genome-wide expression profiling of infected host cells indicates that Neospora is a potent activator of the type I (α/β) interferon pathways typically associated with antiviral responses. Infection of macrophages from mice with targeted deletions in various innate sensing genes demonstrates that host responses to Neospora are dependent on the toll-like receptor Tlr3 and the adapter protein Trif. Consistent with this observation, RNA from Neospora elicits TLR3-dependent type I interferon responses when targeted to the host endo-lysosomal system. Although live Toxoplasma fail to induce type I interferon, heat-killed parasites do trigger this response, albeit much weaker than Neospora, and co-infection studies reveal that T. gondii actively suppresses the production of type I interferon. These findings reveal that eukaryotic pathogens can be potent inducers of type I interferon and that related parasite species interact with this pathway in distinct ways.
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Affiliation(s)
- Daniel P. Beiting
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| | - Lucia Peixoto
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Natalia S. Akopyants
- Department of Molecular Microbiology, Washington University, St. Louis, Missouri, United States of America
| | - Stephen M. Beverley
- Department of Molecular Microbiology, Washington University, St. Louis, Missouri, United States of America
| | - E. John Wherry
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - David A. Christian
- Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Christopher A. Hunter
- Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Igor E. Brodsky
- Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - David S. Roos
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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17
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Martins G, Peixoto L, Teodorescu S, Parpot P, Nogueira R, Brito AG. Impact of an external electron acceptor on phosphorus mobility between water and sediments. Bioresour Technol 2014; 151:419-423. [PMID: 24210650 DOI: 10.1016/j.biortech.2013.10.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 10/08/2013] [Accepted: 10/15/2013] [Indexed: 06/02/2023]
Abstract
The present work assessed the impact of an external electron acceptor on phosphorus fluxes between water and sediment interface. Microcosm experiments simulating a sediment microbial fuel cell (SMFC) were carried out and phosphorus was extracted by an optimized combination of three methods. Despite the low voltage recorded, ~96 mV (SMFC with carbon paper anode) and ~146 mV (SMFC with stainless steel scourer anode), corresponding to a power density of 1.15 and 0.13 mW/m(2), it was enough to produce an increase in the amounts of metal bound phosphorus (14% vs 11%), Ca-bound phosphorus (26% vs 23%), and refractory phosphorus (33% vs 28%). These results indicate an important role of electroactive bacteria in the phosphorus cycling and open a new perspective for preventing metal bound phosphorus dissolution from sediments.
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Affiliation(s)
- G Martins
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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18
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Abstract
Long-term memory formation requires transcription and protein synthesis. Over the past few decades, a great amount of knowledge has been gained regarding the molecular players that regulate the transcriptional program linked to memory consolidation. Epigenetic mechanisms have been shown to be essential for the regulation of neuronal gene expression, and histone acetylation has been one of the most studied and best characterized. In this review, we summarize the lines of evidence that have shown the relevance of histone acetylation in memory in both physiological and pathological conditions. Great advances have been made in identifying the writers and erasers of histone acetylation marks during learning. However, the identities of the upstream regulators and downstream targets that mediate the effect of changes in histone acetylation during memory consolidation remain restricted to a handful of molecules. We outline a general model by which corepressors and coactivators regulate histone acetylation during memory storage and discuss how the recent advances in high-throughput sequencing have the potential to radically change our understanding of how epigenetic control operates in the brain.
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Affiliation(s)
- Lucia Peixoto
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
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19
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Vecsey CG, Peixoto L, Choi JHK, Wimmer M, Jaganath D, Hernandez PJ, Blackwell J, Meda K, Park AJ, Hannenhalli S, Abel T. Genomic analysis of sleep deprivation reveals translational regulation in the hippocampus. Physiol Genomics 2012; 44:981-91. [PMID: 22930738 DOI: 10.1152/physiolgenomics.00084.2012] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Sleep deprivation is a common problem of considerable health and economic impact in today's society. Sleep loss is associated with deleterious effects on cognitive functions such as memory and has a high comorbidity with many neurodegenerative and neuropsychiatric disorders. Therefore, it is crucial to understand the molecular basis of the effect of sleep deprivation in the brain. In this study, we combined genome-wide and traditional molecular biological approaches to determine the cellular and molecular impacts of sleep deprivation in the mouse hippocampus, a brain area crucial for many forms of memory. Microarray analysis examining the effects of 5 h of sleep deprivation on gene expression in the mouse hippocampus found 533 genes with altered expression. Bioinformatic analysis revealed that a prominent effect of sleep deprivation was to downregulate translation, potentially mediated through components of the insulin signaling pathway such as the mammalian target of rapamycin (mTOR), a key regulator of protein synthesis. Consistent with this analysis, sleep deprivation reduced levels of total and phosphorylated mTOR, and levels returned to baseline after 2.5 h of recovery sleep. Our findings represent the first genome-wide analysis of the effects of sleep deprivation on the mouse hippocampus, and they suggest that the detrimental effects of sleep deprivation may be mediated by reductions in protein synthesis via downregulation of mTOR. Because protein synthesis and mTOR activation are required for long-term memory formation, our study improves our understanding of the molecular mechanisms underlying the memory impairments induced by sleep deprivation.
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20
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Peixoto L, Chen F, Harb OS, Davis PH, Beiting DP, Brownback CS, Ouloguem D, Roos DS. Integrative genomic approaches highlight a family of parasite-specific kinases that regulate host responses. Cell Host Microbe 2010; 8:208-18. [PMID: 20709297 DOI: 10.1016/j.chom.2010.07.004] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 04/21/2010] [Accepted: 07/14/2010] [Indexed: 12/24/2022]
Abstract
Apicomplexan parasites release factors via specialized secretory organelles (rhoptries, micronemes) that are thought to control host cell responses. In order to explore parasite-mediated modulation of host cell signaling pathways, we exploited a phylogenomic approach to characterize the Toxoplasma gondii kinome, defining a 44 member family of coccidian-specific secreted kinases, some of which have been previously implicated in virulence. Comparative genomic analysis suggests that "ROPK" genes are under positive selection, and expression profiling demonstrates that most are differentially expressed between strains and/or during differentiation. Integrating diverse genomic-scale analyses points to ROP38 as likely to be particularly important in parasite biology. Upregulating expression of this previously uncharacterized gene in transgenic parasites dramatically suppresses transcriptional responses in the infected cell. Specifically, parasite ROP38 downregulates host genes associated with MAPK signaling and the control of apoptosis and proliferation. These results highlight the value of integrative genomic approaches in prioritizing candidates for functional validation.
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Affiliation(s)
- Lucia Peixoto
- Department of Biology and Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
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21
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Espírito Santo J, Gomes MF, Gomes MJ, Peixoto L, C Pereira S, Acabado A, Freitas J, de Sousa GV. Intravenous immunoglobulin in lupus panniculitis. Clin Rev Allergy Immunol 2010; 38:307-18. [PMID: 19557315 DOI: 10.1007/s12016-009-8162-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Systemic lupus erythematosus (SLE) is a disease of unknown cause that may involve one or many organ or systems. Skin involvement is a major feature in this disease, and a wide variety of skin conditions may be present. Lupus erythematosus panniculitis (LEP) constitutes a rare form of cutaneous lupus characterized by recurrent nodular or plaque lesions that can vary from a benign and mild course to a more disfiguring disease. Initial therapy includes corticosteroids, antimalarials, and azathioprine and, in refractory cases, two antimalarials in association, mycophenolate mofetil, or other immunomodulators. Intravenous immuglobulin (IVIG) is used in many autoimmune disorders, like in SLE, although clinical trials have not yet taken place. In this report, we review skin manifestations of SLE and their treatment, IVIG, and finally a case of LEP successfully treated with IVIG when other therapy modalities failed.
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Abeel T, de Ridder J, Peixoto L. Highlights from the 5th International Society for Computational Biology Student Council Symposium at the 17th Annual International Conference on Intelligent Systems for Molecular Biology and the 8th European Conference on Computational Biology. BMC Bioinformatics 2009; 10 Suppl 13:I1. [PMID: 19840405 PMCID: PMC2764124 DOI: 10.1186/1471-2105-10-s13-i1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Thomas Abeel
- Department of Plant Systems Biology, VIB, Ghent University, Gent, Belgium.
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23
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Peixoto L, Gehlenborg N, Janga SC. Abstracts of the Fourth International Society for Computational Biology (ISCB) Student Council Symposium. Toronto, Canada. July 18, 2008. BMC Bioinformatics 2008; 9 Suppl 10:I1-P6. [PMID: 19007430 PMCID: PMC3226086 DOI: 10.1186/1471-2105-9-s10-i1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this meeting report we give an overview of the talks and presentations from the Fourth International Society for Computational Biology (ISCB) Student Council Symposium held as part of the annual Intelligent Systems for Molecular Biology (ISMB) conference in Toronto, Canada. Furthermore, we detail the role of the Student Council (SC) as an international student body in organizing this symposium series in the context of large, international conferences.
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Affiliation(s)
- Lucia Peixoto
- Biology Department and Penn Genomics Frontier Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Nils Gehlenborg
- European Bioinformatics Institute, Hinxton, UK
- Graduate School of Life Sciences, University of Cambridge, Cambridge, CB2 1RX, UK
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24
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Peixoto L, Roos DS. Genomic scale analysis of lateral gene transfer in Apicomplexan parasites: insights into early eukaryotic evolution, host-pathogen interaction and drug target development. BMC Bioinformatics 2007. [PMCID: PMC4292147 DOI: 10.1186/1471-2105-8-s8-s5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Abstract
The usage of alternative synonymous codons in the completely sequenced, extremely A+T-rich parasite Plasmodium falciparum was studied. Confirming previous studies obtained with less than 3% of the total genes recently described, we found that A- and U-ending triplets predominate but translational selection increases the frequency of a subset of codons in highly expressed genes. However, some new results come from the analysis of the complete sequence. First, there is more variation in GC3 than previously described; second, the effect of natural selection acting at the level of translation has been analysed with real expression data at 4 different stages and third, we found that highly expressed proteins increment the frequency of energetically less expensive amino acids. The implications of these results are discussed.
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Affiliation(s)
- L Peixoto
- Laboratorio de Organización Evolución del Genoma, Facultad de Ciencias, Iguá 4225, Montevideo 11400, Uruguay
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