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Jenkins AK, Ketchesin KD, Becker-Krail DD, McClung CA. Molecular Rhythmicity in Glia: Importance for Brain Health and Relevance to Psychiatric Disease. Biol Psychiatry 2024:S0006-3223(24)01298-8. [PMID: 38735357 DOI: 10.1016/j.biopsych.2024.05.007] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/05/2024] [Accepted: 05/03/2024] [Indexed: 05/14/2024]
Abstract
Circadian rhythms are approximate 24-hour rhythms present in nearly all aspects of human physiology, including proper brain function. These rhythms are produced at the cellular level through a transcriptional-translational feedback loop known as the molecular clock. Diurnal variation in gene expression has been demonstrated in brain tissue from multiple species, including humans, in both cortical and subcortical regions. Interestingly, these rhythms in gene expression have been shown to be disrupted across psychiatric disorders and may be implicated in their underlying pathophysiology. However, little is known regarding molecular rhythms in specific cell types in the brain and how they might be involved in psychiatric disease. Although glial cells (e.g., astrocytes, microglia, and oligodendrocytes) have been historically understudied compared to neurons, evidence of the molecular clock is found within each of these cell subtypes. Here, we review the current literature, which suggests that molecular rhythmicity is essential to functional physiologic outputs from each glial subtype. Furthermore, disrupted molecular rhythms within these cells and the resultant functional deficits may be relevant to specific phenotypes across psychiatric illnesses. Given that circadian rhythm disruptions have been so integrally tied to psychiatric disease, the molecular mechanisms governing these associations could represent exciting new avenues for future research and potential novel pharmacologic targets for treatment.
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Affiliation(s)
- Aaron K Jenkins
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania; Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, 15219
| | - Kyle D Ketchesin
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania; Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, 15219
| | - Darius D Becker-Krail
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania; Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, 15219
| | - Colleen A McClung
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania; Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, 15219.
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2
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DePoy LM, Petersen KA, Zong W, Ketchesin KD, Matthaei RC, Yin R, Perez MS, Vadnie CA, Becker-Krail D, Scott MR, Tseng GC, McClung CA. Cell-type and sex-specific rhythmic gene expression in the nucleus accumbens. Mol Psychiatry 2024:10.1038/s41380-024-02569-7. [PMID: 38678086 DOI: 10.1038/s41380-024-02569-7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 04/10/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
Circadian rhythms are critical for human health and are highly conserved across species. Disruptions in these rhythms contribute to many diseases, including psychiatric disorders. Previous results suggest that circadian genes modulate behavior through specific cell types in the nucleus accumbens (NAc), particularly dopamine D1-expressing medium spiny neurons (MSNs). However, diurnal rhythms in transcript expression have not been investigated in NAc MSNs. In this study we identified and characterized rhythmic transcripts in D1- and D2-expressing neurons and compared rhythmicity results to homogenate as well as astrocyte samples taken from the NAc of male and female mice. We find that all cell types have transcripts with diurnal rhythms and that top rhythmic transcripts are largely core clock genes, which peak at approximately the same time of day in each cell type and sex. While clock-controlled rhythmic transcripts are enriched for protein regulation pathways across cell type, cell signaling and signal transduction related processes are most commonly enriched in MSNs. In contrast to core clock genes, these clock-controlled rhythmic transcripts tend to reach their peak in expression about 2-h later in females than males, suggesting diurnal rhythms in reward may be delayed in females. We also find sex differences in pathway enrichment for rhythmic transcripts peaking at different times of day. Protein folding and immune responses are enriched in transcripts that peak in the dark phase, while metabolic processes are primarily enriched in transcripts that peak in the light phase. Importantly, we also find that several classic markers used to categorize MSNs are rhythmic in the NAc. This is critical since the use of rhythmic markers could lead to over- or under-enrichment of targeted cell types depending on the time at which they are sampled. This study greatly expands our knowledge of how individual cell types contribute to rhythms in the NAc.
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Affiliation(s)
- Lauren M DePoy
- Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine, 15219, Pittsburgh, PA, USA
- Center for Neuroscience, University of Pittsburgh, 15261, Pittsburgh, PA, USA
| | - Kaitlyn A Petersen
- Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine, 15219, Pittsburgh, PA, USA
- Center for Neuroscience, University of Pittsburgh, 15261, Pittsburgh, PA, USA
| | - Wei Zong
- Department of Biostatistics, University of Pittsburgh, 15261, Pittsburgh, PA, USA
| | - Kyle D Ketchesin
- Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine, 15219, Pittsburgh, PA, USA
- Center for Neuroscience, University of Pittsburgh, 15261, Pittsburgh, PA, USA
| | - Ross C Matthaei
- Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine, 15219, Pittsburgh, PA, USA
| | - RuoFei Yin
- Department of Biostatistics, University of Pittsburgh, 15261, Pittsburgh, PA, USA
| | - Megan S Perez
- Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine, 15219, Pittsburgh, PA, USA
- Department of Human Genetics, School of Public Health, University of Pittsburgh, 15261, Pittsburgh, PA, USA
| | - Chelsea A Vadnie
- David O. Robbins Neuroscience Program, Department of Psychology, Ohio Wesleyan University, 43015, Delaware, OH, USA
| | - Darius Becker-Krail
- Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine, 15219, Pittsburgh, PA, USA
- Center for Neuroscience, University of Pittsburgh, 15261, Pittsburgh, PA, USA
| | - Madeline R Scott
- Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine, 15219, Pittsburgh, PA, USA
- Center for Neuroscience, University of Pittsburgh, 15261, Pittsburgh, PA, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, 15261, Pittsburgh, PA, USA
| | - Colleen A McClung
- Department of Psychiatry, Translational Neuroscience Program, University of Pittsburgh School of Medicine, 15219, Pittsburgh, PA, USA.
- Center for Neuroscience, University of Pittsburgh, 15261, Pittsburgh, PA, USA.
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3
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Petersen KA, Zong W, Depoy LM, Scott MR, Shankar VG, Burns JN, Cerwensky AJ, Kim SM, Ketchesin KD, Tseng GC, McClung CA. Comparative rhythmic transcriptome profiling of human and mouse striatal subregions. Neuropsychopharmacology 2024; 49:796-805. [PMID: 38182777 PMCID: PMC10948754 DOI: 10.1038/s41386-023-01788-w] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024]
Abstract
The human striatum can be subdivided into the caudate, putamen, and nucleus accumbens (NAc). In mice, this roughly corresponds to the dorsal medial striatum (DMS), dorsal lateral striatum (DLS), and ventral striatum (NAc). Each of these structures have some overlapping and distinct functions related to motor control, cognitive processing, motivation, and reward. Previously, we used a "time-of-death" approach to identify diurnal rhythms in RNA transcripts in these three human striatal subregions. Here, we identify molecular rhythms across similar striatal subregions collected from C57BL/6J mice across 6 times of day and compare results to the human striatum. Pathway analysis indicates a large degree of overlap between species in rhythmic transcripts involved in processes like cellular stress, energy metabolism, and translation. Notably, a striking finding in humans is that small nucleolar RNAs (snoRNAs) and long non-coding RNAs (lncRNAs) are among the most highly rhythmic transcripts in the NAc and this is not conserved in mice, suggesting the rhythmicity of RNA processing in this region could be uniquely human. Furthermore, the peak timing of overlapping rhythmic genes is altered between species, but not consistently in one direction. Taken together, these studies reveal conserved as well as distinct transcriptome rhythms across the human and mouse striatum and are an important step in understanding the normal function of diurnal rhythms in humans and model organisms in these regions and how disruption could lead to pathology.
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Affiliation(s)
- Kaitlyn A Petersen
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Zong
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lauren M Depoy
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Madeline R Scott
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vaishnavi G Shankar
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jennifer N Burns
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Allison J Cerwensky
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sam-Moon Kim
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kyle D Ketchesin
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Colleen A McClung
- Department of Psychiatry, Translational Neuroscience Program, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA.
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Carlucci M, Lett T, Chavez S, Malinowski A, Lobaugh NJ, Petronis A. Diurnal oscillations of MRI metrics in the brains of male participants. Nat Commun 2023; 14:7044. [PMID: 37923728 PMCID: PMC10624685 DOI: 10.1038/s41467-023-42588-6] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 10/16/2023] [Indexed: 11/06/2023] Open
Abstract
Regulation of biological processes according to a 24-hr rhythm is essential for the normal functioning of an organism. Temporal variation in brain MRI data has often been attributed to circadian or diurnal oscillations; however, it is not clear if such oscillations exist. Here, we provide evidence that diurnal oscillations indeed govern multiple MRI metrics. We recorded cerebral blood flow, diffusion-tensor metrics, T1 relaxation, and cortical structural features every three hours over a 24-hr period in each of 16 adult male controls and eight adult male participants with bipolar disorder. Diurnal oscillations are detected in numerous MRI metrics at the whole-brain level, and regionally. Rhythmicity parameters in the participants with bipolar disorder are similar to the controls for most metrics, except for a larger phase variation in cerebral blood flow. The ubiquitous nature of diurnal oscillations has broad implications for neuroimaging studies and furthers our understanding of the dynamic nature of the human brain.
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Affiliation(s)
- Matthew Carlucci
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, M5T 1R8, ON, Canada
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, LT-10257, Lithuania
| | - Tristram Lett
- Center for Population Neuroscience and Precision Medicine (PONS), Clinic for Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
| | - Sofia Chavez
- Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Alexandra Malinowski
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, M5T 1R8, ON, Canada
| | - Nancy J Lobaugh
- Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Medicine, Division of Neurology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Art Petronis
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, M5T 1R8, ON, Canada.
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, LT-10257, Lithuania.
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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5
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El-Maradny YA, Rubio-Casillas A, Mohamed KI, Uversky VN, Redwan EM. Intrinsic factors behind long-COVID: II. SARS-CoV-2, extracellular vesicles, and neurological disorders. J Cell Biochem 2023; 124:1466-1485. [PMID: 37801299 DOI: 10.1002/jcb.30486] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/04/2023] [Accepted: 09/22/2023] [Indexed: 10/07/2023]
Abstract
With the decline in the number of new Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections, the World Health Organization announced the end of the SARS-CoV-2 pandemic. However, the repercussions of this viral pandemic may remain with us for a longer period of time, as it has remodeled the lives of humankind in many ways, including social and economic. Of course, its most important repercussions remain on the human health level. Long-coronavirus disease (COVID) or post-COVID is a state for which we do not have a concrete definition, a specific international classification of diseases Code, clear diagnostic tools, or well-known effective cures as of yet. In this second article from the Intrinsic Factors behind long-COVID Series, we try to link long-COVID symptoms with their causes, starting from the nervous system. Extracellular vesicles (ECVs) play very complex and ramified roles in the bodies of both healthy and not-healthy individuals. ECVs may facilitate the entry of many bioactive molecules and pathogens into the tissues and cells of the nervous system across the blood-brain barrier. Based on the size, quantity, and quality of their cargo, ECVs are directly proportional to the pathological condition and its severity through intertwined mechanisms that evoke inflammatory immune responses typically accompanied by pathological symptoms over variable time periods according to the type of these symptoms.
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Affiliation(s)
- Yousra A El-Maradny
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg EL-Arab, Egypt
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El-Alamein, Egypt
| | - Alberto Rubio-Casillas
- Biology Laboratory, Autlán Regional Preparatory School, University of Guadalajara, Autlán, Jalisco, Mexico
| | - Kareem I Mohamed
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El-Alamein, Egypt
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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6
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Melloni EMT, Paolini M, Dallaspezia S, Lorenzi C, Poletti S, d'Orsi G, Yoshiike T, Zanardi R, Colombo C, Benedetti F. Melatonin secretion patterns are associated with cognitive vulnerability and brain structure in bipolar depression. Chronobiol Int 2023; 40:1279-1290. [PMID: 37781880 DOI: 10.1080/07420528.2023.2262572] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 09/18/2023] [Indexed: 10/03/2023]
Abstract
Circadian rhythm disruption is a core symptom of bipolar disorder (BD), also reflected in altered patterns of melatonin release. Reductions of grey matter (GM) volumes are well documented in BD. We hypothesized that levels and timing of melatonin secretion in bipolar depression could be associated with depressive psychopathology and brain GM integrity. The onset of melatonin secretion under dim light conditions (DLMO) and the amount of time between DLMO and midsleep (i.e. phase angle difference; PAD) were used as circadian rhythm markers. To study the time course of melatonin secretion, an exponential curve fitting the melatonin values was calculated, and the slope coefficients (SLP) were obtained for each participant. Significant differences were found between HC and BD in PAD measures and melatonin profiles. Correlations between PAD and depressive psychopathology were identified. Melatonin secretion patterns were found to be associated with GM volumes in the Striatum and Supramarginal Gyrus in BD. Our findings emphasized the role of melatonin secretion role as a biological marker of circadian synchronization in bipolar depression and provided a novel insight for a link between melatonin release and brain structure.
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Affiliation(s)
- Elisa M T Melloni
- Psychiatry & Clinical Psychobiology Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milano, Italy
- University Vita-Salute San Raffaele, Milano, Italy
| | - Marco Paolini
- Psychiatry & Clinical Psychobiology Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milano, Italy
- University Vita-Salute San Raffaele, Milano, Italy
| | - Sara Dallaspezia
- Psychiatry & Clinical Psychobiology Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milano, Italy
- University Vita-Salute San Raffaele, Milano, Italy
| | - Cristina Lorenzi
- Psychiatry & Clinical Psychobiology Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milano, Italy
| | - Sara Poletti
- Psychiatry & Clinical Psychobiology Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milano, Italy
- University Vita-Salute San Raffaele, Milano, Italy
| | - Greta d'Orsi
- Psychiatry & Clinical Psychobiology Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milano, Italy
| | - Takuya Yoshiike
- Psychiatry & Clinical Psychobiology Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milano, Italy
- Department of Sleep-Wake Disorders, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Raffaella Zanardi
- University Vita-Salute San Raffaele, Milano, Italy
- IRCCS San Raffaele Scientific Institute, Department of Clinical Neurosciences, Mood Disorder Unit, Milano, Italy
| | - Cristina Colombo
- University Vita-Salute San Raffaele, Milano, Italy
- IRCCS San Raffaele Scientific Institute, Department of Clinical Neurosciences, Mood Disorder Unit, Milano, Italy
| | - Francesco Benedetti
- Psychiatry & Clinical Psychobiology Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milano, Italy
- University Vita-Salute San Raffaele, Milano, Italy
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Zong W, Seney ML, Ketchesin KD, Gorczyca MT, Liu AC, Esser KA, Tseng GC, McClung CA, Huo Z. Experimental design and power calculation in omics circadian rhythmicity detection using the cosinor model. Stat Med 2023; 42:3236-3258. [PMID: 37265194 PMCID: PMC10425922 DOI: 10.1002/sim.9803] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/27/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Circadian clocks are 24-h endogenous oscillators in physiological and behavioral processes. Though recent transcriptomic studies have been successful in revealing the circadian rhythmicity in gene expression, the power calculation for omics circadian analysis have not been fully explored. In this paper, we develop a statistical method, namely CircaPower, to perform power calculation for circadian pattern detection. Our theoretical framework is determined by three key factors in circadian gene detection: sample size, intrinsic effect size and sampling design. Via simulations, we systematically investigate the impact of these key factors on circadian power calculation. We not only demonstrate that CircaPower is fast and accurate, but also show its underlying cosinor model is robust against variety of violations of model assumptions. In real applications, we demonstrate the performance of CircaPower using mouse pan-tissue data and human post-mortem brain data, and illustrate how to perform circadian power calculation using mouse skeleton muscle RNA-Seq pilot as case study. Our method CircaPower has been implemented in an R package, which is made publicly available on GitHub ( https://github.com/circaPower/circaPower).
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Affiliation(s)
- Wei Zong
- Department of Biostatistics, University of Pittsburgh, PA, USA
| | - Marianne L. Seney
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Kyle D. Ketchesin
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Michael T. Gorczyca
- Department of Computational and Systems Biology, University of Pittsburgh, PA, USA
| | - Andrew C. Liu
- Department of Physiology and Aging, University of Florida, FL, USA
| | - Karyn A. Esser
- Department of Physiology and Aging, University of Florida, FL, USA
| | - George C. Tseng
- Department of Biostatistics, University of Pittsburgh, PA, USA
| | - Colleen A. McClung
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, FL, USA
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Bergeron D, Faucher-Giguère L, Emmerichs AK, Choquet K, Song KS, Deschamps-Francoeur G, Fafard-Couture É, Rivera A, Couture S, Churchman LS, Heyd F, Abou Elela S, Scott MS. Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences. Genome Biol 2023; 24:160. [PMID: 37415181 DOI: 10.1186/s13059-023-03002-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/29/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Small nucleolar RNAs (snoRNAs) are abundant noncoding RNAs best known for their involvement in ribosomal RNA maturation. In mammals, most expressed snoRNAs are embedded in introns of longer genes and produced through transcription and splicing of their host. Intronic snoRNAs were long viewed as inert passengers with little effect on host expression. However, a recent study reported a snoRNA influencing the splicing and ultimate output of its host gene. Overall, the general contribution of intronic snoRNAs to host expression remains unclear. RESULTS Computational analysis of large-scale human RNA-RNA interaction datasets indicates that 30% of detected snoRNAs interact with their host transcripts. Many snoRNA-host duplexes are located near alternatively spliced exons and display high sequence conservation suggesting a possible role in splicing regulation. The study of the model SNORD2-EIF4A2 duplex indicates that the snoRNA interaction with the host intronic sequence conceals the branch point leading to decreased inclusion of the adjacent alternative exon. Extended SNORD2 sequence containing the interacting intronic region accumulates in sequencing datasets in a cell-type-specific manner. Antisense oligonucleotides and mutations that disrupt the formation of the snoRNA-intron structure promote the splicing of the alternative exon, shifting the EIF4A2 transcript ratio away from nonsense-mediated decay. CONCLUSIONS Many snoRNAs form RNA duplexes near alternative exons of their host transcripts, placing them in optimal positions to control host output as shown for the SNORD2-EIF4A2 model system. Overall, our study supports a more widespread role for intronic snoRNAs in the regulation of their host transcript maturation.
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Affiliation(s)
- Danny Bergeron
- Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Laurence Faucher-Giguère
- Département de Microbiologie Et d'infectiologie, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Ann-Kathrin Emmerichs
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Laboratory of RNA Biochemistry, Takustrasse 6, 14195, Berlin, Germany
| | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Kristina Sungeun Song
- Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Gabrielle Deschamps-Francoeur
- Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Étienne Fafard-Couture
- Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Andrea Rivera
- Département de Microbiologie Et d'infectiologie, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Sonia Couture
- Département de Microbiologie Et d'infectiologie, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Florian Heyd
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Laboratory of RNA Biochemistry, Takustrasse 6, 14195, Berlin, Germany
| | - Sherif Abou Elela
- Département de Microbiologie Et d'infectiologie, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Michelle S Scott
- Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada.
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9
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Ketchesin KD, Becker-Krail DD, Xue X, Wilson RS, Lam TT, Williams KR, Nairn AC, Tseng GC, Logan RW. Differential Effects of Cocaine and Morphine on the Diurnal Regulation of the Mouse Nucleus Accumbens Proteome. J Proteome Res 2023. [PMID: 37311105 PMCID: PMC10392613 DOI: 10.1021/acs.jproteome.3c00126] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Substance use disorders are associated with disruptions in sleep and circadian rhythms that persist during abstinence and may contribute to relapse risk. Repeated use of substances such as psychostimulants and opioids may lead to significant alterations in molecular rhythms in the nucleus accumbens (NAc), a brain region central to reward and motivation. Previous studies have identified rhythm alterations in the transcriptome of the NAc and other brain regions following the administration of psychostimulants or opioids. However, little is known about the impact of substance use on the diurnal rhythms of the proteome in the NAc. We used liquid chromatography coupled to tandem mass spectrometry-based quantitative proteomics, along with a data-independent acquisition analysis pipeline, to investigate the effects of cocaine or morphine administration on diurnal rhythms of proteome in the mouse NAc. Overall, our data reveal cocaine and morphine differentially alter diurnal rhythms of the proteome in the NAc, with largely independent differentially expressed proteins dependent on time-of-day. Pathways enriched from cocaine altered protein rhythms were primarily associated with glucocorticoid signaling and metabolism, whereas morphine was associated with neuroinflammation. Collectively, these findings are the first to characterize the diurnal regulation of the NAc proteome and demonstrate a novel relationship between the phase-dependent regulation of protein expression and the differential effects of cocaine and morphine on the NAc proteome. The proteomics data in this study are available via ProteomeXchange with identifier PXD042043.
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Affiliation(s)
- Kyle D Ketchesin
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, United States
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Darius D Becker-Krail
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, United States
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xiangning Xue
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Rashaun S Wilson
- Yale/NIDA Neuroproteomics Center, 300 George Street, New Haven, Connecticut 06511, United States
- W.M. Keck Biotechnology Mass Spectrometry (MS) & Proteomics Resource Laboratory, Yale University School of Medicine, New Haven, Connecticut 06511, United States
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - TuKiet T Lam
- Yale/NIDA Neuroproteomics Center, 300 George Street, New Haven, Connecticut 06511, United States
- W.M. Keck Biotechnology Mass Spectrometry (MS) & Proteomics Resource Laboratory, Yale University School of Medicine, New Haven, Connecticut 06511, United States
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Kenneth R Williams
- Yale/NIDA Neuroproteomics Center, 300 George Street, New Haven, Connecticut 06511, United States
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, 300 George Street, New Haven, Connecticut 06511, United States
- Department of Psychiatry, Yale University School of Medicine, Connecticut Mental Health Center, New Haven, Connecticut 06511, United States
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Ryan W Logan
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, United States
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01655, United States
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
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10
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Hickie IB, Merikangas KR, Carpenter JS, Iorfino F, Scott EM, Scott J, Crouse JJ. Does circadian dysrhythmia drive the switch into high- or low-activation states in bipolar I disorder? Bipolar Disord 2023; 25:191-199. [PMID: 36661342 PMCID: PMC10947388 DOI: 10.1111/bdi.13304] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVES Emerging evidence suggests a role of circadian dysrhythmia in the switch between "activation" states (i.e., objective motor activity and subjective energy) in bipolar I disorder. METHODS We examined the evidence with respect to four relevant questions: (1) Are natural or environmental exposures that can disrupt circadian rhythms also related to the switch into high-/low-activation states? (2) Are circadian dysrhythmias (e.g., altered rest/activity rhythms) associated with the switch into activation states in bipolar disorder? (3) Do interventions that affect the circadian system also affect activation states? (4) Are associations between circadian dysrhythmias and activation states influenced by other "third" factors? RESULTS Factors that naturally or experimentally alter circadian rhythms (e.g., light exposure) have been shown to relate to activation states; however future studies need to measure circadian rhythms contemporaneously with these natural/experimental factors. Actigraphic measures of circadian dysrhythmias are associated prospectively with the switch into high- or low-activation states, and more studies are needed to establish the most relevant prognostic actigraphy metrics in bipolar disorder. Interventions that can affect the circadian system (e.g., light therapy, lithium) can also reduce the switch into high-/low-activation states. Whether circadian rhythms mediate these clinical effects is an unknown but valuable question. The influence of age, sex, and other confounders on these associations needs to be better characterised. CONCLUSION Based on the reviewed evidence, our view is that circadian dysrhythmia is a plausible driver of transitions into high- and low-activation states and deserves prioritisation in research in bipolar disorders.
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Affiliation(s)
- Ian B. Hickie
- Youth Mental Health and Technology Team, Brain and Mind Centre, Faculty of Medicine and HealthUniversity of SydneyNew South WalesSydneyAustralia
| | - Kathleen R. Merikangas
- Genetic Epidemiology Research Branch, Division of Intramural Research ProgramNational Institute of Mental HealthBethesdaMarylandUSA
| | - Joanne S. Carpenter
- Youth Mental Health and Technology Team, Brain and Mind Centre, Faculty of Medicine and HealthUniversity of SydneyNew South WalesSydneyAustralia
| | - Frank Iorfino
- Youth Mental Health and Technology Team, Brain and Mind Centre, Faculty of Medicine and HealthUniversity of SydneyNew South WalesSydneyAustralia
| | - Elizabeth M. Scott
- Youth Mental Health and Technology Team, Brain and Mind Centre, Faculty of Medicine and HealthUniversity of SydneyNew South WalesSydneyAustralia
| | - Jan Scott
- Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- Norwegian University of Science and TechnologyTrondheimNorway
- Université de ParisParisFrance
| | - Jacob J. Crouse
- Youth Mental Health and Technology Team, Brain and Mind Centre, Faculty of Medicine and HealthUniversity of SydneyNew South WalesSydneyAustralia
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11
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Ketchesin KD, Becker-Krail DD, Xue X, Wilson RS, Lam TT, Williams KR, Nairn AC, Tseng GC, Logan RW. Differential Effects of Cocaine and Morphine on the Diurnal Regulation of the Mouse Nucleus Accumbens Proteome. bioRxiv 2023:2023.03.01.530696. [PMID: 36909659 PMCID: PMC10002738 DOI: 10.1101/2023.03.01.530696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Substance use disorders (SUDs) are associated with disruptions in sleep and circadian rhythms that persist during abstinence and may contribute to relapse risk. Repeated use of substances such as psychostimulants and opioids may lead to significant alterations in molecular rhythms in the nucleus accumbens (NAc), a brain region central to reward and motivation. Previous studies have identified rhythm alterations in the transcriptome of the NAc and other brain regions following the administration of psychostimulants or opioids. However, little is known about the impact of substance use on the diurnal rhythms of the proteome in the NAc. We used liquid chromatography coupled to tandem mass spectrometry-based (LC-MS/MS) quantitative proteomics, along with a data-independent acquisition (DIA) analysis pipeline, to investigate the effects of cocaine or morphine administration on diurnal rhythms of proteome in the mouse NAc. Overall, our data reveals cocaine and morphine differentially alters diurnal rhythms of the proteome in the NAc, with largely independent differentially expressed proteins dependent on time-of-day. Pathways enriched from cocaine altered protein rhythms were primarily associated with glucocorticoid signaling and metabolism, whereas morphine was associated with neuroinflammation. Collectively, these findings are the first to characterize the diurnal regulation of the NAc proteome and demonstrate a novel relationship between phase-dependent regulation of protein expression and the differential effects of cocaine and morphine on the NAc proteome.
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12
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Ketchesin KD, Zong W, Hildebrand MA, Scott MR, Seney ML, Cahill KM, Shankar VG, Glausier JR, Lewis DA, Tseng GC, McClung CA. Diurnal Alterations in Gene Expression Across Striatal Subregions in Psychosis. Biol Psychiatry 2023; 93:137-148. [PMID: 36302706 PMCID: PMC10411997 DOI: 10.1016/j.biopsych.2022.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Psychosis is a defining feature of schizophrenia and highly prevalent in bipolar disorder. Notably, individuals with these illnesses also have major disruptions in sleep and circadian rhythms, and disturbances of sleep and circadian rhythms can precipitate or exacerbate psychotic symptoms. Psychosis is associated with the striatum, though to our knowledge, no study to date has directly measured molecular rhythms and determined how they are altered in the striatum of subjects with psychosis. METHODS We performed RNA sequencing and both differential expression and rhythmicity analyses to investigate diurnal alterations in gene expression in human postmortem striatal subregions (nucleus accumbens, caudate, and putamen) in subjects with psychosis (n = 36) relative to unaffected comparison subjects (n = 36). RESULTS Across regions, we found differential expression of immune-related transcripts and a substantial loss of rhythmicity in core circadian clock genes in subjects with psychosis. In the nucleus accumbens, mitochondrial-related transcripts had decreased expression in subjects with psychosis, but only in those who died at night. Additionally, we found a loss of rhythmicity in small nucleolar RNAs and a gain of rhythmicity in glutamatergic signaling in the nucleus accumbens of subjects with psychosis. Between-region comparisons indicated that rhythmicity in the caudate and putamen was far more similar in subjects with psychosis than in matched comparison subjects. CONCLUSIONS Together, these findings reveal differential and rhythmic gene expression differences across the striatum that may contribute to striatal dysfunction and psychosis in psychotic disorders.
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Affiliation(s)
- Kyle D Ketchesin
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Wei Zong
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mariah A Hildebrand
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Madeline R Scott
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Marianne L Seney
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kelly M Cahill
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Vaishnavi G Shankar
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jill R Glausier
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - David A Lewis
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania.
| | - Colleen A McClung
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
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13
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Xue X, Zong W, Huo Z, Ketchesin KD, Scott MR, Petersen KA, Logan RW, Seney ML, McClung C, Tseng G. DiffCircaPipeline: a framework for multifaceted characterization of differential rhythmicity. Bioinformatics 2023; 39:btad039. [PMID: 36655766 PMCID: PMC9889843 DOI: 10.1093/bioinformatics/btad039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/05/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
SUMMARY Circadian oscillations of gene expression regulate daily physiological processes, and their disruption is linked to many diseases. Circadian rhythms can be disrupted in a variety of ways, including differential phase, amplitude and rhythm fitness. Although many differential circadian biomarker detection methods have been proposed, a workflow for systematic detection of multifaceted differential circadian characteristics with accurate false positive control is not currently available. We propose a comprehensive and interactive pipeline to capture the multifaceted characteristics of differentially rhythmic biomarkers. Analysis outputs are accompanied by informative visualization and interactive exploration. The workflow is demonstrated in multiple case studies and is extensible to general omics applications. AVAILABILITY AND IMPLEMENTATION R package, Shiny app and source code are available in GitHub (https://github.com/DiffCircaPipeline) and Zenodo (https://doi.org/10.5281/zenodo.7507989). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xiangning Xue
- Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Wei Zong
- Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, Gainesville, FL 32603, USA
| | - Kyle D Ketchesin
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Madeline R Scott
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Kaitlyn A Petersen
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Ryan W Logan
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Marianne L Seney
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Colleen McClung
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - George Tseng
- Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA 15213, USA
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14
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Valeri J, O’Donovan SM, Wang W, Sinclair D, Bollavarapu R, Gisabella B, Platt D, Stockmeier C, Pantazopoulos H. Altered expression of somatostatin signaling molecules and clock genes in the hippocampus of subjects with substance use disorder. Front Neurosci 2022; 16:903941. [PMID: 36161151 PMCID: PMC9489843 DOI: 10.3389/fnins.2022.903941] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Substance use disorders are a debilitating group of psychiatric disorders with a high degree of comorbidity with major depressive disorder. Sleep and circadian rhythm disturbances are commonly reported in people with substance use disorder and major depression and associated with increased risk of relapse. Hippocampal somatostatin signaling is involved in encoding and consolidation of contextual memories which contribute to relapse in substance use disorder. Somatostatin and clock genes also have been implicated in depression, suggesting that these molecules may represent key converging pathways involved in contextual memory processing in substance use and major depression. We used hippocampal tissue from a cohort of subjects with substance use disorder (n = 20), subjects with major depression (n = 20), subjects with comorbid substance use disorder and major depression (n = 24) and psychiatrically normal control subjects (n = 20) to test the hypothesis that expression of genes involved in somatostatin signaling and clock genes is altered in subjects with substance use disorder. We identified decreased expression of somatostatin in subjects with substance use disorder and in subjects with major depression. We also observed increased somatostatin receptor 2 expression in subjects with substance use disorder with alcohol in the blood at death and decreased expression in subjects with major depression. Expression of the clock genes Arntl, Nr1d1, Per2 and Cry2 was increased in subjects with substance use disorder. Arntl and Nr1d1 expression in comparison was decreased in subjects with major depression. We observed decreased expression of Gsk3β in subjects with substance use disorder. Subjects with comorbid substance use disorder and major depression displayed minimal changes across all outcome measures. Furthermore, we observed a significant increase in history of sleep disturbances in subjects with substance use disorder. Our findings represent the first evidence for altered somatostatin and clock gene expression in the hippocampus of subjects with substance use disorder and subjects with major depression. Altered expression of these molecules may impact memory consolidation and contribute to relapse risk.
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Affiliation(s)
- Jake Valeri
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, United States
- Program in Neuroscience, University of Mississippi Medical Center, Jackson, MS, United States
| | - Sinead M. O’Donovan
- Department of Neuroscience, University of Toledo Medical Center, Toledo, OH, United States
| | - Wei Wang
- Department of Medicine and Neurology, Brigham and Women’s Hospital, Boston, MA, United States
| | - David Sinclair
- Department of Neuroscience, University of Toledo Medical Center, Toledo, OH, United States
| | - Ratna Bollavarapu
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, United States
| | - Barbara Gisabella
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, United States
- Program in Neuroscience, University of Mississippi Medical Center, Jackson, MS, United States
| | - Donna Platt
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, United States
- Program in Neuroscience, University of Mississippi Medical Center, Jackson, MS, United States
| | - Craig Stockmeier
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, United States
- Program in Neuroscience, University of Mississippi Medical Center, Jackson, MS, United States
| | - Harry Pantazopoulos
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, United States
- Program in Neuroscience, University of Mississippi Medical Center, Jackson, MS, United States
- *Correspondence: Harry Pantazopoulos,
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15
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Zheng L, Pang Q, Xu H, Guo H, Liu R, Wang T. The Neurobiological Links between Stress and Traumatic Brain Injury: A Review of Research to Date. Int J Mol Sci 2022; 23:ijms23179519. [PMID: 36076917 PMCID: PMC9455169 DOI: 10.3390/ijms23179519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 11/16/2022] Open
Abstract
Neurological dysfunctions commonly occur after mild or moderate traumatic brain injury (TBI). Although most TBI patients recover from such a dysfunction in a short period of time, some present with persistent neurological deficits. Stress is a potential factor that is involved in recovery from neurological dysfunction after TBI. However, there has been limited research on the effects and mechanisms of stress on neurological dysfunctions due to TBI. In this review, we first investigate the effects of TBI and stress on neurological dysfunctions and different brain regions, such as the prefrontal cortex, hippocampus, amygdala, and hypothalamus. We then explore the neurobiological links and mechanisms between stress and TBI. Finally, we summarize the findings related to stress biomarkers and probe the possible diagnostic and therapeutic significance of stress combined with mild or moderate TBI.
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Affiliation(s)
- Lexin Zheng
- Department of Forensic Medicine, School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, China
| | - Qiuyu Pang
- Department of Forensic Medicine, School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, China
| | - Heng Xu
- Department of Forensic Medicine, School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, China
| | - Hanmu Guo
- Department of Forensic Medicine, School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, China
| | - Rong Liu
- Department of Forensic Medicine, School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, China
| | - Tao Wang
- Department of Forensic Medicine, School of Basic Medicine and Biological Sciences, Soochow University, Suzhou 215123, China
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China (Academy of Forensic Science), Shanghai 200063, China
- Correspondence:
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16
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Becker-Krail DD, Walker WH, Nelson RJ. The Ventral Tegmental Area and Nucleus Accumbens as Circadian Oscillators: Implications for Drug Abuse and Substance Use Disorders. Front Physiol 2022; 13:886704. [PMID: 35574492 PMCID: PMC9094703 DOI: 10.3389/fphys.2022.886704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 02/28/2022] [Accepted: 04/04/2022] [Indexed: 12/15/2022] Open
Abstract
Circadian rhythms convergently evolved to allow for optimal synchronization of individuals’ physiological and behavioral processes with the Earth’s 24-h periodic cycling of environmental light and temperature. Whereas the suprachiasmatic nucleus (SCN) is considered the primary pacemaker of the mammalian circadian system, many extra-SCN oscillatory brain regions have been identified to not only exhibit sustainable rhythms in circadian molecular clock function, but also rhythms in overall region activity/function and mediated behaviors. In this review, we present the most recent evidence for the ventral tegmental area (VTA) and nucleus accumbens (NAc) to serve as extra-SCN oscillators and highlight studies that illustrate the functional significance of the VTA’s and NAc’s inherent circadian properties as they relate to reward-processing, drug abuse, and vulnerability to develop substance use disorders (SUDs).
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Affiliation(s)
- Darius D Becker-Krail
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, United States
| | - William H Walker
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, United States
| | - Randy J Nelson
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, United States
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17
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Xue X, Zong W, Glausier JR, Kim SM, Shelton MA, Phan BN, Srinivasan C, Pfenning AR, Tseng GC, Lewis DA, Seney ML, Logan RW. Molecular rhythm alterations in prefrontal cortex and nucleus accumbens associated with opioid use disorder. Transl Psychiatry 2022; 12:123. [PMID: 35347109 PMCID: PMC8960783 DOI: 10.1038/s41398-022-01894-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/03/2022] [Accepted: 03/10/2022] [Indexed: 11/21/2022] Open
Abstract
Severe and persistent disruptions to sleep and circadian rhythms are common in people with opioid use disorder (OUD). Preclinical evidence suggests altered molecular rhythms in the brain modulate opioid reward and relapse. However, whether molecular rhythms are disrupted in the brains of people with OUD remained an open question, critical to understanding the role of circadian rhythms in opioid addiction. Using subjects' times of death as a marker of time of day, we investigated transcriptional rhythms in the brains of subjects with OUD compared to unaffected comparison subjects. We discovered rhythmic transcripts in both the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (NAc), key brain areas involved in OUD, that were largely distinct between OUD and unaffected subjects. Fewer rhythmic transcripts were identified in DLPFC of subjects with OUD compared to unaffected subjects, whereas in the NAc, nearly double the number of rhythmic transcripts was identified in subjects with OUD. In NAc of subjects with OUD, rhythmic transcripts peaked either in the evening or near sunrise, and were associated with an opioid, dopamine, and GABAergic neurotransmission. Associations with altered neurotransmission in NAc were further supported by co-expression network analysis which identified OUD-specific modules enriched for transcripts involved in dopamine, GABA, and glutamatergic synaptic functions. Additionally, rhythmic transcripts in DLPFC and NAc of subjects with OUD were enriched for genomic loci associated with sleep-related GWAS traits, including sleep duration and insomnia. Collectively, our findings connect transcriptional rhythm changes in opioidergic, dopaminergic, GABAergic signaling in the human brain to sleep-related traits in opioid addiction.
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Affiliation(s)
- Xiangning Xue
- grid.21925.3d0000 0004 1936 9000Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Wei Zong
- grid.21925.3d0000 0004 1936 9000Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Jill R. Glausier
- grid.21925.3d0000 0004 1936 9000Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219 USA
| | - Sam-Moon Kim
- grid.21925.3d0000 0004 1936 9000Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219 USA ,grid.21925.3d0000 0004 1936 9000Center for Adolescent Reward, Rhythms, and Sleep, University of Pittsburgh, Pittsburgh, PA 15219 USA
| | - Micah A. Shelton
- grid.21925.3d0000 0004 1936 9000Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219 USA
| | - BaDoi N. Phan
- grid.147455.60000 0001 2097 0344Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213 USA
| | - Chaitanya Srinivasan
- grid.147455.60000 0001 2097 0344Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213 USA
| | - Andreas R. Pfenning
- grid.147455.60000 0001 2097 0344Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213 USA ,grid.147455.60000 0001 2097 0344Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213 USA
| | - George C. Tseng
- grid.21925.3d0000 0004 1936 9000Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - David A. Lewis
- grid.21925.3d0000 0004 1936 9000Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219 USA
| | - Marianne L. Seney
- grid.21925.3d0000 0004 1936 9000Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219 USA ,grid.21925.3d0000 0004 1936 9000Center for Adolescent Reward, Rhythms, and Sleep, University of Pittsburgh, Pittsburgh, PA 15219 USA
| | - Ryan W. Logan
- grid.189504.10000 0004 1936 7558Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118 USA ,grid.189504.10000 0004 1936 7558Center for Systems Neuroscience, Boston University, Boston, MA 02118 USA
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18
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Sharma R, Parikh M, Mishra V, Sahota P, Thakkar M. Activation of dopamine D2 receptors in the medial shell region of the nucleus accumbens increases Per1 expression to enhance alcohol consumption. Addict Biol 2022; 27:e13133. [PMID: 35032086 DOI: 10.1111/adb.13133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 06/29/2021] [Revised: 10/04/2021] [Accepted: 12/10/2021] [Indexed: 11/28/2022]
Abstract
Circadian genes, including Per1, in the medial shell region of nucleus accumbens (mNAcSh), regulate binge alcohol consumption. However, the upstream mechanism regulating circadian genes-induced alcohol consumption is not known. Since activation of dopamine D2 receptors (D2R) increases Per1 gene expression, we hypothesised that local infusion of quinpirole, a D2R agonist, by increasing Per1 gene expression in the mNAcSh, will increase binge alcohol consumption in mice. We performed two experiments on male C57BL/6J mice, instrumented with bilateral guide cannulas above the mNAcSh, and exposed to a 4-day drinking-in-dark (DID) paradigm. The first experiment determined the effects of bilateral infusion of quinpirole (100 ng/300 nl/site) or DMSO (Vehicle group) in the mNAcSh on Per1 gene expression and alcohol consumption. The second experiment determined the effect of antisense-induced downregulation of Per1 in the mNAcSh on the quinpirole-induced increase in alcohol consumption. Control experiments were performed by exposing the animals to sucrose (10% w/v). After the experiment, animals were euthanised, brains removed and processed for localisation of injection sites and analysis of Per1 gene expression in the mNAcSh. As compared with the DMSO, local bilateral infusion of quinpirole significantly increased the expression of Per1 in the mNAcSh along with an increase in the amount of alcohol consumed in mice exposed to DID paradigm. In addition, local antisense-induced downregulation of Per1 significantly attenuated the effects of intro-accumbal infusion of quinpirole on alcohol consumption. Our results suggest that Per1 in the mNAcSh mediates D2R activation-induced increase in alcohol consumption.
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Affiliation(s)
- Rishi Sharma
- Harry S. Truman Memorial Veterans Hospital and Department of Neurology University of Missouri Columbia Missouri USA
| | - Meet Parikh
- Harry S. Truman Memorial Veterans Hospital and Department of Neurology University of Missouri Columbia Missouri USA
| | - Vaibhav Mishra
- Harry S. Truman Memorial Veterans Hospital and Department of Neurology University of Missouri Columbia Missouri USA
| | - Pradeep Sahota
- Harry S. Truman Memorial Veterans Hospital and Department of Neurology University of Missouri Columbia Missouri USA
| | - Mahesh Thakkar
- Harry S. Truman Memorial Veterans Hospital and Department of Neurology University of Missouri Columbia Missouri USA
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19
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Becker-Krail DD, Parekh PK, Ketchesin KD, Yamaguchi S, Yoshino J, Hildebrand MA, Dunham B, Ganapathiraiu MK, Logan RW, McClung CA. Circadian transcription factor NPAS2 and the NAD + -dependent deacetylase SIRT1 interact in the mouse nucleus accumbens and regulate reward. Eur J Neurosci 2022; 55:675-693. [PMID: 35001440 PMCID: PMC9355311 DOI: 10.1111/ejn.15596] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 05/07/2021] [Revised: 12/14/2021] [Accepted: 01/06/2022] [Indexed: 02/03/2023]
Abstract
Substance use disorders are associated with disruptions to both circadian rhythms and cellular metabolic state. At the molecular level, the circadian molecular clock and cellular metabolic state may be interconnected through interactions with the nicotinamide adenine dinucleotide (NAD+ )-dependent deacetylase, sirtuin 1 (SIRT1). In the nucleus accumbens (NAc), a region important for reward, both SIRT1 and the circadian transcription factor neuronal PAS domain protein 2 (NPAS2) are highly enriched, and both are regulated by the metabolic cofactor NAD+ . Substances of abuse, like cocaine, greatly disrupt cellular metabolism and promote oxidative stress; however, their effects on NAD+ in the brain remain unclear. Interestingly, cocaine also induces NAc expression of both NPAS2 and SIRT1, and both have independently been shown to regulate cocaine reward in mice. However, whether NPAS2 and SIRT1 interact in the NAc and/or whether together they regulate reward is unknown. Here, we demonstrate diurnal expression of Npas2, Sirt1 and NAD+ in the NAc, which is altered by cocaine-induced upregulation. Additionally, co-immunoprecipitation reveals NPAS2 and SIRT1 interact in the NAc, and cross-analysis of NPAS2 and SIRT1 chromatin immunoprecipitation sequencing reveals several reward-relevant and metabolic-related pathways enriched among shared gene targets. Notably, NAc-specific Npas2 knock-down or a functional Npas2 mutation in mice attenuates SIRT1-mediated increases in cocaine preference. Together, our data reveal an interaction between NPAS2 and SIRT1 in the NAc, which may serve to integrate cocaine's effects on circadian and metabolic factors, leading to regulation of drug reward.
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Affiliation(s)
- Darius D. Becker-Krail
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA,Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Puja K. Parekh
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA,Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Kyle D. Ketchesin
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA,Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Shintaro Yamaguchi
- Center for Human Nutrition, Division of Geriatrics and Nutritional Science, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jun Yoshino
- Center for Human Nutrition, Division of Geriatrics and Nutritional Science, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Mariah A. Hildebrand
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA,Center for Neuroscience, University of Pittsburgh, PA, USA
| | - Brandon Dunham
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Madhavi K. Ganapathiraiu
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ryan W. Logan
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - Colleen A. McClung
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA,Center for Neuroscience, University of Pittsburgh, PA, USA,Correspondence: Colleen A. McClung,
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20
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Ni RJ, Shu YM, Li T, Zhou JN. Whole-Brain Afferent Inputs to the Caudate Nucleus, Putamen, and Accumbens Nucleus in the Tree Shrew Striatum. Front Neuroanat 2021; 15:763298. [PMID: 34795566 PMCID: PMC8593333 DOI: 10.3389/fnana.2021.763298] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/30/2021] [Indexed: 02/05/2023] Open
Abstract
Day-active tree shrews have a well-developed internal capsule (ic) that clearly separates the caudate nucleus (Cd) and putamen (Pu). The striatum consists of the Cd, ic, Pu, and accumbens nucleus (Acb). Here, we characterized the cytoarchitecture of the striatum and the whole-brain inputs to the Cd, Pu, and Acb in tree shrews by using immunohistochemistry and the retrograde tracer Fluoro-Gold (FG). Our data show the distribution patterns of parvalbumin (PV), nitric oxide synthase (NOS), calretinin (CR), and tyrosine hydroxylase (TH) immunoreactivity in the striatum of tree shrews, which were different from those observed in rats. The Cd and Pu mainly received inputs from the thalamus, motor cortex, somatosensory cortex, subthalamic nucleus, substantia nigra, and other cortical and subcortical regions, whereas the Acb primarily received inputs from the anterior olfactory nucleus, claustrum, infralimbic cortex, thalamus, raphe nucleus, parabrachial nucleus, ventral tegmental area, and so on. The Cd, Pu, and Acb received inputs from different neuronal populations in the ipsilateral (60, 67, and 63 brain regions, respectively) and contralateral (23, 20, and 36 brain regions, respectively) brain hemispheres. Overall, we demonstrate that there are species differences between tree shrews and rats in the density of PV, NOS, CR, and TH immunoreactivity in the striatum. Additionally, we mapped for the first time the distribution of whole-brain input neurons projecting to the striatum of tree shrews with FG injected into the Cd, Pu, and Acb. The similarities and differences in their brain-wide input patterns may provide new insights into the diverse functions of the striatal subregions.
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Affiliation(s)
- Rong-Jun Ni
- Mental Health Center and Psychiatric Laboratory, West China Hospital of Sichuan University, Chengdu, China.,Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China
| | - Yu-Mian Shu
- School of Architecture and Civil Engineering, Chengdu University, Chengdu, China
| | - Tao Li
- Mental Health Center and Psychiatric Laboratory, West China Hospital of Sichuan University, Chengdu, China.,Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China
| | - Jiang-Ning Zhou
- Chinese Academy of Sciences Key Laboratory of Brain Function and Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, China
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21
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Bergeron D, Laforest C, Carpentier S, Calvé A, Fafard-Couture É, Deschamps-Francoeur G, Scott MS. SnoRNA copy regulation affects family size, genomic location and family abundance levels. BMC Genomics 2021; 22:414. [PMID: 34090325 PMCID: PMC8178906 DOI: 10.1186/s12864-021-07757-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 03/17/2021] [Accepted: 05/26/2021] [Indexed: 12/03/2022] Open
Abstract
Background Small nucleolar RNAs (snoRNAs) are an abundant class of noncoding RNAs present in all eukaryotes and best known for their involvement in ribosome biogenesis. In mammalian genomes, many snoRNAs exist in multiple copies, resulting from recombination and retrotransposition from an ancestral snoRNA. To gain insight into snoRNA copy regulation, we used Rfam classification and normal human tissue expression datasets generated using low structure bias RNA-seq to characterize snoRNA families. Results We found that although box H/ACA families are on average larger than box C/D families, the number of expressed members is similar for both types. Family members can cover a wide range of average abundance values, but importantly, expression variability of individual members of a family is preferred over the total variability of the family, especially for box H/ACA snoRNAs, suggesting that while members are likely differentially regulated, mechanisms exist to ensure uniformity of the total family abundance across tissues. Box C/D snoRNA family members are mostly embedded in the same host gene while box H/ACA family members tend to be encoded in more than one different host, supporting a model in which box C/D snoRNA duplication occurred mostly by cis recombination while box H/ACA snoRNA families have gained copy members through retrotransposition. And unexpectedly, snoRNAs encoded in the same host gene can be regulated independently, as some snoRNAs within the same family vary in abundance in a divergent way between tissues. Conclusions SnoRNA copy regulation affects family sizes, genomic location of the members and controls simultaneously member and total family abundance to respond to the needs of individual tissues. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07757-1.
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Affiliation(s)
- Danny Bergeron
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Cédric Laforest
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Stacey Carpentier
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Annabelle Calvé
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Étienne Fafard-Couture
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Gabrielle Deschamps-Francoeur
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada.
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22
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Jacovetti C, Bayazit MB, Regazzi R. Emerging Classes of Small Non-Coding RNAs With Potential Implications in Diabetes and Associated Metabolic Disorders. Front Endocrinol (Lausanne) 2021; 12:670719. [PMID: 34040585 PMCID: PMC8142323 DOI: 10.3389/fendo.2021.670719] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/20/2021] [Indexed: 11/13/2022] Open
Abstract
Most of the sequences in the human genome do not code for proteins but generate thousands of non-coding RNAs (ncRNAs) with regulatory functions. High-throughput sequencing technologies and bioinformatic tools significantly expanded our knowledge about ncRNAs, highlighting their key role in gene regulatory networks, through their capacity to interact with coding and non-coding RNAs, DNAs and proteins. NcRNAs comprise diverse RNA species, including amongst others PIWI-interacting RNAs (piRNAs), involved in transposon silencing, and small nucleolar RNAs (snoRNAs), which participate in the modification of other RNAs such as ribosomal RNAs and transfer RNAs. Recently, a novel class of small ncRNAs generated from the cleavage of tRNAs or pre-tRNAs, called tRNA-derived small RNAs (tRFs) has been identified. tRFs have been suggested to regulate protein translation, RNA silencing and cell survival. While for other ncRNAs an implication in several pathologies is now well established, the potential involvement of piRNAs, snoRNAs and tRFs in human diseases, including diabetes, is only beginning to emerge. In this review, we summarize fundamental aspects of piRNAs, snoRNAs and tRFs biology. We discuss their biogenesis while emphasizing on novel sequencing technologies that allow ncRNA discovery and annotation. Moreover, we give an overview of genomic approaches to decrypt their mechanisms of action and to study their functional relevance. The review will provide a comprehensive landscape of the regulatory roles of these three types of ncRNAs in metabolic disorders by reporting their differential expression in endocrine pancreatic tissue as well as their contribution to diabetes incidence and diabetes-underlying conditions such as inflammation. Based on these discoveries we discuss the potential use of piRNAs, snoRNAs and tRFs as promising therapeutic targets in metabolic disorders.
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Affiliation(s)
- Cécile Jacovetti
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Mustafa Bilal Bayazit
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Romano Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
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23
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Logan RW, Xue X, Ketchesin KD, Hoffman G, Roussos P, Tseng G, McClung CA, Seney ML. Sex Differences in Molecular Rhythms in the Human Cortex. Biol Psychiatry 2021; 91:152-162. [PMID: 33934884 PMCID: PMC8423868 DOI: 10.1016/j.biopsych.2021.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND Diurnal rhythms in gene expression have been detected in the human brain. Previous studies found that males and females exhibit 24-hour rhythms in known circadian genes, with earlier peak expression in females. Whether there are sex differences in large-scale transcriptional rhythms in the cortex that align with observed sex differences in physiological and behavioral rhythms is currently unknown. METHODS Diurnal rhythmicity of gene expression was determined for males and females using RNA sequencing data from human postmortem dorsolateral prefrontal cortex (DLPFC) and anterior cingulate cortex (ACC). Sex differences among rhythmic genes were determined using significance cutoffs, threshold-free analyses, and R2 difference. Phase concordance was assessed across the DLPFC and ACC for males and females. Pathway and transcription factor analyses were also conducted on significantly rhythmic genes. RESULTS Canonical circadian genes had diurnal rhythms in both sexes with similar amplitude and phase. When analyses were expanded to the entire transcriptome, significant sex differences in transcriptional rhythms emerged. There were nearly twice as many rhythmic transcripts in the DLPFC in males and nearly 4 times as many rhythmic transcripts in the ACC in females. Results suggest a diurnal rhythm in synaptic transmission specific to the ACC in females (e.g., GABAergic [gamma-aminobutyric acidergic] and cholinergic neurotransmission). For males, there was phase concordance between the DLPFC and ACC, while phase asynchrony was found in females. CONCLUSIONS There are robust sex differences in molecular rhythms of genes in the DLPFC and ACC, providing potential mechanistic insights into how neurotransmission and synaptic function are modulated in a circadian-dependent and sex-specific manner.
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Affiliation(s)
- Ryan W Logan
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, Massachusetts; Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, Bar Harbor, Maine
| | - Xiangning Xue
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kyle D Ketchesin
- Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania; Translational Neuroscience Program, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania
| | - Gabriel Hoffman
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York
| | - Panos Roussos
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York; Mental Illness Research, Education, and Clinical Center, James J. Peters VA Medical Center, Bronx, New York
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Colleen A McClung
- Center for Systems Neurogenetics of Addiction, The Jackson Laboratory, Bar Harbor, Maine; Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania; Translational Neuroscience Program, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania
| | - Marianne L Seney
- Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania; Translational Neuroscience Program, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania.
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24
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Carpenter JS, Crouse JJ, Scott EM, Naismith SL, Wilson C, Scott J, Merikangas KR, Hickie IB. Circadian depression: A mood disorder phenotype. Neurosci Biobehav Rev 2021; 126:79-101. [PMID: 33689801 DOI: 10.1016/j.neubiorev.2021.02.045] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 02/18/2021] [Accepted: 02/28/2021] [Indexed: 12/15/2022]
Abstract
Major mood syndromes are among the most common and disabling mental disorders. However, a lack of clear delineation of their underlying pathophysiological mechanisms is a major barrier to prevention and optimised treatments. Dysfunction of the 24-h circadian system is a candidate mechanism that has genetic, behavioural, and neurobiological links to mood syndromes. Here, we outline evidence for a new clinical phenotype, which we have called 'circadian depression'. We propose that key clinical characteristics of circadian depression include disrupted 24-h sleep-wake cycles, reduced motor activity, low subjective energy, and weight gain. The illness course includes early age-of-onset, phenomena suggestive of bipolarity (defined by bidirectional associations between objective motor and subjective energy/mood states), poor response to conventional antidepressant medications, and concurrent cardiometabolic and inflammatory disturbances. Identifying this phenotype could be clinically valuable, as circadian-targeted strategies show promise for reducing depressive symptoms and stabilising illness course. Further investigation of underlying circadian disturbances in mood syndromes is needed to evaluate the clinical utility of this phenotype and guide the optimal use of circadian-targeted interventions.
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