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Kubra S, Sun M, Dion W, Catak A, Luong H, Wang H, Pan Y, Liu JJ, Ponna A, Sipula I, Jurczak MJ, Liu S, Zhu B. Epigenetic regulation of global proteostasis dynamics by RBBP5 ensures mammalian organismal health. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.13.612812. [PMID: 39314427 PMCID: PMC11419162 DOI: 10.1101/2024.09.13.612812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Proteostasis is vital for cellular health, with disruptions leading to pathologies including aging, neurodegeneration and metabolic disorders. Traditionally, proteotoxic stress responses were studied as acute reactions to various noxious factors; however, recent evidence reveals that many proteostasis stress-response genes exhibit ~12-hour ultradian rhythms under physiological conditions in mammals. These rhythms, driven by an XBP1s-dependent 12h oscillator, are crucial for managing proteostasis. By exploring the chromatin landscape of the murine 12h hepatic oscillator, we identified RBBP5, a key subunit of the COMPASS complex writing H3K4me3, as an essential epigenetic regulator of proteostasis. RBBP5 is indispensable for regulating both the hepatic 12h oscillator and transcriptional response to acute proteotoxic stress, acting as a co-activator for proteostasis transcription factor XBP1s. RBBP5 ablation leads to increased sensitivity to proteotoxic stress, chronic inflammation, and hepatic steatosis in mice, along with impaired autophagy and reduced cell survival in vitro. In humans, lower RBBP5 expression is associated with reduced adaptive stress-response gene expression and hepatic steatosis. Our findings establish RBBP5 as a central regulator of proteostasis, essential for maintaining mammalian organismal health.
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Affiliation(s)
- Syeda Kubra
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Michelle Sun
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - William Dion
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Ahmet Catak
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Hannah Luong
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Haokun Wang
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | | | - Jia-Jun Liu
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, U.S.A
- Organ Pathobiology and Therapeutics Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Aishwarya Ponna
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Ian Sipula
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Michael J. Jurczak
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
- Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Silvia Liu
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, U.S.A
- Organ Pathobiology and Therapeutics Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, U.S.A
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
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2
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Zhu B, Liu S, David NL, Dion W, Doshi NK, Siegel LB, Amorim T, Andrews RE, Kumar GVN, Li H, Irfan S, Pesaresi T, Sharma AX, Sun M, Fazeli PK, Steinhauser ML. Evidence for ~12-h ultradian gene programs in humans. NPJ BIOLOGICAL TIMING AND SLEEP 2024; 1:4. [PMID: 39148626 PMCID: PMC11325440 DOI: 10.1038/s44323-024-00005-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/11/2024] [Indexed: 08/17/2024]
Abstract
Mice and many marine organisms exhibit ~12-h ultradian rhythms, however, direct evidence of ~12-h ultradian rhythms in humans is lacking. Here, we performed prospective, temporal transcriptome profiling of peripheral white blood cells from three healthy humans. All three participants independently exhibited robust ~12-h transcriptional rhythms in molecular programs involved in RNA and protein metabolism, with strong homology to circatidal gene programs previously identified in Cnidarian marine species.
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Affiliation(s)
- Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA USA
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Silvia Liu
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Natalie L David
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- Neuroendocrinology Unit, Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- Center for Human Integrative Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - William Dion
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Nandini K Doshi
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- Center for Human Integrative Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Lauren B Siegel
- Neuroendocrinology Unit, Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Tânia Amorim
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- Neuroendocrinology Unit, Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- Center for Human Integrative Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Rosemary E Andrews
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- Center for Human Integrative Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - G V Naveen Kumar
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Hanwen Li
- Department of Statistics, Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA USA
| | - Saad Irfan
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Tristan Pesaresi
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- Center for Human Integrative Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Ankit X Sharma
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Michelle Sun
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Pouneh K Fazeli
- Neuroendocrinology Unit, Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- Center for Human Integrative Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Matthew L Steinhauser
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- Center for Human Integrative Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
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Flores CC, Pasetto NA, Wang H, Dimitrov AG, Davis JF, Jiang Z, Davis CJ, Gerstner JR. Sleep and diurnal alternative polyadenylation sites associated with human APA-linked brain disorders. RESEARCH SQUARE 2024:rs.3.rs-4707772. [PMID: 39149473 PMCID: PMC11326403 DOI: 10.21203/rs.3.rs-4707772/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Disruption of sleep and circadian rhythms are a comorbid feature of many pathologies, and can negatively influence many health conditions, including neurodegenerative disease, metabolic illness, cancer, and various neurological disorders. Genetic association studies linking sleep and circadian disturbances with disease susceptibility have mainly focused on changes in gene expression due to mutations, such as single-nucleotide polymorphisms. The interaction between sleep and/or circadian rhythms with the use of Alternative Polyadenylation (APA) has been largely undescribed, particularly in the context of other disorders. APA is a process that generates various transcript isoforms of the same gene affecting its mRNA translation, stability, localization, and subsequent function. Here we identified unique APAs expressed in rat brain over time-of-day, immediately following sleep deprivation, and the subsequent recovery period. From these data, we performed a secondary analysis of these sleep- or time-of-day associated PASs with recently described APA-linked human brain disorder susceptibility genes.
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Wyse CA, Rudderham LM, Nordon EA, Ince LM, Coogan AN, Lopez LM. Circadian Variation in the Response to Vaccination: A Systematic Review and Evidence Appraisal. J Biol Rhythms 2024; 39:219-236. [PMID: 38459699 PMCID: PMC11141079 DOI: 10.1177/07487304241232447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
Molecular timing mechanisms known as circadian clocks drive endogenous 24-h rhythmicity in most physiological functions, including innate and adaptive immunity. Consequently, the response to immune challenge such as vaccination might depend on the time of day of exposure. This study assessed whether the time of day of vaccination (TODV) is associated with the subsequent immune and clinical response by conducting a systematic review of previous studies. The Cochrane Library, PubMed, Google, Medline, and Embase were searched for studies that reported TODV and immune and clinical outcomes, yielding 3114 studies, 23 of which met the inclusion criteria. The global severe acute respiratory syndrome coronavirus 2 vaccination program facilitated investigation of TODV and almost half of the studies included reported data collected during the COVID-19 pandemic. There was considerable heterogeneity in the demography of participants and type of vaccine, and most studies were biased by failure to account for immune status prior to vaccination, self-selection of vaccination time, or confounding factors such as sleep, chronotype, and shiftwork. The optimum TODV was concluded to be afternoon (5 studies), morning (5 studies), morning and afternoon (1 study), midday (1 study), and morning or late afternoon (1 study), with the remaining 10 studies reporting no effect. Further research is required to understand the relationship between TODV and subsequent immune outcome and whether any clinical benefit outweighs the potential effect of this intervention on vaccine uptake.
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Affiliation(s)
- Cathy A. Wyse
- Kathleen Lonsdale Institute for Human Health Research and Department of Biology, Maynooth University, Maynooth, Ireland
| | - Laura M. Rudderham
- Kathleen Lonsdale Institute for Human Health Research and Department of Biology, Maynooth University, Maynooth, Ireland
| | - Enya A. Nordon
- Kathleen Lonsdale Institute for Human Health Research and Department of Biology, Maynooth University, Maynooth, Ireland
| | - Louise M. Ince
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA
| | - Andrew N. Coogan
- Kathleen Lonsdale Institute for Human Health Research and Department of Psychology, Maynooth University, Maynooth, Ireland
| | - Lorna M. Lopez
- Kathleen Lonsdale Institute for Human Health Research and Department of Biology, Maynooth University, Maynooth, Ireland
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Jackson JA, Stewart A, Cable J. Lunar-linked biological rhythms in the immune system of freshwater three-spined stickleback. DISCOVERY IMMUNOLOGY 2024; 3:kyae007. [PMID: 38863794 PMCID: PMC11165434 DOI: 10.1093/discim/kyae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/07/2024] [Accepted: 06/03/2024] [Indexed: 06/13/2024]
Abstract
Immune responses are widely accepted to be under circadian regulation via a molecular clock, with many practical consequences, but much less is known of how other biological rhythms could affect the immune system. In this study, we search for lunar rhythms (circalunar, circasemilunar, and circatidal cycles) in the immune expression of the recently marine-derived freshwater fish, the low-plate morph of the three-spined stickleback. We employed time series of immune expression (mRNA) measurements for 14 immune-associated genes, representing a variety of immunological pathways. Times series measurements were taken on fish populations in the wild, in seminatural outdoor mesocosms, and in the laboratory, according to sampling regimens originally designed to study circannual variation but with the additional potential to provide information about lunar variation. Our evidence best supported the existence of a very small endogenous tidal rhythm. This is consistent with previous suggestions of the existence of a primordial tidal endogenous clock, some elements of which may be conserved in animals evolving outside the marine environment.
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Affiliation(s)
- Joseph A Jackson
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Alexander Stewart
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Joanne Cable
- School of Biosciences, Cardiff University, Cardiff, UK
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Kwiatkowski ER, Rosenthal JJC, Emery P. Clocks at sea: the genome-editing tide is rising. Trends Genet 2024; 40:387-397. [PMID: 38336520 DOI: 10.1016/j.tig.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
The coastline is a particularly challenging environment for its inhabitants. Not only do they have to cope with the solar day and the passing of seasons, but they must also deal with tides. In addition, many marine species track the phase of the moon, especially to coordinate reproduction. Marine animals show remarkable behavioral and physiological adaptability, using biological clocks to anticipate specific environmental cycles. Presently, we lack a basic understanding of the molecular mechanisms underlying circatidal and circalunar clocks. Recent advances in genome engineering and the development of genetically tractable marine model organisms are transforming how we study these timekeeping mechanisms and opening a novel era in marine chronobiology.
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Affiliation(s)
- Erica R Kwiatkowski
- University of Massachusetts Chan Medical School, Department of Neurobiology, Worcester, MA 01605, USA
| | | | - Patrick Emery
- University of Massachusetts Chan Medical School, Department of Neurobiology, Worcester, MA 01605, USA.
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Brase L, Yu Y, McDade E, Harari O, Benitez BA. Comparative gene regulatory networks modulating APOE expression in microglia and astrocytes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.19.24306098. [PMID: 38699303 PMCID: PMC11065001 DOI: 10.1101/2024.04.19.24306098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Background Single-cell technologies have unveiled various transcriptional states in different brain cell types. Transcription factors (TFs) regulate the expression of related gene sets, thereby controlling these diverse expression states. Apolipoprotein E ( APOE ), a pivotal risk-modifying gene in Alzheimer's disease (AD), is expressed in specific glial transcriptional states associated with AD. However, it is still unknown whether the upstream regulatory programs that modulate its expression are shared across brain cell types or specific to microglia and astrocytes. Methods We used pySCENIC to construct state-specific gene regulatory networks (GRNs) for resting and activated cell states within microglia and astrocytes based on single-nucleus RNA sequencing data from AD patients' cortices from the Knight ADRC-DIAN cohort. We then identified replicating TF using data from the ROSMAP cohort. We identified sets of genes co-regulated with APOE by clustering the GRN target genes and identifying genes differentially expressed after the virtual knockout of TFs regulating APOE . We performed enrichment analyses on these gene sets and evaluated their overlap with genes found in AD GWAS loci. Results We identified an average of 96 replicating regulators for each microglial and astrocyte cell state. Our analysis identified the CEBP, JUN, FOS, and FOXO TF families as key regulators of microglial APOE expression. The steroid/thyroid hormone receptor families, including the THR TF family, consistently regulated APOE across astrocyte states, while CEBP and JUN TF families were also involved in resting astrocytes. AD GWAS-associated genes ( PGRN , FCGR3A , CTSH , ABCA1 , MARCKS , CTSB , SQSTM1 , TSC22D4 , FCER1G , and HLA genes) are co-regulated with APOE. We also uncovered that APOE-regulating TFs were linked to circadian rhythm ( BHLHE40 , DBP , XBP1 , CREM , SREBF1 , FOXO3 , and NR2F1 ). Conclusions Our findings reveal a novel perspective on the transcriptional regulation of APOE in the human brain. We found a comprehensive and cell-type-specific regulatory landscape for APOE , revealing distinct and shared regulatory mechanisms across microglia and astrocytes, underscoring the complexity of APOE regulation. APOE -co-regulated genes might also affect AD risk. Furthermore, our study uncovers a potential link between circadian rhythm disruption and APOE regulation, shedding new light on the pathogenesis of AD.
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Dion W, Tao Y, Chambers M, Zhao S, Arbuckle RK, Sun M, Kubra S, Nie Y, Ye M, Larsen MB, Camarco D, Ickes E, DuPont C, Wang H, Wang B, Liu S, Pi S, Chen BB, Chen Y, Chen X, Zhu B. Nuclear speckle rejuvenation alleviates proteinopathies at the expense of YAP1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590103. [PMID: 38659924 PMCID: PMC11042303 DOI: 10.1101/2024.04.18.590103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Current treatments targeting individual protein quality control have limited efficacy in alleviating proteinopathies, highlighting the prerequisite for a common upstream druggable target capable of global proteostasis modulation. Building on our prior research establishing nuclear speckles as pivotal organelles responsible for global proteostasis transcriptional control, we aim to alleviate proteinopathies through nuclear speckle rejuvenation. We identified pyrvinium pamoate as a small-molecule nuclear speckle rejuvenator that enhances protein quality control while suppressing YAP1 signaling via decreasing the surface tension of nuclear speckle condensates through interaction with the intrinsically disordered region of nuclear speckle scaffold protein SON. In pre-clinical models, pyrvinium pamoate reduced tauopathy and alleviated retina degeneration by promoting autophagy and ubiquitin-proteasome system. Aberrant nuclear speckle morphology, reduced protein quality control and increased YAP1 activity were also observed in human tauopathies. Our study uncovers novel therapeutic targets for tackling protein misfolding disorders within an expanded proteostasis framework encompassing nuclear speckles and YAP1.
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Affiliation(s)
- William Dion
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Yuren Tao
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Maci Chambers
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Shanshan Zhao
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Riley K. Arbuckle
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Michelle Sun
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Syeda Kubra
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Yuhang Nie
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Megan Ye
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Mads B. Larsen
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Daniel Camarco
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Eleanor Ickes
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Claire DuPont
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Haokun Wang
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Bingjie Wang
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
| | - Silvia Liu
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, U.S.A
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Shaohua Pi
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
| | - Bill B Chen
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Yuanyuan Chen
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, PA, U.S.A
| | - Xu Chen
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, U.S.A
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
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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] [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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Kembro JM, Flesia AG, Acosta-Rodríguez VA, Takahashi JS, Nieto PS. Dietary restriction modulates ultradian rhythms and autocorrelation properties in mice behavior. Commun Biol 2024; 7:303. [PMID: 38461321 PMCID: PMC10925031 DOI: 10.1038/s42003-024-05991-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/28/2024] [Indexed: 03/11/2024] Open
Abstract
Animal behavior emerges from integration of many processes with different spatial and temporal scales. Dynamical behavioral patterns, including daily and ultradian rhythms and the dynamical microstructure of behavior (i.e., autocorrelations properties), can be differentially affected by external cues. Identifying these patterns is important for understanding how organisms adapt to their environment, yet unbiased methods to quantify dynamical changes over multiple temporal scales are lacking. Herein, we combine a wavelet approach with Detrended Fluctuation Analysis to identify behavioral patterns and evaluate changes over 42-days in mice subjected to different dietary restriction paradigms. We show that feeding restriction alters dynamical patterns: not only are daily rhythms modulated but also the presence, phase and/or strength of ~12h-rhythms, as well as the nature of autocorrelation properties of feed-intake and wheel running behaviors. These results highlight the underlying complexity of behavioral architecture and offer insights into the multi-scale impact of feeding habits on physiology.
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Affiliation(s)
- Jackelyn Melissa Kembro
- Universidad Nacional de Córdoba (UNC), Facultad de Ciencias Exactas, Físicas y Naturales, Instituto de Ciencia y Tecnología de los Alimentos (ICTA) and Departamento de Química, Cátedra de Química Biológica, Córdoba, Córdoba, X5000HUA, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)- UNC, Córdoba, Córdoba, X5000HUA, Argentina
| | - Ana Georgina Flesia
- Universidad Nacional de Córdoba, Facultad de Matemática, Astronomía, Física y Computación, Córdoba, Córdoba, X5000HUA, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigaciones y Estudios de Matemática (CIEM, CONICET-UNC), Córdoba, Córdoba, X5000HUA, Argentina
| | - Victoria América Acosta-Rodríguez
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9111, USA
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9111, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9111, USA
| | - Paula Sofía Nieto
- Universidad Nacional de Córdoba, Facultad de Matemática, Astronomía, Física y Computación, Córdoba, Córdoba, X5000HUA, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Física Enrique Gaviola (IFEG, CONICET-UNC), Universidad Nacional de Córdoba, Córdoba, Córdoba, X5000HUA, Argentina.
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Cornelissen G, Gubin D, Otsuka K. Disease Conditions. CHRONOBIOLOGY AND CHRONOMEDICINE 2024:455-475. [DOI: 10.1039/bk9781839167553-00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/07/2024]
Abstract
Since clock genes are involved in all physiological systems, their role in most disease conditions is not surprising. To complement the information reviewed in Part II for each physiological system considered separately, this chapter illustrates the interdigitating network of interactions taking place within multiple physiological systems in any given disease condition. Circadian disruption, a common factor in disease, is almost inseparable from disturbed sleep, which is present in conditions ranging from psychological to cardio-metabolic and neurodegenerative conditions. Sleep disruption also modifies the immune system. Herein, we highlight the pervasive role played by the circadian system in pathology based on a few examples of selected disease conditions, including some sleep disorders, mental disorders, neurodegenerative conditions, and cancer.
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Affiliation(s)
- Germaine Cornelissen
- aHalberg Chronobiology Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Denis Gubin
- bTyumen State Medical University, Tyumen, Russia
- cTyumen Cardiology Research Center, Tomsk National Research Medical Center, Russian Academy of Science, Tomsk, Russia
| | - Kuniaki Otsuka
- aHalberg Chronobiology Center, University of Minnesota, Minneapolis, Minnesota, USA
- dExecutive Medical Center, Totsuka Royal Clinic, Tokyo Women’s Medical University, Tokyo, Japan
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12
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Unruh BA, Weidemann DE, Miao L, Kojima S. Coordination of rhythmic RNA synthesis and degradation orchestrates 24- and 12-h RNA expression patterns in mouse fibroblasts. Proc Natl Acad Sci U S A 2024; 121:e2314690121. [PMID: 38315868 PMCID: PMC10873638 DOI: 10.1073/pnas.2314690121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Circadian RNA expression is essential to ultimately regulate a plethora of downstream rhythmic biochemical, physiological, and behavioral processes. Both transcriptional and posttranscriptional mechanisms are considered important to drive rhythmic RNA expression; however, the extent to which each regulatory process contributes to the rhythmic RNA expression remains controversial. To systematically address this, we monitored RNA dynamics using metabolic RNA labeling technology during a circadian cycle in mouse fibroblasts. We find that rhythmic RNA synthesis is the primary contributor of 24-h RNA rhythms, while rhythmic degradation is more important for 12-h RNA rhythms. These rhythms were predominantly regulated by Bmal1 and/or the core clock mechanism, and the interplay between rhythmic synthesis and degradation has a significant impact in shaping rhythmic RNA expression patterns. Interestingly, core clock RNAs are regulated by multiple rhythmic processes and have the highest amplitude of synthesis and degradation, presumably critical to sustain robust rhythmicity of cell-autonomous circadian rhythms. Our study yields invaluable insights into the temporal dynamics of both 24- and 12-h RNA rhythms in mouse fibroblasts.
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Affiliation(s)
- Benjamin A. Unruh
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA24061
| | - Douglas E. Weidemann
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA24061
| | - Lin Miao
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA24061
| | - Shihoko Kojima
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA24061
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13
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Flores CC, Pasetto NA, Wang H, Dimitrov A, Davis JF, Jiang Z, Davis CJ, Gerstner JR. Identification of sleep and circadian alternative polyadenylation sites associated with APA-linked human brain disorders. RESEARCH SQUARE 2024:rs.3.rs-3867797. [PMID: 38313253 PMCID: PMC10836116 DOI: 10.21203/rs.3.rs-3867797/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Sleep and circadian rhythm disruptions are comorbid features of many pathologies and can negatively influence numerous health conditions, including degenerative diseases, metabolic illnesses, cancer, and various neurological disorders. Genetic association studies linking sleep and circadian disturbances with disease susceptibility have mainly focused on changes in gene expression due to mutations, such as single-nucleotide polymorphisms. Thus, associations between sleep and/or circadian rhythm and alternative polyadenylation (APA), particularly in the context of other health challenges, are largely undescribed. APA is a process that generates various transcript isoforms from the same gene, resulting in effects on mRNA translation, stability, localization, and subsequent function. Here, we have identified unique APAs in rat brain that exhibit time-of-day-dependent oscillations in expression as well as APAs that are altered by sleep deprivation and the subsequent recovery period. Genes affected by APA usage include Mapt/Tau, Ntrk2, Homer1A, Sin3band Sorl. Sorl1 has two APAs which cycle with a 24 h period, one additional APA cycles with a 12 h period and one more that is reduced during recovery sleep. Finally, we compared sleep- or circadian-associated APAs with recently described APA-linked brain disorder susceptibility genes and found 46 genes in common.
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14
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Zhu B, Liu S, David NL, Dion W, Doshi NK, Siegel LB, Amorim T, Andrews RE, Naveen Kumar GV, Li H, Irfan S, Pesaresi T, Sharma AX, Sun M, Fazeli PK, Steinhauser ML. Evidence for conservation of primordial ~12-hour ultradian gene programs in humans under free-living conditions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539021. [PMID: 37205600 PMCID: PMC10187241 DOI: 10.1101/2023.05.02.539021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
While circadian rhythms are entrained to the once daily light-dark cycle of the sun, many marine organisms exhibit ~12h ultradian rhythms corresponding to the twice daily movement of the tides. Although human ancestors emerged from circatidal environment millions of years ago, direct evidence of ~12h ultradian rhythms in humans is lacking. Here, we performed prospective, temporal transcriptome profiling of peripheral white blood cells and identified robust ~12h transcriptional rhythms from three healthy participants. Pathway analysis implicated ~12h rhythms in RNA and protein metabolism, with strong homology to the circatidal gene programs previously identified in Cnidarian marine species. We further observed ~12h rhythms of intron retention events of genes involved in MHC class I antigen presentation, synchronized to expression of mRNA splicing genes in all three participants. Gene regulatory network inference revealed XBP1, and GABP and KLF transcription factor family members as potential transcriptional regulators of human ~12h rhythms. These results suggest that human ~12h biological rhythms have a primordial evolutionary origin with important implications for human health and disease.
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Affiliation(s)
- Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
- Pittsburgh Liver Research Center, University of Pittsburgh; Pittsburgh, Pennsylvania, USA
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
| | - Silvia Liu
- Pittsburgh Liver Research Center, University of Pittsburgh; Pittsburgh, Pennsylvania, USA
- Department of Pathology, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
| | - Natalie L. David
- Aging Institute of UPMC, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
- Neuroendocrinology Unit, Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
- Center for Human Integrative Physiology, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
| | - William Dion
- Aging Institute of UPMC, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
| | - Nandini K Doshi
- Aging Institute of UPMC, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
- Center for Human Integrative Physiology, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
| | - Lauren B. Siegel
- Neuroendocrinology Unit, Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
| | - Tânia Amorim
- Aging Institute of UPMC, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
- Neuroendocrinology Unit, Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
- Center for Human Integrative Physiology, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
| | - Rosemary E. Andrews
- Aging Institute of UPMC, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
- Center for Human Integrative Physiology, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
| | - GV Naveen Kumar
- Aging Institute of UPMC, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
| | - Hanwen Li
- Department of Statistics, Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh; Pittsburgh, Pennsylvania, USA
| | - Saad Irfan
- Aging Institute of UPMC, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
| | - Tristan Pesaresi
- Aging Institute of UPMC, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
- Center for Human Integrative Physiology, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
| | - Ankit X. Sharma
- Aging Institute of UPMC, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
| | - Michelle Sun
- Aging Institute of UPMC, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
| | - Pouneh K. Fazeli
- Neuroendocrinology Unit, Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
- Center for Human Integrative Physiology, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
| | - Matthew L. Steinhauser
- Aging Institute of UPMC, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
- Center for Human Integrative Physiology, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
- Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania, USA
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15
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Brooks TG, Manjrekar A, Mrcˇela A, Grant GR. Meta-analysis of Diurnal Transcriptomics in Mouse Liver Reveals Low Repeatability of Rhythm Analyses. J Biol Rhythms 2023; 38:556-570. [PMID: 37382061 PMCID: PMC10615793 DOI: 10.1177/07487304231179600] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
To assess the consistency of biological rhythms across studies, 57 public mouse liver tissue timeseries totaling 1096 RNA-seq samples were obtained and analyzed. Only the control groups of each study were included, to create comparable data. Technical factors in RNA-seq library preparation were the largest contributors to transcriptome-level differences, beyond biological or experiment-specific factors such as lighting conditions. Core clock genes were remarkably consistent in phase across all studies. Overlap of genes identified as rhythmic across studies was generally low, with no pair of studies having over 60% overlap. Distributions of phases of significant genes were remarkably inconsistent across studies, but the genes that consistently identified as rhythmic had acrophase clustering near ZT0 and ZT12. Despite the discrepancies between single-study analyses, cross-study analyses found substantial consistency. Running compareRhythms on each pair of studies identified a median of only 11% of the identified rhythmic genes as rhythmic in only 1 of the 2 studies. Data were integrated across studies in a joint and individual variance estimate (JIVE) analysis, which showed that the top 2 components of joint within-study variation are determined by time of day. A shape-invariant model with random effects was fit to the genes to identify the underlying shape of the rhythms, consistent across all studies, including identifying 72 genes with consistently multiple peaks.
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Affiliation(s)
- Thomas G. Brooks
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aditi Manjrekar
- Department of Neuroscience, The University of Texas at Dallas, Richardson, Texas
| | - Antonijo Mrcˇela
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gregory R. Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
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16
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Dubois‐Chevalier J, Gheeraert C, Berthier A, Boulet C, Dubois V, Guille L, Fourcot M, Marot G, Gauthier K, Dubuquoy L, Staels B, Lefebvre P, Eeckhoute J. An extended transcription factor regulatory network controls hepatocyte identity. EMBO Rep 2023; 24:e57020. [PMID: 37424431 PMCID: PMC10481658 DOI: 10.15252/embr.202357020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/11/2023] Open
Abstract
Cell identity is specified by a core transcriptional regulatory circuitry (CoRC), typically limited to a small set of interconnected cell-specific transcription factors (TFs). By mining global hepatic TF regulons, we reveal a more complex organization of the transcriptional regulatory network controlling hepatocyte identity. We show that tight functional interconnections controlling hepatocyte identity extend to non-cell-specific TFs beyond the CoRC, which we call hepatocyte identity (Hep-ID)CONNECT TFs. Besides controlling identity effector genes, Hep-IDCONNECT TFs also engage in reciprocal transcriptional regulation with TFs of the CoRC. In homeostatic basal conditions, this translates into Hep-IDCONNECT TFs being involved in fine tuning CoRC TF expression including their rhythmic expression patterns. Moreover, a role for Hep-IDCONNECT TFs in the control of hepatocyte identity is revealed in dedifferentiated hepatocytes where Hep-IDCONNECT TFs are able to reset CoRC TF expression. This is observed upon activation of NR1H3 or THRB in hepatocarcinoma or in hepatocytes subjected to inflammation-induced loss of identity. Our study establishes that hepatocyte identity is controlled by an extended array of TFs beyond the CoRC.
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Affiliation(s)
| | - Céline Gheeraert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Alexandre Berthier
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Clémence Boulet
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Vanessa Dubois
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
- Basic and Translational Endocrinology (BaTE), Department of Basic and Applied Medical SciencesGhent UniversityGhentBelgium
| | - Loïc Guille
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Marie Fourcot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 – UAR 2014 – PLBSLilleFrance
| | - Guillemette Marot
- Univ. Lille, Inria, CHU Lille, ULR 2694 – METRICS: Évaluation des technologies de santé et des pratiques médicalesLilleFrance
| | - Karine Gauthier
- Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS UMR 5242, INRAE USC 1370, École Normale Supérieure de LyonLyonFrance
| | - Laurent Dubuquoy
- Univ. Lille, Inserm, CHU Lille, U1286 – INFINITE – Institute for Translational Research in InflammationLilleFrance
| | - Bart Staels
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Philippe Lefebvre
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Jérôme Eeckhoute
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
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17
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Unruh BA, Weidemann DE, Kojima S. Coordination of rhythmic RNA synthesis and degradation orchestrates 24-hour and 12-hour RNA expression patterns in mouse fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550672. [PMID: 37546997 PMCID: PMC10402069 DOI: 10.1101/2023.07.26.550672] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Circadian RNA expression is essential to ultimately regulate a plethora of downstream rhythmic biochemical, physiological, and behavioral processes. Both transcriptional and post-transcriptional mechanisms are considered important to drive rhythmic RNA expression, however, the extent to which each regulatory process contributes to the rhythmic RNA expression remains controversial. To systematically address this, we monitored RNA dynamics using metabolic RNA labeling technology during a circadian cycle in mouse fibroblasts. We find that rhythmic RNA synthesis is the primary contributor of 24 hr RNA rhythms, while rhythmic degradation is more important for 12 hr RNA rhythms. These rhythms were predominantly regulated by Bmal1 and/or the core clock mechanism, and interplay between rhythmic synthesis and degradation has a significant impact in shaping rhythmic RNA expression patterns. Interestingly, core clock RNAs are regulated by multiple rhythmic processes and have the highest amplitude of synthesis and degradation, presumably critical to sustain robust rhythmicity of cell-autonomous circadian rhythms. Our study yields invaluable insights into the temporal dynamics of both 24 hr and 12 hr RNA rhythms in mouse fibroblasts.
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Affiliation(s)
- Benjamin A Unruh
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA USA
| | - Douglas E Weidemann
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA USA
| | - Shihoko Kojima
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA USA
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18
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Otsuka K, Cornelissen G, Kubo Y, Shibata K, Mizuno K, Aiba T, Furukawa S, Ohshima H, Mukai C. Methods for assessing change in brain plasticity at night and psychological resilience during daytime between repeated long-duration space missions. Sci Rep 2023; 13:10909. [PMID: 37407662 DOI: 10.1038/s41598-023-36389-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/02/2023] [Indexed: 07/07/2023] Open
Abstract
This study was designed to examine the feasibility of analyzing heart rate variability (HRV) data from repeat-flier astronauts at matching days on two separate missions to assess any effect of repeated missions on brain plasticity and psychological resilience, as conjectured by Demertzi. As an example, on the second mission of a healthy astronaut studied about 20 days after launch, sleep duration lengthened, sleep quality improved, and spectral power (ms2) co-varying with activity of the salience network (SN) increased at night. HF-component (0.15-0.50 Hz) increased by 61.55%, and HF-band (0.30-0.40 Hz) by 92.60%. Spectral power of HRV indices during daytime, which correlate negatively with psychological resilience, decreased, HF-component by 22.18% and HF-band by 37.26%. LF-component and LF-band, reflecting activity of the default mode network, did not change significantly. During the second mission, 24-h acrophases of HRV endpoints did not change but the 12-h acrophase of TF-HRV did (P < 0.0001), perhaps consolidating the circadian system to help adapt to space by taking advantage of brain plasticity at night and psychological resilience during daytime. While this N-of-1 study prevents drawing definitive conclusions, the methodology used herein to monitor markers of brain plasticity could pave the way for further studies that could add to the present results.
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Affiliation(s)
- Kuniaki Otsuka
- Space Biomedical Research Group, Japan Aerospace Exploration Agency, Ibaraki, Japan.
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN, USA.
- Tokyo Women's Medical University, Tokyo, Japan.
| | | | - Yutaka Kubo
- Tokyo Women's Medical University, Tokyo, Japan
| | | | - Koh Mizuno
- Space Biomedical Research Group, Japan Aerospace Exploration Agency, Ibaraki, Japan
- Faculty of Education, Tohoku Fukushi University, Miyagi, Japan
| | - Tatsuya Aiba
- Space Biomedical Research Group, Japan Aerospace Exploration Agency, Ibaraki, Japan
| | - Satoshi Furukawa
- Space Biomedical Research Group, Japan Aerospace Exploration Agency, Ibaraki, Japan
| | - Hiroshi Ohshima
- Space Biomedical Research Group, Japan Aerospace Exploration Agency, Ibaraki, Japan
| | - Chiaki Mukai
- Space Biomedical Research Group, Japan Aerospace Exploration Agency, Ibaraki, Japan
- Tokyo University of Science, Tokyo, Japan
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19
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Zhu B, Liu S. Preservation of ∼12-h ultradian rhythms of gene expression of mRNA and protein metabolism in the absence of canonical circadian clock. Front Physiol 2023; 14:1195001. [PMID: 37324401 PMCID: PMC10267751 DOI: 10.3389/fphys.2023.1195001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/19/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction: Besides the ∼24-h circadian rhythms, ∼12-h ultradian rhythms of gene expression, metabolism and behaviors exist in animals ranging from crustaceans to mammals. Three major hypotheses were proposed on the origin and mechanisms of regulation of ∼12-h rhythms, namely, that they are not cell-autonomous and controlled by a combination of the circadian clock and environmental cues, that they are regulated by two anti-phase circadian transcription factors in a cell autonomous manner, or that they are established by a cell-autonomous ∼12-h oscillator. Methods: To distinguish among these possibilities, we performed a post hoc analysis of two high temporal resolution transcriptome dataset in animals and cells lacking the canonical circadian clock. Results: In both the liver of BMAL1 knockout mice and Drosophila S2 cells, we observed robust and prevalent ∼12-h rhythms of gene expression enriched in fundamental processes of mRNA and protein metabolism that show large convergence with those identified in wild-type mice liver. Bioinformatics analysis further predicted ELF1 and ATF6B as putative transcription factors regulating the ∼12-h rhythms of gene expression independently of the circadian clock in both fly and mice. Discussion: These findings provide additional evidence to support the existence of an evolutionarily conserved 12-h oscillator that controls ∼12-h rhythms of gene expression of protein and mRNA metabolism in multiple species.
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Affiliation(s)
- Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, United States
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Silvia Liu
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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20
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Otsuka K, Murakami S, Okajima K, Shibata K, Kubo Y, Gubin DG, Beaty LA, Cornelissen G. Appropriate Circadian-Circasemidian Coupling Protects Blood Pressure from Morning Surge and Promotes Human Resilience and Wellbeing. Clin Interv Aging 2023; 18:755-769. [PMID: 37193339 PMCID: PMC10183193 DOI: 10.2147/cia.s398957] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 05/02/2023] [Indexed: 05/18/2023] Open
Abstract
Background Blood pressure (BP) variability is involved in the appraisal of threat and safety, and can serve as a potential marker of psychological resilience against stress. The relationship between biological rhythms of BP and resilience was cross-sectionally assessed by 7-day/24-hour chronobiologic screening in a rural Japanese community (Tosa), with focus on the 12-hour component and the "circadian-circasemidian coupling" of systolic (S) BP. Subjects and Methods Tosa residents (N = 239, 147 women, 23-74 years), free of anti-hypertensive medication, completed 7-day/24-hour ambulatory BP monitoring. The circadian-circasemidian coupling was determined individually by computing the difference between the circadian phase and the circasemidian morning-phase of SBP. Participants were classified into three groups: those with a short coupling interval of about 4.5 hours (Group A), those with an intermediate coupling interval of about 6.0 hours (Group B), and those with a long coupling interval of about 8.0 hours (Group C). Results Residents of Group B who showed optimal circadian-circasemidian coordination had less pronounced morning and evening SBP surges, as compared to residents of Group A (10.82 vs 14.29 mmHg, P < 0.0001) and Group C (11.86 vs 15.21 mmHg, P < 0.0001), respectively. The incidence of morning or evening SBP surge was less in Group B than in Group A (P < 0.0001) or Group C (P < 0.0001). Group B residents showed highest measures of wellbeing and psychological resilience, assessed by good relation with friends (P < 0.05), life satisfaction (P < 0.05), and subjective happiness (P < 0.05). A disturbed circadian-circasemidian coupling was associated with elevated BP, dyslipidemia, arteriosclerosis and a depressive mood. Conclusion The circadian-circasemidian coupling of SBP could serve as a new biomarker in clinical practice to guide precision medicine interventions aimed at achieving properly timed rhythms, and thereby resilience and wellbeing.
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Affiliation(s)
- Kuniaki Otsuka
- Tokyo Women’s Medical University, Tokyo, Japan
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN, USA
| | - Shougo Murakami
- Department of Cardiovascular Medicine, Soseikai General Hospital, Kyoto, Japan
| | - Kiyotaka Okajima
- Cardiovascular Internal Medicine, Higashi Omiya General Hospital, Saitama, Japan
| | | | - Yutaka Kubo
- Department of Medicine, Machida Keisen Hospital, Tokyo, Japan
| | - Denis G Gubin
- Laboratory for Chronobiology and Chronomedicine, Research Institute of Biomedicine and Biomedical Technologies, Medical University, Tyumen, 625023, Russia
- Department of Biology, Medical University, Tyumen, 625023, Russia
- Tyumen Cardiology Research Center, Tomsk National Research Medical Center, Russian Academy of Science, Tomsk, Russia
| | - Larry A Beaty
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN, USA
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21
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Zhu B, Liu S. Preservation of ∼12-hour ultradian rhythms of gene expression of mRNA and protein metabolism in the absence of canonical circadian clock. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538977. [PMID: 37205336 PMCID: PMC10187213 DOI: 10.1101/2023.05.01.538977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Besides the ∼24-hour circadian rhythms, ∼12-hour ultradian rhythms of gene expression, metabolism and behaviors exist in animals ranging from crustaceans to mammals. Three major hypotheses were proposed on the origin and mechanisms of regulation of ∼12-hour rhythms, namely that they are not cell-autonomous and controlled by a combination of the circadian clock and environmental cues, that they are regulated by two anti-phase circadian transcriptional factors in a cell-autonomous manner, or that they are established by a cell-autonomous ∼12-hour oscillator. To distinguish among these possibilities, we performed a post-hoc analysis of two high temporal resolution transcriptome dataset in animals and cells lacking the canonical circadian clock. In both the liver of BMAL1 knockout mice and Drosophila S2 cells, we observed robust and prevalent ∼12-hour rhythms of gene expression enriched in fundamental processes of mRNA and protein metabolism that show large convergence with those identified in wild-type mice liver. Bioinformatics analysis further predicted ELF1 and ATF6B as putative transcription factors regulating the ∼12-hour rhythms of gene expression independently of the circadian clock in both fly and mice. These findings provide additional evidence to support the existence of an evolutionarily conserved 12-hour oscillator that controls ∼12-hour rhythms of gene expression of protein and mRNA metabolism in multiple species.
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22
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Kembro JM, Flesia AG, Nieto PS, Caliva JM, Lloyd D, Cortassa S, Aon MA. A dynamically coherent pattern of rhythms that matches between distant species across the evolutionary scale. Sci Rep 2023; 13:5326. [PMID: 37005423 PMCID: PMC10067965 DOI: 10.1038/s41598-023-32286-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/25/2023] [Indexed: 04/04/2023] Open
Abstract
We address the temporal organization of circadian and ultradian rhythms, crucial for understanding biological timekeeping in behavior, physiology, metabolism, and alignment with geophysical time. Using a newly developed five-steps wavelet-based approach to analyze high-resolution time series of metabolism in yeast cultures and spontaneous movement, metabolism, and feeding behavior in mice, rats, and quails, we describe a dynamically coherent pattern of rhythms spanning over a broad range of temporal scales (hours to minutes). The dynamic pattern found shares key features among the four, evolutionary distant, species analyzed. Specifically, a branching appearance given by splitting periods from 24 h into 12 h, 8 h and below in mammalian and avian species, or from 14 h down to 0.07 h in yeast. Scale-free fluctuations with long-range correlations prevail below ~ 4 h. Synthetic time series modeling support a scenario of coexisting behavioral rhythms, with circadian and ultradian rhythms at the center of the emergent pattern observed.
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Affiliation(s)
- J M Kembro
- Instituto de Investigaciones Biológicas y Tecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Facultad de Ciencias Exactas, Físicas y Naturales, Instituto de Ciencia y Tecnología de los Alimentos (ICTA), Universidad Nacional de Córdoba, Córdoba, Argentina
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Departamento de Química, Cátedra de Química Biológica, Córdoba, Argentina
| | - A G Flesia
- Facultad de Matemática, Astronomía, Física y Computación, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigación y Estudios de La Matemática (CIEM, CONICET-UNC), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - P S Nieto
- Facultad de Matemática, Astronomía, Física y Computación, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Física Enrique Gaviola (IFEG, CONICET-UNC), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - J M Caliva
- Instituto de Investigaciones Biológicas y Tecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - D Lloyd
- Schools of Bioscience and Engineering, Cardiff University, Cardiff, Wales, UK
| | - S Cortassa
- Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Baltimore, MD, USA
| | - M A Aon
- Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Baltimore, MD, USA.
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA.
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23
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Asher G, Zhu B. Beyond circadian rhythms: emerging roles of ultradian rhythms in control of liver functions. Hepatology 2023; 77:1022-1035. [PMID: 35591797 PMCID: PMC9674798 DOI: 10.1002/hep.32580] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 12/08/2022]
Abstract
The mammalian liver must cope with various metabolic and physiological changes that normally recur every day and primarily stem from daily cycles of rest-activity and fasting-feeding. Although a large body of evidence supports the reciprocal regulation of circadian rhythms and liver function, the research on the hepatic ultradian rhythms have largely been lagging behind. However, with the advent of more cost-effective high-throughput omics technologies, high-resolution time-lapse imaging, and more robust and powerful mathematical tools, several recent studies have shed new light on the presence and functions of hepatic ultradian rhythms. In this review, we will first very briefly discuss the basic principles of circadian rhythms, and then cover in greater details the recent literature related to ultradian rhythms. Specifically, we will highlight the prevalence and mechanisms of hepatic 12-h rhythms, and 8-h rhythms, which cycle at the second and third harmonics of circadian frequency. Finally, we also refer to ultradian rhythms with other frequencies and examine the limitations of the current approaches as well as the challenges related to identifying ultradian rhythm and addressing their molecular underpinnings.
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Affiliation(s)
- Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pennsylvania, USA
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania, USA
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24
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Otsuka K, Cornelissen G, Weydahl A, Gubin D, Beaty LA, Murase M. Rules of Heliogeomagnetics Diversely Coordinating Biological Rhythms and Promoting Human Health. APPLIED SCIENCES 2023; 13:951. [DOI: 10.3390/app13020951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/07/2024]
Abstract
This investigation reviews how geomagnetic activity affects the circadian variation in blood pressure (BP) and heart rate (HR) and their variabilities of clinically healthy individuals. A small study in Alta, Norway (latitude of 70.0° N), serves to illustrate the methodology used to outline rules of procedure in exploring heliogeomagnetic effects on human physiology. Volunteers in the Alta study were monitored for at least 2 days between 18 March 2002 and 9 January 2005. Estimates of the circadian characteristics of BP and HR by cosinor and the Maximum Entropy Method (MEM) indicate an increase in the circadian amplitude of systolic (S) BP on geomagnetic-disturbance days compared to quiet days (p = 0.0236). Geomagnetic stimulation was found to be circadian-phase dependent, with stimulation in the evening inducing a 49.2% increase in the circadian amplitude of SBP (p = 0.0003), not observed in relation to stimulation in the morning. In two participants monitored for 7 days, the circadian amplitude of SBP decreased by 23.4% on an extremely disturbed day but increased by 50.3% on moderately disturbed days (p = 0.0044), suggesting a biphasic (hormetic) reaction of the circadian SBP rhythm to geomagnetics. These results indicate a possible role of geomagnetic fluctuations in modulating the circadian system.
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Affiliation(s)
- Kuniaki Otsuka
- Tokyo Women’s Medical University, Tokyo 162-8666, Japan
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Germaine Cornelissen
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Andi Weydahl
- School of Sport Sciences, The Arctic University of Norway, Campus Alta, N-9509 Alta, Norway
| | - Denis Gubin
- Laboratory for Chronobiology and Chronomedicine, Research Institute of Biomedicine and Biomedical Technologies, Medical University, 625023 Tyumen, Russia
- Department of Biology, Medical University, 625023 Tyumen, Russia
- Tyumen Cardiology Research Center, Tomsk National Research Medical Center, Russian Academy of Science, 634009 Tomsk, Russia
| | - Larry A. Beaty
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Masatoshi Murase
- Yukawa Institute for Theoretical Physics, Kyoto University, Kyoto 606-8502, Japan
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25
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Scott MR, Zong W, Ketchesin KD, Seney ML, Tseng GC, Zhu B, McClung CA. Twelve-hour rhythms in transcript expression within the human dorsolateral prefrontal cortex are altered in schizophrenia. PLoS Biol 2023; 21:e3001688. [PMID: 36693045 PMCID: PMC9873190 DOI: 10.1371/journal.pbio.3001688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 12/01/2022] [Indexed: 01/25/2023] Open
Abstract
Twelve-hour (12 h) ultradian rhythms are a well-known phenomenon in coastal marine organisms. While 12 h cycles are observed in human behavior and physiology, no study has measured 12 h rhythms in the human brain. Here, we identify 12 h rhythms in transcripts that either peak at sleep/wake transitions (approximately 9 AM/PM) or static times (approximately 3 PM/AM) in the dorsolateral prefrontal cortex, a region involved in cognition. Subjects with schizophrenia (SZ) lose 12 h rhythms in genes associated with the unfolded protein response and neuronal structural maintenance. Moreover, genes involved in mitochondrial function and protein translation, which normally peak at sleep/wake transitions, peak instead at static times in SZ, suggesting suboptimal timing of these essential processes.
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Affiliation(s)
- Madeline R. Scott
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Wei Zong
- Department of Bioinformatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kyle D. Ketchesin
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Marianne L. Seney
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - George C. Tseng
- Department of Bioinformatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Colleen A. McClung
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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26
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Rinsky M, Weizman E, Ben-Asher HW, Eyal G, Zhu B, Levy O. Temporal gene expression patterns in the coral Euphyllia paradivisa reveal the complexity of biological clocks in the cnidarian-algal symbiosis. SCIENCE ADVANCES 2022; 8:eabo6467. [PMID: 36112690 PMCID: PMC9481131 DOI: 10.1126/sciadv.abo6467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/02/2022] [Indexed: 05/25/2023]
Abstract
Studying chronobiology in reef-building corals is challenging due to the tightly coupled symbiosis with their photosynthetic algae, Symbiodiniaceae. Although symbiosis requires metabolic synchronization and coordination of cellular processes in the holobiont, the cross-talk between the host and symbiont's clocks is still puzzling. Here, we use the mesophotic coral Euphyllia paradivisa to examine temporal gene expression patterns in symbiotic and aposymbiotic morphs exposed to natural light/dark cycles and constant darkness. Our comparative transcriptomic analyses revealed circadian and circatidal cycles of gene expression with a predominant diel pattern in both coral morphs. We found a substantial number of transcripts consistently rhythmic under both light conditions, including genes likely involved in the cnidarians' circadian clock, thus indicating that an endogenous clock, which can oscillate independently from the Symbiodiniaceae clock, exists in E. paradivisa. The analysis further manifests the remarkable impacts of symbiosis on transcriptional rhythms and implies that the algae's presence influences the host's biorhythm.
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Affiliation(s)
- Mieka Rinsky
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eviatar Weizman
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Hiba Waldman Ben-Asher
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Gal Eyal
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
- ARC Centre of Excellence for Coral Reef Studies, School of Biological Sciences, University of Queensland St. Lucia, Queensland 4072, Australia
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
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27
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Penny HA, Domingues RG, Krauss MZ, Melo-Gonzalez F, Lawson MA, Dickson S, Parkinson J, Hurry M, Purse C, Jegham E, Godinho-Silva C, Rendas M, Veiga-Fernandes H, Bechtold DA, Grencis RK, Toellner KM, Waisman A, Swann JR, Gibbs JE, Hepworth MR. Rhythmicity of intestinal IgA responses confers oscillatory commensal microbiota mutualism. Sci Immunol 2022; 7:eabk2541. [PMID: 36054336 PMCID: PMC7613662 DOI: 10.1126/sciimmunol.abk2541] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Interactions between the mammalian host and commensal microbiota are enforced through a range of immune responses that confer metabolic benefits and promote tissue health and homeostasis. Immunoglobulin A (IgA) responses directly determine the composition of commensal species that colonize the intestinal tract but require substantial metabolic resources to fuel antibody production by tissue-resident plasma cells. Here, we demonstrate that IgA responses are subject to diurnal regulation over the course of a circadian day. Specifically, the magnitude of IgA secretion, as well as the transcriptome of intestinal IgA+ plasma cells, was found to exhibit rhythmicity. Oscillatory IgA responses were found to be entrained by time of feeding and were also found to be in part coordinated by the plasma cell-intrinsic circadian clock via deletion of the master clock gene Arntl. Moreover, reciprocal interactions between the host and microbiota dictated oscillatory dynamics among the commensal microbial community and its associated transcriptional and metabolic activity in an IgA-dependent manner. Together, our findings suggest that circadian networks comprising intestinal IgA, diet, and the microbiota converge to align circadian biology in the intestinal tract and to ensure host-microbial mutualism.
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Affiliation(s)
- Hugo A. Penny
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, M13 9PL, Manchester, United Kingdom
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, M13 9PL, Manchester, United Kingdom
| | - Rita G. Domingues
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, M13 9PL, Manchester, United Kingdom
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, M13 9PL, Manchester, United Kingdom
| | - Maria Z. Krauss
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, M13 9PL, Manchester, United Kingdom
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, M13 9PL, Manchester, United Kingdom
| | - Felipe Melo-Gonzalez
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, M13 9PL, Manchester, United Kingdom
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, M13 9PL, Manchester, United Kingdom
| | - Melissa A.E. Lawson
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, M13 9PL, Manchester, United Kingdom
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, M13 9PL, Manchester, United Kingdom
| | - Suzanna Dickson
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, M13 9PL, Manchester, United Kingdom
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, M13 9PL, Manchester, United Kingdom
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, M13 9PL, Manchester, United Kingdom
| | - James Parkinson
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, M13 9PL, Manchester, United Kingdom
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, M13 9PL, Manchester, United Kingdom
| | - Madeleine Hurry
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, M13 9PL, Manchester, United Kingdom
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, M13 9PL, Manchester, United Kingdom
| | - Catherine Purse
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, M13 9PL, Manchester, United Kingdom
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, M13 9PL, Manchester, United Kingdom
| | - Emna Jegham
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, M13 9PL, Manchester, United Kingdom
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, M13 9PL, Manchester, United Kingdom
| | | | - Miguel Rendas
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | | | - David A. Bechtold
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, M13 9PL, Manchester, United Kingdom
| | - Richard K. Grencis
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, M13 9PL, Manchester, United Kingdom
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, M13 9PL, Manchester, United Kingdom
- Wellcome Centre for Cell Matrix Research, University of Manchester, M13 9PL, Manchester, United Kingdom
| | - Kai-Michael Toellner
- Institute of Immunology and Immunotherapy, College of Medical & Dental Sciences, Medical School, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ari Waisman
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Jonathan R. Swann
- School of Human Development and Health, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, United Kingdom
| | - Julie E. Gibbs
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, M13 9PL, Manchester, United Kingdom
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, M13 9PL, Manchester, United Kingdom
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, M13 9PL, Manchester, United Kingdom
| | - Matthew R. Hepworth
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, M13 9PL, Manchester, United Kingdom
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, M13 9PL, Manchester, United Kingdom
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28
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Zhu B. Logic of the Temporal Compartmentalization of the Hepatic Metabolic Cycle. Physiology (Bethesda) 2022; 37:0. [PMID: 35658626 PMCID: PMC9394779 DOI: 10.1152/physiol.00003.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/05/2022] [Accepted: 05/28/2022] [Indexed: 12/25/2022] Open
Abstract
The mammalian liver must cope with various metabolic and physiological changes that normally recur every day and result primarily from rest-activity and fasting-feeding cycles. In this article, I present evidence supporting a temporal compartmentalization of rhythmic hepatic metabolic processes into four main clusters: regulation of energy homeostasis, maintenance of information integrity, immune response, and genetic information flow. I further review literatures and discuss how both the circadian and the newly discovered 12-h ultradian clock work together to regulate these four temporally separated processes in mouse liver, which, interestingly, is largely uncoupled from the liver zonation regulation.
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Affiliation(s)
- Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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29
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Unconscious mind activates central cardiovascular network and promotes adaptation to microgravity possibly anti-aging during 1-year-long spaceflight. Sci Rep 2022; 12:11862. [PMID: 35831420 PMCID: PMC9279338 DOI: 10.1038/s41598-022-14858-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 06/14/2022] [Indexed: 12/12/2022] Open
Abstract
The intrinsic cardiovascular regulatory system (β, 0.00013–0.02 Hz) did not adapt to microgravity after a 6-month spaceflight. The infraslow oscillation (ISO, 0.01–0.10 Hz) coordinating brain dynamics via thalamic astrocytes plays a key role in the adaptation to novel environments. We investigate the adaptive process of a healthy astronaut during a 12-month-long spaceflight by analyzing heart rate variability (HRV) in the LF (0.01–0.05 Hz) and MF1 (0.05–0.10 Hz) bands for two consecutive days on four occasions: before launch, at 1-month (ISS01) and 11-month (ISS02) in space, and after return to Earth. Alteration of β during ISS01 improved during ISS02 (P = 0.0167). During ISS01, LF and MF1 bands, reflecting default mode network (DMN) activity, started to increase at night (by 43.1% and 32.0%, respectively), when suprachiasmatic astrocytes are most active, followed by a 25.9% increase in MF1-band throughout the entire day during ISS02, larger at night (47.4%) than during daytime. Magnetic declination correlated positively with β during ISS01 (r = 0.6706, P < 0.0001) and ISS02 (r = 0.3958, P = 0.0095). Magnetic fluctuations may affect suprachiasmatic astrocytes, and the DMN involving ISOs and thalamic astrocytes may then be activated, first at night, then during the entire day, a mechanism that could perhaps promote an anti-aging effect noted in other investigations.
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30
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A novel approach GRNTSTE to reconstruct gene regulatory interactions applied to a case study for rat pineal rhythm gene. Sci Rep 2022; 12:10227. [PMID: 35715583 PMCID: PMC9205975 DOI: 10.1038/s41598-022-14903-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/14/2022] [Indexed: 01/13/2023] Open
Abstract
Accurate inference and prediction of gene regulatory network are very important for understanding dynamic cellular processes. The large-scale time series genomics data are helpful to reveal the molecular dynamics and dynamic biological processes of complex biological systems. Firstly, we collected the time series data of the rat pineal gland tissue in the natural state according to a fixed sampling rate, and performed whole-genome sequencing. The large-scale time-series sequencing data set of rat pineal gland was constructed, which includes 480 time points, the time interval between adjacent time points is 3 min, and the sampling period is 24 h. Then, we proposed a new method of constructing gene expression regulatory network, named the gene regulatory network based on time series data and entropy transfer (GRNTSTE) method. The method is based on transfer entropy and large-scale time-series gene expression data to infer the causal regulatory relationship between genes in a data-driven mode. The comparative experiments prove that GRNTSTE has better performance than dynamical gene network inference with ensemble of trees (dynGENIE3) and SCRIBE, and has similar performance to TENET. Meanwhile, we proved that the performance of GRNTSTE is slightly lower than that of SINCERITIES method and better than other gene regulatory network construction methods in BEELINE framework, which is based on the BEELINE data set. Finally, the rat pineal rhythm gene expression regulatory network was constructed by us based on the GRNTSTE method, which provides an important reference for the study of the pineal rhythm mechanism, and is of great significance to the study of the pineal rhythm mechanism.
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31
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Meng H, Gonzales NM, Jung SY, Lu Y, Putluri N, Zhu B, Dacso CC, Lonard DM, O'Malley BW. Defining the mammalian coactivation of hepatic 12-h clock and lipid metabolism. Cell Rep 2022; 38:110491. [PMID: 35263593 PMCID: PMC8958721 DOI: 10.1016/j.celrep.2022.110491] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/05/2021] [Accepted: 02/14/2022] [Indexed: 12/18/2022] Open
Abstract
The 12-h clock coordinates lipid homeostasis, energy metabolism, and stress rhythms via the transcriptional regulator XBP1. However, the biochemical and physiological bases for integrated control of the 12-h clock and diverse metabolic pathways remain unclear. Here, we show that steroid receptor coactivator SRC-3 coactivates XBP1 transcription and regulates hepatic 12-h cistrome and gene rhythmicity. Mice lacking SRC-3 show abnormal 12-h rhythms in hepatic transcription, metabolic functions, systemic energetics, and rate-limiting lipid metabolic processes, including triglyceride, phospholipid, and cardiolipin pathways. Notably, 12-h clock coactivation is not only preserved, with its cistromic activation priming ahead of the zeitgeber cue of light, but concomitant with rhythmic remodeling in the absence of food. These findings reveal that SRC-3 integrates the mammalian 12-h clock, energy metabolism, and membrane and lipid homeostasis and demonstrates a role for the 12-h clock machinery as an active transcriptional mechanism in anticipating physiological and metabolic energy needs and stresses.
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Affiliation(s)
- Huan Meng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Naomi M Gonzales
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sung Yun Jung
- Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, USA
| | - Nagireddy Putluri
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bokai Zhu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Clifford C Dacso
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - David M Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
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32
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Rock A, Wilcockson D, Last KS. Towards an Understanding of Circatidal Clocks. Front Physiol 2022; 13:830107. [PMID: 35283768 PMCID: PMC8914038 DOI: 10.3389/fphys.2022.830107] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/04/2022] [Indexed: 11/29/2022] Open
Abstract
Circadian clocks are an intrinsic element of life that orchestrate appropriately timed daily physiological and behavioural rhythms entrained to the solar cycle, thereby conferring increased fitness. However, it is thought that the first archaic ‘proto-clocks’ evolved in ancient cyanobacteria in a marine environment, where the dominant time cues (zeitgebers) probably would have been lunar-driven and included tidal cycles. To date, non-circadian ‘marine clocks’ have been described with circatidal (~12.4 h), circasemilunar (~14.8 days), and circalunar (~29.5 days) periodicity, mostly studied in accessible but temporally complex intertidal habitats. In contrast to the well-described circadian clock, their molecular machinery is poorly understood, and fundamental mechanisms remain unclear. We propose that a multi-species approach is the most apposite strategy to resolve the divergence that arose from non-circadian clockwork forged in an evolutionary environment with multiple zeitgebers. We review circatidal clock models with a focus on intertidal organisms, for which robust behavioural, physiological, or genetic underpinnings have been explicated, and discuss their relative experimental merits. Developing a comprehensive mechanistic understanding of circatidal clocks should be a priority because it will ultimately contribute to a more holistic understanding of the origins and evolution of chronobiology itself.
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Affiliation(s)
- Alberto Rock
- Department of Science, Scottish Association for Marine Science, Oban, United Kingdom
| | - David Wilcockson
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
- *Correspondence: David Wilcockson,
| | - Kim S. Last
- Department of Science, Scottish Association for Marine Science, Oban, United Kingdom
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33
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Dion W, Ballance H, Lee J, Pan Y, Irfan S, Edwards C, Sun M, Zhang J, Zhang X, Liu S, Zhu B. Four-dimensional nuclear speckle phase separation dynamics regulate proteostasis. SCIENCE ADVANCES 2022; 8:eabl4150. [PMID: 34985945 PMCID: PMC8730402 DOI: 10.1126/sciadv.abl4150] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/15/2021] [Indexed: 05/15/2023]
Abstract
Phase separation and biorhythms control biological processes in the spatial and temporal dimensions, respectively, but mechanisms of four-dimensional integration remain elusive. Here, we identified an evolutionarily conserved XBP1s-SON axis that establishes a cell-autonomous mammalian 12-hour ultradian rhythm of nuclear speckle liquid-liquid phase separation (LLPS) dynamics, separate from both the 24-hour circadian clock and the cell cycle. Higher expression of nuclear speckle scaffolding protein SON, observed at early morning/early afternoon, generates diffuse and fluid nuclear speckles, increases their interactions with chromatin proactively, transcriptionally amplifies the unfolded protein response, and protects against proteome stress, whereas the opposites are observed following reduced SON level at early evening/late morning. Correlative Son and proteostasis gene expression dynamics are further observed across the entire mouse life span. Our results suggest that by modulating the temporal dynamics of proteostasis, the nuclear speckle LLPS may represent a previously unidentified (chrono)-therapeutic target for pathologies associated with dysregulated proteostasis.
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Affiliation(s)
- William Dion
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Heather Ballance
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jane Lee
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Saad Irfan
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Casey Edwards
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michelle Sun
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jing Zhang
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Silvia Liu
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh
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Kriegermeier A, Hyon A, Sommars M, Hubchak S, LeCuyer B, Liu X, Barish G, Green RM. Hepatic X-Box Binding Protein 1 and Unfolded Protein Response Is Impaired in Weanling Mice With Resultant Hepatic Injury. Hepatology 2021; 74:3362-3375. [PMID: 34170527 PMCID: PMC8886505 DOI: 10.1002/hep.32031] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 06/06/2021] [Accepted: 06/21/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIMS The unfolded protein response (UPR) is a coordinated cellular response to endoplasmic reticulum (ER) stress that functions to maintain cellular homeostasis. When ER stress is unresolved, the UPR can trigger apoptosis. Pathways within the UPR influence bile acid metabolism in adult animal models and adult human liver diseases, however, the UPR has not been studied in young animal models or pediatric liver diseases. In this study we sought to determine whether weanling age mice had altered UPR activation compared with adult mice, which could lead to increased bile acid-induced hepatic injury. APPROACH AND RESULTS We demonstrate that after 7 days of cholic acid (CA) feeding to wild-type animals, weanling age mice have a 2-fold greater serum alanine aminotransferase (ALT) levels compared with adult mice, with increased hepatic apoptosis. Weanling mice fed CA have increased hepatic nuclear X-box binding protein 1 spliced (XBP1s) expression, but cannot increase expression of its protective downstream target's ER DNA J domain-containing protein 4 and ER degradation enhancing α-mannoside. In response to tunicamycin induced ER stress, young mice have blunted expression of several UPR pathways compared with adult mice. CA feeding to adult liver-specific XBP1 knockout (LS-XBP1-/- ) mice, which are unable to resolve hepatic ER stress, leads to increased serum ALT and CCAAT/enhancer binding homologous protein, a proapoptotic UPR molecule, expression to levels similar to CA-fed LS-XBP1-/- weanlings. CONCLUSIONS Weanling mice have attenuated hepatic XBP1 signaling and impaired UPR activation with resultant increased susceptibility to bile acid-induced injury.
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Affiliation(s)
- Alyssa Kriegermeier
- Department of Pediatrics, Northwestern University, Feinberg School of Medicine, Division of Gastroenterology, Hepatology and Nutrition at Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611
| | - Angela Hyon
- Department of Pediatrics, Northwestern University, Feinberg School of Medicine, Division of Gastroenterology, Hepatology and Nutrition at Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611
| | - Meredith Sommars
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Division of Endocrinology, Chicago, IL 60611
| | - Susan Hubchak
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Division of Gastroenterology and Hepatology, Chicago, IL 60611
| | - Brian LeCuyer
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Division of Gastroenterology and Hepatology, Chicago, IL 60611
| | - Xiaoying Liu
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Division of Gastroenterology and Hepatology, Chicago, IL 60611
| | - Grant Barish
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Division of Endocrinology, Chicago, IL 60611
| | - Richard M. Green
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Division of Gastroenterology and Hepatology, Chicago, IL 60611
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35
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Mofatteh M, Echegaray-Iturra F, Alamban A, Dalla Ricca F, Bakshi A, Aydogan MG. Autonomous clocks that regulate organelle biogenesis, cytoskeletal organization, and intracellular dynamics. eLife 2021; 10:e72104. [PMID: 34586070 PMCID: PMC8480978 DOI: 10.7554/elife.72104] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/14/2021] [Indexed: 12/27/2022] Open
Abstract
How do cells perceive time? Do cells use temporal information to regulate the production/degradation of their enzymes, membranes, and organelles? Does controlling biological time influence cytoskeletal organization and cellular architecture in ways that confer evolutionary and physiological advantages? Potential answers to these fundamental questions of cell biology have historically revolved around the discussion of 'master' temporal programs, such as the principal cyclin-dependent kinase/cyclin cell division oscillator and the circadian clock. In this review, we provide an overview of the recent evidence supporting an emerging concept of 'autonomous clocks,' which under normal conditions can be entrained by the cell cycle and/or the circadian clock to run at their pace, but can also run independently to serve their functions if/when these major temporal programs are halted/abrupted. We begin the discussion by introducing recent developments in the study of such clocks and their roles at different scales and complexities. We then use current advances to elucidate the logic and molecular architecture of temporal networks that comprise autonomous clocks, providing important clues as to how these clocks may have evolved to run independently and, sometimes at the cost of redundancy, have strongly coupled to run under the full command of the cell cycle and/or the circadian clock. Next, we review a list of important recent findings that have shed new light onto potential hallmarks of autonomous clocks, suggestive of prospective theoretical and experimental approaches to further accelerate their discovery. Finally, we discuss their roles in health and disease, as well as possible therapeutic opportunities that targeting the autonomous clocks may offer.
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Affiliation(s)
- Mohammad Mofatteh
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Fabio Echegaray-Iturra
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Andrew Alamban
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Francesco Dalla Ricca
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Anand Bakshi
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Mustafa G Aydogan
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
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36
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Aviram R, Adamovich Y, Asher G. Circadian Organelles: Rhythms at All Scales. Cells 2021; 10:2447. [PMID: 34572096 PMCID: PMC8469338 DOI: 10.3390/cells10092447] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Circadian clocks have evolved in most light-sensitive organisms, from unicellular organisms to mammals. Consequently, a myriad of biological functions exhibits circadian rhythmicity, from behavior to physiology, through tissue and cellular functions to subcellular processes. Circadian rhythms in intracellular organelles are an emerging and exciting research arena. We summarize herein the current literature for rhythmicity in major intracellular organelles in mammals. These include changes in the morphology, content, and functions of different intracellular organelles. While these data highlight the presence of rhythmicity in these organelles, a gap remains in our knowledge regarding the underlying molecular mechanisms and their functional significance. Finally, we discuss the importance and challenges faced by spatio-temporal studies on these organelles and speculate on the presence of oscillators in organelles and their potential mode of communication. As circadian biology has been and continues to be studied throughout temporal and spatial axes, circadian organelles appear to be the next frontier.
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Affiliation(s)
| | | | - Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel; (R.A.); (Y.A.)
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37
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Hasanpour M, Mitricheva E, Logothetis N, Noori HR. Intensive longitudinal characterization of multidimensional biobehavioral dynamics in laboratory rats. Cell Rep 2021; 35:108987. [PMID: 33852865 DOI: 10.1016/j.celrep.2021.108987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/04/2021] [Accepted: 03/23/2021] [Indexed: 11/26/2022] Open
Abstract
Rats have been used as animal models for human diseases for more than a century, yet a systematic understanding of basal biobehavioral phenotypes of laboratory rats is still missing. In this study, we utilize wireless tracking technology and videography, collect and analyze more than 130 billion data points to fill this gap, and characterize the evolution of behavior and physiology of group-housed male and female rats (n = 114) of the most commonly used strains (Lister Hooded, Long-Evans, Sprague-Dawley, and Wistar) throughout their development. The resulting intensive longitudinal data suggest the existence of strain and sex differences and bi-stable developmental states. Under standard laboratory 12-h light/12-h dark conditions, our study found the presence of multiple oscillations such as circatidal-like rhythms in locomotor activity. The overall findings further suggest that frequent movement along cage walls or thigmotaxic activity may be a physical feature of motion in constrained spaces, critically affecting the interpretation of basal behavior of rats in cages.
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Affiliation(s)
- Mehrdad Hasanpour
- Department of Physiology of Cognitive Processes, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Ekaterina Mitricheva
- Department of Physiology of Cognitive Processes, Max Planck Institute for Biological Cybernetics, Tübingen, Germany; International Center for Primate Brain Research, Center for Excellence in Brain Science and Intelligence Technology (CEBSIT)/Institute of Neuroscience (ION), Chinese Academy of Sciences, Shanghai, China
| | - Nikos Logothetis
- Department of Physiology of Cognitive Processes, Max Planck Institute for Biological Cybernetics, Tübingen, Germany; International Center for Primate Brain Research, Center for Excellence in Brain Science and Intelligence Technology (CEBSIT)/Institute of Neuroscience (ION), Chinese Academy of Sciences, Shanghai, China; Imaging Science and Biomedical Engineering, University of Manchester, Manchester, UK
| | - Hamid R Noori
- Department of Physiology of Cognitive Processes, Max Planck Institute for Biological Cybernetics, Tübingen, Germany; International Center for Primate Brain Research, Center for Excellence in Brain Science and Intelligence Technology (CEBSIT)/Institute of Neuroscience (ION), Chinese Academy of Sciences, Shanghai, China; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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38
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Revealing the hidden reality of the mammalian 12-h ultradian rhythms. Cell Mol Life Sci 2021; 78:3127-3140. [PMID: 33449146 DOI: 10.1007/s00018-020-03730-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 12/29/2022]
Abstract
Biological oscillations often cycle at different harmonics of the 24-h circadian rhythms, a phenomenon we coined "Musica Universalis" in 2017. Like the circadian rhythm, the 12-h oscillation is also evolutionarily conserved, robust, and has recently gained new traction in the field of chronobiology. Originally thought to be regulated by the circadian clock and/or environmental cues, recent new evidences support the notion that the majority of 12-h rhythms are regulated by a distinct and cell-autonomous pacemaker that includes the unfolded protein response (UPR) transcription factor spliced form of XBP1 (XBP1s). 12-h cycle of XBP1s level in turn transcriptionally generates robust 12-h rhythms of gene expression enriched in the central dogma information flow (CEDIF) pathway. Given the regulatory and functional separation of the 12-h and circadian clocks, in this review, we will focus our attention on the mammalian 12-h pacemaker, and discuss our current understanding of its prevalence, evolutionary origin, regulation, and functional roles in both physiological and pathological processes.
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39
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Abstract
The human striatum can be subdivided into the caudate, putamen, and nucleus accumbens (NAc). Each of these structures have some overlapping and some 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 human cortical regions. Here, we identify molecular rhythms across the three striatal subregions collected from postmortem human brain tissue in subjects without psychiatric or neurological disorders. Core circadian clock genes are rhythmic across all three regions and show strong phase concordance across regions. However, the putamen contains a much larger number of significantly rhythmic transcripts than the other two regions. Moreover, there are many differences in pathways that are rhythmic across regions. Strikingly, the top rhythmic transcripts in NAc (but not the other regions) are predominantly small nucleolar RNAs and long noncoding RNAs, suggesting that a completely different mechanism might be used for the regulation of diurnal rhythms in translation and/or RNA processing in the NAc versus the other regions. Further, although the NAc and putamen are generally in phase with regard to timing of expression rhythms, the NAc and caudate, and caudate and putamen, have several clusters of discordant rhythmic transcripts, suggesting a temporal wave of specific cellular processes across the striatum. Taken together, these studies reveal distinct transcriptome rhythms across the human striatum and are an important step in helping to understand the normal function of diurnal rhythms in these regions and how disruption could lead to pathology.
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40
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Martínez BA, Hoyle RG, Yeudall S, Granade ME, Harris TE, Castle JD, Leitinger N, Bland ML. Innate immune signaling in Drosophila shifts anabolic lipid metabolism from triglyceride storage to phospholipid synthesis to support immune function. PLoS Genet 2020; 16:e1009192. [PMID: 33227003 PMCID: PMC7721134 DOI: 10.1371/journal.pgen.1009192] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 12/07/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
During infection, cellular resources are allocated toward the metabolically-demanding processes of synthesizing and secreting effector proteins that neutralize and kill invading pathogens. In Drosophila, these effectors are antimicrobial peptides (AMPs) that are produced in the fat body, an organ that also serves as a major lipid storage depot. Here we asked how activation of Toll signaling in the larval fat body perturbs lipid homeostasis to understand how cells meet the metabolic demands of the immune response. We find that genetic or physiological activation of fat body Toll signaling leads to a tissue-autonomous reduction in triglyceride storage that is paralleled by decreased transcript levels of the DGAT homolog midway, which carries out the final step of triglyceride synthesis. In contrast, Kennedy pathway enzymes that synthesize membrane phospholipids are induced. Mass spectrometry analysis revealed elevated levels of major phosphatidylcholine and phosphatidylethanolamine species in fat bodies with active Toll signaling. The ER stress mediator Xbp1 contributed to the Toll-dependent induction of Kennedy pathway enzymes, which was blunted by deleting AMP genes, thereby reducing secretory demand elicited by Toll activation. Consistent with ER stress induction, ER volume is expanded in fat body cells with active Toll signaling, as determined by transmission electron microscopy. A major functional consequence of reduced Kennedy pathway induction is an impaired immune response to bacterial infection. Our results establish that Toll signaling induces a shift in anabolic lipid metabolism to favor phospholipid synthesis and ER expansion that may serve the immediate demand for AMP synthesis and secretion but with the long-term consequence of insufficient nutrient storage.
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Affiliation(s)
- Brittany A. Martínez
- Biomedical Sciences Graduate Program, University of Virginia, Charlottesville, VA, United States of America
- Department of Pharmacology, University of Virginia, Charlottesville, VA, United States of America
| | - Rosalie G. Hoyle
- Department of Pharmacology, University of Virginia, Charlottesville, VA, United States of America
| | - Scott Yeudall
- Department of Pharmacology, University of Virginia, Charlottesville, VA, United States of America
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA, United States of America
| | - Mitchell E. Granade
- Biomedical Sciences Graduate Program, University of Virginia, Charlottesville, VA, United States of America
- Department of Pharmacology, University of Virginia, Charlottesville, VA, United States of America
| | - Thurl E. Harris
- Biomedical Sciences Graduate Program, University of Virginia, Charlottesville, VA, United States of America
- Department of Pharmacology, University of Virginia, Charlottesville, VA, United States of America
| | - J. David Castle
- Department of Cell Biology, University of Virginia, Charlottesville, VA, United States of America
| | - Norbert Leitinger
- Biomedical Sciences Graduate Program, University of Virginia, Charlottesville, VA, United States of America
- Department of Pharmacology, University of Virginia, Charlottesville, VA, United States of America
| | - Michelle L. Bland
- Biomedical Sciences Graduate Program, University of Virginia, Charlottesville, VA, United States of America
- Department of Pharmacology, University of Virginia, Charlottesville, VA, United States of America
- * E-mail:
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41
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Zhu B. Decoding the function and regulation of the mammalian 12-h clock. J Mol Cell Biol 2020; 12:752-758. [PMID: 32384155 PMCID: PMC7816679 DOI: 10.1093/jmcb/mjaa021] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/16/2020] [Accepted: 04/24/2020] [Indexed: 11/26/2022] Open
Affiliation(s)
- Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA.,Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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42
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Scrima R, Cela O, Agriesti F, Piccoli C, Tataranni T, Pacelli C, Mazzoccoli G, Capitanio N. Mitochondrial calcium drives clock gene-dependent activation of pyruvate dehydrogenase and of oxidative phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118815. [PMID: 32763264 DOI: 10.1016/j.bbamcr.2020.118815] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/27/2020] [Accepted: 08/03/2020] [Indexed: 12/17/2022]
Abstract
Regulation of metabolism is emerging as a major output of circadian clock circuitry in mammals. Accordingly, mitochondrial oxidative metabolism undergoes both in vivo and in vitro daily oscillatory activities. In a previous study we showed that both glycolysis and mitochondrial oxygen consumption display a similar time-resolved rhythmic activity in synchronized HepG2 cell cultures, which translates in overall bioenergetic changes as here documented by measurement of the ATP level. Treatment of synchronized cells with specific metabolic inhibitors unveiled pyruvate as a major source of reducing equivalents to the respiratory chain with its oxidation driven by the rhythmic (de)phosphorylation of pyruvate dehydrogenase. Further investigation enabled to causally link the autonomous cadenced mitochondrial respiration to a synchronous increase of the mitochondrial Ca2+. The rhythmic change of the mitochondrial respiration was dampened by inhibitors of the mitochondrial Ca2+ uniporter as well as of the ryanodine receptor Ca2+ channel or the ADPR cyclase, indicating that the mitochondrial Ca2+ influx originated from the ER store, likely at contact sites with the mitochondrial compartment. Notably, blockage of the mitochondrial Ca2+ influx resulted in deregulation of the expression of canonical clock genes such as BMALl1, CLOCK, NR1D1. All together our findings unveil a hitherto unexplored function of Ca2+-mediated signaling in time keeping the mitochondrial metabolism and in its feed-back modulation of the circadian clockwork.
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Affiliation(s)
- Rosella Scrima
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy.
| | - Olga Cela
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy.
| | - Francesca Agriesti
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture, PZ, Italy.
| | - Claudia Piccoli
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy.
| | - Tiziana Tataranni
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture, PZ, Italy.
| | - Consiglia Pacelli
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy.
| | - Gianluigi Mazzoccoli
- Department of Medical Sciences and Chronobiology Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, (FG), Italy.
| | - Nazzareno Capitanio
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy.
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Andreatta G, Tessmar-Raible K. The Still Dark Side of the Moon: Molecular Mechanisms of Lunar-Controlled Rhythms and Clocks. J Mol Biol 2020; 432:3525-3546. [PMID: 32198116 PMCID: PMC7322537 DOI: 10.1016/j.jmb.2020.03.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/18/2020] [Accepted: 03/09/2020] [Indexed: 12/22/2022]
Abstract
Starting with the beginning of the last century, a multitude of scientific studies has documented that the lunar cycle times behaviors and physiology in many organisms. It is plausible that even the first life forms adapted to the different rhythms controlled by the moon. Consistently, many marine species exhibit lunar rhythms, and also the number of documented "lunar-rhythmic" terrestrial species is increasing. Organisms follow diverse lunar geophysical/astronomical rhythms, which differ significantly in terms of period length: from hours (circalunidian and circatidal rhythms) to days (circasemilunar and circalunar cycles). Evidence for internal circatital and circalunar oscillators exists for a range of species based on past behavioral studies, but those species with well-documented behaviorally free-running lunar rhythms are not typically used for molecular studies. Thus, the underlying molecular mechanisms are largely obscure: the dark side of the moon. Here we review findings that start to connect molecular pathways with moon-controlled physiology and behaviors. The present data indicate connections between metabolic/endocrine pathways and moon-controlled rhythms, as well as interactions between circadian and circatidal/circalunar rhythms. Moreover, recent high-throughput analyses provide useful leads toward pathways, as well as molecular markers. However, for each interpretation, it is important to carefully consider the, partly substantially differing, conditions used in each experimental paradigm. In the future, it will be important to use lab experiments to delineate the specific mechanisms of the different solar- and lunar-controlled rhythms, but to also start integrating them together, as life has evolved equally long under rhythms of both sun and moon.
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Affiliation(s)
- Gabriele Andreatta
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030 Vienna, Austria; Research Platform "Rhythms of Life", University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030 Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030 Vienna, Austria; Research Platform "Rhythms of Life", University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030 Vienna, Austria.
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