1
|
Zhang X, Procopio SB, Ding H, Semel MG, Schroder EA, Seward TS, Du P, Wu K, Johnson SR, Prabhat A, Schneider DJ, Stumpf IG, Rozmus ER, Huo Z, Delisle BP, Esser KA. New role for cardiomyocyte Bmal1 in the regulation of sex-specific heart transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590181. [PMID: 38659967 PMCID: PMC11042278 DOI: 10.1101/2024.04.18.590181] [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
It has been well established that cardiovascular diseases exhibit significant differences between sexes in both preclinical models and humans. In addition, there is growing recognition that disrupted circadian rhythms can contribute to the onset and progression of cardiovascular diseases. However little is known about sex differences between the cardiac circadian clock and circadian transcriptomes in mice. Here, we show that the the core clock genes are expressed in common in both sexes but the circadian transcriptome of the mouse heart is very sex-specific. Hearts from female mice expressed significantly more rhythmically expressed genes (REGs) than male hearts and the temporal pattern of REGs was distinctly different between sexes. We next used a cardiomyocyte-specific knock out of the core clock gene, Bmal1, to investigate its role in sex-specific gene expression in the heart. All sex differences in the circadian transcriptomes were significantly diminished with cardiomyocyte-specific loss of Bmal1. Surprisingly, loss of cardiomyocyte Bmal1 also resulted in a roughly 8-fold reduction in the number of all the differentially expressed genes between male and female hearts. We conclude that cardiomyocyte-specific Bmal1, and potentially the core clock mechanism, is vital in conferring sex-specific gene expression in the adult mouse heart.
Collapse
Affiliation(s)
- Xiping Zhang
- Department of Physiology and Aging, University of Florida, Gainesville FL, United States
- These authors contributed equally to this paper
| | - Spencer B. Procopio
- Department of Physiology and Aging, University of Florida, Gainesville FL, United States
- These authors contributed equally to this paper
| | - Haocheng Ding
- Department of Biostatics, University of Florida, Gainesville FL, United States
| | - Maya G. Semel
- Department of Physiology and Aging, University of Florida, Gainesville FL, United States
| | - Elizabeth A. Schroder
- Department of Physiology, University of Kentucky, Lexington, KY, United States
- Department of Internal Medicine, University of Kentucky, Lexington, KY, United States
| | - Tanya S. Seward
- Department of Physiology, University of Kentucky, Lexington, KY, United States
| | - Ping Du
- Department of Physiology and Aging, University of Florida, Gainesville FL, United States
| | - Kevin Wu
- Department of Physiology and Aging, University of Florida, Gainesville FL, United States
| | - Sidney R. Johnson
- Department of Physiology, University of Kentucky, Lexington, KY, United States
| | - Abhilash Prabhat
- Department of Physiology, University of Kentucky, Lexington, KY, United States
| | - David J. Schneider
- Department of Physiology, University of Kentucky, Lexington, KY, United States
| | - Isabel G Stumpf
- Department of Physiology, University of Kentucky, Lexington, KY, United States
| | - Ezekiel R Rozmus
- Department of Physiology, University of Kentucky, Lexington, KY, United States
| | - Zhiguang Huo
- Department of Biostatics, University of Florida, Gainesville FL, United States
| | - Brian P. Delisle
- Department of Physiology, University of Kentucky, Lexington, KY, United States
| | - Karyn A. Esser
- Department of Physiology and Aging, University of Florida, Gainesville FL, United States
| |
Collapse
|
2
|
Lévi FA, Okyar A, Hadadi E, Innominato PF, Ballesta A. Circadian Regulation of Drug Responses: Toward Sex-Specific and Personalized Chronotherapy. Annu Rev Pharmacol Toxicol 2024; 64:89-114. [PMID: 37722720 DOI: 10.1146/annurev-pharmtox-051920-095416] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Today's challenge for precision medicine involves the integration of the impact of molecular clocks on drug pharmacokinetics, toxicity, and efficacy toward personalized chronotherapy. Meaningful improvements of tolerability and/or efficacy of medications through proper administration timing have been confirmed over the past decade for immunotherapy and chemotherapy against cancer, as well as for commonly used pharmacological agents in cardiovascular, metabolic, inflammatory, and neurological conditions. Experimental and human studies have recently revealed sexually dimorphic circadian drug responses. Dedicated randomized clinical trials should now aim to issue personalized circadian timing recommendations for daily medical practice, integrating innovative technologies for remote longitudinal monitoring of circadian metrics, statistical prediction of molecular clock function from single-timepoint biopsies, and multiscale biorhythmic mathematical modelling. Importantly, chronofit patients with a robust circadian function, who would benefit most from personalized chronotherapy, need to be identified. Conversely, nonchronofit patients could benefit from the emerging pharmacological class of chronobiotics targeting the circadian clock.
Collapse
Affiliation(s)
- Francis A Lévi
- Chronotherapy, Cancers and Transplantation Research Unit, Faculty of Medicine, Paris-Saclay University, Villejuif, France;
- Gastrointestinal and General Oncology Service, Paul-Brousse Hospital, Assistance Publique-Hôpitaux de Paris, Villejuif, France
- Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Alper Okyar
- Faculty of Pharmacy, Department of Pharmacology, Istanbul University, Beyazit-Istanbul, Turkey
| | - Eva Hadadi
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
- Laboratory for Myeloid Cell Immunology, Center for Inflammation Research VIB, Zwijnaarde, Belgium
| | - Pasquale F Innominato
- Oncology Department, Ysbyty Gwynedd Hospital, Betsi Cadwaladr University Health Board, Bangor, United Kingdom
- Warwick Medical School and Cancer Research Centre, University of Warwick, Coventry, United Kingdom
| | - Annabelle Ballesta
- Inserm Unit 900, Cancer Systems Pharmacology, Institut Curie, MINES ParisTech CBIO-Centre for Computational Biology, PSL Research University, Saint-Cloud, France
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Suen TC, DeBruyne JP. Lysine-independent ubiquitination and degradation of REV-ERBα involves a bi-functional degradation control sequence at its N-terminus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538963. [PMID: 37205588 PMCID: PMC10187254 DOI: 10.1101/2023.05.01.538963] [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
REV-ERBα and REV-ERBβ proteins play crucial roles in linking the circadian system to overt daily rhythms in mammalian physiology and behavior. In most tissues, REV-ERBα protein robustly cycles such that it is detected only within a tight interval of 4-6 hours each day, suggesting both its synthesis and degradation are tightly controlled. Several ubiquitin ligases are known to drive REV-ERBα degradation, but how they interact with REV-ERBα and which lysine residues they ubiquitinate to promote degradation are unknown. In this study, we attempted to identify both ubiquitin-ligase-binding and ubiquitination sites within REV-ERBα required for its degradation. Surprisingly, mutating all lysine residues, the common sites for ubiquitin conjugation, in REV-ERBα to arginines (K20R), did very little to impair its degradation in cells. K20R were degraded much faster by co-expression of two E3 ligases, SIAH2 or SPSB4, suggesting possible N-terminal ubiquitination. To explore this, we examined if small deletions at the N-terminus of REV-ERBα would alter its degradation. Interestingly, deletion of amino acid (AA) residues 2 to 9 (delAA2-9) clearly resulted in a less stable REV-ERBα. We found that it was the length (i.e. 8 AA), and not the specific sequence, that confers stability in this region. Simultaneously, we also mapped the interaction site of the E3 ligase SPSB4 to this same region, specifically requiring AA4-9 of REV-ERBα. Thus, the first 9 AA of REV-ERBα has two opposing roles in regulating REV-ERBα turnover. Further, deleting eight additional AAs (delAA2-17) from the N-terminus strongly prevents REV-ERBα degradation. Combined, these results suggest that complex interactions within the first 25AAs potentially act as an endogenous 'switch' that allows REV-ERBα to exist in a stabilized conformation in order to accumulate at one time of day, but then rapidly shifts to a destabilized form, to enhance its removal at the end of its daily cycle.
Collapse
|
5
|
Lee J, Chen S, Monfared RV, Derdeyn P, Leong K, Chang T, Beier K, Baldi P, Alachkar A. Reanalysis of primate brain circadian transcriptomics reveals connectivity-related oscillations. iScience 2023; 26:107810. [PMID: 37752952 PMCID: PMC10518731 DOI: 10.1016/j.isci.2023.107810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/22/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023] Open
Abstract
Research shows that brain circuits controlling vital physiological processes are closely linked with endogenous time-keeping systems. In this study, we aimed to examine oscillatory gene expression patterns of well-characterized neuronal circuits by reanalyzing publicly available transcriptomic data from a spatiotemporal gene expression atlas of a non-human primate. Unexpectedly, brain structures known for regulating circadian processes (e.g., hypothalamic nuclei) did not exhibit robust cycling expression. In contrast, basal ganglia nuclei, not typically associated with circadian physiology, displayed the most dynamic cycling behavior of its genes marked by sharp temporally defined expression peaks. Intriguingly, the mammillary bodies, considered hypothalamic nuclei, exhibited gene expression patterns resembling the basal ganglia, prompting reevaluation of their classification. Our results emphasize the potential for high throughput circadian gene expression analysis to deepen our understanding of the functional synchronization across brain structures that influence physiological processes and resulting complex behaviors.
Collapse
Affiliation(s)
- Justine Lee
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Siwei Chen
- Department of Computer Science, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA, USA
| | - Roudabeh Vakil Monfared
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Pieter Derdeyn
- Mathematical, Computational, and Systems Biology Program, University of California, Irvine, Irvine, CA, USA
| | - Kenneth Leong
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Tiffany Chang
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Kevin Beier
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
- Department of Physiology and Biophysics, School of medicine, University of California, Irvine, Irvine, CA, USA
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697-4560, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697-4560, USA
- Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, CA 92697, USA
| | - Pierre Baldi
- Department of Computer Science, School of Information and Computer Sciences, University of California, Irvine, Irvine, CA, USA
- Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, CA 92697, USA
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA, USA
| | - Amal Alachkar
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
- Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, CA 92697, USA
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA, USA
| |
Collapse
|
6
|
Obodo D, Outland EH, Hughey JJ. Sex Inclusion in Transcriptome Studies of Daily Rhythms. J Biol Rhythms 2023; 38:3-14. [PMID: 36419398 PMCID: PMC9903005 DOI: 10.1177/07487304221134160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Biomedical research on mammals has traditionally neglected females, raising the concern that some scientific findings may generalize poorly to half the population. Although this lack of sex inclusion has been broadly documented, its extent within circadian genomics remains undescribed. To address this gap, we examined sex inclusion practices in a comprehensive collection of publicly available transcriptome studies on daily rhythms. Among 148 studies having samples from mammals in vivo, we found strong underrepresentation of females across organisms and tissues. Overall, only 23 of 123 studies in mice, 0 of 10 studies in rats, and 9 of 15 studies in humans included samples from females. In addition, studies having samples from both sexes tended to have more samples from males than from females. These trends appear to have changed little over time, including since 2016, when the US National Institutes of Health began requiring investigators to consider sex as a biological variable. Our findings highlight an opportunity to dramatically improve representation of females in circadian research and to explore sex differences in daily rhythms at the genome level.
Collapse
Affiliation(s)
- Dora Obodo
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Elliot H. Outland
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jacob J. Hughey
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee,Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee,Jacob J. Hughey, Department of Biomedical Informatics, Vanderbilt University Medical Center, 2525 West End Ave., Suite 1475, Nashville, TN 37232, USA; e-mail:
| |
Collapse
|
7
|
Abdalla OHMH, Mascarenhas B, Cheng HYM. Death of a Protein: The Role of E3 Ubiquitin Ligases in Circadian Rhythms of Mice and Flies. Int J Mol Sci 2022; 23:ijms231810569. [PMID: 36142478 PMCID: PMC9502492 DOI: 10.3390/ijms231810569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 12/04/2022] Open
Abstract
Circadian clocks evolved to enable organisms to anticipate and prepare for periodic environmental changes driven by the day–night cycle. This internal timekeeping mechanism is built on autoregulatory transcription–translation feedback loops that control the rhythmic expression of core clock genes and their protein products. The levels of clock proteins rise and ebb throughout a 24-h period through their rhythmic synthesis and destruction. In the ubiquitin–proteasome system, the process of polyubiquitination, or the covalent attachment of a ubiquitin chain, marks a protein for degradation by the 26S proteasome. The process is regulated by E3 ubiquitin ligases, which recognize specific substrates for ubiquitination. In this review, we summarize the roles that known E3 ubiquitin ligases play in the circadian clocks of two popular model organisms: mice and fruit flies. We also discuss emerging evidence that implicates the N-degron pathway, an alternative proteolytic system, in the regulation of circadian rhythms. We conclude the review with our perspectives on the potential for the proteolytic and non-proteolytic functions of E3 ubiquitin ligases within the circadian clock system.
Collapse
Affiliation(s)
- Osama Hasan Mustafa Hasan Abdalla
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Brittany Mascarenhas
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Hai-Ying Mary Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
- Correspondence:
| |
Collapse
|