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Sokolowski MBC, Bottet G, Dacher M. Measuring honey bee feeding rhythms with the BeeBox, a platform for nectar foraging insects. Physiol Behav 2024; 283:114598. [PMID: 38821143 DOI: 10.1016/j.physbeh.2024.114598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
In honey bees, most studies of circadian rhythms involve a locomotion test performed in a small tube, a tunnel, or at the hive entrance. However, despite feeding playing an important role in honey bee health or fitness, no demonstration of circadian rhythm on feeding has been performed until recently. Here, we present the BeeBox, a new laboratory platform for bees based on the concept of the Skinner box, which dispenses discrete controlled amounts of food (sucrose syrup) following entrance into an artificial flower. We compared caged groups of bees in 12 h-12 h light/dark cycles, constant darkness and constant light and measured average hourly syrup consumption per living bee. Food intake was higher in constant light and lower in constant darkness; mortality increased in constant light. We observed rhythmic consumption with a period longer than 24 h; this is maintained in darkness without environmental cues, but is damped in the constant light condition. The BeeBox offers many new research perspectives and numerous potential applications in the study of nectar foraging animals.
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Affiliation(s)
| | - Guillaume Bottet
- Université de Picardie - Jules Verne, 1, rue des Louvels, 80000 Amiens, France
| | - Matthieu Dacher
- Sorbonne Université, INRAE, Université Paris Est Créteil, CNRS, IRD - Institute for Ecology and Environnemental Sciences of Paris, iEES Paris, 78026, Versailles, France
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2
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Jankowski MS, Griffith D, Shastry DG, Pelham JF, Ginell GM, Thomas J, Karande P, Holehouse AS, Hurley JM. Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator. Nat Commun 2024; 15:3523. [PMID: 38664421 PMCID: PMC11045787 DOI: 10.1038/s41467-024-47761-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Organismal physiology is widely regulated by the molecular circadian clock, a feedback loop composed of protein complexes whose members are enriched in intrinsically disordered regions. These regions can mediate protein-protein interactions via SLiMs, but the contribution of these disordered regions to clock protein interactions had not been elucidated. To determine the functionality of these disordered regions, we applied a synthetic peptide microarray approach to the disordered clock protein FRQ in Neurospora crassa. We identified residues required for FRQ's interaction with its partner protein FRH, the mutation of which demonstrated FRH is necessary for persistent clock oscillations but not repression of transcriptional activity. Additionally, the microarray demonstrated an enrichment of FRH binding to FRQ peptides with a net positive charge. We found that positively charged residues occurred in significant "blocks" within the amino acid sequence of FRQ and that ablation of one of these blocks affected both core clock timing and physiological clock output. Finally, we found positive charge clusters were a commonly shared molecular feature in repressive circadian clock proteins. Overall, our study suggests a mechanistic purpose for positive charge blocks and yielded insights into repressive arm protein roles in clock function.
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Affiliation(s)
- Meaghan S Jankowski
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Daniel Griffith
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Divya G Shastry
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Jacqueline F Pelham
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joshua Thomas
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Pankaj Karande
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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3
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Force E, Sokolowski MBC, Suray C, Debernard S, Chatterjee A, Dacher M. Regulation of feeding dynamics by the circadian clock, light and sex in an adult nocturnal insect. Front Physiol 2024; 14:1304626. [PMID: 38264330 PMCID: PMC10803417 DOI: 10.3389/fphys.2023.1304626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/26/2023] [Indexed: 01/25/2024] Open
Abstract
Animals invest crucial resources in foraging to support development, sustenance, and reproduction. Foraging and feeding behaviors are rhythmically expressed by most insects. Rhythmic behaviors are modified by exogenous factors like temperature and photoperiod, and internal factors such as the physiological status of the individual. However, the interactions between these factors and the circadian clock to pattern feeding behavior remains elusive. As Drosophila, a standard insect model, spends nearly all its life on food, we rather chose to focus on the adults of a non-model insect, Agrotis ipsilon, a nocturnal cosmopolitan crop pest moth having structured feeding activity. Our study aimed to explore the impact of environmental cues on directly measured feeding behavior rhythms. We took advantage of a new experimental set-up, mimicking an artificial flower, allowing us to specifically monitor feeding behavior in a naturalistic setting, e.g., the need to enter a flower to get food. We show that the frequency of flower visits is under the control of the circadian clock in males and females. Feeding behavior occurs only during the scotophase, informed by internal clock status and external photic input, and females start to visit flowers earlier than males. Shorter duration visits predominate as the night progresses. Importantly, food availability reorganizes the microstructure of feeding behavior, revealing its plasticity. Interestingly, males show a constant number of daily visits during the 5 days of adult life whereas females decrease visitations after the third day of adult life. Taken together, our results provide evidence that the rhythmicity of feeding behavior is sexually dimorphic and controlled by photoperiodic conditions through circadian clock-dependent and independent pathways. In addition, the use of the new experimental set-up provides future opportunities to examine the regulatory mechanisms of feeding behavior paving the way to investigate complex relationships between feeding, mating, and sleep-wake rhythms in insects.
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Affiliation(s)
- Evan Force
- Sorbonne Université, Université Paris-Est Créteil, INRAE, CNRS, IRD, Institute for Ecology and Environmental Sciences of Paris, iEES Paris, Versailles, France
- Sorbonne Université, Université Paris-Est Créteil, INRAE, CNRS, IRD, Institute for Ecology and Environmental Sciences of Paris, iEES Paris, Paris, France
| | | | - Caroline Suray
- Sorbonne Université, Université Paris-Est Créteil, INRAE, CNRS, IRD, Institute for Ecology and Environmental Sciences of Paris, iEES Paris, Versailles, France
| | - Stéphane Debernard
- Sorbonne Université, Université Paris-Est Créteil, INRAE, CNRS, IRD, Institute for Ecology and Environmental Sciences of Paris, iEES Paris, Paris, France
| | - Abhishek Chatterjee
- Sorbonne Université, Université Paris-Est Créteil, INRAE, CNRS, IRD, Institute for Ecology and Environmental Sciences of Paris, iEES Paris, Versailles, France
| | - Matthieu Dacher
- Sorbonne Université, Université Paris-Est Créteil, INRAE, CNRS, IRD, Institute for Ecology and Environmental Sciences of Paris, iEES Paris, Versailles, France
- Sorbonne Université, Université Paris-Est Créteil, INRAE, CNRS, IRD, Institute for Ecology and Environmental Sciences of Paris, iEES Paris, Paris, France
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4
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Bafna A, Lau P, Banks G, Nolan PM. Harvesting mouse suprachiasmatic nucleus by vibrating microtome for diurnal transcriptome analysis. STAR Protoc 2023; 4:102618. [PMID: 37756154 PMCID: PMC10539961 DOI: 10.1016/j.xpro.2023.102618] [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: 07/06/2023] [Revised: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The mammalian suprachiasmatic nucleus (SCN) is the principal circadian clock that synchronizes daily behavioral and physiological responses in response to environmental cues. Here, we present a protocol for harvesting mouse SCN by vibrating microtome for diurnal transcriptome analysis. We describe steps for mouse entrainment, isolation of the SCN, tissue preparation, slicing with a vibratome, and handling of the harvested SCN for RNA extraction. This protocol can also be used for harvesting other mammalian brain regions for genomic studies.
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Affiliation(s)
- Akanksha Bafna
- Medical Research Council, Harwell Science Campus, Oxfordshire, UK.
| | - Petrina Lau
- Medical Research Council, Harwell Science Campus, Oxfordshire, UK; Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Gareth Banks
- Medical Research Council, Harwell Science Campus, Oxfordshire, UK
| | - Patrick M Nolan
- Medical Research Council, Harwell Science Campus, Oxfordshire, UK.
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5
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Bowazolo C, Morse D. Ribosome profiling in the Symbiodiniacean dinoflagellate Fugacium kawagutii shows coordinated protein synthesis of enzymes in different pathways at different times of day. Mol Microbiol 2023; 120:462-471. [PMID: 37545098 DOI: 10.1111/mmi.15137] [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: 04/25/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/08/2023]
Abstract
Dinoflagellates respond to daily changes in light and dark by changes in cellular metabolism, yet the mechanisms used are still unclear. For example, Fugacium (previously Symbiodinium) kawagutii shows little difference in the transcriptome between day and night suggesting little transcriptional control over gene expression. Here, we have performed ribosome profiling at 2 h intervals over a daily light-dark cycle to assess the degree to which protein synthesis rates might change over the daily cycle. The number of F. kawagutii coding sequences with significant differences in the number of ribosome-protected fragments (RPF) over the 24-h cycle was 2923 using JTK_Cycle and 3655 using ECHO. The majority of the regulated transcripts showed peak translation at the onset of the dark period. The regulated sequences were assigned to different KEGG pathways and transcripts that were translated at roughly the same time were termed concurrently regulated. Both analyses revealed concurrent regulation of many transcripts whose gene products were involved in spliceosome or lysosome biogenesis with peak translation rates around the onset of the dark period, while others, involved in nitrate metabolism and ribosomal proteins, were preferentially translated around the onset of the day phase or the end of the night phase, respectively. In addition, some sequences involved in DNA synthesis were preferentially translated at the end of the day. We conclude that light-dark cycles seem able to synchronize translation of some transcripts encoding proteins involved in a range of different cellular processes, and propose that these changes may help the cells adapt and alter their metabolism as a function of the time of day.
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Affiliation(s)
- Carl Bowazolo
- Département de Sciences Biologiques, Institut de Recherche en biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - David Morse
- Département de Sciences Biologiques, Institut de Recherche en biologie Végétale, Université de Montréal, Montréal, Québec, Canada
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Castillo KD, Chapa ED, Lamb TM, Gangopadhyay M, Bell-Pedersen D. Circadian clock control of tRNA synthetases in Neurospora crassa. F1000Res 2023; 11:1556. [PMID: 37841830 PMCID: PMC10576190 DOI: 10.12688/f1000research.125351.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/31/2023] [Indexed: 10/17/2023] Open
Abstract
Background: In Neurospora crassa, the circadian clock controls rhythmic mRNA translation initiation through regulation of the eIF2α kinase CPC-3 (the homolog of yeast and mammalian GCN2). Active CPC-3 phosphorylates and inactivates eIF2α, leading to higher phosphorylated eIF2α (P-eIF2α) levels and reduced translation initiation during the subjective day. This daytime activation of CPC-3 is driven by its binding to uncharged tRNA, and uncharged tRNA levels peak during the day under control of the circadian clock. The daily rhythm in uncharged tRNA levels could arise from rhythmic amino acid levels or aminoacyl-tRNA synthetase (aaRSs) levels. Methods: To determine if and how the clock potentially controls rhythms in aspartyl-tRNA synthetase (AspRS) and glutaminyl-tRNA synthetase (GlnRS), both observed to be rhythmic in circadian genomic datasets, transcriptional and translational fusions to luciferase were generated. These luciferase reporter fusions were examined in wild type (WT), clock mutant Δ frq, and clock-controlled transcription factor deletion strains. Results: Translational and transcriptional fusions of AspRS and GlnRS to luciferase confirmed that their protein levels are clock-controlled with peak levels at night. Moreover, clock-controlled transcription factors NCU00275 and ADV-1 drive robust rhythmic protein expression of AspRS and GlnRS, respectively. Conclusions: These data support a model whereby coordinate clock control of select aaRSs drives rhythms in uncharged tRNAs, leading to rhythmic CPC-3 activation, and rhythms in translation of specific mRNAs.
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Affiliation(s)
- Kathrina D. Castillo
- Biology, Texas A&M University, College Station, TX, 77843, USA
- Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
| | - Emily D. Chapa
- Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Teresa M. Lamb
- Biology, Texas A&M University, College Station, TX, 77843, USA
- Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
| | - Madhusree Gangopadhyay
- Biology, Texas A&M University, College Station, TX, 77843, USA
- Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
| | - Deborah Bell-Pedersen
- Biology, Texas A&M University, College Station, TX, 77843, USA
- Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
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7
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Pelham JF, Mosier AE, Altshuler SC, Rhodes ML, Kirchhoff CL, Fall WB, Mann C, Baik LS, Chiu JC, Hurley JM. Conformational changes in the negative arm of the circadian clock correlate with dynamic interactomes involved in post-transcriptional regulation. Cell Rep 2023; 42:112376. [PMID: 37043358 PMCID: PMC10562519 DOI: 10.1016/j.celrep.2023.112376] [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: 12/07/2021] [Revised: 09/16/2022] [Accepted: 03/24/2023] [Indexed: 04/13/2023] Open
Abstract
Biology is tuned to the Earth's diurnal cycle by the circadian clock, a transcriptional/translational negative feedback loop that regulates physiology via transcriptional activation and other post-transcriptional mechanisms. We hypothesize that circadian post-transcriptional regulation might stem from conformational shifts in the intrinsically disordered proteins that comprise the negative arm of the feedback loop to coordinate variation in negative-arm-centered macromolecular complexes. This work demonstrates temporal conformational fluidity in the negative arm that correlates with 24-h variation in physiologically diverse macromolecular complex components in eukaryotic clock proteins. Short linear motifs on the negative-arm proteins that correspond with the interactors localized to disordered regions and known temporal phosphorylation sites suggesting changes in these macromolecular complexes could be due to conformational changes imparted by the temporal phospho-state. Interactors that oscillate in the macromolecular complexes over circadian time correlate with post-transcriptionally regulated proteins, highlighting how time-of-day variation in the negative-arm protein complexes may tune cellular physiology.
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Affiliation(s)
- Jacqueline F Pelham
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Alexander E Mosier
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Samuel C Altshuler
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Morgan L Rhodes
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | | | - William B Fall
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Catherine Mann
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Lisa S Baik
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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8
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Muthukumarasamy I, Buel SM, Hurley JM, Dordick JS. NOX2 inhibition enables retention of the circadian clock in BV2 microglia and primary macrophages. Front Immunol 2023; 14:1106515. [PMID: 36814920 PMCID: PMC9939898 DOI: 10.3389/fimmu.2023.1106515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/25/2023] [Indexed: 02/09/2023] Open
Abstract
Introduction Sustained neuroinflammation is a major contributor to the progression of neurodegenerative diseases such as Alzheimer's (AD) and Parkinson's (PD) diseases. Neuroinflammation, like other cellular processes, is affected by the circadian clock. Microglia, the resident immune cells in the brain, act as major contributors to neuroinflammation and are under the influence of the circadian clock. Microglial responses such as activation, recruitment, and cytokine expression are rhythmic in their response to various stimuli. While the link between circadian rhythms and neuroinflammation is clear, significant gaps remain in our understanding of this complex relationship. To gain a greater understanding of this relationship, the interaction between the microglial circadian clock and the enzyme NADPH Oxidase Isoform 2 (NOX2) was studied; NOX2 is essential for the production of reactive oxygen species (ROS) in oxidative stress, an integral characteristic of neuroinflammation. Methods BV2 microglia were examined over circadian time, demonstrating oscillations of the clock genes Per2 and Bmal1 and the NOX2 subunits gp91phox and p47phox. Results The BV2 microglial clock exerted significant control over NOX2 expression and inhibition of NOX2 enabled the microglia to retain a functional circadian clock while reducing levels of ROS and inflammatory cytokines. These trends were mirrored in mouse bone marrow-derived primary macrophages. Conclusions NOX2 plays a crucial role in the interaction between the circadian clock and the activation of microglia/macrophages into their pro-inflammatory state, which has important implications in the control of neuroinflammation.
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Affiliation(s)
- Iswarya Muthukumarasamy
- Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Sharleen M. Buel
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Jennifer M. Hurley
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Jonathan S. Dordick
- Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
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9
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Qiu JF, Cui WZ, Zhang Q, Dai TM, Liu K, Li JL, Wang YJ, Sima YH, Xu SQ. Temporal transcriptome reveals that circadian clock is involved in the dynamic regulation of immune response to bacterial infection in Bombyx mori. INSECT SCIENCE 2023; 30:31-46. [PMID: 35446483 DOI: 10.1111/1744-7917.13043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/11/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
The circadian clock plays a critical role in the regulation of host immune defense. However, the mechanistic basis for this regulation is largely unknown. Herein, the core clock gene cryptochrome1 (cry1) knockout line in Bombyx mori, an invertebrate animal model, was constructed to obtain the silkworm with dysfunctional molecular clock, and the dynamic regulation of the circadian clock on the immune responsiveness within 24 h of Staphylococcus aureus infection was analyzed. We found that deletion of cry1 decreased viability of silkworms and significantly reduced resistance of larvae to S. aureus. Time series RNA-seq analysis identified thousands of rhythmically expressed genes, including immune response genes, in the larval immune tissue, fat bodies. Uninfected cry1 knockout silkworms exhibited expression patterns of rhythmically expressed genes similar to wild-type (WT) silkworms infected with S. aureus. However, cry1 knockout silkworms exhibited a seriously weakened response to S. aureus infection. The immune response peaked at 6 and 24 h after infection, during which "transcription storms" occurred, and the expression levels of the immune response genes, PGRP and antimicrobial peptides (AMPs), were significantly upregulated in WT. In contrast, cry1 knockout did not effectively activate Toll, Imd, or NF-κB signaling pathways during the immune adjustment period from 12 to 18 h after infection, resulting in failure to initiate the immune responsiveness peak at 24 h after infection. This may be related to inhibited silkworm fat body energy metabolism. These results demonstrated the dynamic regulation of circadian clock on silkworm immune response to bacterial infection and provided important insights into host antimicrobial defense mechanisms.
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Affiliation(s)
- Jian-Feng Qiu
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China, Jiangsu Province
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China, Jiangsu Province
| | - Wen-Zhao Cui
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China, Jiangsu Province
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China, Jiangsu Province
| | - Qiang Zhang
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China, Jiangsu Province
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China, Jiangsu Province
| | - Tai-Ming Dai
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China, Jiangsu Province
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China, Jiangsu Province
| | - Kai Liu
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China, Jiangsu Province
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China, Jiangsu Province
| | - Jiang-Lan Li
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China, Jiangsu Province
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China, Jiangsu Province
| | - Yu-Jun Wang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, China, Guangxi Province
| | - Yang-Hu Sima
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China, Jiangsu Province
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China, Jiangsu Province
| | - Shi-Qing Xu
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, China, Jiangsu Province
- Institute of Agricultural Biotechnology & Ecology (IABE), Soochow University, Suzhou, China, Jiangsu Province
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10
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Spick M, Hancox TPM, Chowdhury NR, Middleton B, Skene DJ, Morton AJ. Metabolomic Analysis of Plasma in Huntington's Disease Transgenic Sheep (Ovis aries) Reveals Progressive Circadian Rhythm Dysregulation. J Huntingtons Dis 2023; 12:31-42. [PMID: 36617787 DOI: 10.3233/jhd-220552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Metabolic abnormalities have long been predicted in Huntington's disease (HD) but remain poorly characterized. Chronobiological dysregulation has been described in HD and may include abnormalities in circadian-driven metabolism. OBJECTIVE Here we investigated metabolite profiles in the transgenic sheep model of HD (OVT73) at presymptomatic ages. Our goal was to understand changes to the metabolome as well as potential metabolite rhythm changes associated with HD. METHODS We used targeted liquid chromatography mass spectrometry (LC-MS) metabolomics to analyze metabolites in plasma samples taken from female HD transgenic and normal (control) sheep aged 5 and 7 years. Samples were taken hourly across a 27-h period. The resulting dataset was investigated by machine learning and chronobiological analysis. RESULTS The metabolic profiles of HD and control sheep were separable by machine learning at both ages. We found both absolute and rhythmic differences in metabolites in HD compared to control sheep at 5 years of age. An increase in both the number of disturbed metabolites and the magnitude of change of acrophase (the time at which the rhythms peak) was seen in samples from 7-year-old HD compared to control sheep. There were striking similarities between the dysregulated metabolites identified in HD sheep and human patients (notably of phosphatidylcholines, amino acids, urea, and threonine). CONCLUSION This work provides the first integrated analysis of changes in metabolism and circadian rhythmicity of metabolites in a large animal model of presymptomatic HD.
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Affiliation(s)
- Matt Spick
- Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, UK
| | - Thomas P M Hancox
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Namrata R Chowdhury
- Chronobiology, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Benita Middleton
- Chronobiology, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Debra J Skene
- Chronobiology, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - A Jennifer Morton
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, UK
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11
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Moškon M, Režen T, Juvančič M, Verovšek Š. Integrative Analysis of Rhythmicity: From Biology to Urban Environments and Sustainability. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 20:764. [PMID: 36613088 PMCID: PMC9819461 DOI: 10.3390/ijerph20010764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
From biological to socio-technical systems, rhythmic processes are pervasive in our environment. However, methods for their comprehensive analysis are prevalent only in specific fields that limit the transfer of knowledge across scientific disciplines. This hinders interdisciplinary research and integrative analyses of rhythms across different domains and datasets. In this paper, we review recent developments in cross-disciplinary rhythmicity research, with a focus on the importance of rhythmic analyses in urban planning and biomedical research. Furthermore, we describe the current state of the art of (integrative) computational methods for the investigation of rhythmic data. Finally, we discuss the further potential and propose necessary future developments for cross-disciplinary rhythmicity analysis to foster integration of heterogeneous datasets across different domains, as well as guide data-driven decision making beyond the boundaries of traditional intradisciplinary research, especially in the context of sustainable and healthy cities.
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Affiliation(s)
- Miha Moškon
- Faculty of Computer and Information Science, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tadeja Režen
- Centre for Functional Genomics and Bio-Chips, Institute for Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Matevž Juvančič
- Faculty of Architecture, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Špela Verovšek
- Faculty of Architecture, University of Ljubljana, 1000 Ljubljana, Slovenia
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12
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Castillo KD, Wu C, Ding Z, Lopez-Garcia OK, Rowlinson E, Sachs MS, Bell-Pedersen D. A circadian clock translational control mechanism targets specific mRNAs to cytoplasmic messenger ribonucleoprotein granules. Cell Rep 2022; 41:111879. [PMID: 36577368 PMCID: PMC10241597 DOI: 10.1016/j.celrep.2022.111879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 09/13/2022] [Accepted: 12/04/2022] [Indexed: 12/29/2022] Open
Abstract
Phosphorylation of Neurospora crassa eukaryotic initiation factor 2 α (eIF2α), a conserved translation initiation factor, is clock controlled. To determine the impact of rhythmic eIF2α phosphorylation on translation, we performed temporal ribosome profiling and RNA sequencing (RNA-seq) in wild-type (WT), clock mutant Δfrq, eIF2α kinase mutant Δcpc-3, and constitutively active cpc-3c cells. About 14% of mRNAs are rhythmically translated in WT cells, and translation rhythms for ∼30% of these mRNAs, which we named circadian translation-initiation-controlled genes (cTICs), are dependent on the clock and CPC-3. Most cTICs are expressed from arrhythmic mRNAs and contain a P-body (PB) localization motif in their 5' leader sequence. Deletion of SNR-1, a component of cytoplasmic messenger ribonucleoprotein granules (cmRNPgs) that include PBs and stress granules (SGs), and the PB motif on one of the cTIC mRNAs, zip-1, significantly alters zip-1 rhythmic translation. These results reveal that the clock regulates rhythmic translation of specific mRNAs through rhythmic eIF2α activity and cmRNPg metabolism.
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Affiliation(s)
- Kathrina D Castillo
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Zhaolan Ding
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | | | - Emma Rowlinson
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Deborah Bell-Pedersen
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA.
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13
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Brooks R, Monzy J, Aaron B, Zhang X, Kossenkov A, Hayden J, Keeney F, Speicher DW, Zhang L, Dang CV. Circadian lncRNA ADIRF-AS1 binds PBAF and regulates renal clear cell tumorigenesis. Cell Rep 2022; 41:111514. [PMID: 36261012 PMCID: PMC9652615 DOI: 10.1016/j.celrep.2022.111514] [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: 11/09/2021] [Revised: 05/25/2022] [Accepted: 09/26/2022] [Indexed: 11/20/2022] Open
Abstract
We identify ADIRF-AS1 circadian long non-coding RNA (lncRNA). Deletion of ADIRF-AS1 in U2OS cells alters rhythmicity of clock-controlled genes and expression of extracellular matrix genes. ADIRF-AS1 interacts with all components of the PBAF (PBRM1/BRG1) complex in U2OS cells. Because PBRM1 is a tumor suppressor mutated in over 40% of clear cell renal carcinoma (ccRCC) cases, we evaluate ADIRF-AS1 in ccRCC cells. Reducing ADIRF-AS1 expression in ccRCC cells decreases expression of some PBAF-suppressed genes. Expression of these genes is partially rescued by PBRM1 loss, consistent with ADIRF-AS1 acting in part to modulate PBAF. ADIRF-AS1 expression correlates with survival in human ccRCC, particularly in PBRM1 wild-type, but not mutant, tumors. Loss of ADIRF-AS1 eliminates in vivo tumorigenesis, partially rescued by concurrent loss of PBRM1 only when co-injected with Matrigel, suggesting a PBRM1-independent function of ADIRF-AS1. Our findings suggest that ADIRF-AS1 functions partly through PBAF to regulate specific genes as a BMAL1-CLOCK-regulated, oncogenic lncRNA.
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Affiliation(s)
- Rebekah Brooks
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Wistar Institute, Philadelphia, PA, USA; The Ludwig Institute for Cancer Research, New York, NY, USA
| | - Judith Monzy
- The Wistar Institute, Philadelphia, PA, USA; The Ludwig Institute for Cancer Research, New York, NY, USA
| | - Bailey Aaron
- The Wistar Institute, Philadelphia, PA, USA; The Ludwig Institute for Cancer Research, New York, NY, USA
| | - Xue Zhang
- The Wistar Institute, Philadelphia, PA, USA; The Ludwig Institute for Cancer Research, New York, NY, USA
| | | | - James Hayden
- The Ludwig Institute for Cancer Research, New York, NY, USA
| | | | | | - Lin Zhang
- Center for Research on Reproduction & Women's Health, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chi V Dang
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Wistar Institute, Philadelphia, PA, USA; The Ludwig Institute for Cancer Research, New York, NY, USA.
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14
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Buel SM, Debopadhaya S, De los Santos H, Edwards KM, David AM, Dao UH, Bennett KP, Hurley JM. The PAICE suite reveals circadian posttranscriptional timing of noncoding RNAs and spliceosome components in Mus musculus macrophages. G3 (BETHESDA, MD.) 2022; 12:6649694. [PMID: 35876788 PMCID: PMC9434326 DOI: 10.1093/g3journal/jkac176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/27/2022] [Indexed: 01/07/2023]
Abstract
Circadian rhythms broadly regulate physiological functions by tuning oscillations in the levels of mRNAs and proteins to the 24-h day/night cycle. Globally assessing which mRNAs and proteins are timed by the clock necessitates accurate recognition of oscillations in RNA and protein data, particularly in large omics data sets. Tools that employ fixed-amplitude models have previously been used to positive effect. However, the recognition of amplitude change in circadian oscillations required a new generation of analytical software to enhance the identification of these oscillations. To address this gap, we created the Pipeline for Amplitude Integration of Circadian Exploration suite. Here, we demonstrate the Pipeline for Amplitude Integration of Circadian Exploration suite's increased utility to detect circadian trends through the joint modeling of the Mus musculus macrophage transcriptome and proteome. Our enhanced detection confirmed extensive circadian posttranscriptional regulation in macrophages but highlighted that some of the reported discrepancy between mRNA and protein oscillations was due to noise in data. We further applied the Pipeline for Amplitude Integration of Circadian Exploration suite to investigate the circadian timing of noncoding RNAs, documenting extensive circadian timing of long noncoding RNAs and small nuclear RNAs, which control the recognition of mRNA in the spliceosome complex. By tracking oscillating spliceosome complex proteins using the PAICE suite, we noted that the clock broadly regulates the spliceosome, particularly the major spliceosome complex. As most of the above-noted rhythms had damped amplitude changes in their oscillations, this work highlights the importance of the PAICE suite in the thorough enumeration of oscillations in omics-scale datasets.
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Affiliation(s)
| | | | | | - Kaelyn M Edwards
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Alexandra M David
- Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Uyen H Dao
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Kristin P Bennett
- Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA,Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY 12180, USA,Institute for Data Exploration and Applications, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Jennifer M Hurley
- Corresponding author: Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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15
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Narayanan V, Rodrigues AL, Dordick JS. Influence of Circadian Rhythm on Drug Metabolism in 3D Hepatic Spheroids. Biotechnol Bioeng 2022; 119:2842-2856. [PMID: 35822281 DOI: 10.1002/bit.28180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 11/10/2022]
Abstract
Circadian rhythms are characterized as oscillations that fluctuate based on a 24h cycle and are responsible for regulation of physiological functions. While the internal clock synchronizes gene expression using external cues like light, a similar synchronization can be induced in vitro by incubating the cells with an increased percentage of serum followed by its rapid removal. Previous studies have suggested that synchronization of HepG2 cell line induced the rhythmic expression of drug metabolizing enzymes (DME) most specifically the cytochrome P450 enzymes. However, there is a lack of evidence demonstrating the influence of 3D microenvironment on the rhythmicity of these genes. To understand this interplay, gene expression of the circadian machinery and CYP450s were compared using the model human hepatocarcinoma cell line, HepG2. Upon serum shock synchronization, gene and protein expression of core clock regulators was assessed and rhythmic expression of these genes was demonstrated. Further insight into the interrelations between various gene pairs was obtained using statistical analysis. Using RNA sequencing, an in-depth understanding of the widespread effects of circadian regulation on genes involved in metabolic processes in the liver was obtained. This study aids in the better understanding of chronopharmacokinetic events in humans using physiologically relevant 3D culture systems. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Vibha Narayanan
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Andre L Rodrigues
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Departments of Biological Sciences and Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
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16
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Hoopes GM, Zarka D, Feke A, Acheson K, Hamilton JP, Douches D, Buell CR, Farré EM. Keeping time in the dark: Potato diel and circadian rhythmic gene expression reveals tissue-specific circadian clocks. PLANT DIRECT 2022; 6:e425. [PMID: 35844780 PMCID: PMC9277033 DOI: 10.1002/pld3.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/15/2022] [Accepted: 06/24/2022] [Indexed: 05/10/2023]
Abstract
The circadian clock is an internal molecular oscillator and coordinates numerous physiological processes through regulation of molecular pathways. Tissue-specific clocks connected by mobile signals have previously been found to run at different speeds in Arabidopsis thaliana tissues. However, tissue variation in circadian clocks in crop species is unknown. In this study, leaf and tuber global gene expression in cultivated potato under cycling and constant environmental conditions was profiled. In addition, we used a circadian-regulated luciferase reporter construct to study tuber gene expression rhythms. Diel and circadian expression patterns were present among 17.9% and 5.6% of the expressed genes in the tuber. Over 500 genes displayed differential tissue specific diel phases. Intriguingly, few core circadian clock genes had circadian expression patterns, while all such genes were circadian rhythmic in cultivated tomato leaves. Furthermore, robust diel and circadian transcriptional rhythms were observed among detached tubers. Our results suggest alternative regulatory mechanisms and/or clock composition is present in potato, as well as the presence of tissue-specific independent circadian clocks. We have provided the first evidence of a functional circadian clock in below-ground storage organs, holding important implications for other storage root and tuberous crops.
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Affiliation(s)
| | - Daniel Zarka
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Ann Feke
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Kaitlyn Acheson
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - John P. Hamilton
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - David Douches
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - C. Robin Buell
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
- Michigan State University AgBioResearchMichigan State UniversityEast LansingMichiganUSA
| | - Eva M. Farré
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
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17
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Castellana S, Biagini T, Petrizzelli F, Cabibbo A, Mazzoccoli G, Mazza T. RhythmicDB: A Database of Predicted Multi-Frequency Rhythmic Transcripts. Front Genet 2022; 13:882044. [PMID: 35774515 PMCID: PMC9237250 DOI: 10.3389/fgene.2022.882044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
The physiology and behavior of living organisms are featured by time-related variations driven by molecular clockworks that arose during evolution stochastically and heterogeneously. Over the years, several high-throughput experiments were performed to evaluate time-dependent gene expression in different cell types across several species and experimental conditions. Here, these were retrieved, manually curated, and analyzed by two software packages, BioCycle and MetaCycle, to infer circadian or ultradian transcripts across different species. These transcripts were stored in RhythmicDB and made publically available.
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Affiliation(s)
- Stefano Castellana
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo, Italy
| | - Tommaso Biagini
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo, Italy
| | - Francesco Petrizzelli
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo, Italy
| | - Andrea Cabibbo
- Department of Biology, Centro di Bioinformatica Molecolare, University of Rome “Tor Vergata,”, Rome, Italy
| | - Gianluigi Mazzoccoli
- Department of Medical Sciences, Division of Internal Medicine and Chronobiology Laboratory, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo, Italy
- *Correspondence: Tommaso Mazza, ; Gianluigi Mazzoccoli,
| | - Tommaso Mazza
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo, Italy
- *Correspondence: Tommaso Mazza, ; Gianluigi Mazzoccoli,
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18
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Clark GT, Yu Y, Urban CA, Fu G, Wang C, Zhang F, Linhardt RJ, Hurley JM. Circadian control of heparan sulfate levels times phagocytosis of amyloid beta aggregates. PLoS Genet 2022; 18:e1009994. [PMID: 35143487 PMCID: PMC8830681 DOI: 10.1371/journal.pgen.1009994] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/14/2021] [Indexed: 12/17/2022] Open
Abstract
Alzheimer's Disease (AD) is a neuroinflammatory disease characterized partly by the inability to clear, and subsequent build-up, of amyloid-beta (Aβ). AD has a bi-directional relationship with circadian disruption (CD) with sleep disturbances starting years before disease onset. However, the molecular mechanism underlying the relationship of CD and AD has not been elucidated. Myeloid-based phagocytosis, a key component in the metabolism of Aβ, is circadianly-regulated, presenting a potential link between CD and AD. In this work, we revealed that the phagocytosis of Aβ42 undergoes a daily circadian oscillation. We found the circadian timing of global heparan sulfate proteoglycan (HSPG) biosynthesis was the molecular timer for the clock-controlled phagocytosis of Aβ and that both HSPG binding and aggregation may play a role in this oscillation. These data highlight that circadian regulation in immune cells may play a role in the intricate relationship between the circadian clock and AD.
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Affiliation(s)
- Gretchen T. Clark
- Rensselaer Polytechnic Institute, Biological Sciences, Troy, New York, United States of America
| | - Yanlei Yu
- Rensselaer Polytechnic Institute, Chemistry and Chemical Biology, Troy, New York, United States of America
| | - Cooper A. Urban
- Rensselaer Polytechnic Institute, Biological Sciences, Troy, New York, United States of America
| | - Guo Fu
- Rensselaer Polytechnic Institute, Biological Sciences, Troy, New York, United States of America
- Now at the Innovation and Integration Center of New Laser Technology, Chinese Academy of Sciences, Shanghai, China
| | - Chunyu Wang
- Rensselaer Polytechnic Institute, Biological Sciences, Troy, New York, United States of America
- Rensselaer Polytechnic Institute, Chemistry and Chemical Biology, Troy, New York, United States of America
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States of America
| | - Fuming Zhang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States of America
- Rensselaer Polytechnic Institute, Chemical and Biological Engineering, Troy, New York, United States of America
| | - Robert J. Linhardt
- Rensselaer Polytechnic Institute, Biological Sciences, Troy, New York, United States of America
- Rensselaer Polytechnic Institute, Chemistry and Chemical Biology, Troy, New York, United States of America
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States of America
- Rensselaer Polytechnic Institute, Chemical and Biological Engineering, Troy, New York, United States of America
| | - Jennifer M. Hurley
- Rensselaer Polytechnic Institute, Biological Sciences, Troy, New York, United States of America
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States of America
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19
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Circadian Alterations Increase with Progression in a Patient-Derived Cell Culture Model of Breast Cancer. Clocks Sleep 2021; 3:598-608. [PMID: 34842634 PMCID: PMC8628750 DOI: 10.3390/clockssleep3040042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/10/2021] [Accepted: 10/28/2021] [Indexed: 01/20/2023] Open
Abstract
Circadian rhythm disruption can elicit the development of various diseases, including breast cancer. While studies have used cell lines to study correlations between altered circadian rhythms and cancer, these models have different genetic backgrounds and do not mirror the changes that occur with disease development. Isogenic cell models can recapitulate changes across cancer progression. Hence, in this study, a patient-derived breast cancer model, the 21T series, was used to evaluate changes to circadian oscillations of core clock protein transcription as cells progress from normal to malignant states. Three cell lines were used: H16N2 (normal breast epithelium), 21PT (atypical ductal hyperplasia), and 21MT-1 (invasive metastatic carcinoma). The cancerous cells are both HER2+. We assessed the transcriptional profiles of two core clock proteins, BMAL1 and PER2, which represent a positive and negative component of the molecular oscillator. In the normal H16N2 cells, both genes possessed rhythmic mRNA oscillations with close to standard periods and phases. However, in the cancerous cells, consistent changes were observed: both genes had periods that deviated farther from normal and did not have an anti-phase relationship. In the future, mechanistic studies should be undertaken to determine the oncogenic changes responsible for the circadian alterations found.
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20
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De Los Santos H, Bennett KP, Hurley JM. MOSAIC: a joint modeling methodology for combined circadian and non-circadian analysis of multi-omics data. Bioinformatics 2021; 37:767-774. [PMID: 33051654 PMCID: PMC8098022 DOI: 10.1093/bioinformatics/btaa877] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/27/2020] [Accepted: 09/28/2020] [Indexed: 01/01/2023] Open
Abstract
MOTIVATION Circadian rhythms are approximately 24-h endogenous cycles that control many biological functions. To identify these rhythms, biological samples are taken over circadian time and analyzed using a single omics type, such as transcriptomics or proteomics. By comparing data from these single omics approaches, it has been shown that transcriptional rhythms are not necessarily conserved at the protein level, implying extensive circadian post-transcriptional regulation. However, as proteomics methods are known to be noisier than transcriptomic methods, this suggests that previously identified arrhythmic proteins with rhythmic transcripts could have been missed due to noise and may not be due to post-transcriptional regulation. RESULTS To determine if one can use information from less-noisy transcriptomic data to inform rhythms in more-noisy proteomic data, and thus more accurately identify rhythms in the proteome, we have created the Multi-Omics Selection with Amplitude Independent Criteria (MOSAIC) application. MOSAIC combines model selection and joint modeling of multiple omics types to recover significant circadian and non-circadian trends. Using both synthetic data and proteomic data from Neurospora crassa, we showed that MOSAIC accurately recovers circadian rhythms at higher rates in not only the proteome but the transcriptome as well, outperforming existing methods for rhythm identification. In addition, by quantifying non-circadian trends in addition to circadian trends in data, our methodology allowed for the recognition of the diversity of circadian regulation as compared to non-circadian regulation. AVAILABILITY AND IMPLEMENTATION MOSAIC's full interface is available at https://github.com/delosh653/MOSAIC. An R package for this functionality, mosaic.find, can be downloaded at https://CRAN.R-project.org/package=mosaic.find. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hannah De Los Santos
- Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.,Institute for Data Exploration and Applications, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Kristin P Bennett
- Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.,Institute for Data Exploration and Applications, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.,Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.,Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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21
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Hancox TPM, Skene DJ, Dallmann R, Dunn WB. Tick-Tock Consider the Clock: The Influence of Circadian and External Cycles on Time of Day Variation in the Human Metabolome-A Review. Metabolites 2021; 11:328. [PMID: 34069741 PMCID: PMC8161100 DOI: 10.3390/metabo11050328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 12/21/2022] Open
Abstract
The past decade has seen a large influx of work investigating time of day variation in different human biofluid and tissue metabolomes. The driver of this daily variation can be endogenous circadian rhythms driven by the central and/or peripheral clocks, or exogenous diurnal rhythms driven by behavioural and environmental cycles, which manifest as regular 24 h cycles of metabolite concentrations. This review, of all published studies to date, establishes the extent of daily variation with regard to the number and identity of 'rhythmic' metabolites observed in blood, saliva, urine, breath, and skeletal muscle. The probable sources driving such variation, in addition to what metabolite classes are most susceptible in adhering to or uncoupling from such cycles is described in addition to a compiled list of common rhythmic metabolites. The reviewed studies show that the metabolome undergoes significant time of day variation, primarily observed for amino acids and multiple lipid classes. Such 24 h rhythms, driven by various factors discussed herein, are an additional source of intra/inter-individual variation and are thus highly pertinent to all studies applying untargeted and targeted metabolomics platforms, particularly for the construction of biomarker panels. The potential implications are discussed alongside proposed minimum reporting criteria suggested to acknowledge time of day variation as a potential influence of results and to facilitate improved reproducibility.
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Affiliation(s)
- Thomas P. M. Hancox
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Debra J. Skene
- Chronobiology, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK;
| | - Robert Dallmann
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK;
| | - Warwick B. Dunn
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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22
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Jacq A, Becquet D, Bello-Goutierrez MM, Boyer B, Guillen S, Franc JL, François-Bellan AM. Genome-wide screening of circadian and non-circadian impact of Neat1 genetic deletion. Comput Struct Biotechnol J 2021; 19:2121-2132. [PMID: 33995907 PMCID: PMC8085668 DOI: 10.1016/j.csbj.2021.04.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/25/2022] Open
Abstract
Neat1 deletion affects numerous circadian and non-circadian genes. Neat1 deletion causes loss, modification or acquisition of gene circadian pattern. Paraspeckles contribute significantly to the circadian transcriptome.
The functions of the long non-coding RNA, Nuclear enriched abundant transcript 1 (Neat1), are poorly understood. Neat1 is required for the formation of paraspeckles, but its respective paraspeckle-dependent or independent functions are unknown. Several studies including ours reported that Neat1 is involved in the regulation of circadian rhythms. We characterized the impact of Neat1 genetic deletion in a rat pituitary cell line. The mRNAs whose circadian expression pattern or expression level is regulated by Neat1 were identified after high-throughput RNA sequencing of the circadian transcriptome of wild-type cells compared to cells in which Neat1 was deleted by CRISPR/Cas9. The numerous RNAs affected by Neat1 deletion were found to be circadian or non-circadian, targets or non-targets of paraspeckles, and to be associated with many key biological processes showing that Neat1, in interaction with the circadian system or independently, could play crucial roles in key physiological functions through diverse mechanisms.
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23
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Collins EJ, Cervantes-Silva MP, Timmons GA, O'Siorain JR, Curtis AM, Hurley JM. Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states. Genome Res 2021; 31:171-185. [PMID: 33436377 PMCID: PMC7849412 DOI: 10.1101/gr.263814.120] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 11/20/2020] [Indexed: 01/07/2023]
Abstract
Our core timekeeping mechanism, the circadian clock, plays a vital role in immunity. Although the mechanics of circadian control over the immune response is generally explained by transcriptional activation or repression derived from this clock's transcription-translation negative-feedback loop, research suggests that some regulation occurs beyond transcriptional activity. We comprehensively profiled the transcriptome and proteome of murine bone marrow-derived macrophages and found that only 15% of the circadian proteome had corresponding oscillating mRNA, suggesting post-transcriptional regulation influences macrophage clock regulatory output to a greater extent than any other tissue previously profiled. This regulation may be explained by the robust temporal enrichment we identified for proteins involved in degradation and translation. Extensive post-transcriptional temporal-gating of metabolic pathways was also observed and further corresponded with daily variations in ATP production, mitochondrial morphology, and phagocytosis. The disruption of this circadian post-transcriptional metabolic regulation impaired immune functionality. Our results demonstrate that cell-intrinsic post-transcriptional regulation is a primary driver of circadian output in macrophages and that this regulation, particularly of metabolic pathways, plays an important role in determining their response to immune stimuli.
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Affiliation(s)
- Emily J Collins
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Mariana P Cervantes-Silva
- School of Pharmacy and Biomedical Sciences and Tissue Engineering Research Group, Royal College of Surgeons in Ireland, Dublin D02, Ireland
| | - George A Timmons
- School of Pharmacy and Biomedical Sciences and Tissue Engineering Research Group, Royal College of Surgeons in Ireland, Dublin D02, Ireland
| | - James R O'Siorain
- School of Pharmacy and Biomedical Sciences and Tissue Engineering Research Group, Royal College of Surgeons in Ireland, Dublin D02, Ireland
| | - Annie M Curtis
- School of Pharmacy and Biomedical Sciences and Tissue Engineering Research Group, Royal College of Surgeons in Ireland, Dublin D02, Ireland
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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24
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Wu G, Ruben MD, Lee Y, Li J, Hughes ME, Hogenesch JB. Genome-wide studies of time of day in the brain: Design and analysis. BRAIN SCIENCE ADVANCES 2020. [DOI: 10.26599/bsa.2020.9050005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Transcriptome profiling at different times of day is powerful for studying circadian regulation in model organisms and humans. To date, 24 h profiles from many tissue types suggest that about half of all genes are circadian-expressed somewhere in the body. However, few of these studies focused on the brain. Thus, despite known links between circadian disruption and neurological disease, we have virtually no mechanistic understanding. In the coming decade, we expect more genome-wide studies of time of day in different brain diseases, regions, and cell types. We expect just as many different approaches to the design and analysis of these studies. This review considers key principles of circadian tran scriptomics, with the goal of maximizing utility and reproducibility of future studies in the nervous system.
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Affiliation(s)
- Gang Wu
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, U.S.A
| | - Marc D. Ruben
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, U.S.A
| | - Yinyeng Lee
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, U.S.A
| | - Jiajia Li
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO 63310, U.S.A
| | - Michael E. Hughes
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO 63310, U.S.A
| | - John B. Hogenesch
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, U.S.A
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25
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De Los Santos H, Bennett KP, Hurley JM. ENCORE: A Visualization Tool for Insight into Circadian Omics. ACM-BCB ... ... : THE ... ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE 2019; 2019:5-14. [PMID: 31754663 DOI: 10.1145/3307339.3342137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Circadian rhythms are 24-hour biological cycles that control daily molecular rhythms in many organisms. The cellular elements that fall under the regulation of the clock are often studied through the use of omics-scale data sets gathered over time to determine how circadian regulation impacts cellular physiology. Previously, we created the ECHO (Extended Circadian Harmonic Oscillator) tool to identify rhythms in these data sets. Using ECHO, we found that circadian oscillations widely undergo a change in amplitude over time and that these amplitude changes have a biological function in the cell. However, ECHO does not align gene ontologies with the identified oscillating genes to give functional context. Thus, we created ENCORE (ECHO Native Circadian Ontological Rhythmicity Explorer), a novel visualization tool which combines the disparate databases of Gene Ontologies, protein-protein interactions, and auxiliary information to uncover the meaning of circadianly-regulated genes. This freely-available tool performs automatic enrichment and creates publication-worthy visualizations which we used to extend previously-gathered data on circadian regulation of physiology from published omics-scale studies in three circadian model organisms: mouse, fruit fly, and Neurospora crassa.
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Affiliation(s)
- Hannah De Los Santos
- Institute for Data Exploration and Applications/Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY
| | - Kristin P Bennett
- Institute for Data Exploration and Applications/Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY
| | - Jennifer M Hurley
- Department of Biological Sciences/Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY
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