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Rodríguez SG, Crosby P, Hansen LL, Grünewald E, Beale AD, Spangler RK, Rabbitts BM, Partch CL, Stangherlin A, O’Neill JS, van Ooijen G. Potassium rhythms couple the circadian clock to the cell cycle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587153. [PMID: 38617352 PMCID: PMC11014554 DOI: 10.1101/2024.04.02.587153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Circadian (~24 h) rhythms are a fundamental feature of life, and their disruption increases the risk of infectious diseases, metabolic disorders, and cancer1-6. Circadian rhythms couple to the cell cycle across eukaryotes7,8 but the underlying mechanism is unknown. We previously identified an evolutionarily conserved circadian oscillation in intracellular potassium concentration, [K+]i9,10. As critical events in the cell cycle are regulated by intracellular potassium11,12, an enticing hypothesis is that circadian rhythms in [K+]i form the basis of this coupling. We used a minimal model cell, the alga Ostreococcus tauri, to uncover the role of potassium in linking these two cycles. We found direct reciprocal feedback between [K+]i and circadian gene expression. Inhibition of proliferation by manipulating potassium rhythms was dependent on the phase of the circadian cycle. Furthermore, we observed a total inhibition of cell proliferation when circadian gene expression is inhibited. Strikingly, under these conditions a sudden enforced gradient of extracellular potassium was sufficient to induce a round of cell division. Finally, we provide evidence that interactions between potassium and circadian rhythms also influence proliferation in mammalian cells. These results establish circadian regulation of intracellular potassium levels as a primary factor coupling the cell- and circadian cycles across diverse organisms.
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Affiliation(s)
- Sergio Gil Rodríguez
- School of Biological Sciences, University of Edinburgh, Max Born Crescent EH9 3BF Edinburgh, United Kingdom
| | - Priya Crosby
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Louise L. Hansen
- School of Biological Sciences, University of Edinburgh, Max Born Crescent EH9 3BF Edinburgh, United Kingdom
| | - Ellen Grünewald
- School of Biological Sciences, University of Edinburgh, Max Born Crescent EH9 3BF Edinburgh, United Kingdom
| | - Andrew D. Beale
- UKRI MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, CB2 0QH, United Kingdom
| | - Rebecca K. Spangler
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Beverley M. Rabbitts
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Carrie L. Partch
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Alessandra Stangherlin
- Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Institute for Mitochondrial Diseases and Ageing, University of Cologne, Joseph-Stelzmann-Str, 50931, Cologne, Germany
| | - John S. O’Neill
- UKRI MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, CB2 0QH, United Kingdom
| | - Gerben van Ooijen
- School of Biological Sciences, University of Edinburgh, Max Born Crescent EH9 3BF Edinburgh, United Kingdom
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2
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Sharma D, Partch CL. PAS Dimerization at the Nexus of the Mammalian Circadian Clock. J Mol Biol 2024; 436:168341. [PMID: 37924861 DOI: 10.1016/j.jmb.2023.168341] [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: 07/17/2023] [Revised: 10/23/2023] [Accepted: 10/29/2023] [Indexed: 11/06/2023]
Abstract
Circadian rhythms are genetically encoded molecular clocks for internal biological timekeeping. Organisms from single-cell bacteria to humans use these clocks to adapt to the external environment and synchronize their physiology and behavior to solar light/dark cycles. Although the proteins that constitute the molecular 'cogs' and give rise to circadian rhythms are now known, we still lack a detailed understanding of how these proteins interact to generate and sustain the ∼24-hour circadian clock. Structural studies have helped to expand the architecture of clock proteins and have revealed the abundance of the only well-defined structured regions in the mammalian clock called Per-ARNT-Sim (PAS) domains. PAS domains are modular, evolutionarily conserved sensory and signaling domains that typically mediate protein-protein interactions. In the mammalian circadian clock, PAS domains modulate homo and heterodimerization of several core clock proteins that assemble into transcription factors or repressors. This review will focus on the functional importance of the PAS domains in the circadian clock from a biophysical and biochemical standpoint and describe their roles in clock protein interactions and circadian timekeeping.
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Affiliation(s)
- Diksha Sharma
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA, United States
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA, United States; Center for Circadian Biology, University of California San Diego, CA, United States.
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3
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Herrera LR, Johnson RA, McGlynn K, Gibbs ZA, Davis AJ, Whitehurst AW. The cancer testes antigen, HORMAD1, limits genomic instability in cancer cells by protecting stalled replication forks. J Biol Chem 2023; 299:105348. [PMID: 37838177 PMCID: PMC10656231 DOI: 10.1016/j.jbc.2023.105348] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/18/2023] [Accepted: 10/01/2023] [Indexed: 10/16/2023] Open
Abstract
Tumors anomalously induce the expression of meiotic genes, which are otherwise restricted only to developing gametes. If and how these aberrantly expressed meiotic proteins influence DNA metabolism is not clear, but could have important implications for how tumors acquire and mitigate genomic instability. HORMAD1 is a highly conserved meiotic protein that is frequently expressed in lung adenocarincoma where its expression correlates with reduced patient survival and increased mutation burden. Here, we find that HORMAD1 associates with the replisome and is critical for protecting stalled DNA replication forks. Loss of HORMAD1 leads to nascent DNA strand degradation, an event which is mediated by the MRE11-DNA2-BLM pathway. We find that these phenotypes are due to limited RAD51 loading onto stalled replication forks in the absence of HORMAD1. Ultimately, loss of HORMAD1 leads to increased DNA breaks and chromosomal defects, which is exacerbated dramatically by induction of replication stress. Tumor cells proliferate despite encountering chronic replication stress, placing them on the precipice of catastrophic genomic damage. Our data support the hypothesis that the aberrant expression of HORMAD1 is engaged to attenuate the accumulation of excessive DNA damage due to chronic replication stress, which may otherwise lead to accumulation of toxic levels of genomic instability.
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Affiliation(s)
- Luis Reza Herrera
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Ronnesha A Johnson
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Kathleen McGlynn
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Zane A Gibbs
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Anthony J Davis
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas, USA.
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4
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Xing J, Gumerov VM, Zhulin IB. Origin and functional diversification of PAS domain, a ubiquitous intracellular sensor. SCIENCE ADVANCES 2023; 9:eadi4517. [PMID: 37647406 PMCID: PMC10468136 DOI: 10.1126/sciadv.adi4517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
Signal perception is a key function in regulating biological activities and adapting to changing environments. Per-Arnt-Sim (PAS) domains are ubiquitous sensors found in diverse receptors in bacteria, archaea, and eukaryotes, but their origins, distribution across the tree of life, and extent of their functional diversity are not fully characterized. Here, we show that using sequence conservation and structural information, it is possible to propose specific and potential functions for a large portion of nearly 3 million PAS domains. Our analysis suggests that PAS domains originated in bacteria and were horizontally transferred to archaea and eukaryotes. We reveal that gas sensing via a heme cofactor evolved independently in several lineages, whereas redox and light sensing via flavin adenine dinucleotide and flavin mononucleotide cofactors have the same origin. The close relatedness of human PAS domains to those in bacteria provides an opportunity for drug design by exploring potential natural ligands and cofactors for bacterial homologs.
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Affiliation(s)
- Jiawei Xing
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH USA
| | - Vadim M. Gumerov
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH USA
| | - Igor B. Zhulin
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH USA
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5
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Mayshar Y, Raz O, Cheng S, Ben-Yair R, Hadas R, Reines N, Mittnenzweig M, Ben-Kiki O, Lifshitz A, Tanay A, Stelzer Y. Time-aligned hourglass gastrulation models in rabbit and mouse. Cell 2023; 186:2610-2627.e18. [PMID: 37209682 DOI: 10.1016/j.cell.2023.04.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/07/2023] [Accepted: 04/26/2023] [Indexed: 05/22/2023]
Abstract
The hourglass model describes the convergence of species within the same phylum to a similar body plan during development; however, the molecular mechanisms underlying this phenomenon in mammals remain poorly described. Here, we compare rabbit and mouse time-resolved differentiation trajectories to revisit this model at single-cell resolution. We modeled gastrulation dynamics using hundreds of embryos sampled between gestation days 6.0 and 8.5 and compared the species using a framework for time-resolved single-cell differentiation-flows analysis. We find convergence toward similar cell-state compositions at E7.5, supported by the quantitatively conserved expression of 76 transcription factors, despite divergence in surrounding trophoblast and hypoblast signaling. However, we observed noticeable changes in specification timing of some lineages and divergence of primordial germ cell programs, which in the rabbit do not activate mesoderm genes. Comparative analysis of temporal differentiation models provides a basis for studying the evolution of gastrulation dynamics across mammals.
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Affiliation(s)
- Yoav Mayshar
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ofir Raz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Saifeng Cheng
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Raz Ben-Yair
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Hadas
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Netta Reines
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Markus Mittnenzweig
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Oren Ben-Kiki
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Aviezer Lifshitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Amos Tanay
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
| | - Yonatan Stelzer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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6
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Wang B, Stevenson EL, Dunlap JC. Functional analysis of 110 phosphorylation sites on the circadian clock protein FRQ identifies clusters determining period length and temperature compensation. G3 (BETHESDA, MD.) 2023; 13:jkac334. [PMID: 36537198 PMCID: PMC9911066 DOI: 10.1093/g3journal/jkac334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/13/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
In the negative feedback loop driving the Neurospora circadian oscillator, the negative element, FREQUENCY (FRQ), inhibits its own expression by promoting phosphorylation of its heterodimeric transcriptional activators, White Collar-1 (WC-1) and WC-2. FRQ itself also undergoes extensive time-of-day-specific phosphorylation with over 100 phosphosites previously documented. Although disrupting individual or certain clusters of phosphorylation sites has been shown to alter circadian period lengths to some extent, it is still elusive how all the phosphorylations on FRQ control its activity. In this study, we systematically investigated the role in period determination of all 110 reported FRQ phosphorylation sites, using mutagenesis and luciferase reporter assays. Surprisingly, robust FRQ phosphorylation is still detected even when 84 phosphosites were eliminated altogether; further mutating another 26 phosphoresidues completely abolished FRQ phosphorylation. To identify phosphoresidue(s) on FRQ impacting circadian period length, a series of clustered frq phosphomutants covering all the 110 phosphosites were generated and examined for period changes. When phosphosites in the N-terminal and middle regions of FRQ were eliminated, longer periods were typically seen while removal of phosphorylation in the C-terminal tail resulted in extremely short periods, among the shortest reported. Interestingly, abolishing the 11 phosphosites in the C-terminal tail of FRQ not only results in an extremely short period, but also impacts temperature compensation (TC), yielding an overcompensated circadian oscillator. In addition, the few phosphosites in the middle of FRQ are also found to be crucial for TC. When different groups of FRQ phosphomutations were combined intramolecularly, expected additive effects were generally observed except for one novel case of intramolecular epistasis, where arrhythmicity resulting from one cluster of phosphorylation site mutants was restored by eliminating phosphorylation at another group of sites.
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Affiliation(s)
- Bin Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
| | - Elizabeth-Lauren Stevenson
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
| | - Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
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7
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Herrera LR, McGlynn K, Gibbs ZA, Davis AJ, Whitehurst AW. The Cancer Testes Antigen, HORMAD1, is a Tumor-Specific Replication Fork Protection Factor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526348. [PMID: 36778501 PMCID: PMC9915569 DOI: 10.1101/2023.01.31.526348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tumors frequently activate the expression of genes that are only otherwise required for meiosis. HORMAD1, which is essential for meiotic recombination in multiple species, is expressed in over 50% of human lung adenocarcinoma cells (LUAD). We previously found that HORMAD1 promotes DNA double strand break (DSB) repair in LUAD. Here, we report that HORMAD1 takes on an additional role in protecting genomic integrity. Specifically, we find HORMAD1 is critical for protecting stalled DNA replication forks in LUAD. Loss of HORMAD1 leads to nascent DNA degradation, an event which is mediated by the MRE11-DNA2-BLM pathway. Moreover, following exogenous induction of DNA replication stress, HORMAD1 deleted cells accumulate single stranded DNA (ssDNA). We find that these phenotypes are the result of a lack of RAD51 and BRCA2 loading onto stalled replication forks. Ultimately, loss of HORMAD1 leads to increased DSBs and chromosomal aberrations in response to replication stress. Collectively, our data support a model where HORMAD1 expression is selected to mitigate DNA replication stress, which would otherwise induce deleterious genomic instability.
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8
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Philpott HT, Birmingham TB, Fiset B, Walsh LA, Coleman MC, Séguin CA, Appleton CT. Tensile strain and altered synovial tissue metabolism in human knee osteoarthritis. Sci Rep 2022; 12:17367. [PMID: 36253398 PMCID: PMC9576717 DOI: 10.1038/s41598-022-22459-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/14/2022] [Indexed: 01/10/2023] Open
Abstract
Synovium is critical for maintaining joint homeostasis and may contribute to mechanobiological responses during joint movement. We investigated mechanobiological responses of whole synovium from patients with late-stage knee osteoarthritis (OA). Synovium samples were collected during total knee arthroplasty and assigned to histopathology or cyclic 10% tensile strain loading, including (1) static (control); (2) low-frequency (0.3 Hz); and iii) high-frequency (1.0 Hz) for 30-min. After 6-h incubation, tissues were bisected for RNA isolation and immunostaining (3-nitrotyrosine; 3-NT). RNA sequencing was analyzed for differentially expressed genes and pathway enrichment. Cytokines and lactate were measured in conditioned media. Compared to controls, low-frequency strain induced enrichment of pathways related to interferon response, Fc-receptor signaling, and cell metabolism. High-frequency strain induced enrichment of pathways related to NOD-like receptor signaling, high metabolic demand, and redox signaling/stress. Metabolic and redox cell stress was confirmed by increased release of lactate into conditioned media and increased 3-NT formation in the synovial lining. Late-stage OA synovial tissue responses to tensile strain include frequency-dependent increases in inflammatory signaling, metabolism, and redox biology. Based on these findings, we speculate that some synovial mechanobiological responses to strain may be beneficial, but OA likely disturbs synovial homeostasis leading to aberrant responses to mechanical stimuli, which requires further validation.
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Affiliation(s)
- Holly T. Philpott
- grid.39381.300000 0004 1936 8884Faculty of Health Sciences, Western University, London, ON N6G 1H1 Canada ,grid.39381.300000 0004 1936 8884Bone and Joint Institute, Western University, London, ON N6A 5B5 Canada
| | - Trevor B. Birmingham
- grid.39381.300000 0004 1936 8884Faculty of Health Sciences, Western University, London, ON N6G 1H1 Canada ,grid.39381.300000 0004 1936 8884Bone and Joint Institute, Western University, London, ON N6A 5B5 Canada
| | - Benoit Fiset
- grid.14709.3b0000 0004 1936 8649Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3 Canada
| | - Logan A. Walsh
- grid.14709.3b0000 0004 1936 8649Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3 Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montreal, QC H3A 0C7 Canada
| | - Mitchell C. Coleman
- grid.214572.70000 0004 1936 8294Department of Orthopedics and Rehabilitation, University of Iowa, Iowa City, IA 52242 USA ,grid.214572.70000 0004 1936 8294Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242 USA
| | - Cheryle A. Séguin
- grid.39381.300000 0004 1936 8884Bone and Joint Institute, Western University, London, ON N6A 5B5 Canada ,grid.39381.300000 0004 1936 8884Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1 Canada
| | - C. Thomas Appleton
- grid.39381.300000 0004 1936 8884Bone and Joint Institute, Western University, London, ON N6A 5B5 Canada ,grid.39381.300000 0004 1936 8884Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1 Canada ,grid.39381.300000 0004 1936 8884Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1 Canada ,SJHC Rheumatology Centre, 268 Grosvenor St., London, ON N6A 4V2 Canada
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9
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Ectopic expression of meiotic cohesin generates chromosome instability in cancer cell line. Proc Natl Acad Sci U S A 2022; 119:e2204071119. [PMID: 36179046 PMCID: PMC9549395 DOI: 10.1073/pnas.2204071119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
This work originated from mining of cancer genome data and proceeded to analyze the effects of ectopic expression of meiotic cohesins in mitotic cells in culture. In the process, apart from conclusively answering the question on mechanisms for RAD21L toxicity and its underrepresentation in tumor transcriptomes, we found an association of meiotic cohesin binding with BORIS/CTCFL sites in the normal testis. We also elucidated the patterns and outcomes of meiotic cohesin binding to chromosomes in model cell lines. Furthermore, we uncovered that RAD21L-based meiotic cohesin possesses a self-contained chromosome restructuring activity able to trigger sustainable but imperfect mitotic arrest leading to chromosomal instability. The discovered epigenomic and genetic mechanisms can be relevant to chromosome instability in cancer. Many tumors express meiotic genes that could potentially drive somatic chromosome instability. While germline cohesin subunits SMC1B, STAG3, and REC8 are widely expressed in many cancers, messenger RNA and protein for RAD21L subunit are expressed at very low levels. To elucidate the potential of meiotic cohesins to contribute to genome instability, their expression was investigated in human cell lines, predominately in DLD-1. While the induction of the REC8 complex resulted in a mild mitotic phenotype, the expression of the RAD21L complex produced an arrested but viable cell pool, thus providing a source of DNA damage, mitotic chromosome missegregation, sporadic polyteny, and altered gene expression. We also found that genomic binding profiles of ectopically expressed meiotic cohesin complexes were reminiscent of their corresponding specific binding patterns in testis. Furthermore, meiotic cohesins were found to localize to the same sites as BORIS/CTCFL, rather than CTCF sites normally associated with the somatic cohesin complex. These findings highlight the existence of a germline epigenomic memory that is conserved in cells that normally do not express meiotic genes. Our results reveal a mechanism of action by unduly expressed meiotic cohesins that potentially links them to aneuploidy and chromosomal mutations in affected cells.
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10
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Massive Loss of Transcription Factors Promotes the Initial Diversification of Placental Mammals. Int J Mol Sci 2022; 23:ijms23179720. [PMID: 36077118 PMCID: PMC9456351 DOI: 10.3390/ijms23179720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
As one of the most successful group of organisms, mammals occupy a variety of niches on Earth as a result of macroevolution. Transcription factors (TFs), the fundamental regulators of gene expression, may also have evolved. To examine the relationship between TFs and mammalian macroevolution, we analyzed 140,821 de novo-identified TFs and their birth and death histories from 96 mammalian species. Gene tree vs. species tree reconciliation revealed that placental mammals experienced an upsurge in TF losses around 100 million years ago (Mya) and also near the Cretaceous–Paleogene boundary (K–Pg boundary, 66 Mya). Early Euarchontoglires, Laurasiatheria and marsupials appeared between 100 and 95 Mya and underwent initial diversification. The K-Pg boundary was associated with the massive extinction of dinosaurs, which lead to adaptive radiation of mammals. Surprisingly, TF loss decelerated, rather than accelerated, molecular evolutionary rates of their target genes. As the rate of molecular evolution is affected by the mutation rate, the proportion of neutral mutations and the population size, the decrease in molecular evolution may reflect increased functional constraints to survive target genes.
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11
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Albrecht U. Mutational scanning of the CLOCKΔ19 domain identifies amino acids modulating circadian clock dynamics and co-regulator binding. Acta Physiol (Oxf) 2022; 234:e13809. [PMID: 35224861 DOI: 10.1111/apha.13809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Urs Albrecht
- Department of Biology, Biochemistry University of Fribourg Fribourg Switzerland
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12
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Abdo AN, Rintisch C, Gabriel CH, Kramer A. Mutational scanning identified amino acids of the CLOCK exon 19-domain essential for circadian rhythms. Acta Physiol (Oxf) 2022; 234:e13794. [PMID: 35112498 DOI: 10.1111/apha.13794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 12/21/2022]
Abstract
AIM In the mammalian circadian clock, the CLOCK/BMAL1 heterodimer binds to E-box enhancer elements in the promoters of its target genes to activate transcription. The classical Clock mice, the first circadian mouse mutant discovered, are behaviourally arrhythmic. In this mutant, CLOCK lacks a 51 amino acid domain corresponding to exon 19 (CLOCKΔ19), which is required for normal transactivation. While the importance of this CLOCK domain for circadian rhythms is well established, the exact molecular mechanism is still unclear. METHODS Using CRISPR/Cas9 technology, we created a CLOCK knockout - CLOCK rescue system in human circadian reporter cells and performed systematic mutational scanning to assess the functionality of individual amino acids within the CLOCK exon 19-domain. RESULTS CLOCK knockout cells were arrhythmic, and circadian rhythms could be rescued by introducing wild-type CLOCK, but not CLOCKΔ19. In addition, we identified several residues, whose mutation failed to rescue rhythms in CLOCK knockout cells. Many of these are part of the hydrophobic binding interface of the predicted dimer of the CLOCK exon 19-domain. CONCLUSION Our data not only indicate that CLOCK/BMAL1 oligomerization mediated by the exon 19-domain is important for circadian dynamics but also suggest that the exon 19-domain provides a platform for binding coactivators and repressors, which in turn is required for normal circadian rhythms.
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Affiliation(s)
- Ashraf N Abdo
- Laboratory of Chronobiology, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Carola Rintisch
- Laboratory of Chronobiology, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christian H Gabriel
- Laboratory of Chronobiology, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
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13
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Chronoradiobiology of Breast Cancer: The Time Is Now to Link Circadian Rhythm and Radiation Biology. Int J Mol Sci 2022; 23:ijms23031331. [PMID: 35163264 PMCID: PMC8836288 DOI: 10.3390/ijms23031331] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/20/2022] [Accepted: 01/23/2022] [Indexed: 12/13/2022] Open
Abstract
Circadian disruption has been linked to cancer development, progression, and radiation response. Clinical evidence to date shows that circadian genetic variation and time of treatment affect radiation response and toxicity for women with breast cancer. At the molecular level, there is interplay between circadian clock regulators such as PER1, which mediates ATM and p53-mediated cell cycle gating and apoptosis. These molecular alterations may govern aggressive cancer phenotypes, outcomes, and radiation response. Exploiting the various circadian clock mechanisms may enhance the therapeutic index of radiation by decreasing toxicity, increasing disease control, and improving outcomes. We will review the body’s natural circadian rhythms and clock gene-regulation while exploring preclinical and clinical evidence that implicates chronobiological disruptions in the etiology of breast cancer. We will discuss radiobiological principles and the circadian regulation of DNA damage responses. Lastly, we will present potential rational therapeutic approaches that target circadian pathways to improve outcomes in breast cancer. Understanding the implications of optimal timing in cancer treatment and exploring ways to entrain circadian biology with light, diet, and chronobiological agents like melatonin may provide an avenue for enhancing the therapeutic index of radiotherapy.
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14
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Rabinovich-Nikitin I, Rasouli M, Reitz CJ, Posen I, Margulets V, Dhingra R, Khatua TN, Thliveris JA, Martino TA, Kirshenbaum LA. Mitochondrial autophagy and cell survival is regulated by the circadian Clock gene in cardiac myocytes during ischemic stress. Autophagy 2021; 17:3794-3812. [PMID: 34085589 DOI: 10.1080/15548627.2021.1938913] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cardiac function is highly reliant on mitochondrial oxidative metabolism and quality control. The circadian Clock gene is critically linked to vital physiological processes including mitochondrial fission, fusion and bioenergetics; however, little is known of how the Clock gene regulates these vital processes in the heart. Herein, we identified a putative circadian CLOCK-mitochondrial interactome that gates an adaptive survival response during myocardial ischemia. We show by transcriptome and gene ontology mapping in CLOCK Δ19/Δ19 mouse that Clock transcriptionally coordinates the efficient removal of damaged mitochondria during myocardial ischemia by directly controlling transcription of genes required for mitochondrial fission, fusion and macroautophagy/autophagy. Loss of Clock gene activity impaired mitochondrial turnover resulting in the accumulation of damaged reactive oxygen species (ROS)-producing mitochondria from impaired mitophagy. This coincided with ultrastructural defects to mitochondria and impaired cardiac function. Interestingly, wild type CLOCK but not mutations of CLOCK defective for E-Box binding or interaction with its cognate partner ARNTL/BMAL-1 suppressed mitochondrial damage and cell death during acute hypoxia. Interestingly, the autophagy defect and accumulation of damaged mitochondria in CLOCK-deficient cardiac myocytes were abrogated by restoring autophagy/mitophagy. Inhibition of autophagy by ATG7 knockdown abrogated the cytoprotective effects of CLOCK. Collectively, our results demonstrate that CLOCK regulates an adaptive stress response critical for cell survival by transcriptionally coordinating mitochondrial quality control mechanisms in cardiac myocytes. Interdictions that restore CLOCK activity may prove beneficial in reducing cardiac injury in individuals with disrupted circadian CLOCK.Abbreviations: ARNTL/BMAL1: aryl hydrocarbon receptor nuclear translocator-like; ATG14: autophagy related 14; ATG7: autophagy related 7; ATP: adenosine triphosphate; BCA: bovine serum albumin; BECN1: beclin 1, autophagy related; bHLH: basic helix- loop-helix; CLOCK: circadian locomotor output cycles kaput; CMV: cytomegalovirus; COQ5: coenzyme Q5 methyltransferase; CQ: chloroquine; CRY1: cryptochrome 1 (photolyase-like); DNM1L/DRP1: dynamin 1-like; EF: ejection fraction; EM: electron microscopy; FS: fractional shortening; GFP: green fluorescent protein; HPX: hypoxia; i.p.: intraperitoneal; I-R: ischemia-reperfusion; LAD: left anterior descending; LVIDd: left ventricular internal diameter diastolic; LVIDs: left ventricular internal diameter systolic; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MFN2: mitofusin 2; MI: myocardial infarction; mPTP: mitochondrial permeability transition pore; NDUFA4: Ndufa4, mitochondrial complex associated; NDUFA8: NADH: ubiquinone oxidoreductase subunit A8; NMX: normoxia; OCR: oxygen consumption rate; OPA1: OPA1, mitochondrial dynamin like GTPase; OXPHOS: oxidative phosphorylation; PBS: phosphate-buffered saline; PER1: period circadian clock 1; PPARGC1A/PGC-1α: peroxisome proliferative activated receptor, gamma, coactivator 1 alpha; qPCR: quantitative real-time PCR; RAB7A: RAB7, member RAS oncogene family; ROS: reactive oxygen species; RT: room temperature; shRNA: short hairpin RNA; siRNA: small interfering RNA; TFAM: transcription factor A, mitochondrial; TFEB: transcription factor EB; TMRM: tetra-methylrhodamine methyl ester perchlorate; WT: wild -type; ZT: zeitgeber time.
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Affiliation(s)
- Inna Rabinovich-Nikitin
- Department of Physiology and Pathophysiology, The Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, Manitoba, Canada
| | - Mina Rasouli
- Centre for Cardiovascular Investigations, Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Cristine J Reitz
- Centre for Cardiovascular Investigations, Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Illana Posen
- Department of Physiology and Pathophysiology, The Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, Manitoba, Canada
| | - Victoria Margulets
- Department of Physiology and Pathophysiology, The Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, Manitoba, Canada
| | - Rimpy Dhingra
- Department of Physiology and Pathophysiology, The Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, Manitoba, Canada
| | - Tarak N Khatua
- Centre for Cardiovascular Investigations, Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - James A Thliveris
- Department of Human Anatomy and Cell Science, Rady College of Medicine, Max Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Tami A Martino
- Centre for Cardiovascular Investigations, Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Lorrie A Kirshenbaum
- Department of Physiology and Pathophysiology, The Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, Manitoba, Canada.,Department of Pharmacology and Therapeutics, Rady College of Medicine, Max Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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15
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Yi JS, Díaz NM, D'Souza S, Buhr ED. The molecular clockwork of mammalian cells. Semin Cell Dev Biol 2021; 126:87-96. [PMID: 33810978 DOI: 10.1016/j.semcdb.2021.03.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/20/2022]
Abstract
Most organisms contain self-sustained circadian clocks. These clocks can be synchronized by environmental stimuli, but can also oscillate indefinitely in isolation. In mammals this is true at the molecular level for the majority of cell types that have been examined. A core set of "clock genes" form a transcriptional/translational feedback loop (TTFL) which repeats with a period of approximately 24 h. The exact mechanism of the TTFL differs slightly in various cell types, but all involve similar family members of the core cohort of clock genes. The clock has many outputs which are unique for different tissues. Cells in diverse tissues will convert the timing signals provided by the TTFL into uniquely orchestrated transcriptional oscillations of many clock-controlled genes and cellular processes.
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Affiliation(s)
- Jonathan S Yi
- University of Washington, Dept. of Ophthalmology, 750 Republican St., Seattle, WA 98109, USA
| | - Nicolás M Díaz
- University of Washington, Dept. of Ophthalmology, 750 Republican St., Seattle, WA 98109, USA
| | - Shane D'Souza
- Center for Chronobiology, Abrahamson Pediatric Eye Institute, Division of Pediatric Ophthalmology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Ethan D Buhr
- University of Washington, Dept. of Ophthalmology, 750 Republican St., Seattle, WA 98109, USA.
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16
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Cheng H, Liu Z, Wu G, Ho CT, Li D, Xie Z. Dietary compounds regulating the mammal peripheral circadian rhythms and modulating metabolic outcomes. J Funct Foods 2021. [DOI: 10.1016/j.jff.2021.104370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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17
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Cal-Kayitmazbatir S, Kulkoyluoglu-Cotul E, Growe J, Selby CP, Rhoades SD, Malik D, Oner H, Asimgil H, Francey LJ, Sancar A, Kruger WD, Hogenesch JB, Weljie A, Anafi RC, Kavakli IH. CRY1-CBS binding regulates circadian clock function and metabolism. FEBS J 2021; 288:614-639. [PMID: 32383312 PMCID: PMC7648728 DOI: 10.1111/febs.15360] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/09/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022]
Abstract
Circadian disruption influences metabolic health. Metabolism modulates circadian function. However, the mechanisms coupling circadian rhythms and metabolism remain poorly understood. Here, we report that cystathionine β-synthase (CBS), a central enzyme in one-carbon metabolism, functionally interacts with the core circadian protein cryptochrome 1 (CRY1). In cells, CBS augments CRY1-mediated repression of the CLOCK/BMAL1 complex and shortens circadian period. Notably, we find that mutant CBS-I278T protein, the most common cause of homocystinuria, does not bind CRY1 or regulate its repressor activity. Transgenic CbsZn/Zn mice, while maintaining circadian locomotor activity period, exhibit reduced circadian power and increased expression of E-BOX outputs. CBS function is reciprocally influenced by CRY1 binding. CRY1 modulates enzymatic activity of the CBS. Liver extracts from Cry1-/- mice show reduced CBS activity that normalizes after the addition of exogenous wild-type (WT) CRY1. Metabolomic analysis of WT, CbsZn/Zn , Cry1-/- , and Cry2-/- samples highlights the metabolic importance of endogenous CRY1. We observed temporal variation in one-carbon and transsulfuration pathways attributable to CRY1-induced CBS activation. CBS-CRY1 binding provides a post-translational switch to modulate cellular circadian physiology and metabolic control.
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Affiliation(s)
- Sibel Cal-Kayitmazbatir
- Department Molecular Biology and Genetics, Koc University
Rumelifeneri Yolu, Sariyer, Istanbul, Turkey
| | - Eylem Kulkoyluoglu-Cotul
- Department Chemical and Biological Engineering Koc
University Rumelifeneri Yolu, Sariyer, Istanbul, Turkey
| | - Jacqueline Growe
- Systems Pharmacology and Translational Therapeutics,
University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Christopher P. Selby
- Department of Biochemistry and Biophysics, University of
North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Seth D. Rhoades
- Systems Pharmacology and Translational Therapeutics,
University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Dania Malik
- Systems Pharmacology and Translational Therapeutics,
University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Hasimcan Oner
- Department Chemical and Biological Engineering Koc
University Rumelifeneri Yolu, Sariyer, Istanbul, Turkey
| | - Hande Asimgil
- Department Chemical and Biological Engineering Koc
University Rumelifeneri Yolu, Sariyer, Istanbul, Turkey
| | - Lauren J. Francey
- Divisions of Human Genetics and Immunobiology, Cincinnati
Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of
North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Warren D. Kruger
- Cancer Biology Program, Fox Chase Cancer Center,
Philadelphia, PA, USA
| | - John B. Hogenesch
- Systems Pharmacology and Translational Therapeutics,
University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Divisions of Human Genetics and Immunobiology, Cincinnati
Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Aalim Weljie
- Systems Pharmacology and Translational Therapeutics,
University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ron C. Anafi
- Department of Medicine, Chronobiology and Sleep Institute,
University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ibrahim Halil Kavakli
- Department Molecular Biology and Genetics, Koc University
Rumelifeneri Yolu, Sariyer, Istanbul, Turkey
- Department Chemical and Biological Engineering Koc
University Rumelifeneri Yolu, Sariyer, Istanbul, Turkey
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18
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Abstract
Circadian rhythms govern a large array of physiological and metabolic functions. Perturbations of the daily cycle have been linked to elevated risk of developing cancer as well as poor prognosis in patients with cancer. Also, expression of core clock genes or proteins is remarkably attenuated particularly in tumours of a higher stage or that are more aggressive, possibly linking the circadian clock to cellular differentiation. Emerging evidence indicates that metabolic control by the circadian clock underpins specific hallmarks of cancer metabolism. Indeed, to support cell proliferation and biomass production, the clock may direct metabolic processes of cancer cells in concert with non-clock transcription factors to control how nutrients and metabolites are utilized in a time-specific manner. We hypothesize that the metabolic switch between differentiation or stemness of cancer may be coupled to the molecular clockwork. Moreover, circadian rhythms of host organisms appear to dictate tumour growth and proliferation. This Review outlines recent discoveries of the interplay between circadian rhythms, proliferative metabolism and cancer, highlighting potential opportunities in the development of future therapeutic strategies.
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Affiliation(s)
- Kenichiro Kinouchi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA, USA.
- Department of Endocrinology, Metabolism, and Nephrology, School of Medicine, Keio University, Tokyo, Japan.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, U1233 INSERM, Department of Biological Chemistry, University of California, Irvine, CA, USA.
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19
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Abstract
Circadian clocks are cell-autonomous self-sustaining oscillators that allow organisms to anticipate environmental changes throughout the solar day and persist in nearly every cell examined. Environmental or genetic disruption of circadian rhythms increases the risk of several types of cancer, but the underlying mechanisms are not well understood. Here, we discuss evidence connecting circadian rhythms-with emphasis on the cryptochrome proteins (CRY1/2)-to cancer through in vivo models, mechanisms involving known tumor suppressors and oncogenes, chemotherapeutic efficacy, and human cancer risk.
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Affiliation(s)
- Alanna B Chan
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Katja A Lamia
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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20
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van der Watt PJ, Roden LC, Davis KT, Parker MI, Leaner VD. Circadian Oscillations Persist in Cervical and Esophageal Cancer Cells Displaying Decreased Expression of Tumor-Suppressing Circadian Clock Genes. Mol Cancer Res 2020; 18:1340-1353. [PMID: 32503923 DOI: 10.1158/1541-7786.mcr-19-1074] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 04/01/2020] [Accepted: 06/02/2020] [Indexed: 12/24/2022]
Abstract
There is accumulating evidence for a link between circadian clock disruption and cancer progression. In this study, the circadian clock was investigated in cervical and esophageal cancers, to determine whether it is disrupted in these cancer types. Oncomine datamining revealed downregulation of multiple members of the circadian clock gene family in cancer patient tissue compared with matched normal epithelium. Real-time RT-PCR analysis confirmed significant downregulation of CLOCK, PER1, PER2, PER3, CRY1, CRY2, REV-ERBα, and RORα in esophageal tumor tissue. In cell line models, expression of several circadian clock genes was significantly decreased in transformed and cancer cells compared with noncancer controls, and protein levels were dysregulated. These effects were mediated, at least in part, by methylation, where CLOCK, CRY1, and RORα gene promoter regions were found to be methylated in cancer cells. Overexpression of CLOCK and PER2 in cancer cell lines inhibited cell proliferation and activation of RORα and REV-ERBα using agonists resulted in cancer cell death, while having a lesser effect on normal epithelial cells. Despite dysregulated circadian clock gene expression, cervical and esophageal cancer cells maintain functional circadian oscillations after Dexamethasone synchronization, as revealed using real-time bioluminescence imaging, suggesting that their circadian clock mechanisms are intact. IMPLICATIONS: This study is a first to describe dysregulated, yet oscillating, circadian clock gene expression in cervical and esophageal cancer cells, and knowledge of circadian clock functioning in these cancer types has the potential to inform chronotherapy approaches, where the timing of administration of chemotherapy is optimized on the basis of the circadian clock.
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Affiliation(s)
- Pauline J van der Watt
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | - Laura C Roden
- School of Life Sciences, Coventry University, Coventry, United Kingdom
| | - Kate T Davis
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - M Iqbal Parker
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Virna D Leaner
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- SAMRC/UCT Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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21
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Partch CL. Orchestration of Circadian Timing by Macromolecular Protein Assemblies. J Mol Biol 2020; 432:3426-3448. [DOI: 10.1016/j.jmb.2019.12.046] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022]
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22
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Molecular mechanisms and physiological importance of circadian rhythms. Nat Rev Mol Cell Biol 2019; 21:67-84. [PMID: 31768006 DOI: 10.1038/s41580-019-0179-2] [Citation(s) in RCA: 532] [Impact Index Per Article: 106.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2019] [Indexed: 12/12/2022]
Abstract
To accommodate daily recurring environmental changes, animals show cyclic variations in behaviour and physiology, which include prominent behavioural states such as sleep-wake cycles but also a host of less conspicuous oscillations in neurological, metabolic, endocrine, cardiovascular and immune functions. Circadian rhythmicity is created endogenously by genetically encoded molecular clocks, whose components cooperate to generate cyclic changes in their own abundance and activity, with a periodicity of about a day. Throughout the body, such molecular clocks convey temporal control to the function of organs and tissues by regulating pertinent downstream programmes. Synchrony between the different circadian oscillators and resonance with the solar day is largely enabled by a neural pacemaker, which is directly responsive to certain environmental cues and able to transmit internal time-of-day representations to the entire body. In this Review, we discuss aspects of the circadian clock in Drosophila melanogaster and mammals, including the components of these molecular oscillators, the function and mechanisms of action of central and peripheral clocks, their synchronization and their relevance to human health.
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23
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Verlande A, Masri S. Circadian Clocks and Cancer: Timekeeping Governs Cellular Metabolism. Trends Endocrinol Metab 2019; 30:445-458. [PMID: 31155396 PMCID: PMC6679985 DOI: 10.1016/j.tem.2019.05.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/26/2019] [Accepted: 05/02/2019] [Indexed: 12/30/2022]
Abstract
The circadian clock is a biological mechanism that dictates an array of rhythmic physiological processes. Virtually all cells contain a functional clock whose disruption results in altered timekeeping and detrimental systemic effects, including cancer. Recent advances have connected genetic disruption of the clock with multiple transcriptional and signaling networks controlling tumor initiation and progression. An additional feature of this circadian control relies on cellular metabolism, both within the tumor microenvironment and the organism systemically. A discussion of major advances related to cancer metabolism and the circadian clock will be outlined, including new efforts related to metabolic flux of transformed cells, metabolic heterogeneity of tumors, and the implications of circadian control of these pathways.
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Affiliation(s)
- Amandine Verlande
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA; Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92867, USA; Center for Epigenetics and Metabolism, University of California, Irvine, CA 92697, USA
| | - Selma Masri
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA; Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92867, USA; Center for Epigenetics and Metabolism, University of California, Irvine, CA 92697, USA.
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24
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Angelousi A, Kassi E, Ansari-Nasiri N, Randeva H, Kaltsas G, Chrousos G. Clock genes and cancer development in particular in endocrine tissues. Endocr Relat Cancer 2019; 26:R305-R317. [PMID: 30959483 DOI: 10.1530/erc-19-0094] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 04/04/2019] [Indexed: 12/24/2022]
Abstract
Circadian rhythms at a central and peripheral level are operated by transcriptional/translational feedback loops involving a set of genes called 'clock genes' that have been implicated in the development of several diseases, including malignancies. Dysregulation of the Clock system can influence cancer susceptibility by regulating DNA damage and repair mechanisms, as well as apoptosis. A number of oncogenic pathways can be dysregulated via clock genes' epigenetic alterations, including hypermethylation of clock genes' promoters or variants of clock genes. Clock gene disruption has been studied in breast, lung and prostate cancer, and haematological malignancies. However, it is still not entirely clear whether clock gene disruption is the cause or the consequence of tumourigenesis and data in endocrine neoplasms are scarce. Recent findings suggest that clock genes are implicated in benign and malignant adrenocortical neoplasias. They have been also associated with follicular and papillary thyroid carcinomas and parathyroid adenomas, as well as pituitary adenomas and craniopharyngiomas. Dysregulation of clock genes is also encountered in ovarian and testicular tumours and may also be related with their susceptibility to chemotherapeutic agents. The most common clock genes that are implicated in endocrine neoplasms are PER1, CRY1; in most cases their expression is downregulated in tumoural compared to normal tissues. Although there is still a lot to be done for the better understanding of the role of clock genes in endocrine tumourigenenesis, existing evidence could guide research and help identify novel therapeutic targets aiming mainly at the peripheral components of the clock gene system.
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Affiliation(s)
- Anna Angelousi
- Endocrine Unit, 1st Department of Internal Medicine, Laiko Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Eva Kassi
- Endocrine Unit, 1st Department of Internal Medicine, Laiko Hospital, National and Kapodistrian University of Athens, Athens, Greece
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Narjes Ansari-Nasiri
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Harpal Randeva
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism (WISDEM), University Hospitals Coventry and Warwickshire NHS Trust, Coventry, UK
| | - Gregory Kaltsas
- Endocrine Unit, 1st Department of Propaedeutic Medicine, Laiko University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - George Chrousos
- First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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25
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Meira E Cruz M, Miyazawa M, Manfredini R, Cardinali D, Madrid JA, Reiter R, Araujo JF, Agostinho R, Acuña-Castroviejo D. Impact of Daylight Saving Time on circadian timing system: An expert statement. Eur J Intern Med 2019; 60:1-3. [PMID: 30617016 DOI: 10.1016/j.ejim.2019.01.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/02/2019] [Accepted: 01/03/2019] [Indexed: 02/07/2023]
Affiliation(s)
- M Meira E Cruz
- Sleep Unit, Cardiovascular Center, University of Lisbon, Faculty of Medicine, Lisbon, Portugal.
| | - M Miyazawa
- Department of Immunology, Faculty of Medicine and Anti-Aging Center, Kindai University, Osaka, Japan
| | - R Manfredini
- Department of Medical Sciences, Faculty of Medicine, Surgery and Prevention, University of Ferrara, Ferrara, Italy
| | - D Cardinali
- BIOMED-UCA-CONICET, Department of Teaching and Research, Faculty of Medical Sciences, Pontificia Catholic University of Argentina, Buenos Aires, Argentina
| | - J A Madrid
- Department of Physiology, Faculty of Biology, University of Murcia, Spain
| | - R Reiter
- Department of Cell Systems and Anatomy, UT Health, United States
| | - J F Araujo
- Laboratory of Neurobiology and Biological Rhythmicity, Department of Physiology and Biophysics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - R Agostinho
- Institute of Astrophysic and Space Sciences, Department of Physics, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - D Acuña-Castroviejo
- Department of Physiology, Faculty of Medicine, Center of Biomedical Research, Parque Tecnologico de Ciencias de la Salud, University of Granada, Granada, Spain
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26
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Davis K, Roden LC, Leaner VD, van der Watt PJ. The tumour suppressing role of the circadian clock. IUBMB Life 2019; 71:771-780. [DOI: 10.1002/iub.2005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/10/2018] [Accepted: 12/17/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Kate Davis
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences; University of Cape Town; Cape Town South Africa
| | - Laura C. Roden
- School of Life Sciences; Coventry University, Alison Gingell Building Room 2.24; Coventry, CV1 5FB UK
| | - Virna D. Leaner
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences; University of Cape Town; Cape Town South Africa
- SAMRC/UCT Gynaecological Cancer Research Centre; Institute of Infectious Disease and Molecular Medicine, University of Cape Town; Cape Town South Africa
| | - Pauline J. van der Watt
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences; University of Cape Town; Cape Town South Africa
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27
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Antigenic Targets for the Immunotherapy of Acute Myeloid Leukaemia. J Clin Med 2019; 8:jcm8020134. [PMID: 30678059 PMCID: PMC6406328 DOI: 10.3390/jcm8020134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 01/10/2019] [Accepted: 01/20/2019] [Indexed: 12/18/2022] Open
Abstract
One of the most promising approaches to preventing relapse is the stimulation of the body’s own immune system to kill residual cancer cells after conventional therapy has destroyed the bulk of the tumour. In acute myeloid leukaemia (AML), the high frequency with which patients achieve first remission, and the diffuse nature of the disease throughout the periphery, makes immunotherapy particularly appealing following induction and consolidation therapy, using chemotherapy, and where possible stem cell transplantation. Immunotherapy could be used to remove residual disease, including leukaemic stem cells from the farthest recesses of the body, reducing, if not eliminating, the prospect of relapse. The identification of novel antigens that exist at disease presentation and can act as targets for immunotherapy have also proved useful in helping us to gain a better understand of the biology that belies AML. It appears that there is an additional function of leukaemia associated antigens as biomarkers of disease state and survival. Here, we discuss these findings.
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28
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Qu M, Duffy T, Hirota T, Kay SA. Nuclear receptor HNF4A transrepresses CLOCK:BMAL1 and modulates tissue-specific circadian networks. Proc Natl Acad Sci U S A 2018; 115:E12305-E12312. [PMID: 30530698 PMCID: PMC6310821 DOI: 10.1073/pnas.1816411115] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Either expression level or transcriptional activity of various nuclear receptors (NRs) have been demonstrated to be under circadian control. With a few exceptions, little is known about the roles of NRs as direct regulators of the circadian circuitry. Here we show that the nuclear receptor HNF4A strongly transrepresses the transcriptional activity of the CLOCK:BMAL1 heterodimer. We define a central role for HNF4A in maintaining cell-autonomous circadian oscillations in a tissue-specific manner in liver and colon cells. Not only transcript level but also genome-wide chromosome binding of HNF4A is rhythmically regulated in the mouse liver. ChIP-seq analyses revealed cooccupancy of HNF4A and CLOCK:BMAL1 at a wide array of metabolic genes involved in lipid, glucose, and amino acid homeostasis. Taken together, we establish that HNF4A defines a feedback loop in tissue-specific mammalian oscillators and demonstrate its recruitment in the circadian regulation of metabolic pathways.
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Affiliation(s)
- Meng Qu
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089
| | - Tomas Duffy
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, 464-8602 Nagoya, Japan
| | - Steve A Kay
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089;
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29
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Gibbs ZA, Whitehurst AW. Emerging Contributions of Cancer/Testis Antigens to Neoplastic Behaviors. Trends Cancer 2018; 4:701-712. [PMID: 30292353 DOI: 10.1016/j.trecan.2018.08.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 02/07/2023]
Abstract
Tumors of nearly every origin activate the expression of genes normally restricted to gametogenic cells. These genes encode proteins termed cancer/testis (CT) antigens, since expression outside of their naturally immune-privileged site can evoke an immune response. Despite extensive efforts to exploit CT antigens as immunotherapeutic targets, investigation of whether these proteins participate in tumorigenic processes has lagged. Here, we discuss emerging evidence that demonstrates that CT antigens can confer a selective advantage to tumor cells by promoting oncogenic processes or permitting evasion of tumor-suppressive mechanisms. These advances indicate the inherent flexibility of tumor cell regulatory networks to engage aberrantly expressed proteins to promote neoplastic behaviors, which could ultimately present novel therapeutic entry points.
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Affiliation(s)
- Zane A Gibbs
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA; Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Angelique W Whitehurst
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA; Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.
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30
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Nichols BA, Oswald NW, McMillan EA, McGlynn K, Yan J, Kim MS, Saha J, Mallipeddi PL, LaDuke SA, Villalobos PA, Rodriguez-Canales J, Wistuba II, Posner BA, Davis AJ, Minna JD, MacMillan JB, Whitehurst AW. HORMAD1 Is a Negative Prognostic Indicator in Lung Adenocarcinoma and Specifies Resistance to Oxidative and Genotoxic Stress. Cancer Res 2018; 78:6196-6208. [PMID: 30185546 DOI: 10.1158/0008-5472.can-18-1377] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/10/2018] [Accepted: 08/30/2018] [Indexed: 12/21/2022]
Abstract
Cancer testis antigens (CTA) are expressed in testis and placenta and anomalously activated in a variety of tumors. The mechanistic contribution of CTAs to neoplastic phenotypes remains largely unknown. Using a chemigenomics approach, we find that the CTA HORMAD1 correlates with resistance to the mitochondrial complex I inhibitor piericidin A in non-small cell lung cancer (NSCLC). Resistance was due to a reductive intracellular environment that attenuated the accumulation of free radicals. In human lung adenocarcinoma (LUAD) tumors, patients expressing high HORMAD1 exhibited elevated mutational burden and reduced survival. HORMAD1 tumors were enriched for genes essential for homologous recombination (HR), and HORMAD1 promoted RAD51-filament formation, but not DNA resection, during HR. Accordingly, HORMAD1 loss enhanced sensitivity to γ-irradiation and PARP inhibition, and HORMAD1 depletion significantly reduced tumor growth in vivo These results suggest that HORMAD1 expression specifies a novel subtype of LUAD, which has adapted to mitigate DNA damage. In this setting, HORMAD1 could represent a direct target for intervention to enhance sensitivity to DNA-damaging agents or as an immunotherapeutic target in patients.Significance: This study uses a chemigenomics approach to demonstrate that anomalous expression of the CTA HORMAD1 specifies resistance to oxidative stress and promotes HR to support tumor cell survival in NSCLC. Cancer Res; 78(21); 6196-208. ©2018 AACR.
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Affiliation(s)
- Brandt A Nichols
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Nathaniel W Oswald
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas
| | | | - Kathleen McGlynn
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Jingsheng Yan
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, Texas
| | - Min S Kim
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, Texas
| | - Janapriya Saha
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas
| | - Prema L Mallipeddi
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas
| | - Sydnie A LaDuke
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Pamela A Villalobos
- Department of Translational Molecular Pathology, M.D. Anderson Cancer Center, Houston, Texas
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, M.D. Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, M.D. Anderson Cancer Center, Houston, Texas
| | - Bruce A Posner
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas
| | - Anthony J Davis
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas
| | - John D Minna
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas.,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, Texas
| | - John B MacMillan
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California
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31
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van der Veen DR, Riede SJ, Heideman PD, Hau M, van der Vinne V, Hut RA. Flexible clock systems: adjusting the temporal programme. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0254. [PMID: 28993498 DOI: 10.1098/rstb.2016.0254] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2017] [Indexed: 12/20/2022] Open
Abstract
Under natural conditions, many aspects of the abiotic and biotic environment vary with time of day, season or even era, while these conditions are typically kept constant in laboratory settings. The timing information contained within the environment serves as critical timing cues for the internal biological timing system, but how this system drives daily rhythms in behaviour and physiology may also depend on the internal state of the animal. The disparity between timing of these cues in natural and laboratory conditions can result in substantial differences in the scheduling of behaviour and physiology under these conditions. In nature, temporal coordination of biological processes is critical to maximize fitness because they optimize the balance between reproduction, foraging and predation risk. Here we focus on the role of peripheral circadian clocks, and the rhythms that they drive, in enabling adaptive phenotypes. We discuss how reproduction, endocrine activity and metabolism interact with peripheral clocks, and outline the complex phenotypes arising from changes in this system. We conclude that peripheral timing is critical to adaptive plasticity of circadian organization in the field, and that we must abandon standard laboratory conditions to understand the mechanisms that underlie this plasticity which maximizes fitness under natural conditions.This article is part of the themed issue 'Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals'.
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Affiliation(s)
- Daan R van der Veen
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Sjaak J Riede
- Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Paul D Heideman
- Department of Biology, College of William and Mary, Williamsburg, VA, USA
| | - Michaela Hau
- Max-Planck-Institute for Ornithology, Seewiesen, Germany and University of Konstanz, Konstanz, Germany
| | - Vincent van der Vinne
- Neurobiology Department, University of Massachusetts Medical School, Worcester, MA, USA
| | - Roelof A Hut
- Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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32
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Shilts J, Chen G, Hughey JJ. Evidence for widespread dysregulation of circadian clock progression in human cancer. PeerJ 2018; 6:e4327. [PMID: 29404219 PMCID: PMC5797448 DOI: 10.7717/peerj.4327] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/15/2018] [Indexed: 12/12/2022] Open
Abstract
The ubiquitous daily rhythms in mammalian physiology are guided by progression of the circadian clock. In mice, systemic disruption of the clock can promote tumor growth. In vitro, multiple oncogenes can disrupt the clock. However, due to the difficulties of studying circadian rhythms in solid tissues in humans, whether the clock is disrupted within human tumors has remained unknown. We sought to determine the state of the circadian clock in human cancer using publicly available transcriptome data. We developed a method, called the clock correlation distance (CCD), to infer circadian clock progression in a group of samples based on the co-expression of 12 clock genes. Our method can be applied to modestly sized datasets in which samples are not labeled with time of day and coverage of the circadian cycle is incomplete. We used the method to define a signature of clock gene co-expression in healthy mouse organs, then validated the signature in healthy human tissues. By then comparing human tumor and non-tumor samples from twenty datasets of a range of cancer types, we discovered that clock gene co-expression in tumors is consistently perturbed. Subsequent analysis of data from clock gene knockouts in mice suggested that perturbed clock gene co-expression in human cancer is not caused solely by the inactivation of clock genes. Furthermore, focusing on lung cancer, we found that human lung tumors showed systematic changes in expression in a large set of genes previously inferred to be rhythmic in healthy lung. Our findings suggest that clock progression is dysregulated in many solid human cancers and that this dysregulation could have broad effects on circadian physiology within tumors. In addition, our approach opens the door to using publicly available data to infer circadian clock progression in a multitude of human phenotypes.
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Affiliation(s)
- Jarrod Shilts
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - Guanhua Chen
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Jacob J Hughey
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, United States of America.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States of America
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33
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Sertoli cell specific knockdown of RAR-related orphan receptor (ROR) alpha at puberty reduces sperm count in rats. Gene 2018; 641:18-24. [DOI: 10.1016/j.gene.2017.10.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 08/28/2017] [Accepted: 10/11/2017] [Indexed: 12/20/2022]
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34
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Okazaki F, Matsunaga N, Hamamura K, Suzuki K, Nakao T, Okazaki H, Kutsukake M, Fukumori S, Tsuji Y, To H. Administering xCT Inhibitors Based on Circadian Clock Improves Antitumor Effects. Cancer Res 2017; 77:6603-6613. [PMID: 29038345 DOI: 10.1158/0008-5472.can-17-0720] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/22/2017] [Accepted: 10/04/2017] [Indexed: 11/16/2022]
Abstract
Clock genes encoding transcription factors that regulate circadian rhythms may inform chronomodulated chemotherapy, where time-dependent dose alterations might affect drug efficacy and reduce side effects. For example, inhibiting the essential cystine transporter xCT with sulfasalazine induces growth arrest in cancer cells. Although the anticancer effects of sulfasalazine have been studied extensively, its effects on transcriptional control of xCT expression have not been studied. Here, we show that sulfasalazine administration during the period of increased xCT expression improves its anticancer effects and that the Clock gene itself induces xCT expression and regulates its circadian rhythm. Our findings highlight the clinical potential of chronomodulated chemotherapy and the importance of xCT-mediated transcriptional regulation in the utility of such strategies. Cancer Res; 77(23); 6603-13. ©2017 AACR.
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Affiliation(s)
- Fumiyasu Okazaki
- Department of Medical Pharmaceutics, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan.
| | - Naoya Matsunaga
- Department of Glocal Healthcare Science, Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kengo Hamamura
- Department of Chemical Pharmacology, Daiichi University of Pharmacy, Fukuoka, Japan
| | - Kayoko Suzuki
- Department of Medical Pharmaceutics, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Takaharu Nakao
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Okazaki
- Department of Molecular Biology, Daiichi University of Pharmacy, Fukuoka, Japan
| | - Masahiko Kutsukake
- Department of Medical Pharmaceutics, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Shiro Fukumori
- Department of Medical Pharmaceutics, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Yasuhiro Tsuji
- Department of Medical Pharmaceutics, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Hideto To
- Department of Medical Pharmaceutics, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
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35
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Polo A, Singh S, Crispo A, Russo M, Giudice A, Montella M, Colonna G, Costantini S. Evaluating the associations between human circadian rhythms and dysregulated genes in liver cancer cells. Oncol Lett 2017; 14:7353-7359. [PMID: 29250165 PMCID: PMC5727601 DOI: 10.3892/ol.2017.7109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 08/24/2017] [Indexed: 12/14/2022] Open
Abstract
Network analysis is a useful approach in cancer biology as it provides information regarding the genes and proteins. In our previous study, a network analysis was performed on dysregulated genes in HepG2 cells, a hepatoblastoma cell line that lacks the viral infection, compared with normal hepatocytes, identifying the presence of 26 HUB genes. The present study aimed to identify whether these previously identified HUB genes participate in the network that controls the human circadian rhythms. The results of the present study demonstrated that 20/26 HUB genes were associated with the metabolic processes that control human circadian rhythms, which supports the hypothesis that a number of cancer types are dependent from circadian cycles. In addition, it was revealed that the CLOCK circadian regulator gene was associated, via cytoskeleton associated protein 5 (CKAP5), with the HUB genes of the HepG2 network, and that CKAP5 was associated with three other circadian genes (casein kinase 1ε, casein kinase 1δ and histone deacetylase 4) and 10 HepG2 genes (SH2 domain containing, ZW10 interacting kinetochore protein, aurora kinase B, cell division cycle 20, centromere protein A, inner centromere protein, mitotic arrest deficient 2 like 1, baculoviral IAP repeat containing 5, SPC24 NDC80 kinetochore complex component and kinesin family member 2C). Furthermore, the genes that associate the circadian system with liver cancer were demonstrated to encode intrinsically disordered proteins. Finally, the results of the present study identified the microRNAs involved in the network formed by the overlapping of HepG2 and circadian genes.
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Affiliation(s)
- Andrea Polo
- Epidemiology Unit, National Cancer Institute ‘Foundation G. Pascale’, IRCCS, I-80131 Naples, Italy
| | - Sakshi Singh
- Doctorate in Computational Biology, Second University of Naples, I-80131 Naples, Italy
| | - Anna Crispo
- Epidemiology Unit, National Cancer Institute ‘Foundation G. Pascale’, IRCCS, I-80131 Naples, Italy
| | - Marilina Russo
- Oncology Research Center of Mercogliano, National Cancer Institute ‘Foundation G. Pascale’, IRCCS, I-80131 Naples, Italy
| | - Aldo Giudice
- Epidemiology Unit, National Cancer Institute ‘Foundation G. Pascale’, IRCCS, I-80131 Naples, Italy
| | - Maurizio Montella
- Epidemiology Unit, National Cancer Institute ‘Foundation G. Pascale’, IRCCS, I-80131 Naples, Italy
| | - Giovanni Colonna
- Medical Informatics Service, University Hospital, University of Campania ‘Luigi Vanvitelli’, I-80131 Naples, Italy
| | - Susan Costantini
- Oncology Research Center of Mercogliano, National Cancer Institute ‘Foundation G. Pascale’, IRCCS, I-80131 Naples, Italy
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36
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Teplyakov E, Wu Q, Liu J, Pugacheva EM, Loukinov D, Boukaba A, Lobanenkov V, Strunnikov A. The downregulation of putative anticancer target BORIS/CTCFL in an addicted myeloid cancer cell line modulates the expression of multiple protein coding and ncRNA genes. Oncotarget 2017; 8:73448-73468. [PMID: 29088719 PMCID: PMC5650274 DOI: 10.18632/oncotarget.20627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/23/2017] [Indexed: 12/27/2022] Open
Abstract
The BORIS/CTCFL gene, is a testis-specific CTCF paralog frequently erroneously activated in cancer, although its exact role in cancer remains unclear. BORIS is both a transcription factor and an architectural chromatin protein. BORIS' normal role is to establish a germline-like gene expression and remodel the epigenetic landscape in testis; it similarly remodels chromatin when activated in human cancer. Critically, at least one cancer cell line, K562, is dependent on BORIS for its self-renewal and survival. Here, we downregulate BORIS expression in the K562 cancer cell line to investigate downstream pathways regulated by BORIS. RNA-seq analyses of both mRNA and small ncRNAs, including miRNA and piRNA, in the knock-down cells revealed a set of differentially expressed genes and pathways, including both testis-specific and general proliferation factors, as well as proteins involved in transcription regulation and cell physiology. The differentially expressed genes included important transcriptional regulators such as SOX6 and LIN28A. Data indicate that both direct binding of BORIS to promoter regions and locus-control activity via long-distance chromatin domain regulation are involved. The sum of findings suggests that BORIS activation in leukemia does not just recapitulate the germline, but creates a unique regulatory network.
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Affiliation(s)
- Evgeny Teplyakov
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China.,The University of the Chinese Academy of Sciences, Beijing, China
| | - Qiongfang Wu
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Jian Liu
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | | | - Dmitry Loukinov
- NIH, NIAID, Laboratory of Immunogenetics, Rockville, MD, USA
| | - Abdelhalim Boukaba
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | | | - Alexander Strunnikov
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China.,The University of the Chinese Academy of Sciences, Beijing, China
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37
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Hou Z, Su L, Pei J, Grishin NV, Zhang H. Crystal Structure of the CLOCK Transactivation Domain Exon19 in Complex with a Repressor. Structure 2017; 25:1187-1194.e3. [PMID: 28669630 DOI: 10.1016/j.str.2017.05.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/04/2017] [Accepted: 05/25/2017] [Indexed: 11/24/2022]
Abstract
In the canonical clock model, CLOCK:BMAL1-mediated transcriptional activation is feedback regulated by its repressors CRY and PER and, in association with other coregulators, ultimately generates oscillatory gene expression patterns. How CLOCK:BMAL1 interacts with coregulator(s) is not well understood. Here we report the crystal structures of the mouse CLOCK transactivating domain Exon19 in complex with CIPC, a potent circadian repressor that functions independently of CRY and PER. The Exon19:CIPC complex adopts a three-helical coiled-coil bundle conformation containing two Exon19 helices and one CIPC. Unique to Exon19:CIPC, three highly conserved polar residues, Asn341 of CIPC and Gln544 of the two Exon19 helices, are located at the mid-section of the coiled-coil bundle interior and form hydrogen bonds with each other. Combining results from protein database search, sequence analysis, and mutagenesis studies, we discovered for the first time that CLOCK Exon19:CIPC interaction is a conserved transcription regulatory mechanism among mammals, fish, flies, and other invertebrates.
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Affiliation(s)
- Zhiqiang Hou
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lijing Su
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jimin Pei
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hong Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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38
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Lu Y, Zheng X, Hu W, Bian S, Zhang Z, Tao D, Liu Y, Ma Y. Cancer/testis antigen PIWIL2 suppresses circadian rhythms by regulating the stability and activity of BMAL1 and CLOCK. Oncotarget 2017; 8:54913-54924. [PMID: 28903391 PMCID: PMC5589630 DOI: 10.18632/oncotarget.18973] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/18/2017] [Indexed: 02/05/2023] Open
Abstract
Circadian rhythms are regulated by transcriptional and post-translational feedback loops generated by appropriate functions of clock proteins. Rhythmic degradation of the circadian clock proteins is critical for maintenance of the circadian oscillations. Notably, circadian clock does not work during spermatogenesis and can be disrupted in tumors. However, the underlying mechanism that suppresses circadian rhythms in germ cells and cancer cells remains largely unknown. Here we report that the cancer/testis antigen PIWIL2 can repress circadian rhythms both in the testis and cancer cells. By facilitating SRC binding with PI3K, PIWIL2 activates the PI3K-AKT pathway to phosphorylate and deactivate GSK3β, suppressing GSK3β-induced phosphorylation and degradation of circadian protein BMAL1 and CLOCK. Meanwhile, PIWIL2 can bind with E-Box sequences associated with the BMAL1/CLOCK complex to negatively regulate the transcriptional activation activity of promoters of clock-controlled genes. Taken together, our results first described a function for the germline-specific protein PIWIL2 in regulation of the circadian clock, providing a molecular link between spermatogenesis as well as tumorigenesis to the dysfunction of circadian rhythms.
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Affiliation(s)
- Yilu Lu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xulei Zheng
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Wei Hu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shasha Bian
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zhiwei Zhang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Dachang Tao
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yunqiang Liu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yongxin Ma
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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39
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Shostak A. Circadian Clock, Cell Division, and Cancer: From Molecules to Organism. Int J Mol Sci 2017; 18:E873. [PMID: 28425940 PMCID: PMC5412454 DOI: 10.3390/ijms18040873] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 12/21/2022] Open
Abstract
As a response to environmental changes driven by the Earth's axial rotation, most organisms evolved an internal biological timer-the so called circadian clock-which regulates physiology and behavior in a rhythmic fashion. Emerging evidence suggests an intimate interplay between the circadian clock and another fundamental rhythmic process, the cell cycle. However, the precise mechanisms of this connection are not fully understood. Disruption of circadian rhythms has a profound impact on cell division and cancer development and, vice versa, malignant transformation causes disturbances of the circadian clock. Conventional knowledge attributes tumor suppressor properties to the circadian clock. However, this implication might be context-dependent, since, under certain conditions, the clock can also promote tumorigenesis. Therefore, a better understanding of the molecular links regulating the physiological balance between the two cycles will have potential significance for the treatment of cancer and associated disorders.
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Affiliation(s)
- Anton Shostak
- Circadian Rhythms and Molecular Clocks Group, Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany.
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40
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Cai Y, Tsai HC, Yen RWC, Zhang YW, Kong X, Wang W, Xia L, Baylin SB. Critical threshold levels of DNA methyltransferase 1 are required to maintain DNA methylation across the genome in human cancer cells. Genome Res 2017; 27:533-544. [PMID: 28232479 PMCID: PMC5378172 DOI: 10.1101/gr.208108.116] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 02/22/2017] [Indexed: 11/18/2022]
Abstract
Reversing DNA methylation abnormalities and associated gene silencing, through inhibiting DNA methyltransferases (DNMTs) is an important potential cancer therapy paradigm. Maximizing this potential requires defining precisely how these enzymes maintain genome-wide, cancer-specific DNA methylation. To date, there is incomplete understanding of precisely how the three DNMTs, 1, 3A, and 3B, interact for maintaining DNA methylation abnormalities in cancer. By combining genetic and shRNA depletion strategies, we define not only a dominant role for DNA methyltransferase 1 (DNMT1) but also distinct roles of 3A and 3B in genome-wide DNA methylation maintenance. Lowering DNMT1 below a threshold level is required for maximal loss of DNA methylation at all genomic regions, including gene body and enhancer regions, and for maximally reversing abnormal promoter DNA hypermethylation and associated gene silencing to reexpress key genes. It is difficult to reach this threshold with patient-tolerable doses of current DNMT inhibitors (DNMTIs). We show that new approaches, like decreasing the DNMT targeting protein, UHRF1, can augment the DNA demethylation capacities of existing DNA methylation inhibitors for fully realizing their therapeutic potential.
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Affiliation(s)
- Yi Cai
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Hsing-Chen Tsai
- Graduate Institute of Toxicology, National Taiwan University, Taipei, 10051, Taiwan.,Department of Internal Medicine, National Taiwan University Hospital, Taipei, 10002, Taiwan
| | - Ray-Whay Chiu Yen
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Yang W Zhang
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Xiangqian Kong
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Wei Wang
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Limin Xia
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Stephen B Baylin
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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Iida M, Fujii S, Uchida M, Nakamura H, Kagami Y, Agusa T, Hirano M, Bak SM, Kim EY, Iwata H. Identification of aryl hydrocarbon receptor signaling pathways altered in TCDD-treated red seabream embryos by transcriptome analysis. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 177:156-170. [PMID: 27288597 DOI: 10.1016/j.aquatox.2016.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 05/16/2016] [Accepted: 05/20/2016] [Indexed: 06/06/2023]
Abstract
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) induces a broad spectrum of toxic effects including craniofacial malformation and neural damage in fish embryos. These effects are mainly mediated by the aryl hydrocarbon receptor (AHR). However, the mode of action between TCDD-induced AHR activation and adverse outcomes is not yet understood. To provide a comprehensive picture of the AHR signaling pathway in fish embryos exposed to TCDD, red seabream (Pagrus major) embryos were treated with graded concentrations of TCDD (0.3-37nM) in seawater, or with a mixture of TCDD and 500nM CH223191, an AHR-specific antagonist. The transcriptome of red seabream embryos was analyzed using a custom-made microarray with 6000 probes specifically prepared for this species. A Jonckheere-Terpstra test was performed to screen for genes that demonstrated altered mRNA expression levels following TCDD exposure. The signals of 1217 genes (as human homologs) were significantly altered in a TCDD concentration-dependent manner (q-value<0.2). Notably, the TCDD-induced alteration in mRNA expression was alleviated by co-exposure to CH223191, suggesting that the mRNA expression level of these genes was regulated by AHR. To identify TCDD-activated pathways, the microarray data were further subjected to gene set enrichment analysis (GSEA) and functional protein-protein interaction (PPI) network analysis. GSEA demonstrated that the effects of TCDD on sets of genes involved calcium, mitogen-activated protein kinase (MAPK), actin cytoskeleton, chemokine, T cell receptor, melanoma, vascular endothelial growth factor (VEGF), axon guidance, and renal cell carcinoma signaling pathways. These results suggest the hypotheses that TCDD induces immunosuppression via the calcium, MAPK, chemokine, and T cell receptor signaling pathways, neurotoxicity via VEGF signaling, and axon guidance alterations and teratogenicity via the dysregulation of the actin cytoskeleton and melanoma and renal cell carcinoma signaling pathways. Furthermore, the PPI network analysis indicated that the adverse outcome pathways of TCDD in the embryos might be propagated through several hub genes such as cell division control protein 42, phosphoinositide-3-kinase regulatory subunit 1, and guanine nucleotide-binding proteins. Understanding these pathways potentially allows for exploring the adverse outcome pathway of the effects of TCDD on the red seabream embryos.
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Affiliation(s)
- Midori Iida
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, 790-8577, Japan; Computer Science and Systems Engineering, Kyusyu Institute of Technology, Iizuka, 820-0067, Japan.
| | - Satoshi Fujii
- Computer Science and Systems Engineering, Kyusyu Institute of Technology, Iizuka, 820-0067, Japan.
| | | | | | | | - Tetsuro Agusa
- Graduate School of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Kumamoto, 862-0920, Japan.
| | - Masashi Hirano
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, 790-8577, Japan.
| | - Su-Min Bak
- Department of Life and Nanopharmaceutical Science and Department of Biology, Kyung Hee University, Seoul, 130-701, Korea.
| | - Eun-Young Kim
- Department of Life and Nanopharmaceutical Science and Department of Biology, Kyung Hee University, Seoul, 130-701, Korea.
| | - Hisato Iwata
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, 790-8577, Japan.
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42
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Xu ZS, Zhang HX, Zhang YL, Liu TT, Ran Y, Chen LT, Wang YY, Shu HB. PASD1 promotes STAT3 activity and tumor growth by inhibiting TC45-mediated dephosphorylation of STAT3 in the nucleus. J Mol Cell Biol 2016; 8:221-31. [PMID: 26892021 DOI: 10.1093/jmcb/mjw005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 09/22/2015] [Indexed: 12/17/2022] Open
Abstract
Activation of the transcription factor signal transducer and activator of transcription 3 (STAT3) is tightly regulated during various physiological processes, such as cell proliferation, survival, and differentiation, and aberrant STAT3 activation results in tumorigenesis. In this study, we identified the cancer/testis antigen PASD1 as a positive regulator of STAT3 activity. Overexpression of PASD1 activated STAT3 and potentiated IL-6-induced activation of STAT3, whereas knockdown of PASD1 had opposite effects. Endogenous coimmunoprecipitation experiments indicated that PASD1 interacted with STAT3 in the nucleus. Overexpression of PASD1 enhanced both basal and IL-6-induced STAT3 phosphorylation at Y705, whereas knockdown of PASD1 had opposite effects. Mechanistically, PASD1 competed with TC45, a nuclear protein tyrosine phosphatase, to associate with STAT3, thus inhibited TC45-mediated dephosphorylation of STAT3. Consistently, knockdown of PASD1 inhibited expression of many pro-oncogenic genes, leading to suppression of cell proliferation, anchorage-independent growth, cell migration, and tumor growth in nude mice. Our findings demonstrate that PASD1 serves as a critical nuclear positive regulator of STAT3-mediated gene expression and tumorigenesis.
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Affiliation(s)
- Zhi-Sheng Xu
- College of Life Sciences, Medical Research Institute, Collaborative Innovation Center for Viral Immunology, Wuhan University, Wuhan 430072, China
| | - Hong-Xia Zhang
- College of Life Sciences, Medical Research Institute, Collaborative Innovation Center for Viral Immunology, Wuhan University, Wuhan 430072, China
| | - Yu-Long Zhang
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Tian-Tian Liu
- College of Life Sciences, Medical Research Institute, Collaborative Innovation Center for Viral Immunology, Wuhan University, Wuhan 430072, China
| | - Yong Ran
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Liu-Ting Chen
- College of Life Sciences, Medical Research Institute, Collaborative Innovation Center for Viral Immunology, Wuhan University, Wuhan 430072, China
| | - Yan-Yi Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Hong-Bing Shu
- College of Life Sciences, Medical Research Institute, Collaborative Innovation Center for Viral Immunology, Wuhan University, Wuhan 430072, China
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Gérard C, Goldbeter A. Dynamics of the mammalian cell cycle in physiological and pathological conditions. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 8:140-56. [PMID: 26613368 DOI: 10.1002/wsbm.1325] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/22/2015] [Accepted: 10/08/2015] [Indexed: 01/01/2023]
Abstract
A network of cyclin-dependent kinases (Cdks) controls progression along the successive phases G1, S, G2, and M of the mammalian cell cycle. Deregulations in the expression of molecular components in this network often lead to abusive cell proliferation and cancer. Given the complex nature of the Cdk network, it is fruitful to resort to computational models to grasp its dynamical properties. Investigated by means of bifurcation diagrams, a detailed computational model for the Cdk network shows how the balance between quiescence and proliferation is affected by activators (oncogenes) and inhibitors (tumor suppressors) of cell cycle progression, as well as by growth factors and other external factors such as the extracellular matrix (ECM) and cell contact inhibition. Suprathreshold changes in all these factors can trigger a switch in the dynamical behavior of the network corresponding to a bifurcation between a stable steady state, associated with cell cycle arrest, and sustained oscillations of the various cyclin/Cdk complexes, corresponding to cell proliferation. The model for the Cdk network accounts for the dependence or independence of cell proliferation on serum and/or cell anchorage to the ECM. Such computational approach provides an integrated view of the control of cell proliferation in physiological or pathological conditions. Whether the balance is tilted toward cell cycle arrest or cell proliferation depends on the direction in which the threshold associated with the bifurcation is passed once the cell integrates the multiple signals, internal or external to the Cdk network, that promote or impede progression in the cell cycle.
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Affiliation(s)
- Claude Gérard
- Unité de Chronobiologie théorique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Albert Goldbeter
- Unité de Chronobiologie théorique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Marais Street, Stellenbosch, South Africa
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Abstract
PURPOSE OF REVIEW The circadian clock is an intricate biological timekeeper that is subject to fine-tuning mechanisms in order to maintain synchrony with the surrounding environment. One such mechanism is performed by the mammalian sirtuins that provide plasticity to the circadian clock by sensing cellular metabolic state. The sirtuins modulate the circadian epigenome and subsequent transcriptional control, and alterations to this organized system manifest in metabolic consequences, aging phenotypes and possibly cancer. RECENT FINDINGS New information regarding sirtuin-dependent control of the circadian clock has emerged. In addition to sirtuin (SIRT)1 and SIRT3, SIRT6 has been demonstrated as a critical regulator of circadian transcription that also serves as an interface with metabolic homeostasis. Also, new metabolic functions of SIRT1 have been described in the brain, which are critical to relay nutritional inputs to the central clock. SUMMARY This review focuses on the link between the circadian clock and the sirtuins, with an emphasis on new findings. In addition, speculation on the possible connections at the physiological level will be made that could further link the clock to aging and cancer.
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Affiliation(s)
- Selma Masri
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, California, USA
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45
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Khan G, Brooks SE, Mills KI, Guinn BA. Infrequent Expression of the Cancer-Testis Antigen, PASD1, in Ovarian Cancer. BIOMARKERS IN CANCER 2015; 7:31-8. [PMID: 26327782 PMCID: PMC4539101 DOI: 10.4137/bic.s28378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/29/2015] [Accepted: 06/29/2015] [Indexed: 12/13/2022]
Abstract
Ovarian cancer is very treatable in the early stages of disease; however, it is usually detected in the later stages, at which time, treatment is no longer as effective. If discovered early (Stage I), there is a 90% chance of five-year survival. Therefore, it is imperative that early-stage biomarkers are identified to enhance the early detection of ovarian cancer. Cancer-testis antigens (CTAs), such as Per ARNT SIM (PAS) domain containing 1 (PASD1), are unique in that their expression is restricted to immunologically restricted sites, such as the testis and placenta, which do not express MHC class I, and cancer, making them ideally positioned to act as targets for immunotherapy as well as potential biomarkers for cancer detection where expressed. We examined the expression of PASD1a and b in a number of cell lines, as well as eight healthy ovary samples, eight normal adjacent ovarian tissues, and 191 ovarian cancer tissues, which were predominantly stage I (n = 164) and stage II (n = 14) disease. We found that despite the positive staining of skin cancer, only one stage Ic ovarian cancer patient tissue expressed PASD1a and b at detectable levels. This may reflect the predominantly stage I ovarian cancer samples examined. To examine the restriction of PASD1 expression, we examined endometrial tissue arrays and found no expression in 30 malignant tumor tissues, 23 cases of hyperplasia, or 16 normal endometrial tissues. Our study suggests that the search for a single cancer-testes antigen/biomarker that can detect early ovarian cancer must continue.
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Affiliation(s)
- Ghazala Khan
- Department of Life Sciences, University of Bedfordshire, Park Square, Luton, Bedfordshire, UK
| | - Suzanne E Brooks
- Biomedical Imaging Unit, Southampton General Hospital, Southampton, UK
| | - Ken I Mills
- Blood Cancer Research Group, Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, UK
| | - Barbara-Ann Guinn
- Department of Life Sciences, University of Bedfordshire, Park Square, Luton, Bedfordshire, UK
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