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Telmer CA, Karimi K, Chess MM, Agalakov S, Arshinoff BI, Lotay V, Wang DZ, Chu S, Pells TJ, Vize PD, Hinman VF, Ettensohn CA. Echinobase: a resource to support the echinoderm research community. Genetics 2024; 227:iyae002. [PMID: 38262680 PMCID: PMC11075573 DOI: 10.1093/genetics/iyae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/27/2023] [Indexed: 01/25/2024] Open
Abstract
Echinobase (www.echinobase.org) is a model organism knowledgebase serving as a resource for the community that studies echinoderms, a phylum of marine invertebrates that includes sea urchins and sea stars. Echinoderms have been important experimental models for over 100 years and continue to make important contributions to environmental, evolutionary, and developmental studies, including research on developmental gene regulatory networks. As a centralized resource, Echinobase hosts genomes and collects functional genomic data, reagents, literature, and other information for the community. This third-generation site is based on the Xenbase knowledgebase design and utilizes gene-centric pages to minimize the time and effort required to access genomic information. Summary gene pages display gene symbols and names, functional data, links to the JBrowse genome browser, and orthology to other organisms and reagents, and tabs from the Summary gene page contain more detailed information concerning mRNAs, proteins, diseases, and protein-protein interactions. The gene pages also display 1:1 orthologs between the fully supported species Strongylocentrotus purpuratus (purple sea urchin), Lytechinus variegatus (green sea urchin), Patiria miniata (bat star), and Acanthaster planci (crown-of-thorns sea star). JBrowse tracks are available for visualization of functional genomic data from both fully supported species and the partially supported species Anneissia japonica (feather star), Asterias rubens (sugar star), and L. pictus (painted sea urchin). Echinobase serves a vital role by providing researchers with annotated genomes including orthology, functional genomic data aligned to the genomes, and curated reagents and data. The Echinoderm Anatomical Ontology provides a framework for standardizing developmental data across the phylum, and knowledgebase content is formatted to be findable, accessible, interoperable, and reusable by the research community.
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Affiliation(s)
- Cheryl A Telmer
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Macie M Chess
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Sergei Agalakov
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Bradley I Arshinoff
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Vaneet Lotay
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Dong Zhuo Wang
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Stanley Chu
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Troy J Pells
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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Lim SK, Lin WC, Huang SW, Pan YC, Hu CW, Mou CY, Hu CMJ, Mou KY. Bacteria colonization in tumor microenvironment creates a favorable niche for immunogenic chemotherapy. EMBO Mol Med 2024; 16:416-428. [PMID: 38225455 PMCID: PMC10897177 DOI: 10.1038/s44321-023-00022-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024] Open
Abstract
The tumor microenvironment (TME) presents differential selective pressure (DSP) that favors the growth of cancer cells, and monovalent therapy is often inadequate in reversing the cancer cell dominance in the TME. In this work, we introduce bacteria as a foreign species to the TME and explore combinatorial treatment strategies to alter DSP for tumor eradication. We show that cancer-selective chemotherapeutic agents and fasting can provide a strong selection pressure against tumor growth in the presence of bacteria. Moreover, we show that an immunogenic drug (oxaliplatin), but not a non-immunogenic one (5-FU), synergizes with the bacteria to activate both the innate and adaptive immunity in the TME, resulting in complete tumor remission and a sustained anti-tumor immunological memory in mice. The combination of oxaliplatin and bacteria greatly enhances the co-stimulatory and antigen-presenting molecules on antigen-presenting cells, which in turn bridge the cytotoxic T cells for cancer-cell killing. Our findings indicate that rational combination of bacterial therapy and immunogenic chemotherapy can promote anticancer immunity against the immunosuppressive TME.
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Affiliation(s)
- See-Khai Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Wen-Ching Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Sin-Wei Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Chung Pan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Che-Wei Hu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Chung-Yuan Mou
- Department of Chemistry, National Taiwan University, Taipei, 106319, Taiwan
| | - Che-Ming Jack Hu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.
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3
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Evo-devo perspectives on cancer. Essays Biochem 2022; 66:797-815. [PMID: 36250956 DOI: 10.1042/ebc20220041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 12/13/2022]
Abstract
The integration of evolutionary and developmental approaches into the field of evolutionary developmental biology has opened new areas of inquiry- from understanding the evolution of development and its underlying genetic and molecular mechanisms to addressing the role of development in evolution. For the last several decades, the terms 'evolution' and 'development' have been increasingly linked to cancer, in many different frameworks and contexts. This mini-review, as part of a special issue on Evolutionary Developmental Biology, discusses the main areas in cancer research that have been addressed through the lenses of both evolutionary and developmental biology, though not always fully or explicitly integrated in an evo-devo framework. First, it briefly introduces the current views on carcinogenesis that invoke evolutionary and/or developmental perspectives. Then, it discusses the main mechanisms proposed to have specifically evolved to suppress cancer during the evolution of multicellularity. Lastly, it considers whether the evolution of multicellularity and development was shaped by the threat of cancer (a cancer-evo-devo perspective), and/or whether the evolution of developmental programs and life history traits can shape cancer resistance/risk in various lineages (an evo-devo-cancer perspective). A proper evolutionary developmental framework for cancer, both as a disease and in terms of its natural history (in the context of the evolution of multicellularity and development as well as life history traits), could bridge the currently disparate evolutionary and developmental perspectives and uncover aspects that will provide new insights for cancer prevention and treatment.
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4
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Surien O, Ghazali AR, Masre SF. Chemopreventive effects of pterostilbene through p53 and cell cycle in mouse lung of squamous cell carcinoma model. Sci Rep 2021; 11:14862. [PMID: 34290382 PMCID: PMC8295275 DOI: 10.1038/s41598-021-94508-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/13/2021] [Indexed: 12/30/2022] Open
Abstract
Cell proliferation and cell death abnormalities are strongly linked to the development of cancer, including lung cancer. The purpose of this study was to investigate the effect of pterostilbene on cell proliferation and cell death via cell cycle arrest during the transition from G1 to S phase and the p53 pathway. A total of 24 female Balb/C mice were randomly categorized into four groups (n = 6): N-nitroso-tris-chloroethyl urea (NTCU) induced SCC of the lungs, vehicle control, low dose of 10 mg/kg PS + NTCU (PS10), and high dose of 50 mg/kg PS + NTCU (PS50). At week 26, all lungs were harvested for immunohistochemistry and Western blotting analysis. Ki-67 expression is significantly lower, while caspase-3 expression is significantly higher in PS10 and PS50 as compared to the NTCU (p < 0.05). There was a significant decrease in cyclin D1 and cyclin E2 protein expression in PS10 and PS50 when compared to the NTCU (p < 0.05). PS50 significantly increased p53, p21, and p27 protein expression when compared to NTCU (p < 0.05). Pterostilbene is a potential chemoprevention agent for lung SCC as it has the ability to upregulate the p53/p21 pathway, causing cell cycle arrest.
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Affiliation(s)
- Omchit Surien
- Programme of Biomedical Science, Center for Toxicology and Health Risk Studies (CORE), Faculty of Health Sciences, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia
| | - Ahmad Rohi Ghazali
- Programme of Biomedical Science, Center for Toxicology and Health Risk Studies (CORE), Faculty of Health Sciences, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia
| | - Siti Fathiah Masre
- Programme of Biomedical Science, Center for Toxicology and Health Risk Studies (CORE), Faculty of Health Sciences, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia.
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5
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Lineweaver CH, Bussey KJ, Blackburn AC, Davies PCW. Cancer progression as a sequence of atavistic reversions. Bioessays 2021; 43:e2000305. [PMID: 33984158 DOI: 10.1002/bies.202000305] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 12/27/2022]
Abstract
It has long been recognized that cancer onset and progression represent a type of reversion to an ancestral quasi-unicellular phenotype. This general concept has been refined into the atavistic model of cancer that attempts to provide a quantitative analysis and testable predictions based on genomic data. Over the past decade, support for the multicellular-to-unicellular reversion predicted by the atavism model has come from phylostratigraphy. Here, we propose that cancer onset and progression involve more than a one-off multicellular-to-unicellular reversion, and are better described as a series of reversionary transitions. We make new predictions based on the chronology of the unicellular-eukaryote-to-multicellular-eukaryote transition. We also make new predictions based on three other evolutionary transitions that occurred in our lineage: eukaryogenesis, oxidative phosphorylation and the transition to adaptive immunity. We propose several modifications to current phylostratigraphy to improve age resolution to test these predictions. Also see the video abstract here: https://youtu.be/3unEu5JYJrQ.
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Affiliation(s)
- Charles H Lineweaver
- Planetary Science Institute, Research School of Astronomy and Astrophysics & Research School of Earth Sciences, The Australian National University, Canberra, ACT, Australia.,Mt Stromlo Observatory, Canberra, ACT, Australia
| | - Kimberly J Bussey
- Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, Arizona, USA.,Precision Medicine, Midwestern University, Glendale, Arizona, USA
| | - Anneke C Blackburn
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Paul C W Davies
- Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, Arizona, USA
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Tong XY, Quan Y, Zhang HY. NUDT5 as a novel drug target and prognostic biomarker for ER-positive breast cancer. Drug Discov Today 2020; 26:620-625. [PMID: 33276127 DOI: 10.1016/j.drudis.2020.11.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/15/2020] [Accepted: 11/27/2020] [Indexed: 12/22/2022]
Abstract
Breast cancer (BRCA) is the most common malignant tumor in women. The estrogen receptor-positive (ER+) subtype accounts for ∼70% of BRCA cases. Estrogen is a crucial hormone that directly stimulates the growth and development of mammary glands. Recent studies revealed that, as an estrogen cofactor, ATP has an important role in determining the action of estrogen by mediating phase separation. NUDT5 has been recognized as a key factor for ATP production in the nucleus of BRCA cells and, therefore, could represent a novel drug target for ER+ BRCA. Based on a survival analysis of patients with BRCA documented in The Cancer Genome Atlas (TGCA) database, we show that NUDT5 is also a potential prognostic biomarker for ER+ BRCA.
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Affiliation(s)
- Xin-Yu Tong
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuan Quan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China.
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7
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Chevalier RL. Evolution, kidney development, and chronic kidney disease. Semin Cell Dev Biol 2019; 91:119-131. [PMID: 29857053 PMCID: PMC6281795 DOI: 10.1016/j.semcdb.2018.05.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/29/2018] [Accepted: 05/28/2018] [Indexed: 12/21/2022]
Abstract
There is a global epidemic of chronic kidney disease (CKD) characterized by a progressive loss of nephrons, ascribed in large part to a rising incidence of hypertension, metabolic syndrome, and type 2 diabetes mellitus. There is a ten-fold variation in nephron number at birth in the general population, and a 50% overall decrease in nephron number in the last decades of life. The vicious cycle of nephron loss stimulating hypertrophy by remaining nephrons and resulting in glomerulosclerosis has been regarded as maladaptive, and only partially responsive to angiotensin inhibition. Advances over the past century in kidney physiology, genetics, and development have elucidated many aspects of nephron formation, structure and function. Parallel advances have been achieved in evolutionary biology, with the emergence of evolutionary medicine, a discipline that promises to provide new insight into the treatment of chronic disease. This review provides a framework for understanding the origins of contemporary developmental nephrology, and recent progress in evolutionary biology. The establishment of evolutionary developmental biology (evo-devo), ecological developmental biology (eco-devo), and developmental origins of health and disease (DOHaD) followed the discovery of the hox gene family, the recognition of the contribution of cumulative environmental stressors to the changing phenotype over the life cycle, and mechanisms of epigenetic regulation. The maturation of evolutionary medicine has contributed to new investigative approaches to cardiovascular disease, cancer, and infectious disease, and promises the same for CKD. By incorporating these principles, developmental nephrology is ideally positioned to answer important questions regarding the fate of nephrons from embryo through senescence.
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Affiliation(s)
- Robert L Chevalier
- Department of Pediatrics, The University of Virginia, P.O. Box 800386, Charlottesville, VA, United States.
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8
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Tunes LG, Allen JM, Zayas RM, do Monte-Neto RL. Planarians as models to investigate the bioactivity of gold(I) complexes in vivo. Sci Rep 2018; 8:16180. [PMID: 30385794 PMCID: PMC6212559 DOI: 10.1038/s41598-018-34558-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/18/2018] [Indexed: 02/02/2023] Open
Abstract
Gold(I)-containing complexes are used in drug discovery research for rheumatoid arthritis, cancer, and parasitic infections. In this study, we tested the bioactivity of gold(I) complexes in vivo using planarians. The planarian Schmidtea mediterranea possesses orthologues of tumor suppressor genes, such as p53, that, when silenced, cause deregulation of cell proliferation and apoptosis. In this context, we tested two triethylphosphine-gold(I) complexes (AdO and AdT) to determine if they can attenuate phenotypes that result from p53 inhibition. First, we identified the drug concentration that did not affect survival or regeneration and evaluated the drug's effect on cell division and apoptosis. We found that AdT treatment decreased the number of mitotic cells and that all drug treatments increased the number of apoptotic cells. We then performed p53(RNAi) and drug treatments concomitantly and observed the phenotype progression. Drug treatment increased survival three-fold and decreased apoptosis, which resulted in an attenuated phenotype. Our results indicate that planarians can be treated with gold(I) complexes, and that this treatment can diminish the p53(RNAi) phenotype and extend survival. In this work we show that planarians can be used as a model to study the in vivo effect of gold(I) complexes and to further investigate their mechanisms of action.
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Affiliation(s)
- Luiza G Tunes
- Instituto René Rachou - Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
- Department of Biology, San Diego State University, San Diego, California, USA
| | - John M Allen
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Ricardo M Zayas
- Department of Biology, San Diego State University, San Diego, California, USA.
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9
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Cao Y. Tumorigenesis as a process of gradual loss of original cell identity and gain of properties of neural precursor/progenitor cells. Cell Biosci 2017; 7:61. [PMID: 29177029 PMCID: PMC5693707 DOI: 10.1186/s13578-017-0188-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/27/2017] [Indexed: 02/07/2023] Open
Abstract
Cancer is a complex disease without a unified explanation for its cause so far. Our recent work demonstrates that cancer cells share similar regulatory networks and characteristics with embryonic neural cells. Based on the study, I will address the relationship between tumor and neural cells in more details. I collected the evidence from various aspects of cancer development in many other studies, and integrated the information from studies on cancer cell properties, cell fate specification during embryonic development and evolution. Synthesis of the information strongly supports that cancer cells share much more similarities with neural progenitor/stem cells than with mesenchymal-type cells and that tumorigenesis represents a process of gradual loss of cell or lineage identity and gain of characteristics of neural cells. I also discuss cancer EMT, a concept having been under intense debate, and possibly the true meaning of EMT in cancer initiation and development. This synthesis provides fresh insights into a unified explanation for and a previously unrecognized nature of tumorigenesis, which might not be revealed by studies on individual molecular events. The review will also present some brief suggestions for cancer research based on the proposed model of tumorigenesis.
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Affiliation(s)
- Ying Cao
- Model Animal Research Center and MOE Key Laboratory of Model Animals for Disease Study, Nanjing University, 12 Xuefu Road, Pukou High-Tech Zone, Nanjing, 210061 China
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10
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Sahu S, Dattani A, Aboobaker AA. Secrets from immortal worms: What can we learn about biological ageing from the planarian model system? Semin Cell Dev Biol 2017; 70:108-121. [PMID: 28818620 DOI: 10.1016/j.semcdb.2017.08.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/07/2017] [Accepted: 08/09/2017] [Indexed: 12/12/2022]
Abstract
Understanding how some animals are immortal and avoid the ageing process is important. We currently know very little about how they achieve this. Research with genetic model systems has revealed the existence of conserved genetic pathways and molecular processes that affect longevity. Most of these established model organisms have relatively short lifespans. Here we consider the use of planarians, with an immortal life-history that is able to entirely avoid the ageing process. These animals are capable of profound feats of regeneration fueled by a population of adult stem cells called neoblasts. These cells are capable of indefinite self-renewal that has underpinned the evolution of animals that reproduce only by fission, having disposed of the germline, and must therefore be somatically immortal and avoid the ageing process. How they do this is only now starting to be understood. Here we suggest that the evidence so far supports the hypothesis that the lack of ageing is an emergent property of both being highly regenerative and the evolution of highly effective mechanisms for ensuring genome stability in the neoblast stem cell population. The details of these mechanisms could prove to be very informative in understanding how the causes of ageing can be avoided, slowed or even reversed.
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Affiliation(s)
- Sounak Sahu
- Department of Zoology, South Parks Road, University of Oxford, Oxford OX1 3PS, UK
| | - Anish Dattani
- Department of Zoology, South Parks Road, University of Oxford, Oxford OX1 3PS, UK
| | - A Aziz Aboobaker
- Department of Zoology, South Parks Road, University of Oxford, Oxford OX1 3PS, UK.
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11
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Voura EB, Montalvo MJ, Dela Roca KT, Fisher JM, Defamie V, Narala SR, Khokha R, Mulligan ME, Evans CA. Planarians as models of cadmium-induced neoplasia provide measurable benchmarks for mechanistic studies. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 142:544-554. [PMID: 28482323 DOI: 10.1016/j.ecoenv.2017.04.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 04/02/2017] [Accepted: 04/19/2017] [Indexed: 06/07/2023]
Abstract
Bioassays of planarian neoplasia highlight the potential of these organisms as useful standards to assess whether environmental toxins such as cadmium promote tumorigenesis. These studies complement other investigations into the exceptional healing and regeneration of planarians - processes that are driven by a population of active stem cells, or neoblasts, which are likely transformed during planarian tumor growth. Our goal was to determine if planarian tumorigenesis assays are amenable to mechanistic studies of cadmium carcinogenesis. To that end we demonstrate, by examining both counts of cell populations by size, and instances of mitosis, that the activity of the stem cell population can be monitored. We also provide evidence that specific biomodulators can affect the potential of planarian neoplastic growth, in that an inhibitor of metalloproteinases effectively blocked the development of the lesions. From these results, we infer that neoblast activity does respond to cadmium-induced tumor growth, and that metalloproteinases are required for the progression of cancer in the planarian.
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Affiliation(s)
- Evelyn B Voura
- School of Science, Technology and Health Studies, Morrisville State College, 80 Eaton Street, Morrisville, New York 13408, USA.
| | - Melissa J Montalvo
- Department of Math and Science, Dominican College, 470 Western Highway South, Orangeburg, New York 10962, USA
| | - Kevin T Dela Roca
- Department of Math and Science, Dominican College, 470 Western Highway South, Orangeburg, New York 10962, USA
| | - Julia M Fisher
- Colgate University, 13 Oak Drive, Hamilton, New York 13346, USA
| | - Virginie Defamie
- Ontario Cancer Institute, University Health Network, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Swami R Narala
- Ontario Cancer Institute, University Health Network, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Rama Khokha
- Ontario Cancer Institute, University Health Network, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Margaret E Mulligan
- Department of Math and Science, Dominican College, 470 Western Highway South, Orangeburg, New York 10962, USA
| | - Colleen A Evans
- Department of Math and Science, Dominican College, 470 Western Highway South, Orangeburg, New York 10962, USA
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Chu XY, Jiang LH, Zhou XH, Cui ZJ, Zhang HY. Evolutionary Origins of Cancer Driver Genes and Implications for Cancer Prognosis. Genes (Basel) 2017; 8:genes8070182. [PMID: 28708071 PMCID: PMC5541315 DOI: 10.3390/genes8070182] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/27/2017] [Accepted: 07/10/2017] [Indexed: 12/20/2022] Open
Abstract
The cancer atavistic theory suggests that carcinogenesis is a reverse evolution process. It is thus of great interest to explore the evolutionary origins of cancer driver genes and the relevant mechanisms underlying the carcinogenesis. Moreover, the evolutionary features of cancer driver genes could be helpful in selecting cancer biomarkers from high-throughput data. In this study, through analyzing the cancer endogenous molecular networks, we revealed that the subnetwork originating from eukaryota could control the unlimited proliferation of cancer cells, and the subnetwork originating from eumetazoa could recapitulate the other hallmarks of cancer. In addition, investigations based on multiple datasets revealed that cancer driver genes were enriched in genes originating from eukaryota, opisthokonta, and eumetazoa. These results have important implications for enhancing the robustness of cancer prognosis models through selecting the gene signatures by the gene age information.
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Affiliation(s)
- Xin-Yi Chu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ling-Han Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiong-Hui Zhou
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ze-Jia Cui
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
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Chevalier RL. Evolutionary Nephrology. Kidney Int Rep 2017; 2:302-317. [PMID: 28845468 PMCID: PMC5568830 DOI: 10.1016/j.ekir.2017.01.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/11/2017] [Accepted: 01/25/2017] [Indexed: 01/05/2023] Open
Abstract
Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as "maladaptive." In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic) adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ~40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons), evolutionary selection for APOL1 mutations (that provide resistance to trypanosome infection, a tradeoff), and modern life experience (Western diet mismatch leading to diabetes and hypertension). Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo), developmental programming and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.
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Affiliation(s)
- Robert L. Chevalier
- Department of Pediatrics, The University of Virginia, Charlottesville, Virginia, USA
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14
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Cisneros L, Bussey KJ, Orr AJ, Miočević M, Lineweaver CH, Davies P. Ancient genes establish stress-induced mutation as a hallmark of cancer. PLoS One 2017; 12:e0176258. [PMID: 28441401 PMCID: PMC5404761 DOI: 10.1371/journal.pone.0176258] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 04/08/2017] [Indexed: 02/07/2023] Open
Abstract
Cancer is sometimes depicted as a reversion to single cell behavior in cells adapted to live in a multicellular assembly. If this is the case, one would expect that mutation in cancer disrupts functional mechanisms that suppress cell-level traits detrimental to multicellularity. Such mechanisms should have evolved with or after the emergence of multicellularity. This leads to two related, but distinct hypotheses: 1) Somatic mutations in cancer will occur in genes that are younger than the emergence of multicellularity (1000 million years [MY]); and 2) genes that are frequently mutated in cancer and whose mutations are functionally important for the emergence of the cancer phenotype evolved within the past 1000 million years, and thus would exhibit an age distribution that is skewed to younger genes. In order to investigate these hypotheses we estimated the evolutionary ages of all human genes and then studied the probability of mutation and their biological function in relation to their age and genomic location for both normal germline and cancer contexts. We observed that under a model of uniform random mutation across the genome, controlled for gene size, genes less than 500 MY were more frequently mutated in both cases. Paradoxically, causal genes, defined in the COSMIC Cancer Gene Census, were depleted in this age group. When we used functional enrichment analysis to explain this unexpected result we discovered that COSMIC genes with recessive disease phenotypes were enriched for DNA repair and cell cycle control. The non-mutated genes in these pathways are orthologous to those underlying stress-induced mutation in bacteria, which results in the clustering of single nucleotide variations. COSMIC genes were less common in regions where the probability of observing mutational clusters is high, although they are approximately 2-fold more likely to harbor mutational clusters compared to other human genes. Our results suggest this ancient mutational response to stress that evolved among prokaryotes was co-opted to maintain diversity in the germline and immune system, while the original phenotype is restored in cancer. Reversion to a stress-induced mutational response is a hallmark of cancer that allows for effectively searching “protected” genome space where genes causally implicated in cancer are located and underlies the high adaptive potential and concomitant therapeutic resistance that is characteristic of cancer.
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Affiliation(s)
- Luis Cisneros
- NantOmics, Tempe, Arizona, United States of America
- BEYOND Center for Fundamental Concepts in Science, Arizona State University, Tempe, Arizona, United States of America
| | - Kimberly J. Bussey
- NantOmics, Tempe, Arizona, United States of America
- Department of Biomedical Informatics, Arizona State University, Tempe, Arizona, United States of America
- * E-mail:
| | - Adam J. Orr
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Milica Miočević
- Department of Psychology, Arizona State University, Tempe, Arizona, United States of America
| | - Charles H. Lineweaver
- Planetary Science Institute, Research School of Astronomy and Astrophysics and Research School of Earth Sciences, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Paul Davies
- BEYOND Center for Fundamental Concepts in Science, Arizona State University, Tempe, Arizona, United States of America
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15
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Potapova T, Gorbsky GJ. The Consequences of Chromosome Segregation Errors in Mitosis and Meiosis. BIOLOGY 2017; 6:biology6010012. [PMID: 28208750 PMCID: PMC5372005 DOI: 10.3390/biology6010012] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/24/2017] [Accepted: 01/26/2017] [Indexed: 12/21/2022]
Abstract
Mistakes during cell division frequently generate changes in chromosome content, producing aneuploid or polyploid progeny cells. Polyploid cells may then undergo abnormal division to generate aneuploid cells. Chromosome segregation errors may also involve fragments of whole chromosomes. A major consequence of segregation defects is change in the relative dosage of products from genes located on the missegregated chromosomes. Abnormal expression of transcriptional regulators can also impact genes on the properly segregated chromosomes. The consequences of these perturbations in gene expression depend on the specific chromosomes affected and on the interplay of the aneuploid phenotype with the environment. Most often, these novel chromosome distributions are detrimental to the health and survival of the organism. However, in a changed environment, alterations in gene copy number may generate a more highly adapted phenotype. Chromosome segregation errors also have important implications in human health. They may promote drug resistance in pathogenic microorganisms. In cancer cells, they are a source for genetic and phenotypic variability that may select for populations with increased malignance and resistance to therapy. Lastly, chromosome segregation errors during gamete formation in meiosis are a primary cause of human birth defects and infertility. This review describes the consequences of mitotic and meiotic errors focusing on novel concepts and human health.
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Affiliation(s)
- Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
| | - Gary J Gorbsky
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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16
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Wu A, Zhang Q, Lambert G, Khin Z, Gatenby RA, Kim HJ, Pourmand N, Bussey K, Davies PCW, Sturm JC, Austin RH. Ancient hot and cold genes and chemotherapy resistance emergence. Proc Natl Acad Sci U S A 2015; 112:10467-72. [PMID: 26240372 PMCID: PMC4547268 DOI: 10.1073/pnas.1512396112] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We use a microfabricated ecology with a doxorubicin gradient and population fragmentation to produce a strong Darwinian selective pressure that drives forward the rapid emergence of doxorubicin resistance in multiple myeloma (MM) cancer cells. RNA sequencing of the resistant cells was used to examine (i) emergence of genes with high de novo substitution densities (i.e., hot genes) and (ii) genes never substituted (i.e., cold genes). The set of cold genes, which were 21% of the genes sequenced, were further winnowed down by examining excess expression levels. Both the most highly substituted genes and the most highly expressed never-substituted genes were biased in age toward the most ancient of genes. This would support the model that cancer represents a revision back to ancient forms of life adapted to high fitness under extreme stress, and suggests that these ancient genes may be targets for cancer therapy.
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Affiliation(s)
- Amy Wu
- Princeton Institute for the Science and Technology of Materials, Department of Electrical Engineering, Princeton University, Princeton, NJ 08544
| | - Qiucen Zhang
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Guillaume Lambert
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | | | | | - Hyunsung John Kim
- Department of Bioengineering, University of California, Santa Cruz, CA 95064
| | - Nader Pourmand
- Department of Bioengineering, University of California, Santa Cruz, CA 95064
| | - Kimberly Bussey
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Paul C W Davies
- Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ 85287
| | - James C Sturm
- Princeton Institute for the Science and Technology of Materials, Department of Electrical Engineering, Princeton University, Princeton, NJ 08544
| | - Robert H Austin
- Department of Physics, Princeton University, Princeton, NJ 08544
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17
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Wang H, Lööf S, Borg P, Nader GA, Blau HM, Simon A. Turning terminally differentiated skeletal muscle cells into regenerative progenitors. Nat Commun 2015; 6:7916. [PMID: 26243583 PMCID: PMC4765497 DOI: 10.1038/ncomms8916] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/24/2015] [Indexed: 01/09/2023] Open
Abstract
The ability to repeatedly regenerate limbs during the entire lifespan of an animal is restricted to certain salamander species among vertebrates. This ability involves dedifferentiation of post-mitotic cells into progenitors that in turn form new structures. A long-term enigma has been how injury leads to dedifferentiation. Here we show that skeletal muscle dedifferentiation during newt limb regeneration depends on a programmed cell death response by myofibres. We find that programmed cell death-induced muscle fragmentation produces a population of ‘undead' intermediate cells, which have the capacity to resume proliferation and contribute to muscle regeneration. We demonstrate the derivation of proliferating progeny from differentiated, multinucleated muscle cells by first inducing and subsequently intercepting a programmed cell death response. We conclude that cell survival may be manifested by the production of a dedifferentiated cell with broader potential and that the diversion of a programmed cell death response is an instrument to achieve dedifferentiation. Newts can regenerate amputated limbs via unknown mechanism involving dedifferentiation of cells in the stump into progenitors that contribute to the new appendages. Here the authors show that skeletal muscle dedifferentiation in regenerating newt limbs relies on a diverted programmed cell death response by myofibers.
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Affiliation(s)
- Heng Wang
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
| | - Sara Lööf
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
| | - Paula Borg
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
| | - Gustavo A Nader
- Department of Physiology and Pharmacology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, California 94305, United States
| | - András Simon
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
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18
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Abstract
UNLABELLED Our understanding of cancer is being transformed by exploring clonal diversity, drug resistance, and causation within an evolutionary framework. The therapeutic resilience of advanced cancer is a consequence of its character as a complex, dynamic, and adaptive ecosystem engendering robustness, underpinned by genetic diversity and epigenetic plasticity. The risk of mutation-driven escape by self-renewing cells is intrinsic to multicellularity but is countered by multiple restraints, facilitating increasing complexity and longevity of species. But our own species has disrupted this historical narrative by rapidly escalating intrinsic risk. Evolutionary principles illuminate these challenges and provide new avenues to explore for more effective control. SIGNIFICANCE Lifetime risk of cancer now approximates to 50% in Western societies. And, despite many advances, the outcome for patients with disseminated disease remains poor, with drug resistance the norm. An evolutionary perspective may provide a clearer understanding of how cancer clones develop robustness and why, for us as a species, risk is now off the scale. And, perhaps, of what we might best do to achieve more effective control.
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Affiliation(s)
- Mel Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom.
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19
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Abstract
UNLABELLED Our understanding of cancer is being transformed by exploring clonal diversity, drug resistance, and causation within an evolutionary framework. The therapeutic resilience of advanced cancer is a consequence of its character as a complex, dynamic, and adaptive ecosystem engendering robustness, underpinned by genetic diversity and epigenetic plasticity. The risk of mutation-driven escape by self-renewing cells is intrinsic to multicellularity but is countered by multiple restraints, facilitating increasing complexity and longevity of species. But our own species has disrupted this historical narrative by rapidly escalating intrinsic risk. Evolutionary principles illuminate these challenges and provide new avenues to explore for more effective control. SIGNIFICANCE Lifetime risk of cancer now approximates to 50% in Western societies. And, despite many advances, the outcome for patients with disseminated disease remains poor, with drug resistance the norm. An evolutionary perspective may provide a clearer understanding of how cancer clones develop robustness and why, for us as a species, risk is now off the scale. And, perhaps, of what we might best do to achieve more effective control.
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Affiliation(s)
- Mel Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom.
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20
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Chen H, Lin F, Xing K, He X. The reverse evolution from multicellularity to unicellularity during carcinogenesis. Nat Commun 2015; 6:6367. [PMID: 25751731 DOI: 10.1038/ncomms7367] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 01/22/2015] [Indexed: 12/21/2022] Open
Abstract
Theoretical reasoning suggests that cancer may result from a knockdown of the genetic constraints that evolved for the maintenance of metazoan multicellularity. By characterizing the whole-life history of a xenograft tumour, here we show that metastasis is driven by positive selection for general loss-of-function mutations on multicellularity-related genes. Expression analyses reveal mainly downregulation of multicellularity-related genes and an evolving expression profile towards that of embryonic stem cells, the cell type resembling unicellular life in its capacity of unlimited clonal proliferation. Also, the emergence of metazoan multicellularity ~600 Myr ago is accompanied by an elevated birth rate of cancer genes, and there are more loss-of-function tumour suppressors than activated oncogenes in a typical tumour. These data collectively suggest that cancer represents a loss-of-function-driven reverse evolution back to the unicellular 'ground state'. This cancer evolution model may account for inter-/intratumoural genetic heterogeneity, could explain distant-organ metastases and hold implications for cancer therapy.
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Affiliation(s)
- Han Chen
- Key Laboratory of Gene Engineering of Ministry of Education, Cooperative Innovation Center for High Performance Computing, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, China
| | - Fangqin Lin
- Key Laboratory of Gene Engineering of Ministry of Education, Cooperative Innovation Center for High Performance Computing, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, China
| | - Ke Xing
- 1] Key Laboratory of Gene Engineering of Ministry of Education, Cooperative Innovation Center for High Performance Computing, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, China [2] Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xionglei He
- 1] Key Laboratory of Gene Engineering of Ministry of Education, Cooperative Innovation Center for High Performance Computing, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, China [2] Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou 510275, China
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21
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Abstract
ABSTRACT Cancers exhibit differences in metastatic behavior and drug sensitivity that correlate with certain tumor-specific variables such as differentiation grade, growth rate/extent and molecular regulatory aberrations. In practice, patient management is based on the past results of clinical trials adjusted for these biomarkers. Here, it is proposed that treatment strategies could be fine-tuned upfront simply by quantifying tumorigenic spatial (cell growth) and temporal (genetic stability) control losses, as predicted by genetic defects of cell-cycle-regulatory gatekeeper and genome-stabilizing caretaker tumor suppressor genes, respectively. These differential quantifications of tumor dysfunction may in turn be used to create a tumor-specific ‘periodic table’ that guides rational formulation of survival-enhancing anticancer treatment strategies.
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Affiliation(s)
- Richard J Epstein
- *Clinical Informatics & Research Centre, The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst 2010, Sydney, Australia
- Laboratory of Genome Evolution, Garvan Institute for Medical Research, 384 Victoria St, Darlinghurst 2010, Sydney, Australia
- Department of Oncology, & UNSW Clinical School, St Vincent's Hospital, 390 Victoria St, Darlinghurst 2010 Sydney, Australia
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22
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Abstract
Aging is marked by changes that affect organs and resident stem cell function. Shorting of telomeres, DNA damage, oxidative stress, deregulation of genes and proteins, impaired cell-cell communication, and an altered systemic environment cause the eventual demise of cells. At the same time, reparative activities also decline. It is intriguing to correlate aging with the decline of regenerative abilities. Animal models with strong regenerative capabilities imply that aging processes might not be affecting regeneration. In this review, we selectively present age-dependent changes in stem/progenitor cells that are vital for tissue homeostasis and repair. In addition, the aging effect on regeneration following injury in organs such as lung, skeletal muscle, heart, nervous system, cochlear hair, lens, and liver are discussed. These tissues are also known for diseases such as heart attack, stroke, cognitive impairment, cataract, and hearing loss that occur mostly during aging in humans. Conclusively, vertebrate regeneration declines with age with the loss of stem/progenitor cell function. Future studies on improving the function of stem cells, along with studies in fish and amphibians where regeneration does not decline with age, will undoubtedly provide insights into both processes.
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Affiliation(s)
- Konstantinos Sousounis
- Department of Biology and Center for Tissue Regeneration and Engineering, University of Dayton, Dayton, Ohio, USA
| | - Joelle A Baddour
- Department of Chemical and Materials Engineering and Center for Tissue Regeneration and Engineering, University of Dayton, Dayton, Ohio, USA
| | - Panagiotis A Tsonis
- Department of Biology and Center for Tissue Regeneration and Engineering, University of Dayton, Dayton, Ohio, USA.
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23
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Naturally occurring tumours in the basal metazoan Hydra. Nat Commun 2014; 5:4222. [PMID: 24957317 DOI: 10.1038/ncomms5222] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 05/27/2014] [Indexed: 01/04/2023] Open
Abstract
The molecular nature of tumours is well studied in vertebrates, although their evolutionary origin remains unknown. In particular, there is no evidence for naturally occurring tumours in pre-bilaterian animals, such as sponges and cnidarians. This is somewhat surprising given that recent computational studies have predicted that most metazoans might be prone to develop tumours. Here we provide first evidence for naturally occurring tumours in two species of Hydra. Histological, cellular and molecular data reveal that these tumours are transplantable and might originate by differentiation arrest of female gametes. Growth of tumour cells is independent from the cellular environment. Tumour-bearing polyps have significantly reduced fitness. In addition, Hydra tumours show a greatly altered transcriptome that mimics expression shifts in vertebrate cancers. Therefore, this study shows that spontaneous tumours have deep evolutionary roots and that early branching animals may be informative in revealing the fundamental mechanisms of tumorigenesis.
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