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A New Approach toward the Management of Patients with Premature Skin Aging Using the Predictor Effect. COSMETICS 2023. [DOI: 10.3390/cosmetics10020049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Our study aimed to develop a comprehensive approach to the management of patients with involutional skin changes, considering the predictors of premature skin aging. The study included two stages, whereby 78 women with no history of aesthetic procedures that could have affected their perceived age were examined. In the first stage, we examined factors associated with premature skin aging. In the second stage, a blind, comparative placebo-controlled study of the effectiveness of intradermal injections for the treatment of involutional skin changes was conducted. Parameters reflecting skin aging were identified. The sum of these parameters could be used to diagnose premature skin aging in patients with no history of aesthetic treatment. For other patients, we developed indicators that can be applied to determine whether there is a risk of premature skin aging. Patients with premature aging have an increased risk of adverse events, such as impaired regeneration and wound healing, postprocedural hematomas, etc. For the correction of involutional skin changes in patients with premature aging, the collagen product (Collost) had the greatest clinical efficiency and the greatest patient satisfaction. A complex product based on HA (Teosyal Redensity 1) had comparable efficiency, with slightly less patient satisfaction. The product based on native HA (Hyon 1.8%) had low efficiency in the group of patients with premature aging and high efficiency in the group of patients with normal aging.
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2
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Maintenance of Chronological Aging Features in Culture of Normal Human Dermal Fibroblasts from Old Donors. Cells 2022; 11:cells11050858. [PMID: 35269480 PMCID: PMC8909060 DOI: 10.3390/cells11050858] [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: 01/13/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 02/04/2023] Open
Abstract
Chronological aging is defined as a time-dependent decline of tissue homeostasis which severely impacts skin. Understanding the mechanisms of skin aging is an active research area limited by the lack of relevant in vitro models. Being a component of aging, replicative or stress-induced senescence is repeatedly used to mimic skin aging in vitro, thus presenting only a partial view of the complexity of aging. Herein, we aimed to clarify whether primary normal human dermal fibroblasts retained age-related characteristics when cultured in 2D monolayer, and could be used as a relevant model for aging research. We compared three groups of fibroblasts isolated from different aged donors. We observed strongly decreased population doubling capacities, a reduced clonogenic ability, an impairment in extracellular matrix production together with modifications of respiratory metabolism with an increase in age. These disruptions were particularly marked when comparing fibroblasts isolated from old individuals (over 70 years old) to those isolated from young individuals (18–37 years old), while cells from middle-aged donors exhibited an intermediate profile. These alterations of cell features can be related to the signs of dermis aging, thus showing that cultured primary cells indeed retain some characteristics of the original tissue from which they were extracted.
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3
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Danielsson BE, Peters HC, Bathula K, Spear LM, Noll NA, Dahl KN, Conway DE. Progerin-expressing endothelial cells are unable to adapt to shear stress. Biophys J 2022; 121:620-628. [PMID: 34999130 PMCID: PMC8873939 DOI: 10.1016/j.bpj.2022.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/17/2021] [Accepted: 01/05/2022] [Indexed: 11/19/2022] Open
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a rare premature aging disease caused by a single-point mutation in the lamin A gene, resulting in a truncated and farnesylated form of lamin A. This mutant lamin A protein, known as progerin, accumulates at the periphery of the nuclear lamina, resulting in both an abnormal nuclear morphology and nuclear stiffening. Patients with HGPS experience rapid onset of atherosclerosis, with death from heart attack or stroke as teenagers. Progerin expression has been shown to cause dysfunction in both vascular smooth muscle cells and endothelial cells (ECs). In this study, we examined how progerin-expressing endothelial cells adapt to fluid shear stress, the principal mechanical force from blood flow. We compared the response to shear stress for progerin-expressing, wild-type lamin A overexpressing, and control endothelial cells to physiological levels of fluid shear stress. Additionally, we also knocked down ZMPSTE24 in endothelial cells, which results in increased farnesylation of lamin A and similar phenotypes to HGPS. Our results showed that endothelial cells either overexpressing progerin or with ZMPSTE24 knockdown were unable to adapt to shear stress, experiencing significant cell loss at a longer duration of exposure to shear stress (3 days). Endothelial cells overexpressing wild-type lamin A also exhibited similar impairments in adaptation to shear stress, including similar levels of cell loss. Quantification of nuclear morphology showed that progerin-expressing endothelial cells had similar nuclear abnormalities in both static and shear conditions. Treatment of progerin-expressing cells and ZMPSTE24 KD cells with lonafarnib and methystat, drugs previously shown to improve HGPS nuclear morphology, resulted in improvements in adaptation to shear stress. Additionally, the prealignment of cells to shear stress before progerin-expression prevented cell loss. Our results demonstrate that changes in nuclear lamins can affect the ability of endothelial cells to properly adapt to shear stress.
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Affiliation(s)
- Brooke E Danielsson
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia
| | - Hannah C Peters
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia
| | - Kranthi Bathula
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia
| | - Lindsay M Spear
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia
| | - Natalie A Noll
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia
| | - Kris N Dahl
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania; Department, Thornton Tomasetti, New York City, New York
| | - Daniel E Conway
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia.
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4
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Rajeev M, Ratan C, Krishnan K, Vijayan M. Hutchinson-Gilford Progeria Syndrome (Hgps) And Application Of Gene Therapy Based Crispr/Cas Technology As A Promising Innovative Treatment Approach. Recent Pat Biotechnol 2021; 15:266-285. [PMID: 34602042 DOI: 10.2174/1872208315666210928114720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/09/2021] [Accepted: 08/23/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Hutchinson-Gilford progeria syndrome (HGPS) also known as progeria of childhood or progeria is a rare, rapid, autosomal dominant genetic disorder characterized by premature aging which occurs shortly after birth. HGPS occurs as a result of de novo point mutation in the gene recognized as LMNA gene that encodes two proteins Lamin A protein and Lamin C protein which are the structural components of the nuclear envelope. Mutations in the gene trigger abnormal splicing and induce internal deletion of 50 amino acids leading to the development of a truncated form of Lamin A protein known as Progerin. Progerin generation can be considered as the crucial step in HGPS since the protein is highly toxic to human cells, permanently farnesylated, and exhibits variation in several biochemical and structural properties within the individual. HGPS also produces complications such as skin alterations, growth failure, atherosclerosis, hair and fat loss, and bone and joint diseases. We have also revised all relevant patents relating to Hutchinson-gilford progeria syndrome and its therapy in the current article. METHOD The goal of the present review article is to provide information about Hutchinson-Gilford progeria syndrome (HGPS) and the use of CRISPR/Cas technology as a promising treatment approach in the treatment of the disease. The review also discusses about different pharmacological and non-pharmacological methods of treatment currently used for HGPS. RESULTS The main limitation associated with progeria is the lack of a definitive cure. The existing treatment modality provides only symptomatic relief. Therefore, it is high time to develop a therapeutic method that hastens premature aging in such patients. CONCLUSION CRISPR/Cas technology is a novel gene-editing tool that allows genome editing at specific loci, and is found to be a promising therapeutic approach for the treatment of genetic disorders such as HGPS where dominant-negative mutations take place.
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Affiliation(s)
- Mekha Rajeev
- Amrita School of Pharmacy, Amrita Vihwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P. O., Kochi, Kerala 682041. India
| | - Chameli Ratan
- Amrita School of Pharmacy, Amrita Vihwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P. O., Kochi, Kerala 682041. India
| | - Karthik Krishnan
- Amrita School of Pharmacy, Amrita Vihwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P. O., Kochi, Kerala 682041. India
| | - Meenu Vijayan
- Amrita School of Pharmacy, Amrita Vihwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P. O., Kochi, Kerala 682041. India
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5
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Imran SAM, Yazid MD, Idrus RBH, Maarof M, Nordin A, Razali RA, Lokanathan Y. Is There an Interconnection between Epithelial-Mesenchymal Transition (EMT) and Telomere Shortening in Aging? Int J Mol Sci 2021; 22:ijms22083888. [PMID: 33918710 PMCID: PMC8070110 DOI: 10.3390/ijms22083888] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
Epithelial–Mesenchymal Transition (EMT) was first discovered during the transition of cells from the primitive streak during embryogenesis in chicks. It was later discovered that EMT holds greater potential in areas other than the early development of cells and tissues since it also plays a vital role in wound healing and cancer development. EMT can be classified into three types based on physiological functions. EMT type 3, which involves neoplastic development and metastasis, has been the most thoroughly explored. As EMT is often found in cancer stem cells, most research has focused on its association with other factors involving cancer progression, including telomeres. However, as telomeres are also mainly involved in aging, any possible interaction between the two would be worth noting, especially as telomere dysfunction also contributes to cancer and other age-related diseases. Ascertaining the balance between degeneration and cancer development is crucial in cell biology, in which telomeres function as a key regulator between the two extremes. The essential roles that EMT and telomere protection have in aging reveal a potential mutual interaction that has not yet been explored, and which could be used in disease therapy. In this review, the known functions of EMT and telomeres in aging are discussed and their potential interaction in age-related diseases is highlighted.
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Affiliation(s)
- Siti A. M. Imran
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia; (S.A.M.I.); (M.D.Y.); (R.B.H.I.); (M.M.); (A.N.); (R.A.R.)
| | - Muhammad Dain Yazid
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia; (S.A.M.I.); (M.D.Y.); (R.B.H.I.); (M.M.); (A.N.); (R.A.R.)
| | - Ruszymah Bt Hj Idrus
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia; (S.A.M.I.); (M.D.Y.); (R.B.H.I.); (M.M.); (A.N.); (R.A.R.)
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia
| | - Manira Maarof
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia; (S.A.M.I.); (M.D.Y.); (R.B.H.I.); (M.M.); (A.N.); (R.A.R.)
| | - Abid Nordin
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia; (S.A.M.I.); (M.D.Y.); (R.B.H.I.); (M.M.); (A.N.); (R.A.R.)
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia
| | - Rabiatul Adawiyah Razali
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia; (S.A.M.I.); (M.D.Y.); (R.B.H.I.); (M.M.); (A.N.); (R.A.R.)
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia
| | - Yogeswaran Lokanathan
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia; (S.A.M.I.); (M.D.Y.); (R.B.H.I.); (M.M.); (A.N.); (R.A.R.)
- Correspondence: ; Tel.: +60-391457704
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6
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Using proteomic and transcriptomic data to assess activation of intracellular molecular pathways. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:1-53. [PMID: 34340765 DOI: 10.1016/bs.apcsb.2021.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Analysis of molecular pathway activation is the recent instrument that helps to quantize activities of various intracellular signaling, structural, DNA synthesis and repair, and biochemical processes. This may have a deep impact in fundamental research, bioindustry, and medicine. Unlike gene ontology analyses and numerous qualitative methods that can establish whether a pathway is affected in principle, the quantitative approach has the advantage of exactly measuring the extent of a pathway up/downregulation. This results in emergence of a new generation of molecular biomarkers-pathway activation levels, which reflect concentration changes of all measurable pathway components. The input data can be the high-throughput proteomic or transcriptomic profiles, and the output numbers take both positive and negative values and positively reflect overall pathway activation. Due to their nature, the pathway activation levels are more robust biomarkers compared to the individual gene products/protein levels. Here, we review the current knowledge of the quantitative gene expression interrogation methods and their applications for the molecular pathway quantization. We consider enclosed bioinformatic algorithms and their applications for solving real-world problems. Besides a plethora of applications in basic life sciences, the quantitative pathway analysis can improve molecular design and clinical investigations in pharmaceutical industry, can help finding new active biotechnological components and can significantly contribute to the progressive evolution of personalized medicine. In addition to the theoretical principles and concepts, we also propose publicly available software for the use of large-scale protein/RNA expression data to assess the human pathway activation levels.
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7
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Sorokin M, Borisov N, Kuzmin D, Gudkov A, Zolotovskaia M, Garazha A, Buzdin A. Algorithmic Annotation of Functional Roles for Components of 3,044 Human Molecular Pathways. Front Genet 2021; 12:617059. [PMID: 33633781 PMCID: PMC7900570 DOI: 10.3389/fgene.2021.617059] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/20/2021] [Indexed: 12/16/2022] Open
Abstract
Current methods of high-throughput molecular and genomic analyses enabled to reconstruct thousands of human molecular pathways. Knowledge of molecular pathways structure and architecture taken along with the gene expression data can help interrogating the pathway activation levels (PALs) using different bioinformatic algorithms. In turn, the pathway activation profiles can characterize molecular processes, which are differentially regulated and give numeric characteristics of the extent of their activation or inhibition. However, different pathway nodes may have different functions toward overall pathway regulation, and calculation of PAL requires knowledge of molecular function of every node in the pathway in terms of its activator or inhibitory role. Thus, high-throughput annotation of functional roles of pathway nodes is required for the comprehensive analysis of the pathway activation profiles. We proposed an algorithm that identifies functional roles of the pathway components and applied it to annotate 3,044 human molecular pathways extracted from the Biocarta, Reactome, KEGG, Qiagen Pathway Central, NCI, and HumanCYC databases and including 9,022 gene products. The resulting knowledgebase can be applied for the direct calculation of the PALs and establishing large scale profiles of the signaling, metabolic, and DNA repair pathway regulation using high throughput gene expression data. We also provide a bioinformatic tool for PAL data calculations using the current pathway knowledgebase.
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Affiliation(s)
- Maxim Sorokin
- Omicsway Corp., Walnut, CA, United States.,Laboratory of Clinical Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.,Laboratory for Translational Bioinformatics, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Nicolas Borisov
- Omicsway Corp., Walnut, CA, United States.,Laboratory for Translational Bioinformatics, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Denis Kuzmin
- Laboratory for Translational Bioinformatics, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Alexander Gudkov
- Laboratory of Clinical Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Marianna Zolotovskaia
- Laboratory for Translational Bioinformatics, Moscow Institute of Physics and Technology, Moscow, Russia
| | | | - Anton Buzdin
- Omicsway Corp., Walnut, CA, United States.,Laboratory for Translational Bioinformatics, Moscow Institute of Physics and Technology, Moscow, Russia.,Laboratory of Systems Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov First Moscow State Medical University, Moscow, Russia
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8
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Belyi AA, Alekseev AA, Fedintsev AY, Balybin SN, Proshkina EN, Shaposhnikov MV, Moskalev AA. The Resistance of Drosophila melanogaster to Oxidative, Genotoxic, Proteotoxic, Osmotic Stress, Infection, and Starvation Depends on Age According to the Stress Factor. Antioxidants (Basel) 2020; 9:antiox9121239. [PMID: 33297320 PMCID: PMC7762242 DOI: 10.3390/antiox9121239] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/20/2020] [Accepted: 11/30/2020] [Indexed: 01/05/2023] Open
Abstract
We studied how aging affects the ability of Drosophila melanogaster to tolerate various types of stress factors. Data were obtained on the resistance of D. melanogaster to oxidative and genotoxic (separately paraquat, Fe3+, Cu2+, and Zn2+ ions), proteotoxic (hyperthermia, Cd2+ ions), and osmotic (NaCl) stresses, starvation, and infection with the pathological Beauveria bassiana fungus at different ages. In all cases, we observed a strong negative correlation between age and stress tolerance. The largest change in the age-dependent decline in survival occurred under oxidative and osmotic stress. In most experiments, we observed that young Drosophila females have higher stress resistance than males. We checked whether it is possible to accurately assess the biological age of D. melanogaster based on an assessment of stress tolerance. We have proposed a new approach for assessing a biological age of D. melanogaster using a two-parameter survival curve model. For the model, we used an algorithm that evaluated the quality of age prediction for different age and gender groups. The best predictions were obtained for females who were exposed to CdCl2 and ZnCl2 with an average error of 0.32 days and 0.36 days, respectively. For males, the best results were observed for paraquat and NaCl with an average error of 0.61 and 0.68 days, respectively. The average accuracy for all stresses in our model was 1.73 days.
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Affiliation(s)
- Alexei A. Belyi
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russia; (A.A.B.); (A.Y.F.); (E.N.P.); (M.V.S.)
| | - Alexey A. Alekseev
- Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.A.A.); (S.N.B.)
| | - Alexander Y. Fedintsev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russia; (A.A.B.); (A.Y.F.); (E.N.P.); (M.V.S.)
| | - Stepan N. Balybin
- Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.A.A.); (S.N.B.)
| | - Ekaterina N. Proshkina
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russia; (A.A.B.); (A.Y.F.); (E.N.P.); (M.V.S.)
| | - Mikhail V. Shaposhnikov
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russia; (A.A.B.); (A.Y.F.); (E.N.P.); (M.V.S.)
| | - Alexey A. Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russia; (A.A.B.); (A.Y.F.); (E.N.P.); (M.V.S.)
- Correspondence: ; Tel.: +78-21-231-2894
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9
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Villa-Bellosta R. Dietary magnesium supplementation improves lifespan in a mouse model of progeria. EMBO Mol Med 2020; 12:e12423. [PMID: 32875720 PMCID: PMC7539193 DOI: 10.15252/emmm.202012423] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 01/11/2023] Open
Abstract
Aging is associated with redox imbalance according to the redox theory of aging. Consistently, a mouse model of premature aging (LmnaG609G/+) showed an increased level of mitochondrial reactive oxygen species (ROS) and a reduced basal antioxidant capacity, including loss of the NADPH‐coupled glutathione redox system. LmnaG609G/+ mice also exhibited reduced mitochondrial ATP synthesis secondary to ROS‐induced mitochondrial dysfunction. Treatment of LmnaG609G/+ vascular smooth muscle cells with magnesium‐enriched medium improved the intracellular ATP level, enhanced the antioxidant capacity, and thereby reduced mitochondrial ROS production. Moreover, treatment of LmnaG609G/+ mice with dietary magnesium improved the proton pumps (complexes I, III, and IV), stimulated extramitochondrial NADH oxidation and enhanced the coupled mitochondrial membrane potential, and thereby increased H+‐coupled mitochondrial NADPH and ATP synthesis, which is necessary for cellular energy supply and survival. Consistently, magnesium treatment reduced calcification of vascular smooth muscle cells in vitro and in vivo, and improved the longevity of mice. This antioxidant property of magnesium may be beneficial in children with HGPS.
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Affiliation(s)
- Ricardo Villa-Bellosta
- Fundación Instituto de Investigación Sanitaria, Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
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10
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Abstract
DNA damage response (DDR) and DNA repair pathways determine neoplastic cell transformation and therapeutic responses, as well as the aging process. Altered DDR functioning results in accumulation of unrepaired DNA damage, increased frequency of tumorigenic mutations, and premature aging. Recent evidence suggests that polypeptide hormones play a role in modulating DDR and DNA damage repair, while DNA damage accumulation may also affect hormonal status. We review the available reports elucidating involvement of insulin-like growth factor 1 (IGF1), growth hormone (GH), α-melanocyte stimulating hormone (αMSH), and gonadotropin-releasing hormone (GnRH)/gonadotropins in DDR and DNA repair as well as the current understanding of pathways enabling these actions. We discuss effects of DNA damage pathway mutations, including Fanconi anemia, on endocrine function and consider mechanisms underlying these phenotypes. (Endocrine Reviews 41: 1 - 19, 2020).
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Affiliation(s)
- Vera Chesnokova
- Pituitary Center, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shlomo Melmed
- Pituitary Center, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
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11
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Aliper AM, Bozdaganyan ME, Orekhov PS, Zhavoronkov A, Osipov AN. Replicative and radiation-induced aging: a comparison of gene expression profiles. Aging (Albany NY) 2020; 11:2378-2387. [PMID: 31002655 PMCID: PMC6520014 DOI: 10.18632/aging.101921] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/13/2019] [Indexed: 01/04/2023]
Abstract
All living organisms are subject to the aging process and experience the effect of ionizing radiation throughout their life. There have been a number of studies that linked ionizing radiation process to accelerated aging, but comprehensive signalome analysis of both processes was rarely conducted. Here we present a comparative signaling pathway based analysis of the transcriptomes of fibroblasts irradiated with different doses of ionizing radiation, replicatively aged fibroblasts and fibroblasts collected from young, middle age and old patients. We demonstrate a significant concordance between irradiation-induced and replicative senescence signalome signatures of fibroblasts. Additionally, significant differences in transcriptional response were also observed between fibroblasts irradiated with high and low dose. Our data shows that the transcriptome of replicatively aged fibroblasts is more similar to the transcriptome of the cells irradiated with 2 Gy, than with 5 сGy.This work revealed a number of signaling pathways that are shared between senescence and irradiation processes and can potentially be targeted by the new generation of gero- and radioprotectors.
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Affiliation(s)
| | | | - Philipp S Orekhov
- Inсilico Medicine, Inc., Baltimore, MD 21218, USA.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Andreyan N Osipov
- Inсilico Medicine, Inc., Baltimore, MD 21218, USA.,State Research Center-Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency (SRC-FMBC), Moscow 123098, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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12
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Saxena S, Kumar S. Pharmacotherapy to gene editing: potential therapeutic approaches for Hutchinson-Gilford progeria syndrome. GeroScience 2020; 42:467-494. [PMID: 32048129 PMCID: PMC7205988 DOI: 10.1007/s11357-020-00167-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/04/2020] [Indexed: 12/11/2022] Open
Abstract
Hutchinson-Gilford progeria syndrome (HGPS), commonly called progeria, is an extremely rare disorder that affects only one child per four million births. It is characterized by accelerated aging in affected individuals leading to premature death at an average age of 14.5 years due to cardiovascular complications. The main cause of HGPS is a sporadic autosomal dominant point mutation in LMNA gene resulting in differently spliced lamin A protein known as progerin. Accumulation of progerin under nuclear lamina and activation of its downstream effectors cause perturbation in cellular morphology and physiology which leads to a systemic disorder that mainly impairs the cardiovascular system, bones, skin, and overall growth. Till now, no cure has been found for this catastrophic disorder; however, several therapeutic strategies are under development. The current review focuses on the overall progress in the field of therapeutic approaches for the management/cure of HGPS. We have also discussed the new disease models that have been developed for the study of this rare disorder. Moreover, we have highlighted the therapeutic application of extracellular vesicles derived from stem cells against aging and aging-related disorders and, therefore, suggest the same for the treatment of HGPS.
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Affiliation(s)
- Saurabh Saxena
- Department of Medical Laboratory Sciences, Lovely Professional University, Jalandhar - Delhi G.T. Road, Phagwara, Punjab, 144411, India.
| | - Sanjeev Kumar
- Faculty of Technology and Sciences, Lovely Professional University, Jalandhar - Delhi G.T. Road, Phagwara, Punjab, 144411, India
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13
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Borisov N, Sorokin M, Garazha A, Buzdin A. Quantitation of Molecular Pathway Activation Using RNA Sequencing Data. Methods Mol Biol 2020; 2063:189-206. [PMID: 31667772 DOI: 10.1007/978-1-0716-0138-9_15] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Intracellular molecular pathways (IMPs) control all major events in the living cell. IMPs are considered hotspots in biomedical sciences and thousands of IMPs have been discovered for humans and model organisms. Knowledge of IMPs activation is essential for understanding biological functions and differences between the biological objects at the molecular level. Here we describe the Oncobox system for accurate quantitative scoring activities of up to several thousand molecular pathways based on high throughput molecular data. Although initially designed for gene expression and mainly RNA sequencing data, Oncobox is now also applicable for quantitative proteomics, microRNA and transcription factor binding sites mapping data. The Oncobox system includes modules of gene expression data harmonization, aggregation and comparison and a recursive algorithm for automatic annotation of molecular pathways. The universal rationale of Oncobox enables scoring of signaling, metabolic, cytoskeleton, immunity, DNA repair, and other pathways in a multitude of biological objects. The Oncobox system can be helpful to all those working in the fields of genetics, biochemistry, interactomics, and big data analytics in molecular biomedicine.
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Affiliation(s)
- Nicolas Borisov
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Omicsway Corp., Walnut, CA, USA
| | - Maxim Sorokin
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Omicsway Corp., Walnut, CA, USA
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Anton Buzdin
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.
- Omicsway Corp., Walnut, CA, USA.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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14
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The role of transposable elements activity in aging and their possible involvement in laminopathic diseases. Ageing Res Rev 2020; 57:100995. [PMID: 31786372 DOI: 10.1016/j.arr.2019.100995] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/17/2019] [Accepted: 11/25/2019] [Indexed: 01/17/2023]
Abstract
Eukaryotic genomes contain a large number of transposable elements, part of which are still active and able to transpose in the host genome. Mobile element activation is repressed to avoid deleterious effects, such as gene mutations or chromosome rearrangements. Control of transposable elements includes a variety of mechanisms comprising silencing pathways, which are based on the production of small non-coding RNAs. Silencing can occur either through transposable element RNA degradation or through the targeting of DNA sequences by heterochromatin formation and consequent transcriptional inhibition. Since the important role of the heterochromatin silencing, the gradual loss of heterochromatin marks in constitutive heterochromatin regions during the aging process promotes derepression of transposable elements, which is considered a cause of the progressive increase in genomic instability and of the activation of inflammatory responses. This review provides an overview of the effects of heterochromatin loss on the activity of transposable elements during the aging process and the possible impact on genome function. In this context, we discuss the possible role of the nuclear lamina, a major player in heterochromatin dynamics, in the regulation of transposable element activity and potential implications in laminopathic diseases.
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15
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Mamoshina P, Kochetov K, Putin E, Cortese F, Aliper A, Lee WS, Ahn SM, Uhn L, Skjodt N, Kovalchuk O, Scheibye-Knudsen M, Zhavoronkov A. Population Specific Biomarkers of Human Aging: A Big Data Study Using South Korean, Canadian, and Eastern European Patient Populations. J Gerontol A Biol Sci Med Sci 2019; 73:1482-1490. [PMID: 29340580 PMCID: PMC6175034 DOI: 10.1093/gerona/gly005] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Indexed: 12/16/2022] Open
Abstract
Accurate and physiologically meaningful biomarkers for human aging are key to assessing antiaging therapies. Given ethnic differences in health, diet, lifestyle, behavior, environmental exposures, and even average rate of biological aging, it stands to reason that aging clocks trained on datasets obtained from specific ethnic populations are more likely to account for these potential confounding factors, resulting in an enhanced capacity to predict chronological age and quantify biological age. Here, we present a deep learning-based hematological aging clock modeled using the large combined dataset of Canadian, South Korean, and Eastern European population blood samples that show increased predictive accuracy in individual populations compared to population specific hematologic aging clocks. The performance of models was also evaluated on publicly available samples of the American population from the National Health and Nutrition Examination Survey (NHANES). In addition, we explored the association between age predicted by both population specific and combined hematological clocks and all-cause mortality. Overall, this study suggests (a) the population specificity of aging patterns and (b) hematologic clocks predicts all-cause mortality. The proposed models were added to the freely-available Aging.AI system expanding the range of tools for analysis of human aging.
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Affiliation(s)
- Polina Mamoshina
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, Maryland.,Computer Science Department, University of Oxford, UK
| | - Kirill Kochetov
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, Maryland.,Computer Technologies Lab, ITMO University, St. Petersburg, Russia
| | - Evgeny Putin
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, Maryland.,Computer Technologies Lab, ITMO University, St. Petersburg, Russia
| | - Franco Cortese
- Department of Biomedical and Molecular Sciences, Queen's University School of Medicine, Queen's University, Kingston, Ontario, Canada.,Biogerontology Research Foundation, Oxford, UK.,Canadian Longevity Alliance, Ontario, Canada
| | - Alexander Aliper
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, Maryland
| | - Won-Suk Lee
- Gachon University Gil Medical Center, Incheon, South Korea
| | - Sung-Min Ahn
- Gachon University Gil Medical Center, Incheon, South Korea
| | - Lee Uhn
- Gachon University Gil Medical Center, Incheon, South Korea
| | - Neil Skjodt
- Canada Cancer and Aging Research Laboratories, Lethbridge, Alberta, Canada.,University of Lethbridge, Alberta, Canada
| | - Olga Kovalchuk
- Canada Cancer and Aging Research Laboratories, Lethbridge, Alberta, Canada.,University of Lethbridge, Alberta, Canada
| | - Morten Scheibye-Knudsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark
| | - Alex Zhavoronkov
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, Maryland.,Biogerontology Research Foundation, Oxford, UK
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16
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Ashapkin VV, Kutueva LI, Kurchashova SY, Kireev II. Are There Common Mechanisms Between the Hutchinson-Gilford Progeria Syndrome and Natural Aging? Front Genet 2019; 10:455. [PMID: 31156709 PMCID: PMC6529819 DOI: 10.3389/fgene.2019.00455] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/30/2019] [Indexed: 12/25/2022] Open
Abstract
The Hutchinson–Gilford progeria syndrome (HGPS) is a premature aging disease caused by mutations of the LMNA gene leading to increased production of a partially processed form of the nuclear fibrillar protein lamin A – progerin. Progerin acts as a dominant factor that leads to multiple morphological anomalies of cell nuclei and disturbances in heterochromatin organization, mitosis, DNA replication and repair, and gene transcription. Progerin-positive cells are present in primary fibroblast cultures obtained from the skin of normal donors at advanced ages. These cells display HGPS-like defects in nuclear morphology, decreased H3K9me3 and HP1, and increased histone H2AX phosphorylation marks of the DNA damage loci. Inhibition of progerin production in cells of aged non-HGPS donors in vivo increases the proliferative activity, H3K9me3, and HP1, and decreases the senescence markers p21, IGFBP3, and GADD45B to the levels of young donor cells. Thus, progerin-dependent mechanisms act in natural aging. Excessive activity of the same mechanisms may well be the cause of premature aging in HGPS. Telomere attrition is widely regarded to be one of the primary hallmarks of aging. Progerin expression in normal human fibroblasts accelerates the loss of telomeres. Changes in lamina organization may directly affect telomere attrition resulting in accelerated replicative senescence and progeroid phenotypes. The chronological aging in normal individuals and the premature aging in HGPS patients are mediated by similar changes in the activity of signaling pathways, including downregulation of DNA repair and chromatin organization, and upregulation of ERK, mTOR, GH-IGF1, MAPK, TGFβ, and mitochondrial dysfunction. Multiple epigenetic changes are common to premature aging in HGPS and natural aging. Recent studies showed that epigenetic systems could play an active role as drivers of both forms of aging. It may be suggested that these systems translate the effects of various internal and external factors into universal molecular hallmarks, largely common between natural and accelerated forms of aging. Drugs acting at both natural aging and HGPS are likely to exist. For example, vitamin D3 reduces the progerin production and alleviates most HGPS features, and also slows down epigenetic aging in overweight and obese non-HGPS individuals with suboptimal vitamin D status.
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Affiliation(s)
- Vasily V Ashapkin
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Lyudmila I Kutueva
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Svetlana Y Kurchashova
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Igor I Kireev
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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17
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Rezaei G, Daghighi SM, Haririan I, Yousefi I, Raoufi M, Rezaee F, Dinarvand R. Protein corona variation in nanoparticles revisited: A dynamic grouping strategy. Colloids Surf B Biointerfaces 2019; 179:505-516. [PMID: 31009853 DOI: 10.1016/j.colsurfb.2019.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 03/31/2019] [Accepted: 04/02/2019] [Indexed: 12/27/2022]
Abstract
Bio-nano interface investigation models are mainly based on the type of proteins present on corona, bio-nano interaction responses and the evaluation of final outcomes. Due to the extensive diversity in correlative models for investigation of nanoparticles biological responses, a comprehensive model considering different aspects of bio-nano interface from nanoparticles properties to protein corona fingerprints appeared to be essential and cannot be ignored. In order to minimize divergence in studies in the era of bio-nano interface and protein corona with following therapeutic implications, a useful investigation model on the basis of RADAR concept is suggested. The contents of RADAR concept consist of five modules: 1- Reshape of our strategy for synthesis of nanoparticles (NPs), 2- Application of NPs selected based on human fluid, 3- Delivery strategy of NPs selected based on target tissue, 4- Analysis of proteins present on corona using correct procedures and 5- Risk assessment and risk reduction upon the collection and analysis of results to increase drug delivery efficiency and drug efficacy. RADAR grouping strategy for revisiting protein corona phenomenon as a key of success will be discussed with respect to the current state of knowledge.
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Affiliation(s)
- Ghassem Rezaei
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| | - Seyed Mojtaba Daghighi
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Ismael Haririan
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Medical Biomaterials Research Center (MBRC), Tehran University of Medical Sciences, Tehran, Iran
| | - Iman Yousefi
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Canada
| | - Mohammad Raoufi
- Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| | - Farhad Rezaee
- Department of Gastroenterology-Hepatology, Erasmus Medical Center, Rotterdam, the Netherlands; Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
| | - Rassoul Dinarvand
- Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran; Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
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18
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New Insights into the Role of Epithelial⁻Mesenchymal Transition during Aging. Int J Mol Sci 2019; 20:ijms20040891. [PMID: 30791369 PMCID: PMC6412502 DOI: 10.3390/ijms20040891] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/08/2019] [Accepted: 02/15/2019] [Indexed: 12/29/2022] Open
Abstract
Epithelial–mesenchymal transition (EMT) is a cellular process by which differentiated epithelial cells undergo a phenotypic conversion to a mesenchymal nature. The EMT has been increasingly recognized as an essential process for tissue fibrogenesis during disease and normal aging. Higher levels of EMT proteins in aged tissues support the involvement of EMT as a possible cause and/or consequence of the aging process. Here, we will highlight the existing understanding of EMT supporting the phenotypical alterations that occur during normal aging or pathogenesis, covering the impact of EMT deregulation in tissue homeostasis and stem cell function.
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19
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Sen P, Lan Y, Li CY, Sidoli S, Donahue G, Dou Z, Frederick B, Chen Q, Luense LJ, Garcia BA, Dang W, Johnson FB, Adams PD, Schultz DC, Berger SL. Histone Acetyltransferase p300 Induces De Novo Super-Enhancers to Drive Cellular Senescence. Mol Cell 2019; 73:684-698.e8. [PMID: 30773298 DOI: 10.1016/j.molcel.2019.01.021] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 10/10/2018] [Accepted: 01/14/2019] [Indexed: 12/12/2022]
Abstract
Accumulation of senescent cells during aging contributes to chronic inflammation and age-related diseases. While senescence is associated with profound alterations of the epigenome, a systematic view of epigenetic factors in regulating senescence is lacking. Here, we curated a library of short hairpin RNAs for targeted silencing of all known epigenetic proteins and performed a high-throughput screen to identify key candidates whose downregulation can delay replicative senescence of primary human cells. This screen identified multiple new players including the histone acetyltransferase p300 that was found to be a primary driver of the senescent phenotype. p300, but not the paralogous CBP, induces a dynamic hyper-acetylated chromatin state and promotes the formation of active enhancer elements in the non-coding genome, leading to a senescence-specific gene expression program. Our work illustrates a causal role of histone acetyltransferases and acetylation in senescence and suggests p300 as a potential therapeutic target for senescence and age-related diseases.
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Affiliation(s)
- Payel Sen
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yemin Lan
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Catherine Y Li
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simone Sidoli
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Greg Donahue
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhixun Dou
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brian Frederick
- High Throughput Screening Core, Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qijun Chen
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lacey J Luense
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weiwei Dang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - F Bradley Johnson
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK
| | - David C Schultz
- High Throughput Screening Core, Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA.
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20
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Mamoshina P, Kochetov K, Cortese F, Kovalchuk A, Aliper A, Putin E, Scheibye-Knudsen M, Cantor CR, Skjodt NM, Kovalchuk O, Zhavoronkov A. Blood Biochemistry Analysis to Detect Smoking Status and Quantify Accelerated Aging in Smokers. Sci Rep 2019; 9:142. [PMID: 30644411 PMCID: PMC6333803 DOI: 10.1038/s41598-018-35704-w] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 10/11/2018] [Indexed: 01/25/2023] Open
Abstract
There is an association between smoking and cancer, cardiovascular disease and all-cause mortality. However, currently, there are no affordable and informative tests for assessing the effects of smoking on the rate of biological aging. In this study we demonstrate for the first time that smoking status can be predicted using blood biochemistry and cell count results andthe recent advances in artificial intelligence (AI). By employing age-prediction models developed using supervised deep learning techniques, we found that smokers exhibited higher aging rates than nonsmokers, regardless of their cholesterol ratios and fasting glucose levels. We further used those models to quantify the acceleration of biological aging due to tobacco use. Female smokers were predicted to be twice as old as their chronological age compared to nonsmokers, whereas male smokers were predicted to be one and a half times as old as their chronological age compared to nonsmokers. Our findings suggest that deep learning analysis of routine blood tests could complement or even replace the current error-prone method of self-reporting of smoking status and could be expanded to assess the effect of other lifestyle and environmental factors on aging.
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Affiliation(s)
- Polina Mamoshina
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., 9601 Medical Center Dr, Suite 127, JHU, Rockville, MD, 20850, USA.,Canada Cancer and Aging Research Laboratories, Ltd, Lethbridge, Alberta, T1K7X8, Canada.,Computer Science Department, University of Oxford, Oxford, United Kingdom
| | - Kirill Kochetov
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., 9601 Medical Center Dr, Suite 127, JHU, Rockville, MD, 20850, USA.,Canada Cancer and Aging Research Laboratories, Ltd, Lethbridge, Alberta, T1K7X8, Canada.,Computer Technologies Lab, ITMO University, St. Petersburg, 197101, Russia
| | - Franco Cortese
- Biogerontology Research Foundation, Research Department, Oxford, United Kingdom.,Canadian Longevity Alliance, Ontario, Canada
| | - Anna Kovalchuk
- Canada Cancer and Aging Research Laboratories, Ltd, Lethbridge, Alberta, T1K7X8, Canada.,University of Lethbridge, Lethbridge, Alberta, T1K3M4, Canada.,Leaders in Medicine Program, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Alexander Aliper
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., 9601 Medical Center Dr, Suite 127, JHU, Rockville, MD, 20850, USA.,Canada Cancer and Aging Research Laboratories, Ltd, Lethbridge, Alberta, T1K7X8, Canada
| | - Evgeny Putin
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., 9601 Medical Center Dr, Suite 127, JHU, Rockville, MD, 20850, USA.,Canada Cancer and Aging Research Laboratories, Ltd, Lethbridge, Alberta, T1K7X8, Canada.,Computer Technologies Lab, ITMO University, St. Petersburg, 197101, Russia
| | - Morten Scheibye-Knudsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Charles R Cantor
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, 02215, USA
| | - Neil M Skjodt
- Canada Cancer and Aging Research Laboratories, Ltd, Lethbridge, Alberta, T1K7X8, Canada.,University of Lethbridge, Lethbridge, Alberta, T1K3M4, Canada
| | - Olga Kovalchuk
- Canada Cancer and Aging Research Laboratories, Ltd, Lethbridge, Alberta, T1K7X8, Canada. .,University of Lethbridge, Lethbridge, Alberta, T1K3M4, Canada.
| | - Alex Zhavoronkov
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., 9601 Medical Center Dr, Suite 127, JHU, Rockville, MD, 20850, USA. .,Canada Cancer and Aging Research Laboratories, Ltd, Lethbridge, Alberta, T1K7X8, Canada. .,Biogerontology Research Foundation, Research Department, Oxford, United Kingdom. .,Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA.
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21
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Choi H, Kim TH, Jeong JK, Strandgren C, Eriksson M, Cho ES. Expression of the Hutchinson-Gilford Progeria Mutation Leads to Aberrant Dentin Formation. Sci Rep 2018; 8:15368. [PMID: 30337599 PMCID: PMC6193977 DOI: 10.1038/s41598-018-33764-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/05/2018] [Indexed: 12/24/2022] Open
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a rare accelerated senescence disease, manifesting dental abnormalities and several symptoms suggestive of premature aging. Although irregular secondary dentin formation in HGPS patients has been reported, pathological mechanisms underlying aberrant dentin formation remain undefined. In this study, we analyzed the mandibular molars of a tissue-specific mouse model that overexpresses the most common HGPS mutation (LMNA, c.1824C > T, p.G608G) in odontoblasts. In the molars of HGPS mutant mice at postnatal week 13, targeted expression of the HGPS mutation in odontoblasts results in excessive dentin formation and pulp obliteration. Circumpulpal dentin of HGPS mutants was clearly distinguished from secondary dentin of wild-type (WT) littermates and its mantle dentin by considering the irregular porous structure and loss of dentinal tubules. However, the dentin was significantly thinner in the molars of HGPS mutants at postnatal weeks 3 and 5 than in those of WT mice. In vitro analyses using MDPC-23, a mouse odontoblastic cell line, showed cellular senescence, defects of signaling pathways and consequential downregulation of matrix protein expression in progerin-expressing odontoblasts. These results indicate that expression of the HGPS mutation in odontoblasts disturbs physiological secondary dentin formation. In addition, progerin-expressing odontoblasts secrete paracrine factors that can stimulate odontogenic differentiation of dental pulp cells. Taken together, our results suggest that the aberrant circumpulpal dentin of HGPS mutants results from defects in physiological secondary dentin formation and consequential pathologic response stimulated by paracrine factors from neighboring progerin-expressing odontoblasts.
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Affiliation(s)
- Hwajung Choi
- Cluster for Craniofacial Development and Regeneration Research, Institute of Oral Biosciences, Chonbuk National University School of Dentistry, Jeonju, 54896, South Korea
| | - Tak-Heun Kim
- Cluster for Craniofacial Development and Regeneration Research, Institute of Oral Biosciences, Chonbuk National University School of Dentistry, Jeonju, 54896, South Korea
| | - Ju-Kyeong Jeong
- Cluster for Craniofacial Development and Regeneration Research, Institute of Oral Biosciences, Chonbuk National University School of Dentistry, Jeonju, 54896, South Korea
| | - Charlotte Strandgren
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, SE-14183, Sweden
| | - Maria Eriksson
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, SE-14183, Sweden
| | - Eui-Sic Cho
- Cluster for Craniofacial Development and Regeneration Research, Institute of Oral Biosciences, Chonbuk National University School of Dentistry, Jeonju, 54896, South Korea.
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22
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Mamoshina P, Kochetov K, Putin E, Cortese F, Aliper A, Lee WS, Ahn SM, Uhn L, Skjodt N, Kovalchuk O, Scheibye-Knudsen M, Zhavoronkov A. Population Specific Biomarkers of Human Aging: A Big Data Study Using South Korean, Canadian, and Eastern European Patient Populations. J Gerontol A Biol Sci Med Sci 2018. [PMID: 29340580 DOI: 10.1093/gerona/gly005/4801287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Accurate and physiologically meaningful biomarkers for human aging are key to assessing antiaging therapies. Given ethnic differences in health, diet, lifestyle, behavior, environmental exposures, and even average rate of biological aging, it stands to reason that aging clocks trained on datasets obtained from specific ethnic populations are more likely to account for these potential confounding factors, resulting in an enhanced capacity to predict chronological age and quantify biological age. Here, we present a deep learning-based hematological aging clock modeled using the large combined dataset of Canadian, South Korean, and Eastern European population blood samples that show increased predictive accuracy in individual populations compared to population specific hematologic aging clocks. The performance of models was also evaluated on publicly available samples of the American population from the National Health and Nutrition Examination Survey (NHANES). In addition, we explored the association between age predicted by both population specific and combined hematological clocks and all-cause mortality. Overall, this study suggests (a) the population specificity of aging patterns and (b) hematologic clocks predicts all-cause mortality. The proposed models were added to the freely-available Aging.AI system expanding the range of tools for analysis of human aging.
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Affiliation(s)
- Polina Mamoshina
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, Maryland.,Computer Science Department, University of Oxford, UK
| | - Kirill Kochetov
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, Maryland.,Computer Technologies Lab, ITMO University, St. Petersburg, Russia
| | - Evgeny Putin
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, Maryland.,Computer Technologies Lab, ITMO University, St. Petersburg, Russia
| | - Franco Cortese
- Department of Biomedical and Molecular Sciences, Queen's University School of Medicine, Queen's University, Kingston, Ontario, Canada.,Biogerontology Research Foundation, Oxford, UK.,Canadian Longevity Alliance, Ontario, Canada
| | - Alexander Aliper
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, Maryland
| | - Won-Suk Lee
- Gachon University Gil Medical Center, Incheon, South Korea
| | - Sung-Min Ahn
- Gachon University Gil Medical Center, Incheon, South Korea
| | - Lee Uhn
- Gachon University Gil Medical Center, Incheon, South Korea
| | - Neil Skjodt
- Canada Cancer and Aging Research Laboratories, Lethbridge, Alberta, Canada.,University of Lethbridge, Alberta, Canada
| | - Olga Kovalchuk
- Canada Cancer and Aging Research Laboratories, Lethbridge, Alberta, Canada.,University of Lethbridge, Alberta, Canada
| | - Morten Scheibye-Knudsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark
| | - Alex Zhavoronkov
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University, Baltimore, Maryland.,Biogerontology Research Foundation, Oxford, UK
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23
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Larrieu D, Viré E, Robson S, Breusegem SY, Kouzarides T, Jackson SP. Inhibition of the acetyltransferase NAT10 normalizes progeric and aging cells by rebalancing the Transportin-1 nuclear import pathway. Sci Signal 2018; 11:eaar5401. [PMID: 29970603 PMCID: PMC6331045 DOI: 10.1126/scisignal.aar5401] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is an incurable premature aging disease. Identifying deregulated biological processes in HGPS might thus help define novel therapeutic strategies. Fibroblasts from HGPS patients display defects in nucleocytoplasmic shuttling of the GTP-bound form of the small GTPase Ran (RanGTP), which leads to abnormal transport of proteins into the nucleus. We report that microtubule stabilization in HGPS cells sequestered the nonclassical nuclear import protein Transportin-1 (TNPO1) in the cytoplasm, thus affecting the nuclear localization of its cargo, including the nuclear pore protein NUP153. Consequently, nuclear Ran, nuclear anchorage of the nucleoporin TPR, and chromatin organization were disrupted, deregulating gene expression and inducing senescence. Inhibiting N-acetyltransferase 10 (NAT10) ameliorated HGPS phenotypes by rebalancing the nuclear to cytoplasmic ratio of TNPO1. This restored nuclear pore complex integrity and nuclear Ran localization, thereby correcting HGPS cellular phenotypes. We observed a similar mechanism in cells from healthy aged individuals. This study identifies a nuclear import pathway affected in aging and underscores the potential for NAT10 inhibition as a possible therapeutic strategy for HGPS and perhaps also for pathologies associated with normal aging.
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Affiliation(s)
- Delphine Larrieu
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN, UK.
| | - Emmanuelle Viré
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN, UK
| | - Samuel Robson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN, UK
| | - Sophia Y Breusegem
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN, UK
| | - Tony Kouzarides
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN, UK
| | - Stephen P Jackson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN, UK.
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24
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Chen Y, Zhao X, Zhang X, Liu Y, Zhou P, Ni H, Ma J, Ming D. Age-related early/late variations of functional connectivity across the human lifespan. Neuroradiology 2018; 60:403-412. [PMID: 29383434 DOI: 10.1007/s00234-017-1973-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/28/2017] [Indexed: 12/18/2022]
Abstract
PURPOSE Many questions remain regarding how the brain develops, matures, and ages across the lifespan. The functional connectivity networks in the resting-state brain can reflect many of the characteristic changes in the brain that are associated with increasing age. Functional connectivity has been shown to be time-dependent over the course of a lifespan and even over the course of minutes. The lifespan strategies of all cognitive networks and how dynamic functional connectivity is associated with age are unclear. METHODS In this paper, studies employing both linear and quadratic models to define new specific lifespan strategies, including early/late increase/decrease models, were conducted to explore the lifespan functional changes. A large data sample was retrieved from the publicly available data from the Nathan Kline Institute (N = 149 and ages 9-85). Both static and dynamic functional connectivity indexes were calculated including the static functional connectivity, the mean of the dynamic functional connectivity and variations in dynamic functional connectivity. RESULTS The between-network connectivity results revealed early increases in the default-mode (DF) and cingulo-opercular network (CO)-associated network connectivities and a late increase in the fronto-parietal (FP)-associated network connectivity. These results depicted various lifespan strategies for different development stages and different cognitive networks across the lifespan. Additionally, the static FC and mean dynamic FC exhibited consistent results, and their variation exhibited a constant decrease with age across the entire age range. CONCLUSION These results (FDR-corrected p value < 0.05) suggest that the early/late variations in lifespan strategies could reflect an association between varied and complex circumstances and brain development.
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Affiliation(s)
- Yuanyuan Chen
- College of Microelectronics, Tianjin University, Tianjin, China.,Tianjin International Joint Research Center for Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Xin Zhao
- Tianjin International Joint Research Center for Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China.,Department of Biomedical Engineering, College of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin, China
| | - Xiong Zhang
- Tianjin International Joint Research Center for Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China.,Department of Biomedical Engineering, College of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin, China
| | - Ya'nan Liu
- Tianjin International Joint Research Center for Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China.,Department of Biomedical Engineering, College of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin, China
| | - Peng Zhou
- Tianjin International Joint Research Center for Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China.,Department of Biomedical Engineering, College of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin, China
| | - Hongyan Ni
- Department of Radiology, Tianjin First Center Hospital, Tianjin, China
| | - Jianguo Ma
- College of Microelectronics, Tianjin University, Tianjin, China
| | - Dong Ming
- Tianjin International Joint Research Center for Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China. .,Department of Biomedical Engineering, College of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin, China.
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25
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Freitas-Rodríguez S, Rodríguez F, Folgueras AR. GDF11 administration does not extend lifespan in a mouse model of premature aging. Oncotarget 2018; 7:55951-55956. [PMID: 27507054 PMCID: PMC5302888 DOI: 10.18632/oncotarget.11096] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/22/2016] [Indexed: 11/25/2022] Open
Abstract
GDF11 has recently emerged as a powerful anti-aging candidate, found in young blood, capable of rejuvenating a number of aged tissues, such as heart, skeletal muscle and brain. However, recent reports have shown contradictory data questioning its capacity to reverse age-related tissue dysfunction. The availability of a mouse model of accelerated aging, which shares most of the features occurring in physiological aging, gives us an excellent opportunity to test in vivo therapies aimed at extending lifespan both in pathological and normal aging. On this basis, we wondered whether the proposed anti-aging functions of GDF11 would have an overall effect on longevity. We first confirmed the existence of a reduction in GDF11/8 levels in our mouse model of accelerated aging compared with wild-type littermates. However, we show herein that GDF11 daily administration does not extend lifespan of premature-aged mice.
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Affiliation(s)
- Sandra Freitas-Rodríguez
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Francisco Rodríguez
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Alicia R Folgueras
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
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26
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Sorokin M, Kholodenko R, Grekhova A, Suntsova M, Pustovalova M, Vorobyeva N, Kholodenko I, Malakhova G, Garazha A, Nedoluzhko A, Vasilov R, Poddubskaya E, Kovalchuk O, Adamyan L, Prassolov V, Allina D, Kuzmin D, Ignatev K, Osipov A, Buzdin A. Acquired resistance to tyrosine kinase inhibitors may be linked with the decreased sensitivity to X-ray irradiation. Oncotarget 2017; 9:5111-5124. [PMID: 29435166 PMCID: PMC5797037 DOI: 10.18632/oncotarget.23700] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 12/11/2017] [Indexed: 01/08/2023] Open
Abstract
Acquired resistance to chemotherapy and radiation therapy is one of the major obstacles decreasing efficiency of treatment of the oncologic diseases. In this study, on the two cell lines (ovarian carcinoma SKOV-3 and neuroblastoma NGP-127), we modeled acquired resistance to five target anticancer drugs. The cells were grown on gradually increasing concentrations of the clinically relevant tyrosine kinase inhibitors (TKIs) Sorafenib, Pazopanib and Sunitinib, and rapalogs Everolimus and Temsirolimus, for 20 weeks. After 20 weeks of culturing, the half-inhibitory concentrations (IC50) increased by 25 – 186% for the particular combinations of the drugs and cell types. We next subjected cells to 10 Gy irradiation, a dose frequently used in clinical radiation therapy. For the SKOV-3, but not NGP-127 cells, for the TKIs Sorafenib, Pazopanib and Sunitinib, we noticed statistically significant increase in capacity to repair radiation-induced DNA double strand breaks compared to naïve control cells not previously treated with TKIs. These peculiarities were linked with the increased activation of ATM DNA repair pathway in the TKI-treated SKOV-3, but not NGP-127 cells. Our results provide a new cell culture model for studying anti-cancer therapy efficiency and evidence that there may be a tissue-specific radioresistance emerging as a side effect of treatment with TKIs.
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Affiliation(s)
- Maxim Sorokin
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117198, Russia.,National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow 123182, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Roman Kholodenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Anna Grekhova
- State Research Center-Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow 123098, Russia
| | - Maria Suntsova
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117198, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Margarita Pustovalova
- State Research Center-Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow 123098, Russia
| | - Natalia Vorobyeva
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117198, Russia.,State Research Center-Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow 123098, Russia
| | - Irina Kholodenko
- Orekhovich Institute of Biomedical Chemistry, Moscow 119121, Russia
| | - Galina Malakhova
- National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow 123182, Russia
| | - Andrew Garazha
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117198, Russia.,OmicsWay Corp., Walnut, CA 91789, USA
| | - Artem Nedoluzhko
- National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow 123182, Russia
| | - Raif Vasilov
- National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow 123182, Russia
| | | | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K3M4, Canada
| | - Leila Adamyan
- Department of Reproductive Medicine and Surgery, Moscow State University of Medicine and Dentistry, Moscow 127206, Russia
| | - Vladimir Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Daria Allina
- Pathology Department, Morozov Children's City Hospital, Moscow 119049, Russia
| | | | - Kirill Ignatev
- Republic Oncological Hospital, Petrozavodsk 185000, Russia
| | - Andreyan Osipov
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117198, Russia.,State Research Center-Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow 123098, Russia
| | - Anton Buzdin
- National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow 123182, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,OmicsWay Corp., Walnut, CA 91789, USA
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27
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Abstract
Aberrant signal transduction downstream of the Ras GTPase has a well-established role in tumorigenesis. Mutations that result in hyperactivation of Ras are responsible for a third of all human cancers. Hence, small molecule inhibitors of the Ras signal transduction cascade have been under intense focus as potential cancer treatments. In both invertebrate and mammalian models, emerging evidence has also implicated components of the Ras signaling pathway in aging and metabolic regulation. Here, I review the current evidence for Ras signaling in these newly discovered roles highlighting the interactions between the Ras pathway and other longevity assurance mechanisms. Defining the role of Ras signaling in maintaining age-related health may have important implications for the development of interventions that could not only increase lifespan but also delay the onset and/or progression of age-related functional decline.
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Affiliation(s)
- Cathy Slack
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, UK
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28
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Deep biomarkers of human aging: Application of deep neural networks to biomarker development. Aging (Albany NY) 2017; 8:1021-33. [PMID: 27191382 PMCID: PMC4931851 DOI: 10.18632/aging.100968] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 05/09/2016] [Indexed: 01/05/2023]
Abstract
One of the major impediments in human aging research is the absence of a comprehensive and actionable set of biomarkers that may be targeted and measured to track the effectiveness of therapeutic interventions. In this study, we designed a modular ensemble of 21 deep neural networks (DNNs) of varying depth, structure and optimization to predict human chronological age using a basic blood test. To train the DNNs, we used over 60,000 samples from common blood biochemistry and cell count tests from routine health exams performed by a single laboratory and linked to chronological age and sex. The best performing DNN in the ensemble demonstrated 81.5 % epsilon-accuracy r = 0.90 with R2 = 0.80 and MAE = 6.07 years in predicting chronological age within a 10 year frame, while the entire ensemble achieved 83.5% epsilon-accuracy r = 0.91 with R2 = 0.82 and MAE = 5.55 years. The ensemble also identified the 5 most important markers for predicting human chronological age: albumin, glucose, alkaline phosphatase, urea and erythrocytes. To allow for public testing and evaluate real-life performance of the predictor, we developed an online system available at http://www.aging.ai. The ensemble approach may facilitate integration of multi-modal data linked to chronological age and sex that may lead to simple, minimally invasive, and affordable methods of tracking integrated biomarkers of aging in humans and performing cross-species feature importance analysis.
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29
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Aliper A, Belikov AV, Garazha A, Jellen L, Artemov A, Suntsova M, Ivanova A, Venkova L, Borisov N, Buzdin A, Mamoshina P, Putin E, Swick AG, Moskalev A, Zhavoronkov A. In search for geroprotectors: in silico screening and in vitro validation of signalome-level mimetics of young healthy state. Aging (Albany NY) 2017; 8:2127-2152. [PMID: 27677171 PMCID: PMC5076455 DOI: 10.18632/aging.101047] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 09/10/2016] [Indexed: 12/19/2022]
Abstract
Populations in developed nations throughout the world are rapidly aging, and the search for geroprotectors, or anti-aging interventions, has never been more important. Yet while hundreds of geroprotectors have extended lifespan in animal models, none have yet been approved for widespread use in humans. GeroScope is a computational tool that can aid prediction of novel geroprotectors from existing human gene expression data. GeroScope maps expression differences between samples from young and old subjects to aging-related signaling pathways, then profiles pathway activation strength (PAS) for each condition. Known substances are then screened and ranked for those most likely to target differential pathways and mimic the young signalome. Here we used GeroScope and shortlisted ten substances, all of which have lifespan-extending effects in animal models, and tested 6 of them for geroprotective effects in senescent human fibroblast cultures. PD-98059, a highly selective MEK1 inhibitor, showed both life-prolonging and rejuvenating effects. Natural compounds like N-acetyl-L-cysteine, Myricetin and Epigallocatechin gallate also improved several senescence-associated properties and were further investigated with pathway analysis. This work not only highlights several potential geroprotectors for further study, but also serves as a proof-of-concept for GeroScope, Oncofinder and other PAS-based methods in streamlining drug prediction, repurposing and personalized medicine.
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Affiliation(s)
- Alexander Aliper
- Insilico Medicine, Inc, Research Department, Baltimore, MD 21218, USA
| | - Aleksey V Belikov
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | - Andrew Garazha
- Insilico Medicine, Inc, Research Department, Baltimore, MD 21218, USA.,Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia.,Center for Biogerontology and Regenerative Medicine, Moscow, 121099, Russia
| | - Leslie Jellen
- Insilico Medicine, Inc, Research Department, Baltimore, MD 21218, USA.,Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Artem Artemov
- Insilico Medicine, Inc, Research Department, Baltimore, MD 21218, USA
| | - Maria Suntsova
- D. Rogachev Federal Research and Clinical Center for Pediatric Hematology, Oncology, and Immunology, Moscow, 117997, Russia
| | - Alena Ivanova
- D. Rogachev Federal Research and Clinical Center for Pediatric Hematology, Oncology, and Immunology, Moscow, 117997, Russia
| | - Larisa Venkova
- Insilico Medicine, Inc, Research Department, Baltimore, MD 21218, USA.,Pathway Pharmaceuticals, Ltd, Hong Kong, Hong Kong
| | - Nicolas Borisov
- Insilico Medicine, Inc, Research Department, Baltimore, MD 21218, USA.,Pathway Pharmaceuticals, Ltd, Hong Kong, Hong Kong
| | - Anton Buzdin
- Pathway Pharmaceuticals, Ltd, Hong Kong, Hong Kong
| | - Polina Mamoshina
- Insilico Medicine, Inc, Research Department, Baltimore, MD 21218, USA
| | - Evgeny Putin
- Insilico Medicine, Inc, Research Department, Baltimore, MD 21218, USA
| | | | - Alexey Moskalev
- Insilico Medicine, Inc, Research Department, Baltimore, MD 21218, USA.,Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia.,Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, 167982, Russia.,School of Systems Biology, George Mason University (GMU), Fairfax, VA 22030, USA.,Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alex Zhavoronkov
- Insilico Medicine, Inc, Research Department, Baltimore, MD 21218, USA.,The Biogerontology Research Foundation, Oxford, UK
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30
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Serebryannyy L, Misteli T. Protein sequestration at the nuclear periphery as a potential regulatory mechanism in premature aging. J Cell Biol 2017; 217:21-37. [PMID: 29051264 PMCID: PMC5748986 DOI: 10.1083/jcb.201706061] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/10/2017] [Accepted: 08/17/2017] [Indexed: 12/19/2022] Open
Abstract
Serebryannyy and Misteli provide a perspective on how protein sequestration at the inner nuclear membrane and nuclear lamina might influence aging. Despite the extensive description of numerous molecular changes associated with aging, insights into the driver mechanisms of this fundamental biological process are limited. Based on observations in the premature aging syndrome Hutchinson–Gilford progeria, we explore the possibility that protein regulation at the inner nuclear membrane and the nuclear lamina contributes to the aging process. In support, sequestration of nucleoplasmic proteins to the periphery impacts cell stemness, the response to cytotoxicity, proliferation, changes in chromatin state, and telomere stability. These observations point to the nuclear periphery as a central regulator of the aging phenotype.
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Affiliation(s)
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD
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31
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Stamatas GN, Wu J, Pappas A, Mirmirani P, McCormick TS, Cooper KD, Consolo M, Schastnaya J, Ozerov IV, Aliper A, Zhavoronkov A. An analysis of gene expression data involving examination of signaling pathways activation reveals new insights into the mechanism of action of minoxidil topical foam in men with androgenetic alopecia. Cell Cycle 2017; 16:1578-1584. [PMID: 28594262 DOI: 10.1080/15384101.2017.1327492] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Androgenetic alopecia is the most common form of hair loss. Minoxidil has been approved for the treatment of hair loss, however its mechanism of action is still not fully clarified. In this study, we aimed to elucidate the effects of 5% minoxidil topical foam on gene expression and activation of signaling pathways in vertex and frontal scalp of men with androgenetic alopecia. We identified regional variations in gene expression and perturbed signaling pathways using in silico Pathway Activation Network Decomposition Analysis (iPANDA) before and after treatment with minoxidil. Vertex and frontal scalp of patients showed a generally similar response to minoxidil. Both scalp regions showed upregulation of genes that encode keratin associated proteins and downregulation of ILK, Akt, and MAPK signaling pathways after minoxidil treatment. Our results provide new insights into the mechanism of action of minoxidil topical foam in men with androgenetic alopecia.
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Affiliation(s)
- Georgios N Stamatas
- a Emerging Science & Innovation, Johnson & Johnson Santé Beauté France , Johnson & Johnson Group of Consumer Companies , Issy-les-Moulineaux , France
| | - Jeff Wu
- b Hair Care R&D, Johnson & Johnson Consumer Worldwide , Johnson & Johnson Family of Consumer Companies, Inc. , Skillman , NJ , USA
| | - Apostolos Pappas
- c Emerging Science & Innovation, Johnson & Johnson Consumer Worldwide , Johnson & Johnson Family of Consumer Companies, Inc. , Skillman , NJ , USA
| | - Paradi Mirmirani
- d Department of Dermatology , The Permanente Medical Group , Vallejo , CA , USA.,e Department of Dermatology , University of California , San Francisco , CA , USA.,f Department of Dermatology , Case Western Reserve University, University Hospitals Cleveland Medical Center , Cleveland , OH , USA
| | - Thomas S McCormick
- f Department of Dermatology , Case Western Reserve University, University Hospitals Cleveland Medical Center , Cleveland , OH , USA
| | - Kevin D Cooper
- f Department of Dermatology , Case Western Reserve University, University Hospitals Cleveland Medical Center , Cleveland , OH , USA
| | - Mary Consolo
- f Department of Dermatology , Case Western Reserve University, University Hospitals Cleveland Medical Center , Cleveland , OH , USA
| | - Jane Schastnaya
- g Insilico Medicine, Inc., Emerging Technology Centers , Johns Hopkins University at Eastern , Baltimore , MD , USA
| | - Ivan V Ozerov
- g Insilico Medicine, Inc., Emerging Technology Centers , Johns Hopkins University at Eastern , Baltimore , MD , USA
| | - Alexander Aliper
- g Insilico Medicine, Inc., Emerging Technology Centers , Johns Hopkins University at Eastern , Baltimore , MD , USA
| | - Alex Zhavoronkov
- g Insilico Medicine, Inc., Emerging Technology Centers , Johns Hopkins University at Eastern , Baltimore , MD , USA
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32
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Kang HT, Park JT, Choi K, Choi HJC, Jung CW, Kim GR, Lee YS, Park SC. Chemical screening identifies ROCK as a target for recovering mitochondrial function in Hutchinson-Gilford progeria syndrome. Aging Cell 2017; 16:541-550. [PMID: 28317242 PMCID: PMC5418208 DOI: 10.1111/acel.12584] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2017] [Indexed: 12/29/2022] Open
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) constitutes a genetic disease wherein an aging phenotype manifests in childhood. Recent studies indicate that reactive oxygen species (ROS) play important roles in HGPS phenotype progression. Thus, pharmacological reduction in ROS levels has been proposed as a potentially effective treatment for patient with this disorder. In this study, we performed high-throughput screening to find compounds that could reduce ROS levels in HGPS fibroblasts and identified rho-associated protein kinase (ROCK) inhibitor (Y-27632) as an effective agent. To elucidate the underlying mechanism of ROCK in regulating ROS levels, we performed a yeast two-hybrid screen and discovered that ROCK1 interacts with Rac1b. ROCK activation phosphorylated Rac1b at Ser71 and increased ROS levels by facilitating the interaction between Rac1b and cytochrome c. Conversely, ROCK inactivation with Y-27632 abolished their interaction, concomitant with ROS reduction. Additionally, ROCK activation resulted in mitochondrial dysfunction, whereas ROCK inactivation with Y-27632 induced the recovery of mitochondrial function. Furthermore, a reduction in the frequency of abnormal nuclear morphology and DNA double-strand breaks was observed along with decreased ROS levels. Thus, our study reveals a novel mechanism through which alleviation of the HGPS phenotype is mediated by the recovery of mitochondrial function upon ROCK inactivation.
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Affiliation(s)
- Hyun Tae Kang
- Well Aging Research Center; Samsung Advanced Institute of Technology; Samsung Electronics; Suwon-si Korea
| | - Joon Tae Park
- Well Aging Research Center; Samsung Advanced Institute of Technology; Samsung Electronics; Suwon-si Korea
| | - Kobong Choi
- Well Aging Research Center; Samsung Advanced Institute of Technology; Samsung Electronics; Suwon-si Korea
| | - Hyo Jei Claudia Choi
- Well Aging Research Center; Samsung Advanced Institute of Technology; Samsung Electronics; Suwon-si Korea
| | - Chul Won Jung
- Well Aging Research Center; Samsung Advanced Institute of Technology; Samsung Electronics; Suwon-si Korea
| | - Gyu Ree Kim
- Well Aging Research Center; DGIST; Daegu Korea
| | - Young-Sam Lee
- Well Aging Research Center; DGIST; Daegu Korea
- Department of New Biology; DGIST; Daegu Korea
| | - Sang Chul Park
- Well Aging Research Center; DGIST; Daegu Korea
- Department of New Biology; DGIST; Daegu Korea
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33
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Hilton BA, Liu J, Cartwright BM, Liu Y, Breitman M, Wang Y, Jones R, Tang H, Rusinol A, Musich PR, Zou Y. Progerin sequestration of PCNA promotes replication fork collapse and mislocalization of XPA in laminopathy-related progeroid syndromes. FASEB J 2017; 31:3882-3893. [PMID: 28515154 DOI: 10.1096/fj.201700014r] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 04/24/2017] [Indexed: 02/06/2023]
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disorder that is caused by a point mutation in the LMNA gene, resulting in production of a truncated farnesylated-prelamin A protein (progerin). We previously reported that XPA mislocalized to the progerin-induced DNA double-strand break (DSB) sites, blocking DSB repair, which led to DSB accumulation, DNA damage responses, and early replication arrest in HGPS. In this study, the XPA mislocalization to DSBs occurred at stalled or collapsed replication forks, concurrent with a significant loss of PCNA at the forks, whereas PCNA efficiently bound to progerin. This PCNA sequestration likely exposed ds-ssDNA junctions at replication forks for XPA binding. Depletion of XPA or progerin each significantly restored PCNA at replication forks. Our results suggest that although PCNA is much more competitive than XPA in binding replication forks, PCNA sequestration by progerin may shift the equilibrium to favor XPA binding. Furthermore, we demonstrated that progerin-induced apoptosis could be rescued by XPA, suggesting that XPA-replication fork binding may prevent apoptosis in HGPS cells. Our results propose a mechanism for progerin-induced genome instability and accelerated replicative senescence in HGPS.-Hilton, B. A., Liu, J., Cartwright, B. M., Liu, Y., Breitman, M., Wang, Y., Jones, R., Tang, H., Rusinol, A., Musich, P. R., Zou, Y. Progerin sequestration of PCNA promotes replication fork collapse and mislocalization of XPA in laminopathy-related progeroid syndromes.
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Affiliation(s)
- Benjamin A Hilton
- Department of Biomedical Sciences, J. H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
| | - Ji Liu
- Department of Biochemistry and Molecular Biology, West China Center of Medical Sciences, Sichuan University, Chengdu, China
| | - Brian M Cartwright
- Department of Biomedical Sciences, J. H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
| | - Yiyong Liu
- Department of Biomedical Sciences, J. H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
| | - Maya Breitman
- Department of Biomedical Sciences, J. H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
| | - Youjie Wang
- Ministry of Education (MOE) Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rowdy Jones
- Department of Biomedical Sciences, J. H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
| | - Hui Tang
- Department of Biomedical Sciences, J. H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
| | - Antonio Rusinol
- Department of Biomedical Sciences, J. H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
| | - Phillip R Musich
- Department of Biomedical Sciences, J. H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
| | - Yue Zou
- Department of Biomedical Sciences, J. H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA;
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34
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Caravia XM, Roiz-Valle D, Morán-Álvarez A, López-Otín C. Functional relevance of miRNAs in premature ageing. Mech Ageing Dev 2017; 168:10-19. [PMID: 28502819 DOI: 10.1016/j.mad.2017.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 03/30/2017] [Accepted: 05/09/2017] [Indexed: 02/06/2023]
Abstract
Ageing is a complex biological process characterized by the progressive loss of biological fitness due to the accumulation of macromolecular and cellular damage that affects most living organisms. Moreover, ageing is an important risk factor for many pathologies, including cardiovascular diseases, neurological disorders, and cancer. However, the ageing rate can be modulated by genetic, nutritional, and pharmacological factors, highlighting the concept of "ageing plasticity". Progeroid syndromes are a group of rare genetic diseases that resemble many characteristics of physiological ageing. Accordingly, studies on these diseases have been very useful for gaining mechanistic insights in ageing biology. In recent years, a great effort has been made in ageing research and several works have confirmed that geromiRs, the growing subgroup of miRNAs implicated in ageing, are able to modulate organismal lifespan. However, very little is still known about the impact of miRNA in premature ageing. In this review, we will address the functional relevance of this class of small non-coding RNAs in the regulation of the hallmarks of progeroid syndromes. In addition, we will discuss the potential strategies for managing progeria based on geromiR modulation.
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Affiliation(s)
- Xurde M Caravia
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - David Roiz-Valle
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Alba Morán-Álvarez
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain; Centro de Investigación Biomédica en Red de Cáncer, Spain.
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35
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Park SK, Shin OS. Metformin alleviates ageing cellular phenotypes in Hutchinson-Gilford progeria syndrome dermal fibroblasts. Exp Dermatol 2017; 26:889-895. [PMID: 28192606 DOI: 10.1111/exd.13323] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2017] [Indexed: 12/21/2022]
Abstract
Metformin is a popular antidiabetic biguanide, which has been considered as a candidate drug for cancer treatment and ageing prevention. Hutchinson-Gilford progeria syndrome (HGPS) is a devastating disease characterized by premature ageing and severe age-associated complications leading to death. The effects of metformin on HGPS dermal fibroblasts remain largely undefined. In this study, we investigated whether metformin could exert a beneficial effect on nuclear abnormalities and delay senescence in fibroblasts derived from HGPS patients. Metformin treatment partially restored normal nuclear phenotypes, delayed senescence, activated the phosphorylation of AMP-activated protein kinase and decreased reactive oxygen species formation in HGPS dermal fibroblasts. Interestingly, metformin reduced the number of phosphorylated histone variant H2AX-positive DNA damage foci and suppressed progerin protein expression, compared to the control. Furthermore, metformin-supplemented aged mice showed higher splenocyte proliferation and mRNA expression of the antioxidant enzyme, superoxide dismutase 2 than the control mice. Collectively, our results show that metformin treatment alleviates the nuclear defects and premature ageing phenotypes in HGPS fibroblasts. Thus, metformin can be considered a promising therapeutic approach for life extension in HGPS.
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Affiliation(s)
- Seul-Ki Park
- Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Ok Sarah Shin
- Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
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36
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Moskalev A, Chernyagina E, Kudryavtseva A, Shaposhnikov M. Geroprotectors: A Unified Concept and Screening Approaches. Aging Dis 2017; 8:354-363. [PMID: 28580190 PMCID: PMC5440114 DOI: 10.14336/ad.2016.1022] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/22/2016] [Indexed: 12/20/2022] Open
Abstract
Although the geroprotectors discovery is a new biomedicine trend and more than 200 compounds can slow aging and increase the lifespan of the model organism, there are still no geroprotectors on the market. The reasons may be partly related to the lack of a unified concept of geroprotector, accepted by the scientific community. Such concept as a system of criteria for geroprotector identification and classification can form a basis for an analytical model of anti-aging drugs, help to consolidate the efforts of various research initiatives in this area and compare their results. Here, we review the existing classification and characteristics of geroprotectors based on their effect on the survival of a group of individuals or pharmaceutics classes, according to the proposed mechanism of their geroprotective action or theories of aging. After discussing advantages and disadvantages of these approaches, we offer a new concept based on the maintenance of homeostatic capacity because aging can be considered as exponential shrinkage of homeostatic capacity leading to the onset of age-related diseases and death. Besides, we review the most promising current screening approaches to finding new geroprotectors. Establishing the classification of existing geroprotectors based on physiology and current understanding of the nature of aging is essential for putting the existing knowledge into a single system. This system could be useful to formulate standards for finding and creating new geroprotectors. Standardization, in turn, would allow easier comparison and combination of experimental data obtained by different research groups.
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Affiliation(s)
- Alexey Moskalev
- 1Laboratory of postgenomic studies, Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russia.,2Laboratory of genetics of aging and longevity, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia.,3Laboratory of molecular radiobiology and gerontology, Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, 167982, Russia
| | - Elizaveta Chernyagina
- 2Laboratory of genetics of aging and longevity, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | - Anna Kudryavtseva
- 1Laboratory of postgenomic studies, Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russia
| | - Mikhail Shaposhnikov
- 3Laboratory of molecular radiobiology and gerontology, Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, 167982, Russia
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37
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Siman-Tov T, Bosak N, Sprecher E, Paz R, Eran A, Aharon-Peretz J, Kahn I. Early Age-Related Functional Connectivity Decline in High-Order Cognitive Networks. Front Aging Neurosci 2017; 8:330. [PMID: 28119599 PMCID: PMC5223363 DOI: 10.3389/fnagi.2016.00330] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 12/19/2016] [Indexed: 12/15/2022] Open
Abstract
As the world ages, it becomes urgent to unravel the mechanisms underlying brain aging and find ways of intervening with them. While for decades cognitive aging has been related to localized brain changes, growing attention is now being paid to alterations in distributed brain networks. Functional connectivity magnetic resonance imaging (fcMRI) has become a particularly useful tool to explore large-scale brain networks; yet, the temporal course of connectivity lifetime changes has not been established. Here, an extensive cross-sectional sample (21-85 years old, N = 887) from a public fcMRI database was used to characterize adult lifespan connectivity dynamics within and between seven brain networks: the default mode, salience, dorsal attention, fronto-parietal control, auditory, visual and motor networks. The entire cohort was divided into young (21-40 years, mean ± SD: 25.5 ± 4.8, n = 543); middle-aged (41-60 years, 50.6 ± 5.4, n = 238); and old (61 years and above, 69.0 ± 6.3, n = 106) subgroups. Correlation matrices as well as a mixed model analysis of covariance indicated that within high-order cognitive networks a considerable connectivity decline is already evident by middle adulthood. In contrast, a motor network shows increased connectivity in middle adulthood and a subsequent decline. Additionally, alterations in inter-network interactions are noticeable primarily in the transition between young and middle adulthood. These results provide evidence that aging-related neural changes start early in adult life.
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Affiliation(s)
- Tali Siman-Tov
- Cognitive Neurology Institute, Rambam Health Care Campus Haifa, Israel
| | - Noam Bosak
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology Haifa, Israel
| | - Elliot Sprecher
- Laboratory of Clinical Neurophysiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of TechnologyHaifa, Israel; Department of Neurology, Rambam Health Care CampusHaifa, Israel
| | - Rotem Paz
- Cognitive Neurology Institute, Rambam Health Care Campus Haifa, Israel
| | - Ayelet Eran
- Department of Diagnostic Imaging, Rambam Health Care Campus Haifa, Israel
| | - Judith Aharon-Peretz
- Cognitive Neurology Institute, Rambam Health Care CampusHaifa, Israel; Department of Neurology, Rambam Health Care CampusHaifa, Israel
| | - Itamar Kahn
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology Haifa, Israel
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38
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Buzdin AA, Prassolov V, Zhavoronkov AA, Borisov NM. Bioinformatics Meets Biomedicine: OncoFinder, a Quantitative Approach for Interrogating Molecular Pathways Using Gene Expression Data. Methods Mol Biol 2017; 1613:53-83. [PMID: 28849558 DOI: 10.1007/978-1-4939-7027-8_4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We propose a biomathematical approach termed OncoFinder (OF) that enables performing both quantitative and qualitative analyses of the intracellular molecular pathway activation. OF utilizes an algorithm that distinguishes the activator/repressor role of every gene product in a pathway. This method is applicable for the analysis of any physiological, stress, malignancy, and other conditions at the molecular level. OF showed a strong potential to neutralize background-caused differences between experimental gene expression data obtained using NGS, microarray and modern proteomics techniques. Importantly, in most cases, pathway activation signatures were better markers of cancer progression compared to the individual gene products. OF also enables correlating pathway activation with the success of anticancer therapy for individual patients. We further expanded this approach to analyze impact of micro RNAs (miRs) on the regulation of cellular interactome. Many alternative sources provide information about miRs and their targets. However, instruments elucidating higher level impact of the established total miR profiles are still largely missing. A variant of OncoFinder termed MiRImpact enables linking miR expression data with its estimated outcome on the regulation of molecular processes, such as signaling, metabolic, cytoskeleton, and DNA repair pathways. MiRImpact was used to establish cancer-specific and cytomegaloviral infection-linked interactomic signatures for hundreds of molecular pathways. Interestingly, the impact of miRs appeared orthogonal to pathway regulation at the mRNA level, which stresses the importance of combining all available levels of gene regulation to build a more objective molecular model of cell.
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Affiliation(s)
- Anton A Buzdin
- Pathway Pharmaceuticals, Wan Chai, Hong Kong SAR.
- Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, National Research Centre "Kurchatov Institute", Bldg 140, Suite 415, 1, Akademika Kurchatova sq., Moscow, 123182, Russia.
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Laboratory of Bioinformatics, D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.
| | - Vladimir Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova street 32, Mosow, 119991, Russia
| | - Alex A Zhavoronkov
- Pathway Pharmaceuticals, Wan Chai, Hong Kong SAR
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Nikolay M Borisov
- Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, National Research Centre "Kurchatov Institute", Bldg 140, Suite 415, 1, Akademika Kurchatova sq., Moscow, 123182, Russia
- Department of Personalized Medicine, First Oncology Research and Advisory Center, Moscow, Russia
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39
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Yamamoto Y, Ihara M. Disruption of transforming growth factor-β superfamily signaling: A shared mechanism underlying hereditary cerebral small vessel disease. Neurochem Int 2016; 107:211-218. [PMID: 28034724 DOI: 10.1016/j.neuint.2016.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/02/2016] [Accepted: 12/07/2016] [Indexed: 11/20/2022]
Abstract
Cerebral small vessel disease (SVD) is not only one of the leading causes of cognitive impairment but also an important contributory factor in Alzheimer's disease. SVD and related white matter changes are common in the elderly, but the underlying pathogenic mechanism remains unclear. The end-stage pathology of SVD often involves replacement of vascular smooth muscle cells with collagenous or other nontensile fibrillary material. Recent studies on hereditary SVD have revealed a close relationship between small vessel pathology and disruption of transforming growth factor-β (TGF-β) superfamily signaling. TGF-β superfamily members, such as TGF-β and bone morphogenetic proteins, are multifunctional proteins that regulate production of extracellular matrix proteins, which in turn control the bioavailability of TGF-β superfamily members and modulate their signaling activities. This article reviews hereditary disorders with small vessel pathology and their relation to TGF-β superfamily signaling.
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Affiliation(s)
- Yumi Yamamoto
- Department of Regenerative Medicine and Tissue Engineering, National Cerebral and Cardiovascular Center, 5-7-1 Fujishirodai, Suita, Osaka, 565-8565, Japan
| | - Masafumi Ihara
- Department of Neurology, National Cerebral and Cardiovascular Center, 5-7-1 Fujishirodai, Suita, Osaka, 565-8565, Japan.
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40
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Buzdin AA, Artcibasova AV, Fedorova NF, Suntsova MV, Garazha AV, Sorokin MI, Allina D, Shalatonin M, Borisov NM, Zhavoronkov AA, Kovalchuk I, Kovalchuk O, Kushch AA. Early stage of cytomegalovirus infection suppresses host microRNA expression regulation in human fibroblasts. Cell Cycle 2016; 15:3378-3389. [PMID: 28051642 PMCID: PMC5224468 DOI: 10.1080/15384101.2016.1241928] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/12/2016] [Accepted: 09/21/2016] [Indexed: 12/11/2022] Open
Abstract
Responses to human cytomegalovirus (HCMV) infection are largely individual and cell type specific. We investigated molecular profiles in 2 primary cell cultures of human fibroblasts, which are highly or marginally sensitive to HCMV infection, respectively. We screened expression of genes and microRNAs (miRs) at the early (3 hours) stage of infection. To assess molecular pathway activation profiles, we applied bioinformatic algorithms OncoFinder and MiRImpact. In both cell types, pathway regulation properties at mRNA and miR levels were markedly different. Surprisingly, in the infected highly sensitive cells, we observed a "freeze" of miR expression profiles compared to uninfected controls. Our results evidence that in the sensitive cells, HCMV blocks intracellular regulation of microRNA expression already at the earliest stage of infection. These data suggest somewhat new functions for HCMV products and demonstrate dependence of miR expression arrest on the host-encoded factors.
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Affiliation(s)
- Anton A. Buzdin
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- National Research Centre “Kurchatov Institute”, Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia
| | - Alina V. Artcibasova
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR
| | - Natalya F. Fedorova
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Maria V. Suntsova
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Andrew V. Garazha
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
| | | | - Daria Allina
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
- First Oncology Research and Advisory Center, Moscow, Russia
| | | | - Nikolay M. Borisov
- National Research Centre “Kurchatov Institute”, Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia
- First Oncology Research and Advisory Center, Moscow, Russia
| | - Alex A. Zhavoronkov
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Alla A. Kushch
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, Moscow, Russia
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41
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Artcibasova AV, Korzinkin MB, Sorokin MI, Shegay PV, Zhavoronkov AA, Gaifullin N, Alekseev BY, Vorobyev NV, Kuzmin DV, Kaprin АD, Borisov NM, Buzdin AA. MiRImpact, a new bioinformatic method using complete microRNA expression profiles to assess their overall influence on the activity of intracellular molecular pathways. Cell Cycle 2016; 15:689-98. [PMID: 27027999 PMCID: PMC4845938 DOI: 10.1080/15384101.2016.1147633] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
MicroRNAs (miRs) are short noncoding RNA molecules that regulate expression of target mRNAs. Many published sources provide information about miRs and their targets. However, bioinformatic tools elucidating higher level impact of the established total miR profiles, are still largely missing. Recently, we developed a method termed OncoFinder enabling quantification of the activities of intracellular molecular pathways basing on gene expression data. Here we propose a new technique, MiRImpact, which enables to link miR expression data with its estimated outcome on the regulation of molecular pathways, like signaling, metabolic, cytoskeleton rearrangement, and DNA repair pathways. MiRImpact uses OncoFinder rationale for pathway activity calculations, with the major distinctions that (i) it deals with the concentrations of miRs - known regulators of gene products participating in molecular pathways, and (ii) miRs are considered as negative regulators of target molecules, if other is not specified. MiRImpact operates with 2 types of databases: for molecular targets of miRs and for gene products participating in molecular pathways. We applied MiRImpact to compare regulation of human bladder cancer-specific signaling pathways at the levels of mRNA and miR expression. We took 2 most complete alternative databases of experimentally validated miR targets – miRTarBase and DianaTarBase, and an OncoFinder database featuring 2725 gene products and 271 signaling pathways. We showed that the impact of miRs is orthogonal to pathway regulation at the mRNA level, which stresses the importance of studying posttranscriptional regulation of gene expression. We also report characteristic set of miR and mRNA regulation features linked with bladder cancer.
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Affiliation(s)
- Alina V Artcibasova
- a Pathway Pharmaceuticals , Wan Chai , Hong Kong, Hong Kong SAR.,b Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | | | - Maksim I Sorokin
- a Pathway Pharmaceuticals , Wan Chai , Hong Kong, Hong Kong SAR.,c First Oncology Research and Advisory Center , Moscow , Russia
| | - Peter V Shegay
- d P.A. Herzen Moscow Oncological Research Institute , Moscow , Russia
| | - Alex A Zhavoronkov
- b Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | - Nurshat Gaifullin
- e Moscow State University, Faculty of Fundamental Medicine , Moscow , Russia
| | - Boris Y Alekseev
- d P.A. Herzen Moscow Oncological Research Institute , Moscow , Russia
| | | | - Denis V Kuzmin
- f Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia
| | - Аndrey D Kaprin
- d P.A. Herzen Moscow Oncological Research Institute , Moscow , Russia
| | - Nikolay M Borisov
- g National Research Centre "Kurchatov Institute," Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies , Moscow , Russia
| | - Anton A Buzdin
- b Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia.,f Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia.,g National Research Centre "Kurchatov Institute," Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies , Moscow , Russia
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42
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Shepelin D, Korzinkin M, Vanyushina A, Aliper A, Borisov N, Vasilov R, Zhukov N, Sokov D, Prassolov V, Gaifullin N, Zhavoronkov A, Bhullar B, Buzdin A. Molecular pathway activation features linked with transition from normal skin to primary and metastatic melanomas in human. Oncotarget 2016; 7:656-70. [PMID: 26624979 PMCID: PMC4808024 DOI: 10.18632/oncotarget.6394] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 11/11/2015] [Indexed: 12/14/2022] Open
Abstract
Melanoma is the most aggressive and dangerous type of skin cancer, but its molecular mechanisms remain largely unclear. For transcriptomic data of 478 primary and metastatic melanoma, nevi and normal skin samples, we performed high-throughput analysis of intracellular molecular networks including 592 signaling and metabolic pathways. We showed that at the molecular pathway level, the formation of nevi largely resembles transition from normal skin to primary melanoma. Using a combination of bioinformatic machine learning algorithms, we identified 44 characteristic signaling and metabolic pathways connected with the formation of nevi, development of primary melanoma, and its metastases. We created a model describing formation and progression of melanoma at the level of molecular pathway activation. We discovered six novel associations between activation of metabolic molecular pathways and progression of melanoma: for allopregnanolone biosynthesis, L-carnitine biosynthesis, zymosterol biosynthesis (inhibited in melanoma), fructose 2, 6-bisphosphate synthesis and dephosphorylation, resolvin D biosynthesis (activated in melanoma), D-myo-inositol hexakisphosphate biosynthesis (activated in primary, inhibited in metastatic melanoma). Finally, we discovered fourteen tightly coordinated functional clusters of molecular pathways. This study helps to decode molecular mechanisms underlying the development of melanoma.
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Affiliation(s)
- Denis Shepelin
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.,Group for Genomic Analysis of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Mikhail Korzinkin
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.,First Oncology Research and Advisory Center, Moscow, Russia
| | - Anna Vanyushina
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Alexander Aliper
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Nicolas Borisov
- First Oncology Research and Advisory Center, Moscow, Russia.,National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia
| | - Raif Vasilov
- National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia
| | - Nikolay Zhukov
- First Oncology Research and Advisory Center, Moscow, Russia.,Pirogov Russian National Research Medical University, Department of Oncology, Hematology and Radiotherapy, Moscow, Russia
| | | | - Vladimir Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Mosow, Russia
| | - Nurshat Gaifullin
- Moscow State University, Faculty of Fundamental Medicine, Moscow, Russia
| | - Alex Zhavoronkov
- Insilico Medicine, Inc, ETC, Johns Hopkins University, Baltimore, MD, USA
| | | | - Anton Buzdin
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.,Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia
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43
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Kim JA, Park SK, Kumar M, Lee CH, Shin OS. Insights into the role of immunosenescence during varicella zoster virus infection (shingles) in the aging cell model. Oncotarget 2016; 6:35324-43. [PMID: 26473290 PMCID: PMC4742108 DOI: 10.18632/oncotarget.6117] [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: 08/29/2015] [Accepted: 09/25/2015] [Indexed: 12/11/2022] Open
Abstract
Varicella zoster virus (VZV) is the etiological agent of shingles, a painful skin rash that affects a significant proportion of the elderly population. In the present study, we used two aging cell models, Hutchinson-Gilford progeria syndrome (HGPS) fibroblasts and stress or replicative senescence-induced normal human dermal fibroblasts (NHDFs), to investigate age-associated susceptibility to VZV infection. VZV infectivity titers were significantly associated with donor age in HGPS fibroblasts and senescence induction in NHDFs. High throughput RNA-sequencing (RNA-seq) analysis was performed to assess global and dynamic changes in the host transcriptomes of VZV-infected aging cells. Analysis of differentially expressed genes (DEGs) indicated that VZV infection in aged HGPS fibroblasts resembled that in senescent NHDFs, particularly in terms of genes associated with pattern recognition receptors in virus sensing network, providing novel insights into the mechanisms of senescence-associated susceptibility to VZV infection. Additionally, we identified stimulator of interferon genes (STING) as a potential VZV sensing receptor. Knockdown of STING expression resulted in increased viral replication in primary fibroblasts, whereas STING overexpression led to suppression of VZV plaque formation. In conclusion, our findings highlight the important role of immunosenescence following VZV infection and provide significant insights into the mechanisms underlying cellular sensing of VZV infection and the induction of immune responses in aged skin cells.
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Affiliation(s)
- Ji-Ae Kim
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Seul-Ki Park
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Mukesh Kumar
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, Pacific Center for Emerging Infectious Diseases Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Chan-Hee Lee
- Department of Microbiology, Chungbuk National University, Cheongju, Republic of Korea
| | - Ok Sarah Shin
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, Republic of Korea.,Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
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Venkova L, Aliper A, Suntsova M, Kholodenko R, Shepelin D, Borisov N, Malakhova G, Vasilov R, Roumiantsev S, Zhavoronkov A, Buzdin A. Combinatorial high-throughput experimental and bioinformatic approach identifies molecular pathways linked with the sensitivity to anticancer target drugs. Oncotarget 2016; 6:27227-38. [PMID: 26317900 PMCID: PMC4694985 DOI: 10.18632/oncotarget.4507] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 07/17/2015] [Indexed: 01/01/2023] Open
Abstract
Effective choice of anticancer drugs is important problem of modern medicine. We developed a method termed OncoFinder for the analysis of new type of biomarkers reflecting activation of intracellular signaling and metabolic molecular pathways. These biomarkers may be linked with the sensitivity to anticancer drugs. In this study, we compared the experimental data obtained in our laboratory and in the Genomics of Drug Sensitivity in Cancer (GDS) project for testing response to anticancer drugs and transcriptomes of various human cell lines. The microarray-based profiling of transcriptomes was performed for the cell lines before the addition of drugs to the medium, and experimental growth inhibition curves were built for each drug, featuring characteristic IC50 values. We assayed here four target drugs - Pazopanib, Sorafenib, Sunitinib and Temsirolimus, and 238 different cell lines, of which 11 were profiled in our laboratory and 227 - in GDS project. Using the OncoFinder-processed transcriptomic data on ∼600 molecular pathways, we identified pathways showing significant correlation between pathway activation strength (PAS) and IC50 values for these drugs. Correlations reflect relationships between response to drug and pathway activation features. We intersected the results and found molecular pathways significantly correlated in both our assay and GDS project. For most of these pathways, we generated molecular models of their interaction with known molecular target(s) of the respective drugs. For the first time, our study uncovered mechanisms underlying cancer cell response to drugs at the high-throughput molecular interactomic level.
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Affiliation(s)
- Larisa Venkova
- Drug Research and Design Department, Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.,Department of Personalized Medicine, First Oncology Research and Advisory Center, Moscow, Russia
| | - Alexander Aliper
- Drug Research and Design Department, Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.,Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Maria Suntsova
- Drug Research and Design Department, Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.,Department of Personalized Medicine, First Oncology Research and Advisory Center, Moscow, Russia.,Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Roman Kholodenko
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Denis Shepelin
- Drug Research and Design Department, Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.,Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Nicolas Borisov
- Drug Research and Design Department, Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.,Department of Personalized Medicine, First Oncology Research and Advisory Center, Moscow, Russia
| | - Galina Malakhova
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Raif Vasilov
- National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia
| | - Sergey Roumiantsev
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Pirogov Russian National Research Medical University, Department of Oncology, Hematology and Radiotherapy, Moscow, Russia.,Moscow Institute of Physics and Technology, Department of Translational and Regenerative Medicine, Dolgoprudny, Moscow Region, Russia
| | - Alex Zhavoronkov
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Insilico Medicine, Inc, ETC, Johns Hopkins University, Baltimore, MD, USA
| | - Anton Buzdin
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia
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45
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Artemov A, Aliper A, Korzinkin M, Lezhnina K, Jellen L, Zhukov N, Roumiantsev S, Gaifullin N, Zhavoronkov A, Borisov N, Buzdin A. A method for predicting target drug efficiency in cancer based on the analysis of signaling pathway activation. Oncotarget 2016; 6:29347-56. [PMID: 26320181 PMCID: PMC4745731 DOI: 10.18632/oncotarget.5119] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 07/24/2015] [Indexed: 02/07/2023] Open
Abstract
A new generation of anticancer therapeutics called target drugs has quickly developed in the 21st century. These drugs are tailored to inhibit cancer cell growth, proliferation, and viability by specific interactions with one or a few target proteins. However, despite formally known molecular targets for every "target" drug, patient response to treatment remains largely individual and unpredictable. Choosing the most effective personalized treatment remains a major challenge in oncology and is still largely trial and error. Here we present a novel approach for predicting target drug efficacy based on the gene expression signature of the individual tumor sample(s). The enclosed bioinformatic algorithm detects activation of intracellular regulatory pathways in the tumor in comparison to the corresponding normal tissues. According to the nature of the molecular targets of a drug, it predicts whether the drug can prevent cancer growth and survival in each individual case by blocking the abnormally activated tumor-promoting pathways or by reinforcing internal tumor suppressor cascades. To validate the method, we compared the distribution of predicted drug efficacy scores for five drugs (Sorafenib, Bevacizumab, Cetuximab, Sorafenib, Imatinib, Sunitinib) and seven cancer types (Clear Cell Renal Cell Carcinoma, Colon cancer, Lung adenocarcinoma, non-Hodgkin Lymphoma, Thyroid cancer and Sarcoma) with the available clinical trials data for the respective cancer types and drugs. The percent of responders to a drug treatment correlated significantly (Pearson's correlation 0.77 p = 0.023) with the percent of tumors showing high drug scores calculated with the current algorithm.
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Affiliation(s)
- Artem Artemov
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.,D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Alexander Aliper
- D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,First Oncology Research and Advisory Center, Moscow, Russia
| | | | | | - Leslie Jellen
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Nikolay Zhukov
- D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,First Oncology Research and Advisory Center, Moscow, Russia.,Pirogov Russian National Research Medical University, Department of Oncology, Hematology and Radiotherapy, Moscow, Russia
| | - Sergey Roumiantsev
- D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Pirogov Russian National Research Medical University, Department of Oncology, Hematology and Radiotherapy, Moscow, Russia
| | - Nurshat Gaifullin
- Moscow State University, Faculty of Fundamental Medicine, Moscow, Russia
| | - Alex Zhavoronkov
- Insilico Medicine, Inc., ETC, Johns Hopkins University, Baltimore, MD, USA
| | | | - Anton Buzdin
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.,D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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46
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Makarev E, Fortney K, Litovchenko M, Braunewell KH, Zhavoronkov A, Atala A. Quantifying signaling pathway activation to monitor the quality of induced pluripotent stem cells. Oncotarget 2016; 6:23204-12. [PMID: 26327604 PMCID: PMC4695112 DOI: 10.18632/oncotarget.4673] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/10/2015] [Indexed: 11/25/2022] Open
Abstract
Many attempts have been made to evaluate the safety and potency of human induced pluripotent stem cells (iPSCs) for clinical applications using transcriptome data, but results so far have been ambiguous or even contradictory. Here, we characterized stem cells at the pathway level, rather than at the gene level as has been the focus of previous work. We meta-analyzed publically-available gene expression data sets and evaluated signaling and metabolic pathway activation profiles for 20 human embryonic stem cell (ESC) lines, 12 human iPSC lines, five embryonic body lines, and six fibroblast cell lines. We demonstrated the close resemblance of iPSCs with ESCs at the pathway level, and provided examples of how pathway activity can be applied to identify iPSC line abnormalities or to predict in vitro differentiation potential. Our results indicate that pathway activation profiling is a promising strategy for evaluating the safety and potency of iPSC lines in translational medicine applications.
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Affiliation(s)
- Eugene Makarev
- Atlas Regeneration, Inc, Winston-Salem, NC, USA.,Insilico Medicine, Inc, ETC, Johns Hopkins University, Baltimore, MD, USA
| | - Kristen Fortney
- Atlas Regeneration, Inc, Winston-Salem, NC, USA.,Department of Developmental Biology, Stanford University Medical Center, Stanford, CA, USA
| | - Maria Litovchenko
- Department of Computational Genomics, Ludwig Maximilian University of Munich, Germany
| | - Karl H Braunewell
- Department of Neurophysiology, Medical Faculty, Ruhr University Bochum, Germany
| | - Alex Zhavoronkov
- Insilico Medicine, Inc, ETC, Johns Hopkins University, Baltimore, MD, USA.,The Biogerontology Research Foundation, London, UK
| | - Anthony Atala
- Atlas Regeneration, Inc, Winston-Salem, NC, USA.,Department of Urology, Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
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47
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Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease. Aging (Albany NY) 2016; 7:616-28. [PMID: 26342919 PMCID: PMC4600621 DOI: 10.18632/aging.100799] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the level of interest in aging research increases, there is a growing number of geroprotectors, or therapeutic interventions that aim to extend the healthy lifespan and repair or reduce aging-related damage in model organisms and, eventually, in humans. There is a clear need for a manually-curated database of geroprotectors to compile and index their effects on aging and age-related diseases and link these effects to relevant studies and multiple biochemical and drug databases. Here, we introduce the first such resource, Geroprotectors (http://geroprotectors.org). Geroprotectors is a public, rapidly explorable database that catalogs over 250 experiments involving over 200 known or candidate geroprotectors that extend lifespan in model organisms. Each compound has a comprehensive profile complete with biochemistry, mechanisms, and lifespan effects in various model organisms, along with information ranging from chemical structure, side effects, and toxicity to FDA drug status. These are presented in a visually intuitive, efficient framework fit for casual browsing or in-depth research alike. Data are linked to the source studies or databases, providing quick and convenient access to original data. The Geroprotectors database facilitates cross-study, cross-organism, and cross-discipline analysis and saves countless hours of inefficient literature and web searching. Geroprotectors is a one-stop, knowledge-sharing, time-saving resource for researchers seeking healthy aging solutions.
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Pitrez P, Rosa S, Praça C, Ferreira L. Vascular disease modeling using induced pluripotent stem cells: Focus in Hutchinson-Gilford Progeria Syndrome. Biochem Biophys Res Commun 2016; 473:710-8. [DOI: 10.1016/j.bbrc.2015.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 10/02/2015] [Indexed: 02/03/2023]
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49
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Zhavoronkov A, Moskalev A. Editorial: Should We Treat Aging as a Disease? Academic, Pharmaceutical, Healthcare Policy, and Pension Fund Perspectives. Front Genet 2016; 7:17. [PMID: 26909101 PMCID: PMC4754422 DOI: 10.3389/fgene.2016.00017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 01/29/2016] [Indexed: 12/31/2022] Open
Affiliation(s)
- Alex Zhavoronkov
- The Biogerontology Research FoundationOxford, UK; Insilico Medicine Inc.Baltimore, MD, USA; Laboratory of Regenerative Medicine, Federal Research and Clinical Centre of Pediatric Hematology, Oncology and ImmunologyMoscow, Russia
| | - Alexey Moskalev
- Insilico Medicine Inc.Baltimore, MD, USA; Radiation Ecology, Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of Ural Branch of RASSyktyvkar, Russia; Biological and Medical Physics Department, Moscow Institute of Physics and Technology (State University)Dolgoprudny, Russia
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50
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Mendelsohn AR, Larrick JW. Aging Stem Cells Lose the Capability to Distribute Damaged Proteins Asymmetrically. Rejuvenation Res 2015; 18:581-4. [PMID: 26650679 DOI: 10.1089/rej.2015.1800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Understanding the interplay between reversible epigenetic changes and potentially more difficult to reverse accumulation of damaged macromolecules is a central challenge in developing treatments for aging-associated dysfunction. One hypothesis is that epigenetic drift leads to subtle losses of homeostatic maintenance mechanisms, that in turn, lead to the accumulation of damaged macromolecules, which then further degrade homeostasis. A key mechanism of maintaining optimal cell function is asymmetrical division, whereby cellular damage is segregated away from cells that need to undergo further proliferation, such as stem cells. Such asymmetrical distribution of damaged macromolecules has been observed during cell division in many organisms, from yeast to human embryonic stem cells, and depends on diffusion barriers (DBs) in the membrane of the endoplasmic reticulum (ER). In a recent study, these results have been extended to neural stem cells (NSCs), in which the ability of the ER DB to promote asymmetrical distribution of damaged proteins deteriorates with age. NSC function declines with age as proliferative capacity is reduced. The loss of asymmetric protein distribution correlates with the loss of NSC proliferative capacity. Ectopic expression of progerin, an altered form of lamin A, is associated with the premature aging disorder, Hutchinson-Gilford progeria syndrome (HGPS). Progerin's expression also increases with normal aging due to mis-splicing, weakening the ER DB. Recent work suggests that many cell signaling pathway changes associated with HGPS are replicated during normal aging in cultured cells. Moreover, the detrimental changes associated with progerin expression in HGPS are partially reversible experimentally after treatment with statins, a farnesyltransferase inhibitor, a isoprenylcysteine carboxyl methyltransferase inhibitor, or sulforaphane. It will be of great interest if these compounds can also reverse the aging-associated permeability of the ER DB and restore stem cell function.
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