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Jo M, Kim S, Park J, Chang YT, Gwon Y. Reduced dynamicity and increased high-order protein assemblies in dense fibrillar component of the nucleolus under cellular senescence. Redox Biol 2024; 75:103279. [PMID: 39111063 PMCID: PMC11347067 DOI: 10.1016/j.redox.2024.103279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/27/2024] [Accepted: 07/20/2024] [Indexed: 08/23/2024] Open
Abstract
Cellular senescence, which is triggered by various stressors, manifests as irreversible cell cycle arrest, resulting in the disruption of multiple nuclear condensates. One of the affected structures is the nucleolus, whose tripartite layout, separated into distinct liquid phases, allows for the stepwise progression of ribosome biogenesis. The dynamic properties of dense fibrillar components, a sub-nucleolar phase, are crucial for mediating pre-rRNA processing. However, the mechanistic link between the material properties of dense fibrillar components and cellular senescence remains unclear. We established a significant association between cellular senescence and alterations in nucleolar materiality and characteristics, including the number, size, and sphericity of individual subphases of the nucleolus. Senescent cells exhibit reduced fibrillarin dynamics, aberrant accumulation of high-order protein assemblies, such as oligomers and fibrils, and increased dense fibrillar component density. Intriguingly, the addition of RNA-interacting entities mirrored the diminished diffusion of fibrillarin in the nucleolus during cellular senescence. Thus, our findings contribute to a broader understanding of the intricate changes in the materiality of the nucleolus associated with cellular senescence and shed light on nucleolar dynamics in the context of aging and cellular stress.
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Affiliation(s)
- Minjeong Jo
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Soomin Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Jeongeun Park
- Department of MetaBioHealth, Sungkyunkwan University Institute for Convergence, Suwon, 16419, Republic of Korea
| | - Young-Tae Chang
- Department of Chemistry, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Youngdae Gwon
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea; Department of MetaBioHealth, Sungkyunkwan University Institute for Convergence, Suwon, 16419, Republic of Korea; KIST-SKKU Brain Research Center, Sungkyunkwan University Institute for Convergence, Suwon, 16419, Republic of Korea.
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Yoshioka Y, Huang Y, Jin X, Ngo KX, Kumaki T, Jin M, Toyoda S, Takayama S, Inotsume M, Fujita K, Homma H, Ando T, Tanaka H, Okazawa H. PQBP3 prevents senescence by suppressing PSME3-mediated proteasomal Lamin B1 degradation. EMBO J 2024; 43:3968-3999. [PMID: 39103492 PMCID: PMC11405525 DOI: 10.1038/s44318-024-00192-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/12/2024] [Accepted: 07/22/2024] [Indexed: 08/07/2024] Open
Abstract
Senescence of nondividing neurons remains an immature concept, with especially the regulatory molecular mechanisms of senescence-like phenotypes and the role of proteins associated with neurodegenerative diseases in triggering neuronal senescence remaining poorly explored. In this study, we reveal that the nucleolar polyglutamine binding protein 3 (PQBP3; also termed NOL7), which has been linked to polyQ neurodegenerative diseases, regulates senescence as a gatekeeper of cytoplasmic DNA leakage. PQBP3 directly binds PSME3 (proteasome activator complex subunit 3), a subunit of the 11S proteasome regulator complex, decreasing PSME3 interaction with Lamin B1 and thereby preventing Lamin B1 degradation and senescence. Depletion of endogenous PQBP3 causes nuclear membrane instability and release of genomic DNA from the nucleus to the cytosol. Among multiple tested polyQ proteins, ataxin-1 (ATXN1) partially sequesters PQBP3 to inclusion bodies, reducing nucleolar PQBP3 levels. Consistently, knock-in mice expressing mutant Atxn1 exhibit decreased nuclear PQBP3 and a senescence phenotype in Purkinje cells of the cerebellum. Collectively, these results suggest homologous roles of the nucleolar protein PQBP3 in cellular senescence and neurodegeneration.
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Affiliation(s)
- Yuki Yoshioka
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Yong Huang
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Xiaocen Jin
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kien Xuan Ngo
- Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Tomohiro Kumaki
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Meihua Jin
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Saori Toyoda
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Sumire Takayama
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Maiko Inotsume
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kyota Fujita
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Research Center for Child Mental Development, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Hidenori Homma
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Toshio Ando
- Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Hikari Tanaka
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Hitoshi Okazawa
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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Qanmber G, You Q, Yang Z, Fan L, Zhang Z, Chai M, Gao B, Li F, Yang Z. Transcriptional and translational landscape fine-tune genome annotation and explores translation control in cotton. J Adv Res 2024; 58:13-30. [PMID: 37207930 PMCID: PMC10982868 DOI: 10.1016/j.jare.2023.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/21/2023] Open
Abstract
INTRODUCTION The unavailability of intergenic region annotation in whole genome sequencing and pan-genomics hinders efforts to enhance crop improvement. OBJECTIVES Despite advances in research, the impact of post-transcriptional regulation on fiber development and translatome profiling at different stages of fiber growth in cotton (G. hirsutum) remains unexplored. METHODS We utilized a combination of reference-guided de novo transcriptome assembly and ribosome profiling techniques to uncover the hidden mechanisms of translational control in eight distinct tissues of upland cotton. RESULTS Our study identified P-site distribution at three-nucleotide periodicity and dominant ribosome footprint at 27 nucleotides. Specifically, we have detected 1,589 small open reading frames (sORFs), including 1,376 upstream ORFs (uORFs) and 213 downstream ORFs (dORFs), as well as 552 long non-coding RNAs (lncRNAs) with potential coding functions, which fine-tune the annotation of the cotton genome. Further, we have identified novel genes and lncRNAs with strong translation efficiency (TE), while sORFs were found to affect mRNA transcription levels during fiber elongation. The reliability of these findings was confirmed by the high consistency in correlation and synergetic fold change between RNA-sequencing (RNA-seq) and Ribosome-sequencing (Ribo-seq) analyses. Additionally, integrated omics analysis of the normal fiber ZM24 and short fiber pag1 cotton mutant revealed several differentially expressed genes (DEGs), and fiber-specific expressed (high/low) genes associated with sORFs (uORFs and dORFs). These findings were further supported by the overexpression and knockdown of GhKCS6, a gene associated with sORFs in cotton, and demonstrated the potential regulation of the mechanism governing fiber elongation on both the transcriptional and post-transcriptional levels. CONCLUSION Reference-guided transcriptome assembly and the identification of novel transcripts fine-tune the annotation of the cotton genome and predicted the landscape of fiber development. Our approach provided a high-throughput method, based on multi-omics, for discovering unannotated ORFs, hidden translational control, and complex regulatory mechanisms in crop plants.
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Affiliation(s)
- Ghulam Qanmber
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Qi You
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Zhaoen Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Liqiang Fan
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Zhibin Zhang
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Mao Chai
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Baibai Gao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Zuoren Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
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Kołacz K, Robaszkiewicz A. PARP1 at the crossroad of cellular senescence and nucleolar processes. Ageing Res Rev 2024; 94:102206. [PMID: 38278370 DOI: 10.1016/j.arr.2024.102206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Senescent cells that occur in response to telomere shortening, oncogenes, extracellular and intracellular stress factors are characterized by permanent cell cycle arrest, the morphological and structural changes of the cell that include the senescence-associated secretory phenotype (SASP) and nucleoli rearrangement. The associated DNA lesions induce DNA damage response (DDR), which activates the DNA repair protein - poly-ADP-ribose polymerase 1 (PARP1). This protein consumes NAD+ to synthesize ADP-ribose polymer (PAR) on its own protein chain and on other interacting proteins. The involvement of PARP1 in nucleoli processes, such as rRNA transcription and ribosome biogenesis, the maintenance of heterochromatin and nucleoli structure, as well as controlling the crucial DDR protein release from the nucleoli to nucleus, links PARP1 with cellular senescence and nucleoli functioning. In this review we describe and discuss the impact of PARP1-mediated ADP-ribosylation on early cell commitment to senescence with the possible role of senescence-induced PARP1 transcriptional repression and protein degradation on nucleoli structure and function. The cause-effect interplay between PARP1 activation/decline and nucleoli functioning during senescence needs to be studied in detail.
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Affiliation(s)
- Kinga Kołacz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, University of Lodz, Banacha 12 /16, 90-237 Lodz, Poland.
| | - Agnieszka Robaszkiewicz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research (IFBR), 600 5th Street South, St. Petersburgh, FL 33701, USA.
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Lu X, Yuan F, Qiao L, Liu Y, Gu Q, Qi X, Li J, Li D, Liu M. AS1041, a novel derivative of marine natural compound Aspergiolide A, induces senescence of leukemia cells via oxidative stress-induced DNA damage and BCR-ABL degradation. Biomed Pharmacother 2024; 171:116099. [PMID: 38171244 DOI: 10.1016/j.biopha.2023.116099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/18/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
Chronic myelogenous leukemia (CML) is characterized by the constitutive activation of BCR-ABL tyrosine kinase. Imatinib was approved for CML therapy, however, BCR-ABL-dependent drug resistance, especially BCR-ABL-T315I mutation, restricts its clinical application. In this study, we reported anthraquinone lactone AS1041, a synthesized derivative of marine natural compound Aspergiolide A, showed anti-leukemia effect in vitro and in vivo by promoting cell senescence. Mechanistic study revealed the pro-senescence effect of AS1041 was dependent on oxidative stress-induced DNA damage, and the resultant activation of P53/P21 and P16INK4a/Rb. Also, AS1041 promoted ubiquitin proteasome system (UPS)-mediated BCR-ABL degradation, which also contributed to AS1041-induced senescence. In vivo, AS1041-induced senescence promoted tumor growth inhibition. In summary, the in vitro and in vivo antitumor effect of AS1041 suggests it can serve as a pro-senescence agent for alternative antileukemia therapy and imatinib-resistant cancer therapy by enhancing cellular oxidative stress and BCR-ABL degradation.
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Affiliation(s)
- Xuxiu Lu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Fengli Yuan
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Liang Qiao
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Gannan Normal University, Ganzhou 341000, China
| | - Yankai Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qianqun Gu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xin Qi
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jing Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Sanya Oceanographic Institute, Ocean University of China, Sanya 572024, China.
| | - Ming Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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Kang D, Hwang HJ, Baek Y, Sung JY, Kim K, Park HJ, Ko YG, Kim YN, Lee JS. TRIM22 induces cellular senescence by targeting PHLPP2 in hepatocellular carcinoma. Cell Death Dis 2024; 15:26. [PMID: 38199981 PMCID: PMC10781680 DOI: 10.1038/s41419-024-06427-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024]
Abstract
The ubiquitin-proteasome system is a vital protein degradation system that is involved in various cellular processes, such as cell cycle progression, apoptosis, and differentiation. Dysregulation of this system has been implicated in numerous diseases, including cancer, vascular disease, and neurodegenerative disorders. Induction of cellular senescence in hepatocellular carcinoma (HCC) is a potential anticancer strategy, but the precise role of the ubiquitin-proteasome system in cellular senescence remains unclear. In this study, we show that the E3 ubiquitin ligase, TRIM22, plays a critical role in the cellular senescence of HCC cells. TRIM22 expression is transcriptionally upregulated by p53 in HCC cells experiencing ionizing radiation (IR)-induced senescence. Overexpression of TRIM22 triggers cellular senescence by targeting the AKT phosphatase, PHLPP2. Mechanistically, the SPRY domain of TRIM22 directly associates with the C-terminal domain of PHLPP2, which contains phosphorylation sites that are subject to IKKβ-mediated phosphorylation. The TRIM22-mediated PHLPP2 degradation leads to activation of AKT-p53-p21 signaling, ultimately resulting in cellular senescence. In both human HCC databases and patient specimens, the levels of TRIM22 and PHLPP2 show inverse correlations at the mRNA and protein levels. Collectively, our findings reveal that TRIM22 regulates cancer cell senescence by modulating the proteasomal degradation of PHLPP2 in HCC cells, suggesting that TRIM22 could potentially serve as a therapeutic target for treating cancer.
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Affiliation(s)
- Donghee Kang
- Research Center for Controlling Intercellular Communication, College of Medicine, Inha University, Incheon, 22212, Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, 22212, Korea
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon, 22212, Korea
| | - Hyun Jung Hwang
- Research Center for Controlling Intercellular Communication, College of Medicine, Inha University, Incheon, 22212, Korea
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon, 22212, Korea
| | - Yurim Baek
- Research Center for Controlling Intercellular Communication, College of Medicine, Inha University, Incheon, 22212, Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, 22212, Korea
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon, 22212, Korea
| | - Jee Young Sung
- Metastasis Branch, Division of Cancer Biology, National Cancer Center, Goyang, 10408, Korea
| | - KyeongJin Kim
- Research Center for Controlling Intercellular Communication, College of Medicine, Inha University, Incheon, 22212, Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, 22212, Korea
| | - Heon Joo Park
- Research Center for Controlling Intercellular Communication, College of Medicine, Inha University, Incheon, 22212, Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, 22212, Korea
- Department of Microbiology, College of Medicine, Inha University, Incheon, 22212, Korea
| | - Young-Gyu Ko
- Division of Life Sciences, Korea University, Seoul, 02841, Korea
| | - Yong-Nyun Kim
- Metastasis Branch, Division of Cancer Biology, National Cancer Center, Goyang, 10408, Korea
| | - Jae-Seon Lee
- Research Center for Controlling Intercellular Communication, College of Medicine, Inha University, Incheon, 22212, Korea.
- Program in Biomedical Science & Engineering, Inha University, Incheon, 22212, Korea.
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon, 22212, Korea.
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Deschênes-Simard X, Malleshaiah M, Ferbeyre G. Extracellular Signal-Regulated Kinases: One Pathway, Multiple Fates. Cancers (Basel) 2023; 16:95. [PMID: 38201521 PMCID: PMC10778234 DOI: 10.3390/cancers16010095] [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: 11/23/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
This comprehensive review delves into the multifaceted aspects of ERK signaling and the intricate mechanisms underlying distinct cellular fates. ERK1 and ERK2 (ERK) govern proliferation, transformation, epithelial-mesenchymal transition, differentiation, senescence, or cell death, contingent upon activation strength, duration, and context. The biochemical mechanisms underlying these outcomes are inadequately understood, shaped by signaling feedback and the spatial localization of ERK activation. Generally, ERK activation aligns with the Goldilocks principle in cell fate determination. Inadequate or excessive ERK activity hinders cell proliferation, while balanced activation promotes both cell proliferation and survival. Unraveling the intricacies of how the degree of ERK activation dictates cell fate requires deciphering mechanisms encompassing protein stability, transcription factors downstream of ERK, and the chromatin landscape.
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Affiliation(s)
- Xavier Deschênes-Simard
- Montreal University Hospital Center (CHUM), Université de Montréal, Montréal, QC H3T 1J4, Canada;
| | - Mohan Malleshaiah
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada;
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Gerardo Ferbeyre
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Montreal Cancer Institute, CR-CHUM, Université de Montréal, Montréal, QC H3T 1J4, Canada
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Oguma Y, Alessio N, Aprile D, Dezawa M, Peluso G, Di Bernardo G, Galderisi U. Meta-analysis of senescent cell secretomes to identify common and specific features of the different senescent phenotypes: a tool for developing new senotherapeutics. Cell Commun Signal 2023; 21:262. [PMID: 37770897 PMCID: PMC10537976 DOI: 10.1186/s12964-023-01280-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/15/2023] [Indexed: 09/30/2023] Open
Abstract
DNA damage resulting from genotoxic injury can initiate cellular senescence, a state characterized by alterations in cellular metabolism, lysosomal activity, and the secretion of factors collectively known as the senescence-associated secretory phenotype (SASP). Senescence can have beneficial effects on our bodies, such as anti-cancer properties, wound healing, and tissue development, which are attributed to the SASP produced by senescent cells in their intermediate stages. However, senescence can also promote cancer and aging, primarily due to the pro-inflammatory activity of SASP.Studying senescence is complex due to various factors involved. Genotoxic stimuli cause random damage to cellular macromolecules, leading to variations in the senescent phenotype from cell to cell, despite a shared program. Furthermore, senescence is a dynamic process that cannot be analyzed as a static endpoint, adding further complexity.Investigating SASP is particularly intriguing as it reveals how a senescence process triggered in a few cells can spread to many others, resulting in either positive or negative consequences for health. In our study, we conducted a meta-analysis of the protein content of SASP obtained from different research groups, including our own. We categorized the collected omic data based on: i) cell type, ii) harmful agent, and iii) senescence stage (early and late senescence).By employing Gene Ontology and Network analysis on the omic data, we identified common and specific features of different senescent phenotypes. This research has the potential to pave the way for the development of new senotherapeutic drugs aimed at combating the negative consequences associated with the senescence process. Video Abstract.
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Affiliation(s)
- Yo Oguma
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Nicola Alessio
- Department of Experimental Medicine, Luigi Vanvitelli Campania University, Naples, Italy
| | - Domenico Aprile
- Department of Experimental Medicine, Luigi Vanvitelli Campania University, Naples, Italy
| | - Mari Dezawa
- Department of Stem Cell Biology and Histology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Giovanni Di Bernardo
- Department of Experimental Medicine, Luigi Vanvitelli Campania University, Naples, Italy
| | - Umberto Galderisi
- Department of Experimental Medicine, Luigi Vanvitelli Campania University, Naples, Italy.
- Genome and Stem Cell Center (GENKÖK), Erciyes University, Kayseri, Turkey.
- Center for Biotechnology, Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA, USA.
- Dip. Medicina Sperimentale, Via Luigi De Crecchio 7, 80138, Naples, Italy.
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Feng D, Zhu W, Shi X, Wei W, Han P, Wei Q, Yang L. Leucine zipper protein 2 serves as a prognostic biomarker for prostate cancer correlating with immune infiltration and epigenetic regulation. Heliyon 2022; 8:e10750. [PMID: 36217461 PMCID: PMC9547219 DOI: 10.1016/j.heliyon.2022.e10750] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/19/2022] [Accepted: 09/20/2022] [Indexed: 11/04/2022] Open
Abstract
Background We sought to determine whether leucine zipper protein 2 (LUZP2) could benefit men with prostate cancer (PCa) undergoing radical radiotherapy (RT) or prostatectomy (RP). Methods Analysis was done on differentiating expression, clinical prognosis, co-expressed genes, immune infiltration, and epigenetic changes. All of our analyses were done using the R software (version 3.6.3) and the appropriate packages. Results In terms of PCa, tumor samples expressed LUZP2 more than normal samples did. In the TCGA database and GSE116918, we found that LUZP2 was the only independent risk factor for PCa. The shared enriched pathways for patients undergoing RP or RT were cell-cell adhesion, regulation of filopodium assembly, and extracellular matrix containing collagen. With the exception of TNFRSF14, we discovered that LUZP2 was negatively correlated with 21 immune checkpoints in PCa patients receiving RT. We found a significant inverse relationship between LUZP2 expression and the tumor immune environment, which included B cells, CD4+ T cells, neutrophils, macrophages, dendritic cells, stromal score, immune score, and estimate score, in patients receiving RP or RT. Additionally, tumor purity was positively correlated with LUZP2. We found that the drug bortezomib may be susceptible to the LUZP2. DNA methylation was significantly associated with the mRNA expression of LUZP2 in PCa patients from the TCGA database, and LUZP2 methylation was positively correlated with immune cells. The proliferative activity of various PCa cells, which correlated to different stages of this disease, was also found to be significantly reduced by LUZP2 reduction, according to the results of our experimental work. Conclusions We proposed a relatively comprehensive understanding of the roles of LUZP2 on PCa from the fresh perspective of senescence.
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Dungan CM, Figueiredo VC, Wen Y, VonLehmden GL, Zdunek CJ, Thomas NT, Mobley CB, Murach KA, Brightwell CR, Long DE, Fry CS, Kern PA, McCarthy JJ, Peterson CA. Senolytic treatment rescues blunted muscle hypertrophy in old mice. GeroScience 2022; 44:1925-1940. [PMID: 35325353 PMCID: PMC9616988 DOI: 10.1007/s11357-022-00542-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/06/2022] [Indexed: 01/07/2023] Open
Abstract
With aging, skeletal muscle plasticity is attenuated in response to exercise. Here, we report that senescent cells, identified using senescence-associated β-galactosidase (SA β-Gal) activity and p21 immunohistochemistry, are very infrequent in resting muscle, but emerge approximately 2 weeks after a bout of resistance exercise in humans. We hypothesized that these cells contribute to blunted hypertrophic potential in old age. Using synergist ablation-induced mechanical overload (MOV) of the plantaris muscle to model resistance training in adult (5-6-month) and old (23-24-month) male C57BL/6 J mice, we found increased senescent cells in both age groups during hypertrophy. Consistent with the human data, there were negligible senescent cells in plantaris muscle from adult and old sham controls, but old mice had significantly more senescent cells 7 and 14 days following MOV relative to young. Old mice had blunted whole-muscle hypertrophy when compared to adult mice, along with smaller muscle fibers, specifically glycolytic type 2x + 2b fibers. To ablate senescent cells using a hit-and-run approach, old mice were treated with vehicle or a senolytic cocktail consisting of 5 mg/kg dasatinib and 50 mg/kg quercetin (D + Q) on days 7 and 10 during 14 days of MOV; control mice underwent sham surgery with or without senolytic treatment. Old mice given D + Q had larger muscles and muscle fibers after 14 days of MOV, fewer senescent cells when compared to vehicle-treated old mice, and changes in the expression of genes (i.e., Igf1, Ddit4, Mmp14) that are associated with hypertrophic growth. Our data collectively show that senescent cells emerge in human and mouse skeletal muscle following a hypertrophic stimulus and that D + Q improves muscle growth in old mice.
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Affiliation(s)
- Cory M Dungan
- Center for Muscle Biology, University of Kentucky, Lexington, KY, USA.
- Department of Physical Therapy, University of Kentucky, Lexington, KY, USA.
- College of Health Sciences, University of Kentucky, 900 S. Limestone, CTW 445, Lexington, KY, 40536, USA.
| | | | - Yuan Wen
- Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Physical Therapy, University of Kentucky, Lexington, KY, USA
| | | | | | - Nicholas T Thomas
- Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington, KY, USA
| | - C Brooks Mobley
- Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- School of Kinesiology, Auburn University, Auburn, AL, USA
| | - Kevin A Murach
- Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, USA
| | - Camille R Brightwell
- Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington, KY, USA
| | - Douglas E Long
- Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Physical Therapy, University of Kentucky, Lexington, KY, USA
| | - Christopher S Fry
- Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington, KY, USA
| | - Philip A Kern
- Department of Internal Medicine, Division of Endocrinology, University of Kentucky, Lexington, KY, USA
| | - John J McCarthy
- Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Charlotte A Peterson
- Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Physical Therapy, University of Kentucky, Lexington, KY, USA
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11
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The Downregulation of Both Giant HERCs, HERC1 and HERC2, Is an Unambiguous Feature of Chronic Myeloid Leukemia, and HERC1 Levels Are Associated with Leukemic Cell Differentiation. J Clin Med 2022; 11:jcm11020324. [PMID: 35054018 PMCID: PMC8778248 DOI: 10.3390/jcm11020324] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 01/27/2023] Open
Abstract
Large HERC E3 ubiquitin ligase family members, HERC1 and HERC2, are staggeringly complex proteins that can intervene in a wide range of biological processes, such as cell proliferation, DNA repair, neurodevelopment, and inflammation. Therefore, mutations or dysregulation of large HERCs is associated with neurological disorders, DNA repair defects, and cancer. Though their role in solid tumors started to be investigated some years ago, our knowledge about HERCs in non-solid neoplasm is greatly lagging behind. Chronic Myeloid Leukemia (CML) is a model onco-hematological disorder because of its unique and unambiguous relation between genotype and phenotype due to a single genetic alteration. In the present study, we ascertained that the presence of the BCR-ABL fusion gene was inversely associated with the expression of the HERC1 and HERC2 genes. Upon the achievement of remission, both HERC1 and HERC2 mRNAs raised again to levels comparable to those of the healthy donors. Additionally, our survey unveiled that their gene expression is sensitive to different Tyrosine Kinases Inhibitors (TKIs) in a time-dependent fashion. Interestingly, for the first time, we also observed a differential HERC1 expression when the leukemic cell lines were induced to differentiate towards different lineages revealing that HERC1 protein expression is associated with the differentiation process in a lineage-specific manner. Taken together, our findings suggest that HERC1 might act as a novel potential player in blood cell differentiation. Overall, we believe that our results are beneficial to initiate exploring the role/s of large HERCs in non-solid neoplasms.
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12
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Valerio HP, Ravagnani FG, Ronsein GE, Di Mascio P. A single dose of Ultraviolet-A induces proteome remodeling and senescence in primary human keratinocytes. Sci Rep 2021; 11:23355. [PMID: 34857819 PMCID: PMC8639817 DOI: 10.1038/s41598-021-02658-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/19/2021] [Indexed: 01/10/2023] Open
Abstract
Epidermal photoaging contributes to skin fragility over time and it is a risk factor for skin cancer. Photoaging has been associated for a long time with exposure to Ultraviolet-A (UVA) light, the predominant component of the solar ultraviolet radiation. While the cellular mechanisms underlying UVA-induced photoaging in the dermis have been well characterized, UVA's action on the epidermis remains elusive. Here, proteomic analysis was conducted to derive the cellular responses induced by an environmentally relevant dose of UVA in primary human keratinocytes. We also investigated the effects of UVA on non-transformed immortalized keratinocytes (HaCaT cells), bearing potentially oncogenic mutations. We showed that UVA induces proteome remodeling and senescence in primary keratinocytes, eliciting potent antioxidant and pro-inflammatory responses. Additionally, we showed that UVA modulates the secretory phenotype of these cells to the extent of inducing paracrine oxidative stress and immune system activation in pre-malignant keratinocytes. These observations offer insights into the cellular mechanisms by which UVA drives photoaging in the skin.
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Affiliation(s)
- Hellen Paula Valerio
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil.
| | - Felipe Gustavo Ravagnani
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Graziella Eliza Ronsein
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil.
| | - Paolo Di Mascio
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil.
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13
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Igelmann S, Lessard F, Uchenunu O, Bouchard J, Fernandez-Ruiz A, Rowell MC, Lopes-Paciencia S, Papadopoli D, Fouillen A, Ponce KJ, Huot G, Mignacca L, Benfdil M, Kalegari P, Wahba HM, Pencik J, Vuong N, Quenneville J, Guillon J, Bourdeau V, Hulea L, Gagnon E, Kenner L, Moriggl R, Nanci A, Pollak MN, Omichinski JG, Topisirovic I, Ferbeyre G. A hydride transfer complex reprograms NAD metabolism and bypasses senescence. Mol Cell 2021; 81:3848-3865.e19. [PMID: 34547241 DOI: 10.1016/j.molcel.2021.08.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 06/25/2021] [Accepted: 08/20/2021] [Indexed: 01/23/2023]
Abstract
Metabolic rewiring and redox balance play pivotal roles in cancer. Cellular senescence is a barrier for tumorigenesis circumvented in cancer cells by poorly understood mechanisms. We report a multi-enzymatic complex that reprograms NAD metabolism by transferring reducing equivalents from NADH to NADP+. This hydride transfer complex (HTC) is assembled by malate dehydrogenase 1, malic enzyme 1, and cytosolic pyruvate carboxylase. HTC is found in phase-separated bodies in the cytosol of cancer or hypoxic cells and can be assembled in vitro with recombinant proteins. HTC is repressed in senescent cells but induced by p53 inactivation. HTC enzymes are highly expressed in mouse and human prostate cancer models, and their inactivation triggers senescence. Exogenous expression of HTC is sufficient to bypass senescence, rescue cells from complex I inhibitors, and cooperate with oncogenic RAS to transform primary cells. Altogether, we provide evidence for a new multi-enzymatic complex that reprograms metabolism and overcomes cellular senescence.
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Affiliation(s)
- Sebastian Igelmann
- CRCHUM, 900 Saint-Denis St, Montréal, QC H2X 0A9, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Frédéric Lessard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Oro Uchenunu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T1E2, Canada; Department of Experimental Medicine, McGill University, Montreal, QC H4A3T2, Canada
| | - Jacob Bouchard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | | | | | | | - David Papadopoli
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T1E2, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A3T2, Canada
| | - Aurélien Fouillen
- Faculté de médecine dentaire, Université de Montréal, Montréal, QC H3C 3J7, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Katia Julissa Ponce
- Faculté de médecine dentaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Geneviève Huot
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Lian Mignacca
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Mehdi Benfdil
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Paloma Kalegari
- CRCHUM, 900 Saint-Denis St, Montréal, QC H2X 0A9, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Haytham M Wahba
- Department of Biochemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62521, Egypt; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Jan Pencik
- Department of Pathology, Medical University of Vienna, Vienna, Austria; Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Center for Biomarker Research in Medicine, 8010 Graz, Austria
| | - Nhung Vuong
- CRCHUM, 900 Saint-Denis St, Montréal, QC H2X 0A9, Canada
| | - Jordan Quenneville
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Jordan Guillon
- CRCHUM, 900 Saint-Denis St, Montréal, QC H2X 0A9, Canada
| | - Véronique Bourdeau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Laura Hulea
- Maisonneuve-Rosemont Hospital Research Centre, Montréal, QC H1T 2M4, Canada, Département de Médecine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Etienne Gagnon
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Lukas Kenner
- Department of Pathology, Medical University of Vienna, Vienna, Austria; Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria; Christian Doppler Laboratory for Applied Metabolomics, Vienna, Austria; CBmed GmbH - Center for Biomarker Research in Medicine, Graz, Styria, Austria
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Antonio Nanci
- Faculté de médecine dentaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Michael N Pollak
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T1E2, Canada
| | - James G Omichinski
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Ivan Topisirovic
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T1E2, Canada; Department of Experimental Medicine, McGill University, Montreal, QC H4A3T2, Canada; Department of Biochemistry, McGill University, Montreal, QC H4A 3T2, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A3T2, Canada.
| | - Gerardo Ferbeyre
- CRCHUM, 900 Saint-Denis St, Montréal, QC H2X 0A9, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada.
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14
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Zhu W, Xu J, Chen S, Chen J, Liang Y, Zhang C, Li Q, Lai J, Li L. Large-scale translatome profiling annotates the functional genome and reveals the key role of genic 3' untranslated regions in translatomic variation in plants. PLANT COMMUNICATIONS 2021; 2:100181. [PMID: 34327320 PMCID: PMC8299070 DOI: 10.1016/j.xplc.2021.100181] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 05/12/2023]
Abstract
The translatome, a profile of the translational status of genetic information within cells, provides a new perspective on gene expression. Although many plant genomes have been sequenced, comprehensive translatomic annotations are not available for plants due to a lack of efficient translatome profiling techniques. Here, we developed a new technique termed 3' ribosome-profiling sequencing (3'Ribo-seq) for reliable, robust translatomic profiling. 3'Ribo-seq combines polysome profiling and 3' selection with a barcoding and pooling strategy. Systematic translatome profiling of different tissues of Arabidopsis, rice, and maize using conventional ribosome profiling (Ribo-seq) and 3'Ribo-seq revealed many novel translational genomic loci, thereby complementing functional genome annotation in plants. Using the low-cost, efficient 3'Ribo-seq technique and genome-wide association mapping of translatome expression (eGWAS), we performed a population-level dissection of the translatomes of 159 diverse maize inbred lines and identified 1,777 translational expression quantitative trait loci (eQTLs). Notably, local eQTLs are significantly enriched in the 3' untranslated regions of genes. Detailed eQTL analysis suggested that sequence variation around the polyadenylation (polyA) signal motif plays a key role in translatomic variation. Our study provides a comprehensive translatome annotation of plant functional genomes and introduces 3'Ribo-seq, which paves the way for deep translatomic analysis at the population level.
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Affiliation(s)
- Wanchao Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Sijia Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yan Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author
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15
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LRRK2 Kinase Inhibitor Rejuvenates Oxidative Stress-Induced Cellular Senescence in Neuronal Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:9969842. [PMID: 34306319 PMCID: PMC8282384 DOI: 10.1155/2021/9969842] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/11/2021] [Indexed: 12/12/2022]
Abstract
Background Leucine-rich repeat kinase 2 (LRRK2) plays a critical role in the pathogenesis of Parkinson's disease (PD). Aging is the most critical risk factor for the progression of PD. The correlation between aging and cellular senescence has been established. Cellular senescence is correlated with the dysregulation of the proteolytic pathway and mitochondrial dysfunction, which are also associated with the aggregation of α-synuclein (α-syn). Methods Human dopaminergic neuron-like cells (differentiated SH-SY5Y cells) were treated with rotenone in the presence or absence of the LRRK2 kinase inhibitor GSK2578215A (GSK-KI) for 48 h. The markers of cellular senescence, including p53, p21Waf1/Cip1 (p21), β-galactosidase (β-gal), Rb phosphorylation, senescence-associated (SA) β-gal activity, and lysosomal activity, were examined. The dSH cells and rat primary cortical neurons were treated with α-syn fibrils 30 min before treatment with rotenone in the presence or absence of GSK-KI for 48 h. Mice were intraperitoneally injected with rotenone and MLi-2 (LRRK2 kinase inhibitor) once every two days for two weeks. Results Rotenone upregulated LRRK2 phosphorylation and β-gal levels through the activation of the p53-p21 signaling axis and downregulated Rb phosphorylation. Additionally, rotenone upregulated SA β-gal activity, reactive oxygen species levels, and LRRK2 phosphorylation and inhibited lysosome activity. Rotenone-induced LRRK2 upregulation impaired the clearance of α-syn fibrils. Treatment with LRRK2 inhibitor mitigated rotenone-induced cellular senescence and α-syn accumulation. Conclusions Rotenone-induced upregulation of LRRK2 kinase activity promoted cellular senescence, which enhanced α-syn accumulation. However, the administration of an LRRK2 kinase inhibitor rejuvenated rotenone-induced cellular senescence.
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16
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Dabrowska M, Uram L, Dabrowski M, Sikora E. Antigen presentation capability and AP-1 activation accompany methotrexate-induced colon cancer cell senescence in the context of aberrant β-catenin signaling. Mech Ageing Dev 2021; 197:111517. [PMID: 34139213 DOI: 10.1016/j.mad.2021.111517] [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: 12/05/2020] [Revised: 05/19/2021] [Accepted: 06/09/2021] [Indexed: 01/10/2023]
Abstract
Reversible cellular senescence was demonstrated previously to constitute colon cancer cell response to methotrexate. The current study presents a comparison of two senescent states of colon cancer cells, arrested and reversing, resulting from respectively, 120 h exposure to the drug, and 48 h exposure followed by 96 h regrowth in drug-free media. The upregulation of immunoproteasome subunit-coding genes and the increase in human leukocyte antigen HLA-A/B/C membrane level indicated MHC-I-restricted antigen presentation as common to both senescent states. Nuclear factor NF-κB p65 level decreased and activating protein AP-1: c-Jun, Fra2 and JunB nuclear levels increased in both senescent cell populations. Notably, the increase in AP-1- dependent transcription occurred after 48 h exposure to methotrexate. β-catenin nuclear level increased after 48 h exposure to the drug and remained as such only in senescence-arrested cells. β-catenin level was found uncoupled from the protein phosphorylation status indicating the deregulation of β-catenin signaling in colon cancer cells employed in the study. These findings carry implications for both, a general mechanism of senescence establishment and putative advantages for colon cancer treatment.
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Affiliation(s)
- Magdalena Dabrowska
- Laboratory of Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093, Warszawa, Poland.
| | - Lukasz Uram
- Faculty of Chemistry, Rzeszow University of Technology, 6 Powstancow Warszawy Ave., 35-959, Rzeszow, Poland.
| | - Michal Dabrowski
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093, Warszawa, Poland.
| | - Ewa Sikora
- Laboratory of Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093, Warszawa, Poland.
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17
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Moreira R, Romero A, Rey-Campos M, Pereiro P, Rosani U, Novoa B, Figueras A. Stimulation of Mytilus galloprovincialis Hemocytes With Different Immune Challenges Induces Differential Transcriptomic, miRNomic, and Functional Responses. Front Immunol 2020; 11:606102. [PMID: 33391272 PMCID: PMC7773633 DOI: 10.3389/fimmu.2020.606102] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022] Open
Abstract
Mediterranean mussels (Mytilus galloprovincialis) are marine bivalve molluscs with high resilience to biotic and abiotic stress. This resilience is one of the reasons why this species is such an interesting model for studying processes such as the immune response. In this work, we stimulated mussel hemocytes with poly I:C, β-glucans, and LPS and then sequenced hemocyte mRNAs (transcriptome) and microRNAs (miRNome) to investigate the molecular basis of the innate immune responses against these pathogen-associated molecular patterns (PAMPs). An immune transcriptome comprising 219,765 transcripts and an overview of the mussel miRNome based on 5,175,567 non-redundant miRNA reads were obtained. The expression analyses showed opposite results in the transcriptome and miRNome; LPS was the stimulus that triggered the highest transcriptomic response, with 648 differentially expressed genes (DEGs), while poly I:C was the stimulus that triggered the highest miRNA response, with 240 DE miRNAs. Our results reveal a powerful immune response to LPS as well as activation of certain immunometabolism- and ageing/senescence-related processes in response to all the immune challenges. Poly I:C exhibited powerful stimulating properties in mussels, since it triggered the highest miRNomic response and modulated important genes related to energy demand; these effects could be related to the stronger activation of these hemocytes (increased phagocytosis, increased NO synthesis, and increased velocity and accumulated distance). The transcriptome results suggest that after LPS stimulation, pathogen recognition, homeostasis and cell survival processes were activated, and phagocytosis was induced by LPS. β-glucans elicited a response related to cholesterol metabolism, which is important during the immune response, and it was the only stimulus that induced the synthesis of ROS. These results suggest a specific and distinct response of hemocytes to each stimulus from a transcriptomic, miRNomic, and functional point of view.
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Affiliation(s)
- Rebeca Moreira
- Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Vigo, Spain
| | - Alejandro Romero
- Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Vigo, Spain
| | - Magalí Rey-Campos
- Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Vigo, Spain
| | - Patricia Pereiro
- Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Vigo, Spain
| | - Umberto Rosani
- Department of Biology, University of Padova, Padova, Italy.,Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute (AWI), List auf Sylt, Germany
| | - Beatriz Novoa
- Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Vigo, Spain
| | - Antonio Figueras
- Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Vigo, Spain
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18
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Tundo GR, Sbardella D, Santoro AM, Coletta A, Oddone F, Grasso G, Milardi D, Lacal PM, Marini S, Purrello R, Graziani G, Coletta M. The proteasome as a druggable target with multiple therapeutic potentialities: Cutting and non-cutting edges. Pharmacol Ther 2020; 213:107579. [PMID: 32442437 PMCID: PMC7236745 DOI: 10.1016/j.pharmthera.2020.107579] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 01/10/2023]
Abstract
Ubiquitin Proteasome System (UPS) is an adaptable and finely tuned system that sustains proteostasis network under a large variety of physiopathological conditions. Its dysregulation is often associated with the onset and progression of human diseases; hence, UPS modulation has emerged as a promising new avenue for the development of treatments of several relevant pathologies, such as cancer and neurodegeneration. The clinical interest in proteasome inhibition has considerably increased after the FDA approval in 2003 of bortezomib for relapsed/refractory multiple myeloma, which is now used in the front-line setting. Thereafter, two other proteasome inhibitors (carfilzomib and ixazomib), designed to overcome resistance to bortezomib, have been approved for treatment-experienced patients, and a variety of novel inhibitors are currently under preclinical and clinical investigation not only for haematological malignancies but also for solid tumours. However, since UPS collapse leads to toxic misfolded proteins accumulation, proteasome is attracting even more interest as a target for the care of neurodegenerative diseases, which are sustained by UPS impairment. Thus, conceptually, proteasome activation represents an innovative and largely unexplored target for drug development. According to a multidisciplinary approach, spanning from chemistry, biochemistry, molecular biology to pharmacology, this review will summarize the most recent available literature regarding different aspects of proteasome biology, focusing on structure, function and regulation of proteasome in physiological and pathological processes, mostly cancer and neurodegenerative diseases, connecting biochemical features and clinical studies of proteasome targeting drugs.
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Affiliation(s)
- G R Tundo
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy.
| | | | - A M Santoro
- CNR, Institute of Crystallography, Catania, Italy
| | - A Coletta
- Department of Chemistry, University of Aarhus, Aarhus, Denmark
| | - F Oddone
- IRCCS-Fondazione Bietti, Rome, Italy
| | - G Grasso
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - D Milardi
- CNR, Institute of Crystallography, Catania, Italy
| | - P M Lacal
- Laboratory of Molecular Oncology, IDI-IRCCS, Rome, Italy
| | - S Marini
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy
| | - R Purrello
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - G Graziani
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - M Coletta
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy.
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Kong MY, Li LY, Lou YM, Chi HY, Wu JJ. Chinese herbal medicines for prevention and treatment of colorectal cancer: From molecular mechanisms to potential clinical applications. JOURNAL OF INTEGRATIVE MEDICINE-JIM 2020; 18:369-384. [PMID: 32758397 DOI: 10.1016/j.joim.2020.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023]
Abstract
Worldwide, colorectal cancer (CRC) is one of the most common malignant tumors, leading to immense social and economic burdens. Currently, the main treatments for CRC include surgery, chemotherapy, radiotherapy and immunotherapy. Despite advances in the diagnosis and treatment of CRC, the prognosis for CRC patients remains poor. Furthermore, the occurrence of side effects and toxicities severely limits the clinical use of these therapies. Therefore, alternative medications with high efficacy but few side effects are needed. An increasing number of modern pharmacological studies and clinical trials have supported the effectiveness of Chinese herbal medicines (CHMs) for the prevention and treatment of CRC. CHMs may be able to effectively reduce the risk of CRC, alleviate the adverse reactions caused by chemotherapy, and prolong the survival time of patients with advanced CRC. Studies of molecular mechanisms have provided deeper insight into the roles of molecules from CHMs in treating CRC. This paper summarizes the current understanding of the use of CHMs for the prevention and treatment of CRC, the main molecular mechanisms involved in these processes, the role of CHMs in modulating chemotherapy-induced adverse reactions, and CHM's potential role in epigenetic regulation of CRC. The current study provides beneficial information on the use of CHMs for the prevention and treatment of CRC in the clinic, and suggests novel directions for new drug discovery against CRC.
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Affiliation(s)
- Mu-Yan Kong
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China
| | - Le-Yan Li
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China
| | - Yan-Mei Lou
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China
| | - Hong-Yu Chi
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China
| | - Jin-Jun Wu
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China.
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20
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Sun Y, Zheng X, Yuan H, Chen G, Ouyang J, Liu J, Liu X, Xing X, Zhao B. Proteomic analyses reveal divergent ubiquitylation patterns in hepatocellula carcinoma cell lines with different metastasis potential. J Proteomics 2020; 225:103834. [PMID: 32454254 DOI: 10.1016/j.jprot.2020.103834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/13/2020] [Accepted: 05/18/2020] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignant tumours, metastasis and recurrence remain the primary reasons for poor prognosis. Ubiquitination serves as a degradation mechanism of proteins, but it is involved in additional cellular processes including metastasis. Here, by using label-free quantification, double-glycine (di-Gly) antibody affinity purification and high-resolution liquid chromatography tandem mass spectrometry (LC-MS/MS), we investigated quantitative proteome, ubiquitylome, and the crosstalk between the two datasets in HCC cell lines with different metastasis potential to identify biomarkers associated with HCC metastasis. In total, 83 ubiquitinated proteins significantly and steadily changed their abundance according to their metastatic potential, and the participated biological processes of these ubiquitinated proteins were tightly associated with tumour metastasis. Further signaling pathway analysis revealed that the ribosome and proteasome were significantly over-activated in the highly metastatic cells. Furthermore, we analyzed the crosstalk between the whole proteome and the ubiquitylome, and further discussed the mechanism that how ubiquitination events affect HCC metastasis. Eventually, the ubiquitination of Ku80 was validated to be significantly down-regulated in the high-metastatic cells comparing with the low-metastatic cells. We believe that these findings will help us better understand the underlying molecular mechanisms of the metastasis of HCC. SIGNIFICANCE: In this manuscript, we used label free based proteomics combined with diglycine antibody (di-Gly) affinity purification approach to identify biomarkers associated with HCC recurrence/metastasis in in a serial HCC cell lines with increasing invasion and metastasis potential. And then, we analyzed the crosstalk between the whole proteome and the ubiquitylome. Eventually, the ubiquitination of Ku80 was confirm to be closely associated with invasion and migration of HCC cells. As far as we know, this is the first time to use quantitative proteomic approach to study the ubiquitylomics in HCC cell lines with increasing metastasis ability.
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Affiliation(s)
- Ying Sun
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China; School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, People's Republic of China; Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, People's Republic of China
| | - Xiaoyuan Zheng
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Hui Yuan
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Geng Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Jiahe Ouyang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Jingfeng Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China; School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, People's Republic of China; Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, People's Republic of China
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China; School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, People's Republic of China; Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, People's Republic of China
| | - Xiaohua Xing
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China; The School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, People's Republic of China.
| | - Bixing Zhao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China.
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Tempo-spatial alternative polyadenylation analysis reveals that 3' UTR lengthening of Mdm2 regulates p53 expression and cellular senescence in aged rat testis. Biochem Biophys Res Commun 2020; 523:1046-1052. [PMID: 31973811 DOI: 10.1016/j.bbrc.2020.01.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/11/2020] [Indexed: 12/21/2022]
Abstract
Although tissue aging is accompanied with cellular senescence, it is much complicated than senescence given both types and number of cells change with age. Alternative polyadenylation (APA) had shown tissue specificity and APA-mediated 3' untranslated region (3' UTR) lengthening could regulate senescence-associated phenotypes. However, whether tissue aging shows similar trends remains unknown. Here, we performed a comprehensive analysis on RNA-seq datasets derived from multiple cells and rat tissues of young and old age. Although APA-mediated 3' UTR lengthening in various senescent cells reinforced the previous discovery, tissue aging showed much more complexity in APA. Interestingly, testis was the only tissue displaying dramatic 3' UTR lengthening and decreased expression trend of corresponding genes in aged rat. Genes with longer 3' UTR in aged testis were enriched in senescence-associated pathways, among which, Mdm2, encoding an E3 ligase of p53, favored distal poly(A) site resulting in lengthened 3' UTR and decreased expression. Longer 3' UTR of Mdm2 generated less protein, and decreased Mdm2 expression led to senescence-associated phenotypes along with increased p53 and p21 protein abundance, which could all be reversed by Mdm2 overexpression. Our work revealed complicated APA changes during tissue aging and discovered APA-mediated 3' UTR lengthening of Mdm2 is a hidden layer in regulating the well-known senescence-related p53-p21 signal axis during testis aging, and also has potential implications regarding declined male fertility along aging.
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Santos-Otte P, Leysen H, van Gastel J, Hendrickx JO, Martin B, Maudsley S. G Protein-Coupled Receptor Systems and Their Role in Cellular Senescence. Comput Struct Biotechnol J 2019; 17:1265-1277. [PMID: 31921393 PMCID: PMC6944711 DOI: 10.1016/j.csbj.2019.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 12/17/2022] Open
Abstract
Aging is a complex biological process that is inevitable for nearly all organisms. Aging is the strongest risk factor for development of multiple neurodegenerative disorders, cancer and cardiovascular disorders. Age-related disease conditions are mainly caused by the progressive degradation of the integrity of communication systems within and between organs. This is in part mediated by, i) decreased efficiency of receptor signaling systems and ii) an increasing inability to cope with stress leading to apoptosis and cellular senescence. Cellular senescence is a natural process during embryonic development, more recently it has been shown to be also involved in the development of aging disorders and is now considered one of the major hallmarks of aging. G-protein-coupled receptors (GPCRs) comprise a superfamily of integral membrane receptors that are responsible for cell signaling events involved in nearly every physiological process. Recent advances in the molecular understanding of GPCR signaling complexity have expanded their therapeutic capacity tremendously. Emerging data now suggests the involvement of GPCRs and their associated proteins in the development of cellular senescence. With the proven efficacy of therapeutic GPCR targeting, it is reasonable to now consider GPCRs as potential platforms to control cellular senescence and the consequently, age-related disorders.
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Key Words
- ADP-ribosylation factor GTPase-activating protein, (Arf-GAP)
- AT1R blockers, (ARB)
- Aging
- Angiotensin II, (Ang II)
- Ataxia telangiectasia mutated, (ATM)
- Cellular senescence
- G protein-coupled receptor kinase interacting protein 2 (GIT2)
- G protein-coupled receptor kinase interacting protein 2, (GIT2)
- G protein-coupled receptor kinase, (GRK)
- G protein-coupled receptors (GPCRs)
- G protein-coupled receptors, (GPCRs)
- Hutchinson–Gilford progeria syndrome, (HGPS)
- Lysophosphatidic acid, (LPA)
- Regulator of G-protein signaling, (RGS)
- Relaxin family receptor 3, (RXFP3)
- active state, (R*)
- angiotensin type 1 receptor, (AT1R)
- angiotensin type 2 receptor, (AT2R)
- beta2-adrenergic receptor, (β2AR)
- cyclin-dependent kinase 2, (CDK2)
- cyclin-dependent kinase inhibitor 1, (cdkn1A/p21)
- endothelial cell differentiation gene, (Edg)
- inactive state, (R)
- latent semantic indexing, (LSI)
- mitogen-activated protein kinase, (MAPK)
- nuclear factor kappa-light-chain-enhancer of activated B cells, (NF- κβ)
- protein kinases, (PK)
- purinergic receptors family, (P2Y)
- renin-angiotensin system, (RAS)
- retinoblastoma, (RB)
- senescence associated secretory phenotype, (SASP)
- stress-induced premature senescence, (SIPS)
- transcription factor E2F3, (E2F3)
- transmembrane, (TM)
- tumor suppressor gene PTEN, (PTEN)
- tumor suppressor protein 53, (p53)
- vascular smooth muscle cells, (VSMC)
- β-Arrestin
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Affiliation(s)
- Paula Santos-Otte
- Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, 01062 Dresden, Germany
| | - Hanne Leysen
- Receptor Biology Lab, University of Antwerp, 2610 Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Jaana van Gastel
- Receptor Biology Lab, University of Antwerp, 2610 Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Jhana O. Hendrickx
- Receptor Biology Lab, University of Antwerp, 2610 Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Bronwen Martin
- Receptor Biology Lab, University of Antwerp, 2610 Antwerp, Belgium
| | - Stuart Maudsley
- Receptor Biology Lab, University of Antwerp, 2610 Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
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23
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Liang S, Bellato HM, Lorent J, Lupinacci FCS, Oertlin C, van Hoef V, Andrade VP, Roffé M, Masvidal L, Hajj GNM, Larsson O. Polysome-profiling in small tissue samples. Nucleic Acids Res 2019; 46:e3. [PMID: 29069469 PMCID: PMC5758873 DOI: 10.1093/nar/gkx940] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/10/2017] [Indexed: 01/01/2023] Open
Abstract
Polysome-profiling is commonly used to study translatomes and applies laborious extraction of efficiently translated mRNA (associated with >3 ribosomes) from a large volume across many fractions. This property makes polysome-profiling inconvenient for larger experimental designs or samples with low RNA amounts. To address this, we optimized a non-linear sucrose gradient which reproducibly enriches for efficiently translated mRNA in only one or two fractions, thereby reducing sample handling 5-10-fold. The technique generates polysome-associated RNA with a quality reflecting the starting material and, when coupled with smart-seq2 single-cell RNA sequencing, translatomes in small tissues from biobanks can be obtained. Translatomes acquired using optimized non-linear gradients resemble those obtained with the standard approach employing linear gradients. Polysome-profiling using optimized non-linear gradients in serum starved HCT-116 cells with or without p53 showed that p53 status associates with changes in mRNA abundance and translational efficiency leading to changes in protein levels. Moreover, p53 status also induced translational buffering whereby changes in mRNA levels are buffered at the level of mRNA translation. Thus, here we present a polysome-profiling technique applicable to large study designs, primary cells and frozen tissue samples such as those collected in biobanks.
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Affiliation(s)
- Shuo Liang
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | | | - Julie Lorent
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | | | - Christian Oertlin
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Vincent van Hoef
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Victor P Andrade
- Department of Pathology, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Martín Roffé
- International Research Center, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Laia Masvidal
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Glaucia N M Hajj
- International Research Center, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
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Del Toro N, Fernandez-Ruiz A, Mignacca L, Kalegari P, Rowell MC, Igelmann S, Saint-Germain E, Benfdil M, Lopes-Paciencia S, Brakier-Gingras L, Bourdeau V, Ferbeyre G, Lessard F. Ribosomal protein RPL22/eL22 regulates the cell cycle by acting as an inhibitor of the CDK4-cyclin D complex. Cell Cycle 2019; 18:759-770. [PMID: 30874462 DOI: 10.1080/15384101.2019.1593708] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Senescence is a tumor suppressor program characterized by a stable growth arrest while maintaining cell viability. Senescence-associated ribogenesis defects (SARD) have been shown to regulate senescence through the ability of the ribosomal protein S14 (RPS14 or uS11) to bind and inhibit the cyclin-dependent kinase 4 (CDK4). Here we report another ribosomal protein that binds and inhibits CDK4 in senescent cells: L22 (RPL22 or eL22). Enforcing the expression of RPL22/eL22 is sufficient to induce an RB and p53-dependent cellular senescent phenotype in human fibroblasts. Mechanistically, RPL22/eL22 can interact with and inhibit CDK4-Cyclin D1 to decrease RB phosphorylation both in vitro and in cells. Briefly, we show that ribosome-free RPL22/eL22 causes a cell cycle arrest which could be relevant during situations of nucleolar stress such as cellular senescence or the response to cancer chemotherapy.
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Affiliation(s)
- Neylen Del Toro
- a Department of Biochemistry and Molecular Medicine , Université de Montréal , Montréal , Québec , Canada
| | - Ana Fernandez-Ruiz
- a Department of Biochemistry and Molecular Medicine , Université de Montréal , Montréal , Québec , Canada.,b CRCHUM , Montréal , QC , Canada
| | - Lian Mignacca
- a Department of Biochemistry and Molecular Medicine , Université de Montréal , Montréal , Québec , Canada
| | - Paloma Kalegari
- a Department of Biochemistry and Molecular Medicine , Université de Montréal , Montréal , Québec , Canada.,b CRCHUM , Montréal , QC , Canada
| | - Marie-Camille Rowell
- a Department of Biochemistry and Molecular Medicine , Université de Montréal , Montréal , Québec , Canada.,b CRCHUM , Montréal , QC , Canada
| | - Sebastian Igelmann
- a Department of Biochemistry and Molecular Medicine , Université de Montréal , Montréal , Québec , Canada
| | - Emmanuelle Saint-Germain
- a Department of Biochemistry and Molecular Medicine , Université de Montréal , Montréal , Québec , Canada
| | - Mehdi Benfdil
- a Department of Biochemistry and Molecular Medicine , Université de Montréal , Montréal , Québec , Canada
| | - Stéphane Lopes-Paciencia
- a Department of Biochemistry and Molecular Medicine , Université de Montréal , Montréal , Québec , Canada.,b CRCHUM , Montréal , QC , Canada
| | - Léa Brakier-Gingras
- a Department of Biochemistry and Molecular Medicine , Université de Montréal , Montréal , Québec , Canada
| | - Véronique Bourdeau
- a Department of Biochemistry and Molecular Medicine , Université de Montréal , Montréal , Québec , Canada
| | - Gerardo Ferbeyre
- a Department of Biochemistry and Molecular Medicine , Université de Montréal , Montréal , Québec , Canada.,b CRCHUM , Montréal , QC , Canada
| | - Frédéric Lessard
- a Department of Biochemistry and Molecular Medicine , Université de Montréal , Montréal , Québec , Canada
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25
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Ogrodnik M, Salmonowicz H, Gladyshev VN. Integrating cellular senescence with the concept of damage accumulation in aging: Relevance for clearance of senescent cells. Aging Cell 2019; 18:e12841. [PMID: 30346102 PMCID: PMC6351832 DOI: 10.1111/acel.12841] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 07/31/2018] [Accepted: 08/20/2018] [Indexed: 12/12/2022] Open
Abstract
Understanding the aging process and ways to manipulate it is of major importance for biology and medicine. Among the many aging theories advanced over the years, the concept most consistent with experimental evidence posits the buildup of numerous forms of molecular damage as a foundation of the aging process. Here, we discuss that this concept integrates well with recent findings on cellular senescence, offering a novel view on the role of senescence in aging and age‐related disease. Cellular senescence has a well‐established role in cellular aging, but its impact on the rate of organismal aging is less defined. One of the most prominent features of cellular senescence is its association with macromolecular damage. The relationship between cell senescence and damage concerns both damage as a molecular signal of senescence induction and accelerated accumulation of damage in senescent cells. We describe the origin, regulatory mechanisms, and relevance of various damage forms in senescent cells. This view on senescent cells as carriers and inducers of damage puts new light on senescence, considering it as a significant contributor to the rise in organismal damage. Applying these ideas, we critically examine current evidence for a role of cellular senescence in aging and age‐related diseases. We also discuss the differential impact of longevity interventions on senescence burden and other types of age‐related damage. Finally, we propose a model on the role of aging‐related damage accumulation and the rate of aging observed upon senescent cell clearance.
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Affiliation(s)
- Mikolaj Ogrodnik
- Institute for Cell and Molecular Biosciences; Newcastle University Institute for Ageing; Newcastle upon Tyne UK
| | - Hanna Salmonowicz
- Institute for Cell and Molecular Biosciences; Newcastle University Institute for Ageing; Newcastle upon Tyne UK
| | - Vadim N. Gladyshev
- Division of Genetics; Department of Medicine; Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
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26
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Targeting Proteotoxic Stress in Cancer: A Review of the Role that Protein Quality Control Pathways Play in Oncogenesis. Cancers (Basel) 2019; 11:cancers11010066. [PMID: 30634515 PMCID: PMC6356294 DOI: 10.3390/cancers11010066] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/24/2018] [Accepted: 12/07/2018] [Indexed: 02/06/2023] Open
Abstract
Despite significant advances in cancer diagnostics and therapeutics the majority of cancer unfortunately remains incurable, which has led to continued research to better understand its exceptionally diverse biology. As a result of genomic instability, cancer cells typically have elevated proteotoxic stress. Recent appreciation of this functional link between the two secondary hallmarks of cancer: aneuploidy (oxidative stress) and proteotoxic stress, has therefore led to the development of new anticancer therapies targeting this emerging “Achilles heel” of malignancy. This review highlights the importance of managing proteotoxic stress for cancer cell survival and provides an overview of the integral role proteostasis pathways play in the maintenance of protein homeostasis. We further review the efforts undertaken to exploit proteotoxic stress in multiple myeloma (as an example of a hematologic malignancy) and triple negative breast cancer (as an example of a solid tumor), and give examples of: (1) FDA-approved therapies in routine clinical use; and (2) promising therapies currently in clinical trials. Finally, we provide new insights gleaned from the use of emerging technologies to disrupt the protein secretory pathway and repurpose E3 ligases to achieve targeted protein degradation.
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27
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Ferbeyre G. Aberrant signaling and senescence associated protein degradation. Exp Gerontol 2018; 107:50-54. [DOI: 10.1016/j.exger.2017.06.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/20/2017] [Accepted: 06/23/2017] [Indexed: 11/17/2022]
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28
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Senescence-associated ribosome biogenesis defects contributes to cell cycle arrest through the Rb pathway. Nat Cell Biol 2018; 20:789-799. [PMID: 29941930 DOI: 10.1038/s41556-018-0127-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/21/2018] [Indexed: 01/05/2023]
Abstract
Cellular senescence is a tumour suppressor programme characterized by a stable cell cycle arrest. Here we report that cellular senescence triggered by a variety of stimuli leads to diminished ribosome biogenesis and the accumulation of both rRNA precursors and ribosomal proteins. These defects were associated with reduced expression of several ribosome biogenesis factors, the knockdown of which was also sufficient to induce senescence. Genetic analysis revealed that Rb but not p53 was required for the senescence response to altered ribosome biogenesis. Mechanistically, the ribosomal protein S14 (RPS14 or uS11) accumulates in the soluble non-ribosomal fraction of senescent cells, where it binds and inhibits CDK4 (cyclin-dependent kinase 4). Overexpression of RPS14 is sufficient to inhibit Rb phosphorylation, inducing cell cycle arrest and senescence. Here we describe a mechanism for maintaining the senescent cell cycle arrest that may be relevant for cancer therapy, as well as biomarkers to identify senescent cells.
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29
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Sun XY, Liu QH, Huang J. iTRAQ-based quantitative proteomic analysis of differentially expressed proteins in Litopenaeus vannamei
in response to infection with WSSV strains varying in virulence. Lett Appl Microbiol 2018; 67:113-122. [DOI: 10.1111/lam.13004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 11/30/2022]
Affiliation(s)
- X.-Y. Sun
- Laboratory for Marine Fisheries Science and Food Production Processes; Qingdao National Laboratory for Marine Science and Technology; Key Laboratory of Maricultural Organism Disease Control; Ministry of Agriculture; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute; Chinese Academy of Fishery Sciences; Qingdao China
| | - Q.-H. Liu
- Laboratory for Marine Fisheries Science and Food Production Processes; Qingdao National Laboratory for Marine Science and Technology; Key Laboratory of Maricultural Organism Disease Control; Ministry of Agriculture; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute; Chinese Academy of Fishery Sciences; Qingdao China
| | - J. Huang
- Laboratory for Marine Fisheries Science and Food Production Processes; Qingdao National Laboratory for Marine Science and Technology; Key Laboratory of Maricultural Organism Disease Control; Ministry of Agriculture; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute; Chinese Academy of Fishery Sciences; Qingdao China
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30
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Carracedo J, Ramírez-Carracedo R, Martínez de Toda I, Vida C, Alique M, De la Fuente M, Ramírez-Chamond R. Protein Carbamylation: A Marker Reflecting Increased Age-Related Cell Oxidation. Int J Mol Sci 2018; 19:ijms19051495. [PMID: 29772765 PMCID: PMC5983744 DOI: 10.3390/ijms19051495] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 12/30/2022] Open
Abstract
Carbamylation is a post-translational modification of proteins that may partake in the oxidative stress-associated cell damage, and its increment has been recently proposed as a “hallmark of aging”. The molecular mechanisms associated with aging are related to an increased release of free radicals. We have studied whether carbamylated proteins from the peripheral blood of healthy subjects are related to oxidative damage and aging, taking into account the gender and the immune profile of the subjects. The study was performed in healthy human volunteers. The detection of protein carbamylation and malondialdehyde (MDA) levels was evaluated using commercial kits. The immune profile was calculated using parameters of immune cell function. The results show that the individuals from the elderly group (60–79 years old) have increased carbamylated protein and MDA levels. When considered by gender, only men between 60 and 79 years old showed significantly increased carbamylated proteins and MDA levels. When those subjects were classified by their immune profile, the carbamylated protein levels were higher in those with an older immune profile. In conclusion, the carbamylation of proteins in peripheral blood is related to age-associated oxidative damage and to an aging functional immunological signature. Our results suggest that carbamylated proteins may play an important role at the cellular level in the aging process.
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Affiliation(s)
- Julia Carracedo
- Department of Genetics, Physiology, and Microbiology, Faculty of Biology, Complutense University/Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28040 Madrid, Spain.
| | - Rafael Ramírez-Carracedo
- Cardiovascular Joint Research Unit, Francisco de Vitoria University/Hospital Ramon y Cajal Research Unit (IRYCIS), 28223 Madrid, Spain.
| | - Irene Martínez de Toda
- Department of Genetics, Physiology, and Microbiology, Faculty of Biology, Complutense University/Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28040 Madrid, Spain.
| | - Carmen Vida
- Department of Genetics, Physiology, and Microbiology, Faculty of Biology, Complutense University/Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28040 Madrid, Spain.
| | - Matilde Alique
- Biology Systems Department, Physiology, Alcala University, Alcala de Henares, 28805 Madrid, Spain.
| | - Mónica De la Fuente
- Department of Genetics, Physiology, and Microbiology, Faculty of Biology, Complutense University/Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28040 Madrid, Spain.
| | - Rafael Ramírez-Chamond
- Biology Systems Department, Physiology, Alcala University, Alcala de Henares, 28805 Madrid, Spain.
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Abstract
PURPOSE OF REVIEW Premature activation of aging-associated molecular mechanisms is emerging as an important contributor to many diseases, including scleroderma. Among central regulators of the aging process are a group of histone deacetylases called sirtuins (SIRTs). Recent findings implicate these molecules as pathophysiological players in scleroderma skin and lung fibrosis. The goal of this article is to review recent studies on the involvement of SIRTs in scleroderma from the perspective of aging-related molecular mechanisms. RECENT FINDINGS Despite a degree of controversy in this rapidly developing field, the majority of data suggest that SIRT levels are decreased in tissues from patients with scleroderma compared to healthy controls as well as in animal models of scleroderma. Molecular studies reveal several mechanisms through which declining SIRT levels contribute to fibrosis, with the most attention given to modulation of the TGF-β signaling pathway. Activation of SIRTs in cell culture and in animal models elicits antifibrotic effects. Declining SIRT levels and activity are emerging as pathophysiological contributors to scleroderma. Restoration of SIRTs may be therapeutic in patients with scleroderma.
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Copper accumulation in senescent cells: Interplay between copper transporters and impaired autophagy. Redox Biol 2018; 16:322-331. [PMID: 29579719 PMCID: PMC5953000 DOI: 10.1016/j.redox.2018.03.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 12/24/2022] Open
Abstract
Cellular senescence is characterized by irreversible growth arrest incurred through either replicative exhaustion or by pro-oncogenic cellular stressors (radioactivity, oxidative stress, oncogenic activation). The enrichment of senescent cells in tissues with age has been associated with tissue dyshomeostasis and age-related pathologies including cancers, neurodegenerative disorders (e.g. Alzheimer's, Parkinson's, etc.) and metabolic disorders (e.g. diabetes). We identified copper accumulation as being a universal feature of senescent cells [mouse embryonic fibroblasts (MEF), human prostate epithelial cells and human diploid fibroblasts] in vitro. Elevated copper in senescent MEFs was accompanied by elevated levels of high-affinity copper uptake protein 1 (Ctr1), diminished levels of copper-transporting ATPase 1 (Atp7a) (copper export) and enhanced antioxidant defence reflected by elevated levels of glutathione (GSH), superoxide dismutase 1 (SOD1) and glutaredoxin 1 (Grx1). The levels of intracellular copper were further increased in senescent MEFs cultured in copper supplemented medium and in senescent Mottled Brindled (Mobr) MEFs lacking functional Atp7a. Finally, we demonstrated that the restoration/preservation of autophagic-lysosomal degradation in senescent MEFs following rapamycin treatment correlated with attenuation of copper accumulation in these cells despite a further decrease in Atp7a levels. This study for the first time establishes a link between Atp7a and the autophagic-lysosomal pathway, and a requirement for both to effect efficient copper export. Such a connection between cellular autophagy and copper homeostasis is significant, as both have emerged as important facets of age-associated degenerative disease. Copper accumulation is a feature of cellular senescence. Elevated copper in senescent cells is associated with impaired autophagic-lysosomal function. Restoration/preservation of lysosomal function attenuates copper accumulation. Both Atp7a and autophagic-lysosomal function are required for copper export.
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Chen M, Lyu G, Han M, Nie H, Shen T, Chen W, Niu Y, Song Y, Li X, Li H, Chen X, Wang Z, Xia Z, Li W, Tian XL, Ding C, Gu J, Zheng Y, Liu X, Hu J, Wei G, Tao W, Ni T. 3' UTR lengthening as a novel mechanism in regulating cellular senescence. Genome Res 2018; 28:285-294. [PMID: 29440281 PMCID: PMC5848608 DOI: 10.1101/gr.224451.117] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 01/24/2018] [Indexed: 01/09/2023]
Abstract
Cellular senescence has been viewed as a tumor suppression mechanism and also as a contributor to individual aging. Widespread shortening of 3' untranslated regions (3' UTRs) in messenger RNAs (mRNAs) by alternative polyadenylation (APA) has recently been discovered in cancer cells. However, the role of APA in the process of cellular senescence remains elusive. Here, we found that hundreds of genes in senescent cells tended to use distal poly(A) (pA) sites, leading to a global lengthening of 3' UTRs and reduced gene expression. Genes that harbor longer 3' UTRs in senescent cells were enriched in senescence-related pathways. Rras2, a member of the Ras superfamily that participates in multiple signal transduction pathways, preferred longer 3' UTR usage and exhibited decreased expression in senescent cells. Depletion of Rras2 promoted senescence, while rescue of Rras2 reversed senescence-associated phenotypes. Mechanistically, splicing factor TRA2B bound to a core "AGAA" motif located in the alternative 3' UTR of Rras2, thereby reducing the RRAS2 protein level and causing senescence. Both proximal and distal poly(A) signals showed strong sequence conservation, highlighting the vital role of APA regulation during evolution. Our results revealed APA as a novel mechanism in regulating cellular senescence.
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Affiliation(s)
- Meng Chen
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Guoliang Lyu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Miao Han
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Hongbo Nie
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Ting Shen
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Wei Chen
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Yichi Niu
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Yifan Song
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Xueping Li
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Huan Li
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Xinyu Chen
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Ziyue Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Zheng Xia
- Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wei Li
- Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xiao-Li Tian
- Human Aging Research Institute and School of Life Sciences, Nanchang University, Nanchang, 330031 China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Jun Gu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Yufang Zheng
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Xinhua Liu
- School of Pharmacy, Fudan University, Shanghai, 201203 China
| | - Jinfeng Hu
- School of Pharmacy, Fudan University, Shanghai, 201203 China
| | - Gang Wei
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Wei Tao
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
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Palani CD, Ramanathapuram L, Lam-ubol A, Kurago ZB. Toll-like receptor 2 induces adenosine receptor A2a and promotes human squamous carcinoma cell growth via extracellular signal regulated kinases ½. Oncotarget 2018; 9:6814-6829. [PMID: 29467931 PMCID: PMC5805517 DOI: 10.18632/oncotarget.23784] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 12/27/2017] [Indexed: 01/26/2023] Open
Abstract
Patient treatment for oral squamous cell carcinoma (OSCC) not associated with Human papillomavirus remains problematic. OSCC microenvironment is typically inflamed and colonized by microorganisms, providing ligands for toll-like receptors (TLR). In immune cells TLR2 and TLR4 activate NF-kB and extracellular signal regulated kinase (ERK)1/2 pathways, leading to upregulation of inhibitory adenosine receptors A2a and A2b, and reduction in stimulatory A1 and A3. How TLR and adenosine receptors function in SCC cells is not understood. To address this gap, we evaluated TLR and adenosine receptor expression and function in human OSCC cells and keratinocytes. TLR2 and A2a were co-expressed in pre-cancer and SCC cells of 17 oral specimens. In vitro, 5/6 OSCC lines expressed more TLR2 than TLR1, 4 or 6 mRNA. TLR2 ligands stimulated A2a expression in TLR2-high cell lines, but no A1 or A3 was detected with or without stimuli. In TLR2-high OSCC, TLR2/1, 2/6 and adenosine receptor agonists activated ERK1/2. TLR2-mediated ERK1/2 phosphorylation resulted in accumulation of c-FOS, ERK-dependent cell proliferation and reduced caspase-3 activity. Similar ERK1/2-dependent proliferation and decreased caspase-3 activity were caused by combined TLR2 and adenosine receptor stimuli. We conclude that TLR2 and adenosine receptor agonists, known to be present in the tumor microenvironment, may contribute to OSCC progression in part via direct effects on the ERK1/2 pathway in squamous carcinoma cells.
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Affiliation(s)
| | | | - Aroonwan Lam-ubol
- Faculty of Dentistry Srinakharinwirot University, Wattana, Bangkok, Thailand
| | - Zoya B. Kurago
- Dental College of Georgia, Augusta University, Augusta, GA, USA
- Medical College of Georgia, Augusta University, Augusta, GA, USA
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35
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MicroRNA profiling analysis revealed different cellular senescence mechanisms in human mesenchymal stem cells derived from different origin. Genomics 2017; 109:147-157. [DOI: 10.1016/j.ygeno.2017.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/10/2017] [Accepted: 02/11/2017] [Indexed: 01/01/2023]
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36
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Li YJ, Lei YH, Yao N, Wang CR, Hu N, Ye WC, Zhang DM, Chen ZS. Autophagy and multidrug resistance in cancer. CHINESE JOURNAL OF CANCER 2017. [PMID: 28646911 PMCID: PMC5482965 DOI: 10.1186/s40880-017-0219-2] [Citation(s) in RCA: 479] [Impact Index Per Article: 68.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multidrug resistance (MDR) occurs frequently after long-term chemotherapy, resulting in refractory cancer and tumor recurrence. Therefore, combatting MDR is an important issue. Autophagy, a self-degradative system, universally arises during the treatment of sensitive and MDR cancer. Autophagy can be a double-edged sword for MDR tumors: it participates in the development of MDR and protects cancer cells from chemotherapeutics but can also kill MDR cancer cells in which apoptosis pathways are inactive. Autophagy induced by anticancer drugs could also activate apoptosis signaling pathways in MDR cells, facilitating MDR reversal. Therefore, research on the regulation of autophagy to combat MDR is expanding and is becoming increasingly important. We summarize advanced studies of autophagy in MDR tumors, including the variable role of autophagy in MDR cancer cells.
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Affiliation(s)
- Ying-Jie Li
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, Guangdong, P. R. China
| | - Yu-He Lei
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, Guangdong, P. R. China
| | - Nan Yao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, Guangdong, P. R. China
| | - Chen-Ran Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, Guangdong, P. R. China
| | - Nan Hu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, Guangdong, P. R. China
| | - Wen-Cai Ye
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, Guangdong, P. R. China
| | - Dong-Mei Zhang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, Guangdong, P. R. China.
| | - Zhe-Sheng Chen
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, Guangdong, P. R. China. .,Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA.
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37
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Alternative Chk1-independent S/M checkpoint in somatic cells that prevents premature mitotic entry. Med Oncol 2017; 34:70. [PMID: 28349497 DOI: 10.1007/s12032-017-0932-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/23/2017] [Indexed: 12/22/2022]
Abstract
Genomic instability is the hallmark of cancer. Checkpoint kinase-1 (Chk1) is required for cell cycle delay after DNA damage or blocked DNA replication. Chk1-depleted tumor cells undergo premature mitosis and apoptosis. Here we analyzed the depletion of Chk1 in normal somatic cells in the absence of DNA damage in order to investigate alternative cell cycle checkpoint mechanism(s). By means of adenoviruses, flow cytometry, immunofluorescence and Western blotting, Chk1-depleted mouse embryonic fibroblasts (MEFs) were investigated. Chk1-/- MEFs arrested at the S/G2 boundary of the cell cycle with decreased protein levels of many cell cycle key players. Cyclin B1 was predominantly cytoplasmic. Interestingly, overexpression of nuclear dominant Cyclin B1 leads to nuclear translocation and premature mitosis. Chk1-/- MEFs exhibited the absence of double-strand breaks, yet cells showed delayed DNA damage recovery with pan-nuclear immunostaining pattern of Histone H2AX. Activation of this checkpoint would elicit a senescent-like phenotype. Taken together, our elaborated data revealed the existence of an additional S/M checkpoint functioning via γH2AX signaling and cytoplasmic retention of Cyclin B1 in somatic cells.
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38
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Xavier LADC, Bezerra JF, de Rezende AA, Oliveira RADC, Dalmolin RJS, do Amaral VS. Analysis of genome instability biomarkers in children with non-syndromic orofacial clefts. Mutagenesis 2017; 32:313-321. [DOI: 10.1093/mutage/gew068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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39
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Wang Y, Liu H, Liang D, Huang Y, Zeng Y, Xing X, Xia J, Lin M, Han X, Liao N, Liu X, Liu J. Reveal the molecular signatures of hepatocellular carcinoma with different sizes by iTRAQ based quantitative proteomics. J Proteomics 2016; 150:230-241. [PMID: 27693406 DOI: 10.1016/j.jprot.2016.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 08/03/2016] [Accepted: 09/19/2016] [Indexed: 12/12/2022]
Abstract
Tumor size of hepatocellular carcinoma (HCC) is a key parameter for predicting prognosis of HCC patients. The biological behaviors of HCC, such as tumor growth, recurrence and metastasis are significantly associated with tumor size. However, the underlying molecular mechanisms remain unclear. Here, we applied iTRAQ-based proteomic strategy to analyze the proteome differences among small, media, large and huge primary HCC tissues. In brief,88 proteins in small HCC, 69 proteins in media HCC, 118 proteins in large HCC and 215 proteins in huge HCC, were identified by comparing the proteome of cancerous tissues with its corresponding non-cancerous tissues. Further analysis of dysregulated proteins involved in signaling revealed that alteration of ERK1/2 and AKT signaling played important roles in the tumorigenesis or tumor growth in all subtypes. Interestingly, alteration of specific signaling was discovered in small and huge HCC, which might reflect specific molecular mechanisms of tumor growth. Furthermore, the dysregulation degree of a group of proteins has been confirmed to be significantly correlated with the tumor size; these proteins might be potential targets for studying tumor growth of HCC. Overall, we have revealed the molecular signatures of HCC with different tumor sizes, and provided fundamental information for further in-depth study. BIOLOGICAL SIGNIFICANCE In this study, we compared the protein expression profiles among different HCC subtypes, including small HCC, media HCC, large HCC and huge HCC for the first time. The results clearly proved that different molecular alterations and specific signaling pathways were indeed involved in different HCC subtypes, which might explain the different malignancy biological behaviors. In addition, the dysregulation degree of a group of proteins has been confirmed to be significantly correlated with the tumor size. We believe that these findings would help us better understand the underlying molecular mechanisms of the tumorigenesis and development of HCC.
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Affiliation(s)
- Yingchao Wang
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, People's Republic of China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Hongzhi Liu
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, People's Republic of China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China; Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350007, People's Republic of China
| | - Dong Liang
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, People's Republic of China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China; Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350007, People's Republic of China
| | - Yao Huang
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, People's Republic of China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China; Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350007, People's Republic of China
| | - Yongyi Zeng
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, People's Republic of China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China; Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350007, People's Republic of China
| | - Xiaohua Xing
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, People's Republic of China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Jiangbao Xia
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, People's Republic of China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Minjie Lin
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, People's Republic of China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Xiao Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Naishun Liao
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, People's Republic of China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China
| | - Xiaolong Liu
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, People's Republic of China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China.
| | - Jingfeng Liu
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou 350025, People's Republic of China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, People's Republic of China; Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350007, People's Republic of China.
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40
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Xing X, Huang Y, Wang S, Chi M, Zeng Y, Chen L, Li L, Zeng J, Lin M, Han X, Liu X, Liu J. Comparative analysis of primary hepatocellular carcinoma with single and multiple lesions by iTRAQ-based quantitative proteomics. J Proteomics 2015; 128:262-71. [DOI: 10.1016/j.jprot.2015.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 07/16/2015] [Accepted: 08/12/2015] [Indexed: 02/07/2023]
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41
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Affiliation(s)
- Nezahat Ozlem Arat
- a University of Montreal, Institute of Research in Immunology and Cancer ; Montreal , Canada
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