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Ahmed SMQ, Sasikumar J, Laha S, Das SP. Multifaceted role of the DNA replication protein MCM10 in maintaining genome stability and its implication in human diseases. Cancer Metastasis Rev 2024:10.1007/s10555-024-10209-3. [PMID: 39240414 DOI: 10.1007/s10555-024-10209-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 08/29/2024] [Indexed: 09/07/2024]
Abstract
MCM10 plays a vital role in genome duplication and is crucial for DNA replication initiation, elongation, and termination. It coordinates several proteins to assemble at the fork, form a functional replisome, trigger origin unwinding, and stabilize the replication bubble. MCM10 overexpression is associated with increased aggressiveness in breast, cervical, and several other cancers. Disruption of MCM10 leads to altered replication timing associated with initiation site gains and losses accompanied by genome instability. Knockdown of MCM10 affects the proliferation and migration of cancer cells, manifested by DNA damage and replication fork arrest, and has recently been shown to be associated with clinical conditions like CNKD and RCM. Loss of MCM10 function is associated with impaired telomerase activity, leading to the accumulation of abnormal replication forks and compromised telomere length. MCM10 interacts with histones, aids in nucleosome assembly, binds BRCA2 to maintain genome integrity during DNA damage, prevents lesion skipping, and inhibits PRIMPOL-mediated repriming. It also interacts with the fork reversal enzyme SMARCAL1 and inhibits fork regression. Additionally, MCM10 undergoes several post-translational modifications and contributes to transcriptional silencing by interacting with the SIR proteins. This review explores the mechanism associated with MCM10's multifaceted role in DNA replication initiation, chromatin organization, transcriptional silencing, replication stress, fork stability, telomere length maintenance, and DNA damage response. Finally, we discuss the role of MCM10 in the early detection of cancer, its prognostic significance, and its potential use in therapeutics for cancer treatment.
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Affiliation(s)
- Sumayyah M Q Ahmed
- Cell Biology and Molecular Genetics (CBMG), Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Jayaprakash Sasikumar
- Cell Biology and Molecular Genetics (CBMG), Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Suparna Laha
- Cell Biology and Molecular Genetics (CBMG), Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Shankar Prasad Das
- Cell Biology and Molecular Genetics (CBMG), Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, 575018, India.
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Huang QR, Jiang Q, Tan JY, Nong RB, Yan J, Yang XW, Mo LG, Ling GY, Deng T, Gong YZ. The prognostic and immunological role of MCM3 in pan-cancer and validation of prognosis in a clinical lower-grade glioma cohort. Front Pharmacol 2024; 15:1390615. [PMID: 38698811 PMCID: PMC11063780 DOI: 10.3389/fphar.2024.1390615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
Background: Previous studies have shown that MCM3 plays a key role in initiating DNA replication. However, the mechanism of MCM3 function in most cancers is still unknown. The aim of our study was to explore the expression, prognostic role, and immunological characteristics of MCM3 across cancers. Methods: We explored the expression pattern of MCM3 across cancers. We subsequently explored the prognostic value of MCM3 expression by using univariate Cox regression analysis. Spearman correlation analysis was performed to determine the correlations between MCM3 and immune-related characteristics, mismatching repair (MMR) signatures, RNA modulator genes, cancer stemness, programmed cell death (PCD) gene expression, tumour mutation burden (TMB), microsatellite instability (MSI), and neoantigen levels. The role of MCM3 in predicting the response to immune checkpoint blockade (ICB) therapy was further evaluated in four immunotherapy cohorts. Single-cell data from CancerSEA were analysed to assess the biological functions associated with MCM3 in 14 cancers. The clinical correlation and independent prognostic significance of MCM3 were further analysed in the TCGA and CGGA lower-grade glioma (LGG) cohorts, and a prognostic nomogram was constructed. Immunohistochemistry in a clinical cohort was utilized to validate the prognostic utility of MCM3 expression in LGG. Results: MCM3 expression was upregulated in most tumours and strongly associated with patient outcomes in many cancers. Correlation analyses demonstrated that MCM3 expression was closely linked to immune cell infiltration, immune checkpoints, MMR genes, RNA modulator genes, cancer stemness, PCD genes and the TMB in most tumours. There was an obvious difference in outcomes between patients with high MCM3 expression and those with low MCM3 expression in the 4 ICB treatment cohorts. Single-cell analysis indicated that MCM3 was mainly linked to the cell cycle, DNA damage and DNA repair. The expression of MCM3 was associated with the clinical features of LGG patients and was an independent prognostic indicator. Finally, the prognostic significance of MCM3 in LGG was validated in a clinical cohort. Conclusion: Our study suggested that MCM3 can be used as a potential prognostic marker for cancers and may be associated with tumour immunity. In addition, MCM3 is a promising predictor of immunotherapy responses.
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Affiliation(s)
- Qian-Rong Huang
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Qian Jiang
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Ju-Yuan Tan
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Ren-Bao Nong
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Jun Yan
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | | | - Li-Gen Mo
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Guo-Yuan Ling
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Teng Deng
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yi-Zhen Gong
- Department of Clinical Research, Guangxi Medical University Cancer Hospital, Nanning, China
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Li J, Liu F, Mo K, Ni H, Yin Y. Effects of weaning on intestinal longitudinal muscle-myenteric plexus function in piglets. SCIENCE CHINA. LIFE SCIENCES 2024; 67:379-390. [PMID: 37824029 DOI: 10.1007/s11427-022-2391-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 05/18/2023] [Indexed: 10/13/2023]
Abstract
Weaning piglets usually suffer from severe diarrhea (commonly known as postweaning diarrhea, PWD) along with intestinal motility disorder. Intestinal peristalsis is mainly regulated by the longitudinal muscle-myenteric plexus (LM-MP). To understand the relationship between intestinal LM-MP function and the development of PWD, we compared the intestinal electrical activity, and the transcriptional profile of the LM-MP between 21-day-old piglets (just weaned, n=7) and 24-day-old piglets (suffered the most severe weaning stress, n=7). The results showed that 24-day-old piglets exhibited different degrees of diarrhea. A significant increase in the slow-wave frequency in the ileum and colon was observed in 24-day-old piglets, while c-kit expression in the intestinal LM-MPs was significantly decreased, indicating that PWD caused by elevated slow-wave frequency may be associated with loss of c-kit. The real-time quantitative PCR (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA) showed that intestinal LM-MPs in 24-day-old piglets may undergo inflammation and oxidative stress. Significant increases in 8-hydroxy-2'-deoxyguanosine and decreases in thioredoxin suggest that weaning may lead to DNA damage in the LM-MP of 24-day-old piglets. In addition, activating transcription factor 3 was significantly upregulated, indicating nerve damage in the LM-MP of 24-day-old piglets. The transcriptomic results showed that most of the differentially expressed genes in the ileal LM-MP after weaning were downregulated and closely related to the cell cycle process. Subsequent RT-qPCR analysis showed that the relative expression of p21 was upregulated, while the expression of cyclin A2, cyclin B1, and proliferating cell nuclear antigen was downregulated in the ileal and colonic LM-MP of 24-day-old piglets, suggesting that weaning may inhibit cell proliferation and cause G1/S cell cycle arrest in ileal and colonic LM-MP. In conclusion, weaning may lead to cell cycle arrest by causing DNA damage in the LM-MP, impairing intestinal motility regulation, and ultimately leading to diarrhea in piglets.
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Affiliation(s)
- Jing Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Hunan Research Center of Livestock and Poultry Sciences, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Fenfen Liu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Hunan Research Center of Livestock and Poultry Sciences, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- University of Chinese Academy of Sciences, Beijing, 100008, China
| | - Kaibin Mo
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Hunan Research Center of Livestock and Poultry Sciences, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Hengjia Ni
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Hunan Research Center of Livestock and Poultry Sciences, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China.
- University of Chinese Academy of Sciences, Beijing, 100008, China.
| | - Yulong Yin
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Hunan Research Center of Livestock and Poultry Sciences, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China.
- University of Chinese Academy of Sciences, Beijing, 100008, China.
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Baron N, Purushotham R, Pullaiahgari D, Bose P, Zarivach R, Shapira M. LeishIF4E2 is a cap-binding protein that plays a role in Leishmania cell cycle progression. FASEB J 2024; 38:e23367. [PMID: 38095329 DOI: 10.1096/fj.202301665r] [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: 08/16/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023]
Abstract
Leishmania encode six paralogs of the cap-binding protein eIF4E and five eIF4G candidates, forming unique complexes. Two cap-binding proteins, LeishIF4E1 and LeishIF4E2, do not bind any identified LeishIF4Gs, thus their roles are intriguing. Here, we combine structural prediction, proteomic analysis, and interaction assays to shed light on LeishIF4E2 function. A nonconserved C-terminal extension was identified through structure prediction and sequence alignment. m7 GTP-binding assays involving both recombinant and transgenic LeishIF4E2 with and without the C-terminal extension revealed that this extension functions as a regulatory gate, modulating the cap-binding activity of LeishIF4E2. The interactomes of the two LeishIF4E2 versions were investigated, highlighting the role of the C-terminal extension in binding to SLBP2. SLBP2 is known to interact with a stem-loop structure in the 3' UTRs of histone mRNAs. Consistent with the predicted inhibitory effect of SLBP2 on histone expression in Xenopus laevis, a hemizygous deletion mutant of LeishIF4E2, exhibited an upregulation of several histones. We therefore propose that LeishIF4E2 is involved in histone expression, possibly through its interaction between SLBP2 and LeishIF4E2, thus affecting cell cycle progression. In addition, cell synchronization showed that LeishIF4E2 expression decreased during the S-phase, when histones are known to be synthesized. Previous studies in T. brucei also highlighted an association between TbEIF4E2 and SLBP2, and further reported on an interaction between TbIF4E2 and S-phase-abundant mRNAs. Our results show that overexpression of LeishIF4E2 correlates with upregulation of cell cycle and chromosome maintenance proteins. Along with its effect on histone expression, we propose that LeishIF4E2 is involved in cell cycle progression.
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Affiliation(s)
- Nofar Baron
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Rajaram Purushotham
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Priyanka Bose
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Michal Shapira
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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Tshilenge KT, Aguirre CG, Bons J, Gerencser AA, Basisty N, Song S, Rose J, Lopez-Ramirez A, Naphade S, Loureiro A, Battistoni E, Milani M, Wehrfritz C, Holtz A, Hetz C, Mooney SD, Schilling B, Ellerby LM. Proteomic Analysis of Huntington's Disease Medium Spiny Neurons Identifies Alterations in Lipid Droplets. Mol Cell Proteomics 2023; 22:100534. [PMID: 36958627 PMCID: PMC10165459 DOI: 10.1016/j.mcpro.2023.100534] [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: 05/28/2022] [Revised: 03/15/2023] [Accepted: 03/19/2023] [Indexed: 03/25/2023] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disease caused by a CAG repeat expansion in the Huntingtin (HTT) gene. The resulting polyglutamine (polyQ) tract alters the function of the HTT protein. Although HTT is expressed in different tissues, the medium spiny projection neurons (MSNs) in the striatum are particularly vulnerable in HD. Thus, we sought to define the proteome of human HD patient-derived MSNs. We differentiated HD72 induced pluripotent stem cells and isogenic controls into MSNs and carried out quantitative proteomic analysis. Using data-dependent acquisitions with FAIMS for label-free quantification on the Orbitrap Lumos mass spectrometer, we identified 6,323 proteins with at least two unique peptides. Of these, 901 proteins were altered significantly more in the HD72-MSNs than in isogenic controls. Functional enrichment analysis of upregulated proteins demonstrated extracellular matrix and DNA signaling (DNA replication pathway, double-strand break repair, G1/S transition) with the highest significance. Conversely, processes associated with the downregulated proteins included neurogenesis-axogenesis, the brain-derived neurotrophic factor-signaling pathway, Ephrin-A: EphA pathway, regulation of synaptic plasticity, triglyceride homeostasis cholesterol, plasmid lipoprotein particle immune response, interferon-γ signaling, immune system major histocompatibility complex, lipid metabolism and cellular response to stimulus. Moreover, proteins involved in the formation and maintenance of axons, dendrites, and synapses (e.g., Septin protein members) were dysregulated in HD72-MSNs. Importantly, lipid metabolism pathways were altered, and using quantitative image, we found analysis that lipid droplets accumulated in the HD72-MSN, suggesting a deficit in the turnover of lipids possibly through lipophagy. Our proteomics analysis of HD72-MSNs identified relevant pathways that are altered in MSNs and confirm current and new therapeutic targets for HD.
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Affiliation(s)
| | - Carlos Galicia Aguirre
- The Buck Institute for Research on Aging, Novato, California, 94945, USA; University of Southern California, Leonard Davis School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90893, USA
| | - Joanna Bons
- The Buck Institute for Research on Aging, Novato, California, 94945, USA
| | - Akos A Gerencser
- The Buck Institute for Research on Aging, Novato, California, 94945, USA
| | - Nathan Basisty
- The Buck Institute for Research on Aging, Novato, California, 94945, USA; Translational Gerontology Branch, National Institute on Aging (NIA), NIH, Baltimore, Maryland, 21244, USA
| | - Sicheng Song
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Jacob Rose
- The Buck Institute for Research on Aging, Novato, California, 94945, USA
| | | | - Swati Naphade
- The Buck Institute for Research on Aging, Novato, California, 94945, USA
| | - Ashley Loureiro
- The Buck Institute for Research on Aging, Novato, California, 94945, USA
| | - Elena Battistoni
- The Buck Institute for Research on Aging, Novato, California, 94945, USA
| | - Mateus Milani
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile; Center for Geroscience, Brain Health and Metabolism (GERO), Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile
| | - Cameron Wehrfritz
- The Buck Institute for Research on Aging, Novato, California, 94945, USA
| | - Anja Holtz
- The Buck Institute for Research on Aging, Novato, California, 94945, USA
| | - Claudio Hetz
- The Buck Institute for Research on Aging, Novato, California, 94945, USA; Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile; Center for Geroscience, Brain Health and Metabolism (GERO), Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Birgit Schilling
- The Buck Institute for Research on Aging, Novato, California, 94945, USA; University of Southern California, Leonard Davis School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90893, USA.
| | - Lisa M Ellerby
- The Buck Institute for Research on Aging, Novato, California, 94945, USA; University of Southern California, Leonard Davis School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90893, USA.
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Pang D, Yu S, Yang X. A mini-review of the role of condensin in human nervous system diseases. Front Mol Neurosci 2022; 15:889796. [PMID: 35992200 PMCID: PMC9386267 DOI: 10.3389/fnmol.2022.889796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/07/2022] [Indexed: 01/10/2023] Open
Abstract
Mitosis and meiosis are crucial life activities that transmit eukaryotic genetic information to progeny in a stable and orderly manner. The formation and appearance of chromosomes, which are derived from chromatin, are the preconditions and signs of mitosis. When entering mitosis, interphase loose chromatin is highly spiralized and folded to form compact chromosomes. In recent years, it has been found that in addition to the well-known DNA, histones, and topoisomerase, a large protein complex called condensin plays an important role in the process of chromosome formation. Numerous studies have shown that the abnormal function of condensin can lead to incomplete or excessive concentration of chromatin, as well as disorder of genome organization process, abnormal transmission of genetic information, and ultimately lead to various diseases of individual, especially in nervous system diseases. In this review, the biological function of condensin and the potential pathogenic mechanism of condensin in nervous system diseases are briefly summarized. Therefore, the investigation of these mechanisms makes a significant contribution to the understanding of those related diseases and provides new ideas for clinical treatments.
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Affiliation(s)
- Du Pang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Tianjin, China
| | - Shengping Yu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Tianjin, China
- *Correspondence: Shengping Yu Xuejun Yang
| | - Xuejun Yang
- Department of Neurosurgery, Beijing Tsinghua Changgung Hospital, Affiliated Hospital of Tsinghua University, Beijing, China
- *Correspondence: Shengping Yu Xuejun Yang
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ITRAQ-based quantitative proteomic analysis reveals that VPS35 promotes the expression of MCM2-7 genes in HeLa cells. Sci Rep 2022; 12:9700. [PMID: 35690672 PMCID: PMC9188599 DOI: 10.1038/s41598-022-13934-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/13/2022] [Indexed: 11/25/2022] Open
Abstract
Vacuolar protein sorting 35 (VPS35) is a major component of the retromer complex that regulates endosomal trafficking in eukaryotic cells. Recent studies have shown that VPS35 promotes tumor cell proliferation and affects the nuclear accumulation of its interacting partner. In this study, isobaric tags for relative and absolute quantitation (iTRAQ)-based mass spectrometry were used to measure the changes in nuclear protein abundance in VPS35-depleted HeLa cells. A total of 47 differentially expressed proteins were identified, including 27 downregulated and 20 upregulated proteins. Gene ontology (GO) analysis showed that the downregulated proteins included several minichromosome maintenance (MCM) proteins described as cell proliferation markers, and these proteins were present in the MCM2-7 complex, which is essential for DNA replication. Moreover, we validated that loss of VPS35 reduced the mRNA and protein expression of MCM2-7 genes. Notably, re-expression of VPS35 in VPS35 knockout HeLa cells rescued the expression of these genes. Functionally, we showed that VPS35 contributes to cell proliferation and maintenance of genomic stability of HeLa cells. Therefore, these findings reveal that VPS35 is involved in the regulation of MCM2-7 gene expression and establish a link between VPS35 and cell proliferation.
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Tsitsipatis D, Martindale JL, Ubaida‐Mohien C, Lyashkov A, Yanai H, Kashyap A, Shin CH, Herman AB, Ji E, Yang J, Munk R, Dunn C, Lukyanenko Y, Yang X, Chia CW, Karikkineth AC, Zukley L, D’Agostino J, Kaileh M, Cui C, Beerman I, Ferrucci L, Gorospe M. Proteomes of primary skin fibroblasts from healthy individuals reveal altered cell responses across the life span. Aging Cell 2022; 21:e13609. [PMID: 35429111 PMCID: PMC9124301 DOI: 10.1111/acel.13609] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/24/2022] [Indexed: 02/04/2023] Open
Abstract
Changes in the proteome of different human tissues with advancing age are poorly characterized. Here, we studied the proteins present in primary skin fibroblasts collected from 82 healthy individuals across a wide age spectrum (22-89 years old) who participated in the GESTALT (Genetic and Epigenetic Signatures of Translational Aging Laboratory Testing) study of the National Institute on Aging, NIH. Proteins were extracted from lysed fibroblasts and subjected to liquid chromatography-mass spectrometry analysis, and the expression levels of 9341 proteins were analyzed using linear regression models. We identified key pathways associated with skin fibroblast aging, including autophagy, scavenging of reactive oxygen species (ROS), ribosome biogenesis, DNA replication, and DNA repair. Changes in these prominent pathways were corroborated using molecular and cell culture approaches. Our study establishes a framework of the global proteome governing skin fibroblast aging and points to possible biomarkers and therapeutic targets.
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Affiliation(s)
- Dimitrios Tsitsipatis
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Jennifer L. Martindale
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Ceereena Ubaida‐Mohien
- Translational Gerontology BranchNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Alexey Lyashkov
- Translational Gerontology BranchNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Hagai Yanai
- Translational Gerontology BranchNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Amogh Kashyap
- Translational Gerontology BranchNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Chang Hoon Shin
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Allison B. Herman
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Eunbyul Ji
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Jen‐Hao Yang
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Rachel Munk
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Christopher Dunn
- Laboratory of Molecular Biology and ImmunologyNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Yevgeniya Lukyanenko
- Translational Gerontology BranchNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Xiaoling Yang
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Chee W. Chia
- Clinical Research CoreNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Ajoy C. Karikkineth
- Clinical Research CoreNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Linda Zukley
- Clinical Research CoreNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Jarod D’Agostino
- Clinical Research CoreNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Mary Kaileh
- Laboratory of Molecular Biology and ImmunologyNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Chang‐Yi Cui
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Isabel Beerman
- Translational Gerontology BranchNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Luigi Ferrucci
- Translational Gerontology BranchNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Myriam Gorospe
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
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Choi SH, Cho K, Kim ES, Yoo HY. Proline-serine-threonine-repeat region of MDC1 mediates Chk1 phosphorylation and the DNA double-strand break repair. Int J Biochem Cell Biol 2021; 143:106152. [PMID: 34974185 DOI: 10.1016/j.biocel.2021.106152] [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: 09/10/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 11/29/2022]
Abstract
MDC1, a mediator of DNA damage response, recruits other repair proteins on double-strand break (DSB) sites. MDC1 is necessary for activating checkpoint kinases Chk1 and Chk2. It is unclear whether Chk1 interacts with MDC1. MDC1 also comprises many discrete domains. The role of the proline-serine-threonine (PST)-repeat domain of MDC1 in the DNA damage response is unclear. Here, we showed that MDC1 directly binds Chk1 through this PST-repeat region. Phosphorylation of Chk1 by ionizing radiation (IR) also required this PST-repeat domain. Degradation of intact MDC1 was accelerated depending on the PST-repeat domain after IR exposure. In the IR damage response, the PST-repeat-deleted MDC1 levels remained elevated with slow degradation. This abnormal regulation of MDC1 was F-box- and WD40 repeat-containing 7 (FBXW7)-dependent. The mutation of lysine 1413 within the PST-repeat of MDC1 deregulated MDC1 with or without damage. K1413R mutant and PST-deleted MDC1 displayed reduced ability to repair the damaged genome post-IR exposure. These results provide that the PST domain of MDC1 is involved in Chk1 and DNA repair activation. The findings suggest new insights into how MDC1 connects the checkpoint and DNA repair in the DNA damage response.
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Affiliation(s)
- Seung Ho Choi
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea; Samsung Biomedical Research Institute, Research Institute for Future Medicine, Samsung Medical Center, Seoul 06355, Korea
| | - Kyoungjoo Cho
- Department of Life Science, College of Fusion Science, Kyonggi University, Suwon 16227, Korea
| | - Eun Seon Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea; Samsung Biomedical Research Institute, Research Institute for Future Medicine, Samsung Medical Center, Seoul 06355, Korea
| | - Hae Yong Yoo
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea; Samsung Biomedical Research Institute, Research Institute for Future Medicine, Samsung Medical Center, Seoul 06355, Korea.
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10
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Elersek T, Novak M, Mlinar M, Virant I, Bahor N, Leben K, Žegura B, Filipič M. Lethal and Sub-Lethal Effects and Modulation of Gene Expression Induced by T Kinase Inhibitors in Zebrafish (Danio Rerio) Embryos. TOXICS 2021; 10:toxics10010004. [PMID: 35051046 PMCID: PMC8781212 DOI: 10.3390/toxics10010004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/16/2021] [Accepted: 12/21/2021] [Indexed: 12/11/2022]
Abstract
Tyrosine kinase inhibitors (TKIs) are designed for targeted cancer therapy. The consumption of these drugs during the last 20 years has been constantly rising. In the zebrafish (Danio rerio) embryo toxicity test, we assessed the toxicity of six TKIs: imatinib mesylate, erlotinib, nilotinib, dasatinib, sorafenib and regorafenib. Imatinib mesylate and dasatinib induced lethal effects, while regorafenib, sorfenib and dasatinib caused a significant increase of sub-lethal effects, predominantly oedema, no blood circulation and formation of blood aggregates. The analyses of the changes in the expression of selected genes associated with the hormone system after the exposure to imatinib mesylate, dasatinib and regorafenib demonstrated that all three tested TKIs deregulated the expression of oestrogen receptor esr1, cytochrome P450 aromatase (cypa19b) and hydroxysteroid-dehydrogenase (hsd3b), regorafenib, and also thyroglobulin (tg). The expression of genes involved in the DNA damage response (gadd45 and mcm6) and apoptosis (bcl2) was deregulated only by exposure to regorafenib. The data indicate that common mechanisms, namely antiangiogenic activity and interference with steroidogenesis are involved in the TKI induced sub-lethal effects and potential hormone disrupting activity, respectively. The residues of TKIs may represent an environmental hazard; therefore, further ecotoxicological studies focusing also on the effects of their mixtures are warranted.
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Affiliation(s)
- Tina Elersek
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia; (T.E.); (M.N.); (M.M.); (N.B.); (K.L.); (B.Ž.)
| | - Matjaž Novak
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia; (T.E.); (M.N.); (M.M.); (N.B.); (K.L.); (B.Ž.)
| | - Mateja Mlinar
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia; (T.E.); (M.N.); (M.M.); (N.B.); (K.L.); (B.Ž.)
| | - Igor Virant
- Institute of Oncology Ljubljana, Zaloška 2, 1000 Ljubljana, Slovenia;
| | - Nika Bahor
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia; (T.E.); (M.N.); (M.M.); (N.B.); (K.L.); (B.Ž.)
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Karin Leben
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia; (T.E.); (M.N.); (M.M.); (N.B.); (K.L.); (B.Ž.)
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Bojana Žegura
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia; (T.E.); (M.N.); (M.M.); (N.B.); (K.L.); (B.Ž.)
| | - Metka Filipič
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia; (T.E.); (M.N.); (M.M.); (N.B.); (K.L.); (B.Ž.)
- Correspondence:
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11
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Salas-Leiva DE, Tromer EC, Curtis BA, Jerlström-Hultqvist J, Kolisko M, Yi Z, Salas-Leiva JS, Gallot-Lavallée L, Williams SK, Kops GJPL, Archibald JM, Simpson AGB, Roger AJ. Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist. Nat Commun 2021; 12:6003. [PMID: 34650064 PMCID: PMC8516963 DOI: 10.1038/s41467-021-26077-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022] Open
Abstract
Cells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.
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Affiliation(s)
- Dayana E. Salas-Leiva
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada ,grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Eelco C. Tromer
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom ,grid.4830.f0000 0004 0407 1981Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Bruce A. Curtis
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Jon Jerlström-Hultqvist
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Martin Kolisko
- grid.418095.10000 0001 1015 3316Institute of Parasitology, Biology Centre, Czech Acad. Sci, České Budějovice, Czech Republic
| | - Zhenzhen Yi
- grid.263785.d0000 0004 0368 7397Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Joan S. Salas-Leiva
- grid.466575.30000 0001 1835 194XCONACyT-Centro de Investigación en Materiales Avanzados, Departamento de medio ambiente y energía, Miguel de Cervantes 120, Complejo Industrial Chihuahua, 31136 Chihuahua, Chih. México
| | - Lucie Gallot-Lavallée
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Shelby K. Williams
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Geert J. P. L. Kops
- grid.7692.a0000000090126352Oncode Institute, Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - John M. Archibald
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Alastair G. B. Simpson
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Andrew J. Roger
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
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12
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Olivier DW, Pretorius E, Engelbrecht AM. Serum amyloid A1: Innocent bystander or active participant in cell migration in triple-negative breast cancer? Exp Cell Res 2021; 406:112759. [PMID: 34332984 DOI: 10.1016/j.yexcr.2021.112759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 01/26/2023]
Abstract
The Serum Amyloid A (SAA) family of proteins is associated with various pathological conditions, including cancer. However, their role in cancer is incompletely understood. Here, we investigated the role of SAA1 in cell cycle regulation, apoptosis, survival signaling, metabolism, and metastasis in models of triple-negative breast cancer (TNBC), using RNAi. Our data show that in untransformed epithelial cells (MCF12A), the knockdown of SAA1 induces the expression of cell cycle regulators (MCM2, p53), the activation of DNA repair (PARP synthesis), and survival signaling (NFκB). In contrast, knockdown of SAA1 in the TNBC cell line (MDA-MB-231) induced the expression p16 and shifted cells in the cell cycle from the S to G2/M phase, without the activation of DNA repair. Moreover, in SAA1-deficient MDA-MB-231 and HCC70 cells, metabolism (NADH oxidation) continually increased while cell migration (% wound closure and the rate of wound closure) decreased. However, silencing of SAA1 altered epithelial and mesenchymal markers in MCF12A (E-cadherin, Laminin 1β, Vimentin) and MDA-MB-231 (α-Smooth muscle actin) cells, associated with the metastatic program of epithelial-mesenchymal transition. Nonetheless, our data provide evidence that SAA1 could potentially serve as a therapeutic target in TNBC.
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Affiliation(s)
- Daniel Wilhelm Olivier
- Department of Physiological Sciences, Stellenbosch University, Mike De Vries Building, Corner Merriman and Bosman Road, Stellenbosch, 7602, South Africa.
| | - Etheresia Pretorius
- Department of Physiological Sciences, Stellenbosch University, Mike De Vries Building, Corner Merriman and Bosman Road, Stellenbosch, 7602, South Africa.
| | - Anna-Mart Engelbrecht
- Department of Physiological Sciences, Stellenbosch University, Mike De Vries Building, Corner Merriman and Bosman Road, Stellenbosch, 7602, South Africa.
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13
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Tain LS, Sehlke R, Meilenbrock RL, Leech T, Paulitz J, Chokkalingam M, Nagaraj N, Grönke S, Fröhlich J, Atanassov I, Mann M, Beyer A, Partridge L. Tissue-specific modulation of gene expression in response to lowered insulin signalling in Drosophila. eLife 2021; 10:e67275. [PMID: 33879316 PMCID: PMC8060030 DOI: 10.7554/elife.67275] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/18/2021] [Indexed: 01/15/2023] Open
Abstract
Reduced activity of the insulin/IGF signalling network increases health during ageing in multiple species. Diverse and tissue-specific mechanisms drive the health improvement. Here, we performed tissue-specific transcriptional and proteomic profiling of long-lived Drosophila dilp2-3,5 mutants, and identified tissue-specific regulation of >3600 transcripts and >3700 proteins. Most expression changes were regulated post-transcriptionally in the fat body, and only in mutants infected with the endosymbiotic bacteria, Wolbachia pipientis, which increases their lifespan. Bioinformatic analysis identified reduced co-translational ER targeting of secreted and membrane-associated proteins and increased DNA damage/repair response proteins. Accordingly, age-related DNA damage and genome instability were lower in fat body of the mutant, and overexpression of a minichromosome maintenance protein subunit extended lifespan. Proteins involved in carbohydrate metabolism showed altered expression in the mutant intestine, and gut-specific overexpression of a lysosomal mannosidase increased autophagy, gut homeostasis, and lifespan. These processes are candidates for combatting ageing-related decline in other organisms.
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Affiliation(s)
| | - Robert Sehlke
- Max-Planck Institute for Biology of AgeingCologneGermany
- CECAD Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesCologneGermany
| | | | - Thomas Leech
- Max-Planck Institute for Biology of AgeingCologneGermany
| | - Jonathan Paulitz
- Max-Planck Institute for Biology of AgeingCologneGermany
- CECAD Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesCologneGermany
| | - Manopriya Chokkalingam
- CECAD Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesCologneGermany
| | - Nagarjuna Nagaraj
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of BiochemistryMartinsriedGermany
| | | | - Jenny Fröhlich
- Max-Planck Institute for Biology of AgeingCologneGermany
| | | | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of BiochemistryMartinsriedGermany
| | - Andreas Beyer
- CECAD Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesCologneGermany
- Center for Molecular Medicine (CMMC) & Cologne School for Computational Biology (CSCB), University of CologneCologneGermany
| | - Linda Partridge
- Max-Planck Institute for Biology of AgeingCologneGermany
- Institute of Healthy Ageing, and GEE, UCLLondonUnited Kingdom
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14
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Shrestha R, Llaurado Fernandez M, Dawson A, Hoenisch J, Volik S, Lin YY, Anderson S, Kim H, Haegert AM, Colborne S, Wong NKY, McConeghy B, Bell RH, Brahmbhatt S, Lee CH, DiMattia GE, Le Bihan S, Morin GB, Collins CC, Carey MS. Multiomics Characterization of Low-Grade Serous Ovarian Carcinoma Identifies Potential Biomarkers of MEK Inhibitor Sensitivity and Therapeutic Vulnerability. Cancer Res 2021; 81:1681-1694. [PMID: 33441310 DOI: 10.1158/0008-5472.can-20-2222] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/12/2020] [Accepted: 01/11/2021] [Indexed: 11/16/2022]
Abstract
Low-grade serous ovarian carcinoma (LGSOC) is a rare tumor subtype with high case fatality rates in patients with metastatic disease. There is a pressing need to develop effective treatments using newly available preclinical models for therapeutic discovery and drug evaluation. Here, we use multiomics integration of whole-exome sequencing, RNA sequencing, and mass spectrometry-based proteomics on 14 LGSOC cell lines to elucidate novel biomarkers and therapeutic vulnerabilities. Comparison of LGSOC cell line data with LGSOC tumor data enabled predictive biomarker identification of MEK inhibitor (MEKi) efficacy, with KRAS mutations found exclusively in MEKi-sensitive cell lines and NRAS mutations found mostly in MEKi-resistant cell lines. Distinct patterns of Catalogue of Somatic Mutations in Cancer mutational signatures were identified in MEKi-sensitive and MEKi-resistant cell lines. Deletions of CDKN2A/B and MTAP genes were more frequent in cell lines than tumor samples and possibly represent key driver events in the absence of KRAS/NRAS/BRAF mutations. These LGSOC cell lines were representative models of the molecular aberrations found in LGSOC tumors. For prediction of in vitro MEKi efficacy, proteomic data provided better discrimination than gene expression data. Condensin, minichromosome maintenance, and replication factor C protein complexes were identified as potential treatment targets in MEKi-resistant cell lines. This study suggests that CDKN2A/B or MTAP deficiency may be exploited using synthetically lethal treatment strategies, highlighting the importance of using proteomic data as a tool for molecular drug prediction. Multiomics approaches are crucial to improving our understanding of the molecular underpinnings of LGSOC and applying this information to develop new therapies. SIGNIFICANCE: These findings highlight the utility of global multiomics to characterize LGSOC cell lines as research models, to determine biomarkers of MEKi resistance, and to identify potential novel therapeutic targets.
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Affiliation(s)
- Raunak Shrestha
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Marta Llaurado Fernandez
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amy Dawson
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joshua Hoenisch
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stanislav Volik
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Yen-Yi Lin
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shawn Anderson
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Hannah Kim
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anne M Haegert
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Shane Colborne
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Nelson K Y Wong
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology & Laboratory Medicine, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Brian McConeghy
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Robert H Bell
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | | | - Cheng-Han Lee
- Department of Pathology & Laboratory Medicine, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Gabriel E DiMattia
- Translational Ovarian Cancer Research Program, London Health Science Centre, London, Ontario, Canada
| | | | - Gregg B Morin
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Colin C Collins
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada. .,Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark S Carey
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada.
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15
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Novak M, Baebler Š, Žegura B, Rotter A, Gajski G, Gerić M, Garaj-Vrhovac V, Bakos K, Csenki Z, Kovács R, Horváth Á, Gazsi G, Filipič M. Deregulation of whole-transcriptome gene expression in zebrafish (Danio rerio) after chronic exposure to low doses of imatinib mesylate in a complete life cycle study. CHEMOSPHERE 2021; 263:128097. [PMID: 33297093 DOI: 10.1016/j.chemosphere.2020.128097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 06/12/2023]
Abstract
Imatinib mesylate (IM) is an anticancer drug that belongs to tyrosine kinase inhibitors. We report the results of the first investigation of the chronic exposure of zebrafish (Danio rerio) to IM. The exposure to IM (0.01, 1 and 100 μg/L) was initiated in adult fish and continued through hatching and the offspring generation for seven months. In addition to standard toxicological endpoints, induction of genotoxic effects and whole-genome transcriptome of liver samples of offspring generation of zebrafish were analysed. Exposure to IM did not affect the survival and growth of zebrafish, did not cause any histopathological changes, but it induced a marginal increase in the chromosomal damage in blood cells. The whole-genome transcriptome analyses demonstrated dose-dependent increase in the number of differentially expressed genes with a significantly higher number of deregulated genes in female fish compared to male. Differentially expressed genes included genes involved in response to DNA damage, cell cycle control and regulation of circadian rhythm. Based on the low genotoxic activity and the pattern of the changes in DNA damage responsive genes we consider that at current environmental exposure levels, IM represents low risk for genotoxic effects in aquatic organisms. Exposure to IM also induced deregulation of the expression of genes associated with steroidogenesis and hormone metabolism and function, which indicates hormone-disrupting activity of IM that has not been studied so far. The study provide new information on the potential consequences of chronic exposure to the residues of tyrosine kinase inhibitors, which remain to be further explored.
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Affiliation(s)
- Matjaž Novak
- National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia.
| | - Špela Baebler
- National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Bojana Žegura
- National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Ana Rotter
- National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Goran Gajski
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, Ksaverska Cesta 2, 10000, Zagreb, Croatia
| | - Marko Gerić
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, Ksaverska Cesta 2, 10000, Zagreb, Croatia
| | - Vera Garaj-Vrhovac
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, Ksaverska Cesta 2, 10000, Zagreb, Croatia
| | - Katalin Bakos
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Pater Károly U, H-2100, Gödöllo, Hungary
| | - Zsolt Csenki
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Pater Károly U, H-2100, Gödöllo, Hungary
| | - Róbert Kovács
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Pater Károly U, H-2100, Gödöllo, Hungary
| | - Ákos Horváth
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Pater Károly U, H-2100, Gödöllo, Hungary
| | - Gyöngyi Gazsi
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, 1. Pater Károly U, H-2100, Gödöllo, Hungary
| | - Metka Filipič
- National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
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16
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Yang L, Wang X, Jiao X, Tian B, Zhang M, Zhou C, Wang R, Chen H, Wang B, Li J, Liu J, Zhang G, Liu P. Suppressor of Ty 16 promotes lung cancer malignancy and is negatively regulated by miR-1227-5p. Cancer Sci 2020; 111:4075-4087. [PMID: 32860308 PMCID: PMC7648015 DOI: 10.1111/cas.14627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 07/03/2020] [Accepted: 07/27/2020] [Indexed: 01/01/2023] Open
Abstract
Suppressor of Ty 16 (Spt16) is a component of the facilitates chromatin transcription (FACT) complex, which is a histone chaperone and involved in gene transcription, DNA replication, and DNA repair. Previous studies showed that FACT is highly expressed in cancer, and cancer cells are more reliant on FACT than normal cells. However, the relationship between Spt16 and lung cancer remains unclear. In this study, we explored the functions of Spt16 in lung cancer cells. The effects of Spt16 on lung cancer cell proliferation, cell cycle progression, apoptosis, migration, and invasion were examined. We found that knockdown of Spt16 led to obvious decreases of both Rb and MCM7, and further activated the DNA damage response (DDR) pathway. In addition, a novel micro‐RNA, miR‐1227‐5p, directly targeted the 3′‐UTR of Spt16 and regulated the mRNA levels of Spt16. Furthermore, we found that CBL0137, the functional inhibitor of FACT, showed similar effects as loss of Spt16. Together, our data indicated that Spt16 is likely to be an essential regulator for lung cancer malignancy and is negatively regulated by miR‐1227‐5p.
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Affiliation(s)
- Lu Yang
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xing Wang
- Department of Pathology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Xinyan Jiao
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Bixia Tian
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Miao Zhang
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Can Zhou
- Department of Breast Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ruiqi Wang
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - He Chen
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Bo Wang
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Juan Li
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jie Liu
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Guanjun Zhang
- Department of Pathology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Peijun Liu
- Center for Translational Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Fabits M, Gonçalves Magalhães V, Chan B, Girault V, Elbasani E, Rossetti E, Saeland E, Messerle M, Pichlmair A, Lisnić VJ, Brinkmann MM. The Cytomegalovirus Tegument Protein UL35 Antagonizes Pattern Recognition Receptor-Mediated Type I IFN Transcription. Microorganisms 2020; 8:microorganisms8060790. [PMID: 32466380 PMCID: PMC7356634 DOI: 10.3390/microorganisms8060790] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/23/2020] [Accepted: 05/23/2020] [Indexed: 12/16/2022] Open
Abstract
The rapid activation of pattern recognition receptor (PRR)-mediated type I interferon (IFN) signaling is crucial for the host response to infection. In turn, human cytomegalovirus (HCMV) must evade this potent response to establish life-long infection. Here, we reveal that the HCMV tegument protein UL35 antagonizes the activation of type I IFN transcription downstream of the DNA and RNA sensors cGAS and RIG-I, respectively. We show that ectopic expression of UL35 diminishes the type I IFN response, while infection with a recombinant HCMV lacking UL35 induces an elevated type I IFN response compared to wildtype HCMV. With a series of luciferase reporter assays and the analysis of signaling kinetics upon HCMV infection, we observed that UL35 downmodulates PRR signaling at the level of the key signaling factor TANK-binding kinase 1 (TBK1). Finally, we demonstrate that UL35 and TBK1 co-immunoprecipitate when co-expressed in HEK293T cells. In addition, we show that a previously reported cellular binding partner of UL35, O-GlcNAc transferase (OGT), post-translationally GlcNAcylates UL35, but that this modification is not required for the antagonizing effect of UL35 on PRR signaling. In summary, we have identified UL35 as the first HCMV protein to antagonize the type I IFN response at the level of TBK1, thereby enriching our understanding of how this important herpesvirus escapes host immune responses.
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Affiliation(s)
- Markus Fabits
- Institute of Genetics, Technische Universität Braunschweig, 38106 Braunschweig, Germany;
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (V.G.M.); (B.C.)
| | - Vladimir Gonçalves Magalhães
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (V.G.M.); (B.C.)
| | - Baca Chan
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (V.G.M.); (B.C.)
| | - Virginie Girault
- Institute of Virology, Technical University of Munich, School of Medicine, 81675 Munich, Germany; (V.G.); (A.P.)
| | - Endrit Elbasani
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany; (E.E.); (M.M.)
| | - Elisa Rossetti
- Janssen Vaccines & Prevention BV, 2333 CN Leiden, The Netherlands; (E.R.); (E.S.)
| | - Eirikur Saeland
- Janssen Vaccines & Prevention BV, 2333 CN Leiden, The Netherlands; (E.R.); (E.S.)
| | - Martin Messerle
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany; (E.E.); (M.M.)
| | - Andreas Pichlmair
- Institute of Virology, Technical University of Munich, School of Medicine, 81675 Munich, Germany; (V.G.); (A.P.)
| | - Vanda Juranić Lisnić
- Department for Histology and Embryology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia;
| | - Melanie M. Brinkmann
- Institute of Genetics, Technische Universität Braunschweig, 38106 Braunschweig, Germany;
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (V.G.M.); (B.C.)
- Correspondence: ; Tel.: +49-531-6181-3069
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Fang Z, Pan Z. Essential Role of Ubiquitin-Fold Modifier 1 Conjugation in DNA Damage Response. DNA Cell Biol 2019; 38:1030-1039. [PMID: 31368785 DOI: 10.1089/dna.2019.4861] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Both endogenous and exogenous factors can cause DNA damage that compromises genomic integrity and cell viability. A proper DNA damage response (DDR) plays a role in maintaining genome stability and preventing tumorigenesis. DNA double-strand breaks (DSBs) are the most toxic DNA lesion, whose response is dominated by the ataxia-telangiectasia mutated (ATM) protein kinase. After being activated by the sensor Mre11-Rad50-Nbs1 (MRN) complex or acetyltransferase Tip60, ATM rapidly phosphorylates downstream targets to launch DDR signaling when DNA is damaged. However, the exact mechanism of DDR is complex and ambiguous. Ufmylation, one type of ubiquitin-like modification, proceeds mainly through a three-step enzymatic reaction to help ubiquitin-fold modifier 1 (Ufm1), attach to substrates with ubiquitin-like modifier-activating enzyme 5 (Uba5), Ufm1-conjugating enzyme 1 (Ufc1) and Ufm1-specific ligase 1 (Ufl1). Although ubiquitination is essential to the DSBs response, the potential function of ufmylation in DDR is largely unknown. Herein, we review the relationship between ufmylation and DDR to elucidate the function and mechanism of ufmylation in DDR, which would reveal the pathogenesis of some diseases and provide new guidance to create a therapeutic method.
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Affiliation(s)
- Zhi Fang
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Zezheng Pan
- Faculty of Basic Medical Science, Jiangxi Medical College, Nanchang University, Nanchang, China
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