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Feng LL, Bie SY, Deng ZH, Bai SM, Shi J, Qin CL, Liu HL, Li JX, Chen WY, Zhou JY, Jiao CM, Ma Y, Qiu MB, Ai HS, Zheng J, Hung MC, Wang YL, Wan XB, Fan XJ. Ubiquitin-induced RNF168 condensation promotes DNA double-strand break repair. Proc Natl Acad Sci U S A 2024; 121:e2322972121. [PMID: 38968116 DOI: 10.1073/pnas.2322972121] [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: 01/01/2024] [Accepted: 05/22/2024] [Indexed: 07/07/2024] Open
Abstract
Rapid accumulation of repair factors at DNA double-strand breaks (DSBs) is essential for DSB repair. Several factors involved in DSB repair have been found undergoing liquid-liquid phase separation (LLPS) at DSB sites to facilitate DNA repair. RNF168, a RING-type E3 ubiquitin ligase, catalyzes H2A.X ubiquitination for recruiting DNA repair factors. Yet, whether RNF168 undergoes LLPS at DSB sites remains unclear. Here, we identified K63-linked polyubiquitin-triggered RNF168 condensation which further promoted RNF168-mediated DSB repair. RNF168 formed liquid-like condensates upon irradiation in the nucleus while purified RNF168 protein also condensed in vitro. An intrinsically disordered region containing amino acids 460-550 was identified as the essential domain for RNF168 condensation. Interestingly, LLPS of RNF168 was significantly enhanced by K63-linked polyubiquitin chains, and LLPS largely enhanced the RNF168-mediated H2A.X ubiquitination, suggesting a positive feedback loop to facilitate RNF168 rapid accumulation and its catalytic activity. Functionally, LLPS deficiency of RNF168 resulted in delayed recruitment of 53BP1 and BRCA1 and subsequent impairment in DSB repair. Taken together, our finding demonstrates the pivotal effect of LLPS in RNF168-mediated DSB repair.
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Affiliation(s)
- Li-Li Feng
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
- Department of Radiology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Shu-Ying Bie
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Zhi-Heng Deng
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Shao-Mei Bai
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Jie Shi
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510655, China
- Department of Radiation Oncology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Cao-Litao Qin
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510655, China
- Department of Radiation Oncology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Huan-Lei Liu
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jia-Xu Li
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Wan-Ying Chen
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jin-Ying Zhou
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Chun-Mei Jiao
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yi Ma
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Meng-Bo Qiu
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Hua-Song Ai
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jian Zheng
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510655, China
- Department of Radiation Oncology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, Institute of Biochemistry and Molecular Biology, Research Center for Cancer Biology, Cancer Biology and Precision Therapeutics Center, and Center for Molecular Medicine, China Medical University, Taichung 406, Taiwan (Republic of China)
| | - Yun-Long Wang
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xiang-Bo Wan
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xin-Juan Fan
- Department of Pathology, Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
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2
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Koo SY, Park EJ, Noh HJ, Jo SM, Ko BK, Shin HJ, Lee CW. Ubiquitination Links DNA Damage and Repair Signaling to Cancer Metabolism. Int J Mol Sci 2023; 24:ijms24098441. [PMID: 37176148 PMCID: PMC10179089 DOI: 10.3390/ijms24098441] [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: 04/12/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Changes in the DNA damage response (DDR) and cellular metabolism are two important factors that allow cancer cells to proliferate. DDR is a set of events in which DNA damage is recognized, DNA repair factors are recruited to the site of damage, the lesion is repaired, and cellular responses associated with the damage are processed. In cancer, DDR is commonly dysregulated, and the enzymes associated with DDR are prone to changes in ubiquitination. Additionally, cellular metabolism, especially glycolysis, is upregulated in cancer cells, and enzymes in this metabolic pathway are modulated by ubiquitination. The ubiquitin-proteasome system (UPS), particularly E3 ligases, act as a bridge between cellular metabolism and DDR since they regulate the enzymes associated with the two processes. Hence, the E3 ligases with high substrate specificity are considered potential therapeutic targets for treating cancer. A number of small molecule inhibitors designed to target different components of the UPS have been developed, and several have been tested in clinical trials for human use. In this review, we discuss the role of ubiquitination on overall cellular metabolism and DDR and confirm the link between them through the E3 ligases NEDD4, APC/CCDH1, FBXW7, and Pellino1. In addition, we present an overview of the clinically important small molecule inhibitors and implications for their practical use.
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Affiliation(s)
- Seo-Young Koo
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Eun-Ji Park
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Hyun-Ji Noh
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Su-Mi Jo
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Bo-Kyoung Ko
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Hyun-Jin Shin
- Team of Radiation Convergence Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Republic of Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
- SKKU Institute for Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
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4
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Gu L, Yan W, Liu L, Wang S, Zhang X, Lyu M. Research Progress on Rolling Circle Amplification (RCA)-Based Biomedical Sensing. Pharmaceuticals (Basel) 2018; 11:E35. [PMID: 29690513 PMCID: PMC6027247 DOI: 10.3390/ph11020035] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/10/2018] [Accepted: 04/10/2018] [Indexed: 12/26/2022] Open
Abstract
Enhancing the limit of detection (LOD) is significant for crucial diseases. Cancer development could take more than 10 years, from one mutant cell to a visible tumor. Early diagnosis facilitates more effective treatment and leads to higher survival rate for cancer patients. Rolling circle amplification (RCA) is a simple and efficient isothermal enzymatic process that utilizes nuclease to generate long single stranded DNA (ssDNA) or RNA. The functional nucleic acid unit (aptamer, DNAzyme) could be replicated hundreds of times in a short period, and a lower LOD could be achieved if those units are combined with an enzymatic reaction, Surface Plasmon Resonance, electrochemical, or fluorescence detection, and other different kinds of biosensor. Multifarious RCA-based platforms have been developed to detect a variety of targets including DNA, RNA, SNP, proteins, pathogens, cytokines, micromolecules, and diseased cells. In this review, improvements in using the RCA technique for medical biosensors and biomedical applications were summarized and future trends in related research fields described.
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Affiliation(s)
- Lide Gu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Wanli Yan
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Le Liu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Shujun Wang
- Marine Resources Development Institute of Jiangsu, Lianyungang 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
| | - Xu Zhang
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
- Verschuren Centre for Sustainability in Energy & the Environment, Cape Breton University, Sydney, NS B1P 6L2, Canada.
| | - Mingsheng Lyu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
- Marine Resources Development Institute of Jiangsu, Lianyungang 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
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5
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Pietrucha B, Heropolitańska-Pliszka E, Geffers R, Enßen J, Wieland B, Bogdanova NV, Dörk T. Clinical and Biological Manifestation of RNF168 Deficiency in Two Polish Siblings. Front Immunol 2017; 8:1683. [PMID: 29255463 PMCID: PMC5722808 DOI: 10.3389/fimmu.2017.01683] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/15/2017] [Indexed: 11/13/2022] Open
Abstract
Germline mutations in the RING finger protein gene RNF168 have been identified in a combined immunodeficiency disorder called RIDDLE syndrome. Since only two patients have been described with somewhat different phenotypes, there is need to identify further patients. Here, we report on two Polish siblings with RNF168 deficiency due to homozygosity for a novel frameshift mutation, c.295delG, that was identified through exome sequencing. Both patients presented with immunoglobulin deficiency, telangiectasia, cellular radiosensitivity, and increased alpha-fetoprotein (AFP) levels. The younger sibling had a more pronounced neurological and morphological phenotype, and she also carried an ATM gene mutation in the heterozygous state. Immunoblot analyses showed absence of RNF168 protein, whereas ATM levels and function were proficient in lymphoblastoid cells from both patients. Consistent with the absence of RNF168 protein, 53BP1 recruitment to DNA double-strand breaks (DSBs) after irradiation was undetectable in lymphoblasts or primary fibroblasts from either of the two patients. γH2AX foci accumulated normally but they disappeared with significant delay, indicating a severe defect in DSB repair. A comparison with the two previously identified patients indicates immunoglobulin deficiency, cellular radiosensitivity, and increased AFP levels as hallmarks of RNF168 deficiency. The variability in its clinical expression despite similar cellular phenotypes suggests that some manifestations of RNF168 deficiency may be modified by additional genetic or epidemiological factors.
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Affiliation(s)
- Barbara Pietrucha
- Department of Immunology, Children's Memorial Health Institute, Warsaw, Poland
| | | | - Robert Geffers
- Genome Analytics Unit, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Julia Enßen
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Britta Wieland
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Natalia Valerijevna Bogdanova
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany.,Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
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6
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Dumbbell DNA-templated CuNPs as a nano-fluorescent probe for detection of enzymes involved in ligase-mediated DNA repair. Biosens Bioelectron 2017; 94:456-463. [DOI: 10.1016/j.bios.2017.03.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/06/2017] [Accepted: 03/16/2017] [Indexed: 11/23/2022]
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7
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Chinn IK, Sanders RP, Stray-Pedersen A, Coban-Akdemir ZH, Kim VHD, Dadi H, Roifman CM, Quigg T, Lupski JR, Orange JS, Hanson IC. Novel Combined Immune Deficiency and Radiation Sensitivity Blended Phenotype in an Adult with Biallelic Variations in ZAP70 and RNF168. Front Immunol 2017; 8:576. [PMID: 28603521 PMCID: PMC5445153 DOI: 10.3389/fimmu.2017.00576] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/01/2017] [Indexed: 12/11/2022] Open
Abstract
With the advent of high-throughput genomic sequencing techniques, novel genetic etiologies are being uncovered for previously unexplained Mendelian phenotypes, and the underlying genetic architecture of disease is being unraveled. Although most of these “mendelizing” disease traits represent phenotypes caused by single-gene defects, a percentage of patients have blended phenotypes caused by pathogenic variants in multiple genes. We describe an adult patient with susceptibility to bacterial, herpesviral, and fungal infections. Immunologic defects included CD8+ T cell lymphopenia, decreased T cell proliferative responses to mitogens, hypogammaglobulinemia, and radiation sensitivity. Whole-exome sequencing revealed compound heterozygous variants in ZAP70. Biallelic mutations in ZAP70 are known to produce a spectrum of immune deficiency that includes the T cell abnormalities observed in this patient. Analyses for variants in genes associated with radiation sensitivity identified the presence of a homozygous RNF168 variant of unknown significance. RNF168 deficiency causes radiosensitivity, immunodeficiency, dysmorphic features, and learning difficulties syndrome and may account for the radiation sensitivity. Thus, the patient was found to have a novel blended phenotype associated with multilocus genomic variation: i.e., separate and distinct genetic defects. These findings further illustrate the clinical utility of applying genomic testing in patients with primary immunodeficiency diseases.
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Affiliation(s)
- Ivan K Chinn
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, TX, USA.,Center for Human Immunobiology, Texas Children's Hospital, Houston, TX, USA
| | - Robert P Sanders
- Texas Transplant Institute, Methodist Hospital, San Antonio, TX, USA
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Department of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Baylor-Hopkins Center for Mendelian Genomics, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep H Coban-Akdemir
- Baylor-Hopkins Center for Mendelian Genomics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Vy Hong-Diep Kim
- Division of Immunology and Allergy, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Harjit Dadi
- Division of Immunology and Allergy, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.,Canadian Centre for Primary Immunodeficiency, The Jeffrey Model Research Laboratory for the Diagnosis of Primary Immunodeficiency, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Chaim M Roifman
- Division of Immunology and Allergy, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.,Canadian Centre for Primary Immunodeficiency, The Jeffrey Model Research Laboratory for the Diagnosis of Primary Immunodeficiency, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Troy Quigg
- Texas Transplant Institute, Methodist Hospital, San Antonio, TX, USA
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Baylor-Hopkins Center for Mendelian Genomics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jordan S Orange
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, TX, USA.,Center for Human Immunobiology, Texas Children's Hospital, Houston, TX, USA
| | - I Celine Hanson
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, TX, USA
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8
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Morio T. Recent advances in the study of immunodeficiency and DNA damage response. Int J Hematol 2017; 106:357-365. [PMID: 28550350 DOI: 10.1007/s12185-017-2263-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 05/17/2017] [Indexed: 12/13/2022]
Abstract
DNA breaks can be induced by exogenous stimuli or by endogenous stress, but are also generated during recombination of V, D, and J genes (V(D)J recombination), immunoglobulin class switch recombination (CSR). Among various DNA breaks generated, DNA double strand break (DSB) is the most deleterious one. DNA damage response (DDR) is initiated when DSBs are detected, leading to DNA break repair by non-homologous end joining (NHEJ). The process is critically important for the generation of diversity for foreign antigens; and failure to exert DNA repair leads to immunodeficiency such as severe combined immunodeficiency and hyper-IgM syndrome. In V(D)J recombination, DSBs are induced by RAG1/2; and generated post-cleavage hairpins are resolved by Artemis/DNA-PKcs/KU70/KU80. DDR is initiated by ataxia-telangiectasia mutated as a master regulator together with MRE11/RAD50/NBS1 complex. Finally, DSBs are repaired by NHEJ. The defect of one of the molecules shows various degree of immunodeficiency and radiosensitivity. Upon CSR inducing signal, DSBs induced by activation-induced cytidine deaminase and endonucleases elicit DDR. Broken ends are repaired either by NHEJ or by mismatch repair system. Patients with radiosensitive SCID require hematopoietic cell transplantation as a curative therapy; but the procedures for eradication of recipient hematopoietic cells are often associated with severe toxicity.
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Affiliation(s)
- Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan.
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9
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Moens LN, Falk-Sörqvist E, Asplund AC, Bernatowska E, Smith CIE, Nilsson M. Diagnostics of primary immunodeficiency diseases: a sequencing capture approach. PLoS One 2014; 9:e114901. [PMID: 25502423 PMCID: PMC4263707 DOI: 10.1371/journal.pone.0114901] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 11/14/2014] [Indexed: 11/19/2022] Open
Abstract
Primary Immunodeficiencies (PID) are genetically inherited disorders characterized by defects of the immune system, leading to increased susceptibility to infection. Due to the variety of clinical symptoms and the complexity of current diagnostic procedures, accurate diagnosis of PID is often difficult in daily clinical practice. Thanks to the advent of “next generation” sequencing technologies and target enrichment methods, the development of multiplex diagnostic assays is now possible. In this study, we applied a selector-based target enrichment assay to detect disease-causing mutations in 179 known PID genes. The usefulness of this assay for molecular diagnosis of PID was investigated by sequencing DNA from 33 patients, 18 of which had at least one known causal mutation at the onset of the experiment. We were able to identify the disease causing mutations in 60% of the investigated patients, indicating that the majority of PID cases could be resolved using a targeted sequencing approach. Causal mutations identified in the unknown patient samples were located in STAT3, IGLL1, RNF168 and PGM3. Based on our results, we propose a stepwise approach for PID diagnostics, involving targeted resequencing, followed by whole transcriptome and/or whole genome sequencing if causative variants are not found in the targeted exons.
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Affiliation(s)
- Lotte N. Moens
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Elin Falk-Sörqvist
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - A. Charlotta Asplund
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Ewa Bernatowska
- Department of Clinical Immunology, Children's Memorial Health Institute, Warsaw, Poland
| | - C. I. Edvard Smith
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
- * E-mail: (EFS); (MN)
| | - Mats Nilsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- * E-mail: (EFS); (MN)
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10
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Popovic D, Vucic D, Dikic I. Ubiquitination in disease pathogenesis and treatment. Nat Med 2014; 20:1242-53. [PMID: 25375928 DOI: 10.1038/nm.3739] [Citation(s) in RCA: 781] [Impact Index Per Article: 78.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 09/29/2014] [Indexed: 02/07/2023]
Abstract
Ubiquitination is crucial for a plethora of physiological processes, including cell survival and differentiation and innate and adaptive immunity. In recent years, considerable progress has been made in the understanding of the molecular action of ubiquitin in signaling pathways and how alterations in the ubiquitin system lead to the development of distinct human diseases. Here we describe the role of ubiquitination in the onset and progression of cancer, metabolic syndromes, neurodegenerative diseases, autoimmunity, inflammatory disorders, infection and muscle dystrophies. Moreover, we indicate how current knowledge could be exploited for the development of new clinical therapies.
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Affiliation(s)
- Doris Popovic
- 1] Institute of Biochemistry II, Goethe University School of Medicine, University Hospital, Frankfurt, Germany. [2] Buchmann Institute for Molecular Life Sciences, Goethe University School of Medicine, University Hospital, Frankfurt, Germany
| | - Domagoj Vucic
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California, USA
| | - Ivan Dikic
- 1] Institute of Biochemistry II, Goethe University School of Medicine, University Hospital, Frankfurt, Germany. [2] Buchmann Institute for Molecular Life Sciences, Goethe University School of Medicine, University Hospital, Frankfurt, Germany. [3] Department of Immunology, University of Split School of Medicine, Split, Croatia
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11
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Jiang HX, Kong DM, Shen HX. Amplified detection of DNA ligase and polynucleotide kinase/phosphatase on the basis of enrichment of catalytic G-quadruplex DNAzyme by rolling circle amplification. Biosens Bioelectron 2014; 55:133-8. [DOI: 10.1016/j.bios.2013.12.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 11/24/2013] [Accepted: 12/01/2013] [Indexed: 12/01/2022]
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12
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Goodarzi AA, Jeggo PA. The repair and signaling responses to DNA double-strand breaks. ADVANCES IN GENETICS 2013; 82:1-45. [PMID: 23721719 DOI: 10.1016/b978-0-12-407676-1.00001-9] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A DNA double-strand break (DSB) has long been recognized as a severe cellular lesion, potentially representing an initiating event for carcinogenesis or cell death. The evolution of DSB repair pathways as well as additional processes, such as cell cycle checkpoint arrest, to minimize the cellular impact of DSB formation was, therefore, not surprising. However, the depth and complexity of the DNA damage responses being revealed by current studies were unexpected. Perhaps the most surprising finding to emerge is the dramatic changes to chromatin architecture that arise in the DSB vicinity. In this review, we overview the cellular response to DSBs focusing on DNA repair pathways and the interface between them. We consider additional events which impact upon these DSB repair pathways, including regulated arrest of cell cycle progression and chromatin architecture alterations. Finally, we discuss the impact of defects in these processes to human disease.
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Affiliation(s)
- Aaron A Goodarzi
- Department of Biochemistry & Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
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USP-11 as a predictive and prognostic factor following neoadjuvant therapy in women with breast cancer. Cancer J 2013; 19:10-7. [PMID: 23337751 DOI: 10.1097/ppo.0b013e3182801b3a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
PURPOSE USP-11, a member of the ubiquitin-specific protease family, has emerged as an essential regulator of double-strand break repair. Few studies have shown that silencing USP-11 led to hypersensitivity to poly(ADP-ribose) polymerase inhibition, ionizing radiation, and DNA-damaging agents. We sought to examine the predictive and prognostic relevance of USP-11 in patients treated with neoadjuvant systemic therapy (NST) for breast cancer. METHODS Fifty-six women who were treated with NST for breast cancer between 1999 and 2004 were included in the study. The Kaplan-Meier product-limit method was used to estimate disease-free survival and overall survival rates. Logistic regression models were fit to determine the associations between USP-11 status, pathological complete response (pCR), and survival. RESULTS Sixteen patients (29%) had high-USP-11-expressing tumors, and 40 (71%) patients had low-USP-11-expressing tumors. No significant differences were observed in pCR rates with respect to USP-11 status. At a median follow-up of 7.4 years, 33 patients (59%) experienced a disease recurrence or death. Patients with high-USP-11-expressing tumors had a higher risk of recurrence (odds ratio [OR], 3.87; 95% confidence interval [CI], 1.51-9.93; P = 0.005) and death (OR, 6.03; 95% CI, 2.00-18.17; P = 0.001) than those with low-USP-11-expressing tumors. Patients who did not achieve a pCR had an increased risk of recurrence (OR, 5.16; 95% CI, 1.16-23.07; P = 0.03). CONCLUSIONS Our data indicate that USP-11 is not a predictor of a pCR after anthracycline-taxane-containing NST for breast cancer. Low USP-11 expression was independently correlated with better survival outcomes.
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Vaz B, Halder S, Ramadan K. Role of p97/VCP (Cdc48) in genome stability. Front Genet 2013; 4:60. [PMID: 23641252 PMCID: PMC3639377 DOI: 10.3389/fgene.2013.00060] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/05/2013] [Indexed: 11/13/2022] Open
Abstract
Ubiquitin-dependent molecular chaperone p97, also known as valosin-containing protein (VCP) or Cdc48, is an AAA ATPase involved in protein turnover and degradation. p97 converts its own ATPase hydrolysis into remodeling activity on a myriad of ubiquitinated substrates from different cellular locations and pathways. In this way, p97 mediates extraction of targeted protein from cellular compartments or protein complexes. p97-dependent protein extraction from various cellular environments maintains cellular protein homeostasis. In recent years, p97-dependent protein extraction from chromatin has emerged as an essential evolutionarily conserved process for maintaining genome stability. Inactivation of p97 segregase activity leads to accumulation of ubiquitinated substrates on chromatin, consequently leading to protein-induced chromatin stress (PICHROS). PICHROS directly and negatively affects multiple DNA metabolic processes, including replication, damage responses, mitosis, and transcription, leading to genotoxic stress and genome instability. By summarizing and critically evaluating recent data on p97 function in various chromatin-associated protein degradation processes, we propose establishing p97 as a genome caretaker.
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Affiliation(s)
- Bruno Vaz
- Institute of Pharmacology and Toxicology, University Zürich-Vetsuisse Zürich, Switzerland ; Gray Institute for Radiation Oncology and Biology, Department of Oncology, University of Oxford Oxford, UK
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Zhang LY, Chen LS, Sun R, JI SJ, Ding YY, Wu J, Tian Y. Effects of expression level of DNA repair-related genes involved in the NHEJ pathway on radiation-induced cognitive impairment. JOURNAL OF RADIATION RESEARCH 2013; 54:235-242. [PMID: 23135157 PMCID: PMC3589933 DOI: 10.1093/jrr/rrs095] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 09/06/2012] [Accepted: 09/25/2012] [Indexed: 06/01/2023]
Abstract
Cranial radiation therapy can induce cognitive decline. Impairments of hippocampal neurogenesis are thought to be a paramountly important mechanism underlying radiation-induced cognitive dysfunction. In the mature nervous system, DNA double-strand breaks (DSBs) are mainly repaired by non-homologous end-joining (NHEJ) pathways. It has been demonstrated that NHEJ deficiencies are associated with impaired neurogenesis. In our study, rats were randomly divided into five groups to be irradiated by single doses of 0 (control), 0 (anesthesia control), 2, 10, and 20 Gy, respectively. The cognitive function of the irradiated rats was measured by open field, Morris water maze and passive avoidance tests. Real-time PCR was also used to detect the expression level of DNA DSB repair-related genes involved in the NHEJ pathway, such as XRCC4, XRCC5and XRCC6, in the hippocampus. The influence of different radiation doses on cognitive function in rats was investigated. From the results of the behavior tests, we found that rats receiving 20 Gy irradiation revealed poorer learning and memory, while no significant loss of learning and memory existed in rats receiving irradiation from 0-10 Gy. The real-time PCR and Western blot results showed no significant difference in the expression level of DNA repair-related genes between the 10 and 20 Gy groups, which may help to explain the behavioral results, i.e. DNA damage caused by 0-10 Gy exposure was appropriately repaired, however, damage induced by 20 Gy exceeded the body's maximum DSB repair ability. Ionizing radiation-induced cognitive impairments depend on the radiation dose, and more directly on the body's own ability to repair DNA DSBs via the NHEJ pathway.
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Affiliation(s)
| | | | | | | | | | | | - Ye Tian
- Corresponding author: Tel: + 86-512-6778-3430; Fax: + 86-512-6828-4303;
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Dehkordy SF, Aghamohammadi A, Ochs HD, Rezaei N. Primary immunodeficiency diseases associated with neurologic manifestations. J Clin Immunol 2011; 32:1-24. [PMID: 22038677 DOI: 10.1007/s10875-011-9593-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Accepted: 09/09/2011] [Indexed: 01/04/2023]
Abstract
Primary immunodeficiency diseases (PID) are a heterogeneous group of inherited disorders of the immune system, predisposing individuals to recurrent infections, allergy, autoimmunity, and malignancies. A considerable number of these conditions have been found to be also associated with neurologic signs and symptoms. These manifestations are considered core features of some immunodeficiency syndromes, such as ataxia-telangiectasia and purine nucleoside phosphorylase deficiency, or occur less prominently in some others. Diverse pathological mechanisms including defective responses to DNA damage, metabolic errors, and autoimmune phenomena have been associated with neurologic abnormalities; however, several issues remain to be elucidated. Greater awareness of these associated features and gaining a better understanding of the contributing mechanisms will lead to prompt diagnosis and treatment and possibly development of novel preventive and therapeutic strategies. In this review, we aim to provide a brief description of the clinical and genetic characteristics of PID associated with neurologic complications.
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Affiliation(s)
- Soodabeh Fazeli Dehkordy
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, 14194, Iran
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