1
|
Saikia S, Postwala H, Athilingam VP, Anandan A, Padma VV, Kalita PP, Chorawala M, Prajapati B. Single Nucleotide Polymorphisms (SNPs) in the Shadows: Uncovering their Function in Non-Coding Region of Esophageal Cancer. Curr Pharm Biotechnol 2024; 25:1915-1938. [PMID: 38310451 DOI: 10.2174/0113892010265004231116092802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 02/05/2024]
Abstract
Esophageal cancer is a complex disease influenced by genetic and environmental factors. Single nucleotide polymorphisms (SNPs) in non-coding regions of the genome have emerged as crucial contributors to esophageal cancer susceptibility. This review provides a comprehensive overview of the role of SNPs in non-coding regions and their association with esophageal cancer. The accumulation of SNPs in the genome has been implicated in esophageal cancer risk. Various studies have identified specific locations in the genome where SNPs are more likely to occur, suggesting a location-specific response. Chromatin conformational studies have shed light on the localization of SNPs and their impact on gene transcription, posttranscriptional modifications, gene expression regulation, and histone modification. Furthermore, miRNA-related SNPs have been found to play a significant role in esophageal squamous cell carcinoma (ESCC). These SNPs can affect miRNA binding sites, thereby altering target gene regulation and contributing to ESCC development. Additionally, the risk of ESCC has been linked to base excision repair, suggesting that SNPs in this pathway may influence disease susceptibility. Somatic DNA segment alterations and modified expression quantitative trait loci (eQTL) have also been associated with ESCC. These alterations can lead to disrupted gene expression and cellular processes, ultimately contributing to cancer development and progression. Moreover, SNPs have been found to be associated with the long non-coding RNA HOTAIR, which plays a crucial role in ESCC pathogenesis. This review concludes with a discussion of the current and future perspectives in the field of SNPs in non-coding regions and their relevance to esophageal cancer. Understanding the functional implications of these SNPs may lead to the identification of novel therapeutic targets and the development of personalized approaches for esophageal cancer prevention and treatment.
Collapse
Affiliation(s)
- Surovi Saikia
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - Humzah Postwala
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Ahmedabad, India
| | - Vishnu Prabhu Athilingam
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - Aparna Anandan
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - V Vijaya Padma
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - Partha P Kalita
- Program of Biotechnology, Assam Down Town University, Panikhaiti, Guwahati 781026, Assam, India
| | - Mehul Chorawala
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Ahmedabad, India
| | - Bhupendra Prajapati
- Department of Pharmaceutics and Pharmaceutical Technology, Shree. S. K. Patel College of Pharmaceutical Education and Research, Ganpat University, Kherva, Gujarat, India
| |
Collapse
|
2
|
Mousa M, Albarguthi S, Albreiki M, Farooq Z, Sajid S, El Hajj Chehadeh S, ElBait GD, Tay G, Deeb AA, Alsafar H. Whole-Exome Sequencing in Family Trios Reveals De Novo Mutations Associated with Type 1 Diabetes Mellitus. BIOLOGY 2023; 12:biology12030413. [PMID: 36979105 PMCID: PMC10044903 DOI: 10.3390/biology12030413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/16/2023] [Accepted: 02/23/2023] [Indexed: 03/10/2023]
Abstract
Type 1 diabetes mellitus (T1DM) is a chronic autoimmune disease characterized by insulin deficiency and loss of pancreatic islet β-cells. The objective of this study is to identify de novo mutations in 13 trios from singleton families that contribute to the genetic basis of T1DM through the application of whole-exome sequencing (WES). Of the 13 families sampled for this project, 12 had de novo variants, with Family 7 having the highest number (nine) of variants linked to T1DM/autoimmune pathways, whilst Family 4 did not have any variants past the filtering steps. There were 10 variants of 7 genes reportedly associated with T1DM (MST1; TDG; TYRO3; IFIHI; GLIS3; VEGFA; TYK2). There were 20 variants of 13 genes that were linked to endocrine, metabolic, or autoimmune diseases. Our findings demonstrate that trio-based WES is a powerful approach for identifying new candidate genes for the pathogenesis of T1D. Genotyping and functional annotation of the discovered de novo variants in a large cohort is recommended to ascertain their association with disease pathogenesis.
Collapse
Affiliation(s)
- Mira Mousa
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Sara Albarguthi
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Mohammed Albreiki
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Zenab Farooq
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi 127788, United Arab Emirates
| | - Sameeha Sajid
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi 127788, United Arab Emirates
| | - Sarah El Hajj Chehadeh
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Gihan Daw ElBait
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Guan Tay
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Asma Al Deeb
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi 127788, United Arab Emirates
- Department of Endocrinology, Mafraq Hospital, Abu Dhabi 127788, United Arab Emirates
| | - Habiba Alsafar
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
- Correspondence:
| |
Collapse
|
3
|
Qu W, Jeong A, Zhong R, Thieschafer JS, Gram A, Li L. Deletion of Small GTPase H-Ras Rescues Memory Deficits and Reduces Amyloid Plaque-Associated Dendritic Spine Loss in Transgenic Alzheimer's Mice. Mol Neurobiol 2023; 60:495-511. [PMID: 36287323 PMCID: PMC10771223 DOI: 10.1007/s12035-022-03082-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/27/2022] [Indexed: 01/25/2023]
Abstract
Alzheimer's disease (AD) is a fatal neurodegenerative disorder, affecting millions of lives without a cure. While the molecular mechanism of AD remains obscure, emerging evidence suggests that small GTPases, a group of GTP-binding proteins that regulate a plethora of essential cellular events, modulate the pathogenic process of AD. Among those, the small GTPase H-Ras, extensively studied in cancer, regulates synaptic function, and both upstream and downstream signaling pathways of H-Ras have been implicated in AD. However, the role of H-Ras per se in AD pathogenesis had not been explored previously. In the present study, the impact of Hras deletion on cognitive function and amyloid pathology was investigated in transgenic APP/PS1 mice of AD. Behavioral assessments showed that the absence of Hras rescued spatial memory deficit in APP/PS1 mice at 9 months of age. The pathological evaluation demonstrated that Hras deletion reduced cortical amyloid deposition and astrogliosis. Furthermore, Hras deficiency protected against amyloid plaque-associated loss of dendritic spines in APP/PS1 mice. Intriguingly, canonical signaling pathways downstream of H-Ras were not affected by the absence of Hras in the brain. Unbiased transcriptomic analysis revealed that lack of H-Ras affected the expression of select genes in the brain of AD mice and identified a novel connection between H-Ras and Annexin A4, a calcium-dependent phospholipid-binding protein that has been shown to regulate membrane repair, neuroinflammation, and calcium homeostasis. Taken together, these data indicate that H-Ras modifies the pathogenic process of AD and may serve as a potential therapeutic target for AD.
Collapse
Affiliation(s)
- Wenhui Qu
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Pathology & Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Angela Jeong
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Rui Zhong
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Josslen S Thieschafer
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Andrea Gram
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ling Li
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, 55455, USA.
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA.
| |
Collapse
|
4
|
Wang X, Yu J, Wang J. Neural Tube Defects and Folate Deficiency: Is DNA Repair Defective? Int J Mol Sci 2023; 24:ijms24032220. [PMID: 36768542 PMCID: PMC9916799 DOI: 10.3390/ijms24032220] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Neural tube defects (NTDs) are complex congenital malformations resulting from failure of neural tube closure during embryogenesis, which is affected by the interaction of genetic and environmental factors. It is well known that folate deficiency increases the incidence of NTDs; however, the underlying mechanism remains unclear. Folate deficiency not only causes DNA hypomethylation, but also blocks the synthesis of 2'-deoxythymidine-5'-monophosphate (dTMP) and increases uracil misincorporation, resulting in genomic instabilities such as base mismatch, DNA breakage, and even chromosome aberration. DNA repair pathways are essential for ensuring normal DNA synthesis, genomic stability and integrity during embryonic neural development. Genomic instability or lack of DNA repair has been implicated in risk of development of NTDs. Here, we reviewed the relationship between folate deficiency, DNA repair pathways and NTDs so as to reveal the role and significance of DNA repair system in the pathogenesis of NTDs and better understand the pathogenesis of NTDs.
Collapse
|
5
|
Taraschi A, Cimini C, Colosimo A, Ramal-Sanchez M, Valbonetti L, Bernabò N, Barboni B. An interactive analysis of the mouse oviductal miRNA profiles. Front Cell Dev Biol 2022; 10:1015360. [PMID: 36340025 PMCID: PMC9627480 DOI: 10.3389/fcell.2022.1015360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/06/2022] [Indexed: 11/15/2022] Open
Abstract
MicroRNAs are small non-coding molecules that control several cellular functions and act as negative post-transcriptional regulators of the mRNA. While their implication in several biological functions is already known, an important role as regulators of different physiological and pathological processes in fertilization and embryo development is currently emerging. Indeed, miRNAs have been found in the oviductal fluid packaged within the extracellular vesicles, which might act as natural nanoshuttles by transporting lipids, proteins, RNA molecules and miRNAs from the oviduct to the gametes or embryos. Here, an exhaustive bibliography search was carried out, followed by the construction of a computational model based on the networks theory in an attempt to recreate and elucidate the pathways potentially activated by the oviductal miRNA. The omics data published to date were gathered to create the Oviductal MiRNome, in which the miRNA target genes and their interactions are represented by using stringApp and the Network analyzer from Cytoscape 3.7.2. Then, the hyperlinked nodes were identified to investigate the pathways in which they are involved using the gene ontology enrichment analysis. To study the phenotypical effects after the removal of key genes on the reproductive system and embryo, knockout mouse lines for every protein-coding gene were investigated by using the International Mouse Phenotyping Consortium database. The creation of the Oviductal MiRNome revealed the presence of important genes and their interactions within the network. The functional enrichment analysis revealed that the hyperlinked nodes are involved in fundamental cellular functions, both structural and regulatory/signaling, suggesting their implication in fertilization and early embryo development. This fact was as well evidenced by the effects of the gene deletion in KO mice on the reproductive system and embryo development. The present study highlights the importance of studying the miRNA profiles and their enormous potential as tools to improve the assisted reproductive techniques currently used in human and animal reproduction.
Collapse
Affiliation(s)
- Angela Taraschi
- Faculty of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
- Istituto Zooprofilattico Sperimentale Dell’Abruzzo e Del Molise “G. Caporale”, Teramo, Italy
| | - Costanza Cimini
- Faculty of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Alessia Colosimo
- Faculty of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Marina Ramal-Sanchez
- Faculty of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Luca Valbonetti
- Faculty of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
- Institute of Biochemistry and Cell Biology (CNR-IBBC/EMMA/Infrafrontier/IMPC), National Research Council, Rome, Italy
| | - Nicola Bernabò
- Faculty of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
- Institute of Biochemistry and Cell Biology (CNR-IBBC/EMMA/Infrafrontier/IMPC), National Research Council, Rome, Italy
- *Correspondence: Nicola Bernabò,
| | - Barbara Barboni
- Faculty of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| |
Collapse
|
6
|
Jiang N, Yang M, Han Y, Zhao H, Sun L. PRDM16 Regulating Adipocyte Transformation and Thermogenesis: A Promising Therapeutic Target for Obesity and Diabetes. Front Pharmacol 2022; 13:870250. [PMID: 35462933 PMCID: PMC9024053 DOI: 10.3389/fphar.2022.870250] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Given that obesity and diabetes have been major public health concerns and that disease morbidities have been rising continuously, effective treatment for these diseases is urgently needed. Because adipose tissue metabolism is involved in the progression of obesity and diabetes, it might be efficient to target adipocyte metabolic pathways. Positive regulatory domain zinc finger region protein 16 (PRDM16), a transcription factor that is highly expressed in adipocytes, plays a key role in adipose tissue metabolism, such as the browning and thermogenesis of adipocytes, the beigeing of adipocytes, the adipogenic differentiation of myoblasts, and the conversion of visceral adipocytes to subcutaneous adipocytes. Furthermore, clinical and basic studies have shown that the expression of PRDM16 is associated with obesity and diabetes and that PRDM16 signaling participates in the treatment of the two diseases. For example, metformin promotes thermogenesis and alleviates obesity by activating the AMPK/αKG/PRDM16 signaling pathway; rosiglitazone alleviates obesity under the synergistic effect of PRDM16; resveratrol plays an antiobesity role by inducing the expression of PRDM16; liraglupeptide improves insulin resistance by inducing the expression of PRDM16; and mulberry leaves play an anti-inflammatory and antidiabetes role by activating the expression of brown fat cell marker genes (including PRDM16). In this review, we summarize the evidence of PRDM16 involvement in the progression of obesity and diabetes and that PRDM16 may be a promising therapy for obesity and diabetes.
Collapse
|
7
|
Policarpo R, Sierksma A, De Strooper B, d'Ydewalle C. From Junk to Function: LncRNAs in CNS Health and Disease. Front Mol Neurosci 2021; 14:714768. [PMID: 34349622 PMCID: PMC8327212 DOI: 10.3389/fnmol.2021.714768] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/25/2021] [Indexed: 12/26/2022] Open
Abstract
Recent advances in RNA sequencing technologies helped to uncover the existence of tens of thousands of long non-coding RNAs (lncRNAs) that arise from the dark matter of the genome. These lncRNAs were originally thought to be transcriptional noise but an increasing number of studies demonstrate that these transcripts can modulate protein-coding gene expression by a wide variety of transcriptional and post-transcriptional mechanisms. The spatiotemporal regulation of lncRNA expression is particularly evident in the central nervous system, suggesting that they may directly contribute to specific brain processes, including neurogenesis and cellular homeostasis. Not surprisingly, lncRNAs are therefore gaining attention as putative novel therapeutic targets for disorders of the brain. In this review, we summarize the recent insights into the functions of lncRNAs in the brain, their role in neuronal maintenance, and their potential contribution to disease. We conclude this review by postulating how these RNA molecules can be targeted for the treatment of yet incurable neurological disorders.
Collapse
Affiliation(s)
- Rafaela Policarpo
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium.,Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., Beerse, Belgium
| | - Annerieke Sierksma
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Bart De Strooper
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium.,UK Dementia Research Institute, University College London, London, United Kingdom
| | - Constantin d'Ydewalle
- Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., Beerse, Belgium
| |
Collapse
|
8
|
Chen SL, Wang GP, Shi DR, Yao SH, Chen KD, Yao HP. RON in hepatobiliary and pancreatic cancers: Pathogenesis and potential therapeutic targets. World J Gastroenterol 2021; 27:2507-2520. [PMID: 34092972 PMCID: PMC8160627 DOI: 10.3748/wjg.v27.i20.2507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/04/2021] [Accepted: 04/09/2021] [Indexed: 02/06/2023] Open
Abstract
The receptor protein tyrosine kinase RON belongs to the c-MET proto-oncogene family. Research has shown that RON has a role in cancer pathogenesis, which places RON on the frontline of the development of novel cancer therapeutic strategies. Hepatobiliary and pancreatic (HBP) cancers have a poor prognosis, being reported as having higher rates of cancer-related death. Therefore, to combat these malignant diseases, the mechanism underlying the aberrant expression and signaling of RON in HBP cancer pathogenesis, and the development of RON as a drug target for therapeutic intervention should be investigated. Abnormal RON expression and signaling have been identified in HBP cancers, and also act as tumorigenic determinants for HBP cancer malignant behaviors. In addition, RON is emerging as an important mediator of the clinical prognosis of HBP cancers. Thus, not only is RON significant in HBP cancers, but also RON-targeted therapeutics could be developed to treat these cancers, for example, therapeutic monoclonal antibodies and small-molecule inhibitors. Among them, antibody-drug conjugates have become increasingly popular in current research and their potential as novel anti-cancer biotherapeutics will be determined in future clinical trials.
Collapse
Affiliation(s)
- Shao-Long Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310000, Zhejiang Province, China
| | - Guo-Ping Wang
- Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310000, Zhejiang Province, China
| | - Dan-Rong Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang Province, China
| | - Shu-Hao Yao
- Department of Stomatology, Wenzhou Medical University Renji College, Wenzhou 325035, Zhejiang Province, China
| | - Ke-Da Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310000, Zhejiang Province, China
| | - Hang-Ping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang Province, China
| |
Collapse
|
9
|
Gu S, Bodai Z, Cowan QT, Komor AC. Base Editors: Expanding the Types of DNA Damage Products Harnessed for Genome Editing. ACTA ACUST UNITED AC 2021; 1. [PMID: 34368792 DOI: 10.1016/j.ggedit.2021.100005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Base editors are an innovative addition to the genome editing toolbox that introduced a new genome editing strategy to the field. Instead of using double-stranded DNA breaks, base editors use nucleobase modification chemistry to efficiently and precisely incorporate single nucleotide variants (SNVs) into the genome of living cells. Two classes of DNA base editors currently exist: deoxycytidine deamination-derived editors (CBEs, which facilitate C•G to T•A mutations) and deoxyadenosine deamination-derived base editors (ABEs, which facilitate A•T to G•C mutations). More recently, the development of mitochondrial base editors allowed the introduction of C•G to T•A mutations into mitochondrial DNA as well. Base editors show great potential as therapeutic agents and research tools, and extensive studies have been carried out to improve upon the original base editor constructs to aid researchers in a variety of disciplines. Despite their widespread use, there are few publications that focus on elucidating the biological pathways involved during the processing of base editor intermediates. Because base editors introduce unique types of DNA damage products (a U•G mismatch with a DNA backbone nick for CBEs, and an I•T mismatch with a DNA backbone nick for ABEs) to facilitate genome editing, a deep understanding of the DNA damage repair pathways that facilitate or impede base editing represents an important aspect for the further expansion and improvement of the technologies. Here, we first review canonical deoxyuridine, deoxyinosine, and single-stranded break repair. Then, we discuss how interactions among these different repair processes can lead to different base editing outcomes. Through this review, we hope to promote thoughtful discussions on the DNA repair mechanisms of base editing, as well as help researchers in the improvement of the current base editors and the development of new base editors.
Collapse
Affiliation(s)
- Sifeng Gu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Zsolt Bodai
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Quinn T Cowan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| |
Collapse
|
10
|
Wang B, Chen Y, Zhang X, Jiang Z, Wang Y, Chen K, Wang F, Weng X, Zhou X. A far-red emissive two-photon fluorescent probe for quantification of uracil in genomic DNA. Chem Commun (Camb) 2021; 57:2784-2787. [PMID: 33599665 DOI: 10.1039/d1cc00016k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a new method for dU detection in genomic DNA combined with UNG excision and fluorescent probe labeling. UNG can remove uracil bases to introduce abasic sites, which can react with NRNO to produce intense fluorescence because of the inhibition of the PET effect. It can also cause the polymerase extension to stop to provide details of dU site information.
Collapse
Affiliation(s)
- Bingyao Wang
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Yi Chen
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Xiong Zhang
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Zhuoran Jiang
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Yafen Wang
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Kun Chen
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Fang Wang
- Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Xiaocheng Weng
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Xiang Zhou
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| |
Collapse
|
11
|
Wang W, Chen Y, Xu A, Cai M, Cao J, Zhu H, Yang B, Shao X, Ying M, He Q. Protein phase separation: A novel therapy for cancer? Br J Pharmacol 2020; 177:5008-5030. [PMID: 32851637 DOI: 10.1111/bph.15242] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/18/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
In recent years, phase separation has been increasingly reported to play a pivotal role in a wide range of biological processes. Due to the close relationships between cancer and disorders in intracellular physiological function, the identification of new mechanisms involved in intracellular regulation has been regarded as a new direction for cancer therapy. Introducing the concept of phase separation into complex descriptions of disease mechanisms may provide many different insights. Here, we review the recent findings on the phase separation of cancer-related proteins, describing the possible relationships between phase separation and key proteins associated with cancer and indicate possible regulatory modalities, especially drug candidates for phase separation, which may provide more effective strategies for cancer therapy.
Collapse
Affiliation(s)
- Wei Wang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yingqian Chen
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Aixiao Xu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Minyi Cai
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Ji Cao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Hong Zhu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xuejing Shao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Meidan Ying
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
12
|
Antibody-drug conjugates targeting RON receptor tyrosine kinase as a novel strategy for treatment of triple-negative breast cancer. Drug Discov Today 2020; 25:1160-1173. [PMID: 32479905 DOI: 10.1016/j.drudis.2020.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/05/2020] [Accepted: 05/18/2020] [Indexed: 12/17/2022]
Abstract
Treatment of triple-negative breast cancer (TNBC) is a challenge to oncologists. Currently, the lack of effective therapy has fostered a major effort to discover new targets and therapeutics to combat this disease. The recepteur d'origine nantais (RON) receptor has been implicated in the pathogenesis of TNBC. Clinical studies have revealed that aberrant RON expression is crucial in regulating TNBC malignant phenotypes. Increased RON expression also has prognostic value for breast cancer progress. These features provide the rationale to target RON for TNBC treatment. In this review, we discuss the importance of RON in TNBC tumorigenesis and the development of anti-RON antibody-drug conjugates (ADCs) for clinical application. The findings from preclinical studies lay the foundation for clinical trials of this novel biotherapeutic for TNBC therapy.
Collapse
|
13
|
Yao HP, Suthe SR, Tong XM, Wang MH. Targeting RON receptor tyrosine kinase for treatment of advanced solid cancers: antibody-drug conjugates as lead drug candidates for clinical trials. Ther Adv Med Oncol 2020; 12:1758835920920069. [PMID: 32426050 PMCID: PMC7222236 DOI: 10.1177/1758835920920069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/27/2020] [Indexed: 02/06/2023] Open
Abstract
The recepteur d'origine nantais (RON) receptor tyrosine kinase, belonging to the mesenchymal-to-epithelial transition proto-oncogene family, has been implicated in the pathogenesis of cancers derived from the colon, lung, breast, and pancreas. These findings lay the foundation for targeting RON for cancer treatment. However, development of RON-targeted therapeutics has not gained sufficient attention for the last decade. Although therapeutic monoclonal antibodies (TMABs) targeting RON have been validated in preclinical studies, results from clinical trials have met with limited success. This outcome diminishes pharmaceutical enthusiasm for further development of RON-targeted therapeutics. Recently, antibody-drug conjugates (ADCs) targeting RON have drawn special attention owing to their increased therapeutic activity. The rationale for developing anti-RON ADCs is based on the observation that cancer cells are not sufficiently addicted to RON signaling for survival. Thus, TMAB-mediated inhibition of RON signaling is ineffective for clinical application. In contrast, anti-RON ADCs combine a target-specific antibody with potent cytotoxins for cancer cell killing. This approach not only overcomes the shortcomings in TMAB-targeted therapies but also holds the promise for advancing anti-RON ADCs into clinical trials. In this review, we discuss the latest advancements in the development of anti-RON ADCs for targeted cancer therapy including drug conjugation profile, pharmacokinetic properties, cytotoxic effect in vitro, efficacy in tumor models, and toxicological activities in primates.
Collapse
Affiliation(s)
- Hang-Ping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Sreedhar Reddy Suthe
- Cancer Biology Research Center, Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, USA
| | - Xiang-Min Tong
- Department of Hematology, Zhejiang Provincial People’s Hospital and People’s Hospital of Hangzhou Medical College, Hangzhou, China
| | - Ming-Hai Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Biology Research Center, Texas Tech University Health Sciences Jerry H. Hodge School of Pharmacy, 1406 Coulter Street, Amarillo, TX 79106, USA
| |
Collapse
|
14
|
Koliadenko V, Wilanowski T. Additional functions of selected proteins involved in DNA repair. Free Radic Biol Med 2020; 146:1-15. [PMID: 31639437 DOI: 10.1016/j.freeradbiomed.2019.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 12/30/2022]
Abstract
Protein moonlighting is a phenomenon in which a single polypeptide chain can perform a number of different unrelated functions. Here we present our analysis of moonlighting in the case of selected DNA repair proteins which include G:T mismatch-specific thymine DNA glycosylase (TDG), methyl-CpG-binding domain protein 4 (MBD4), apurinic/apyrimidinic endonuclease 1 (APE1), AlkB homologs, poly (ADP-ribose) polymerase 1 (PARP-1) and single-strand selective monofunctional uracil DNA glycosylase 1 (SMUG1). Most of their additional functions are not accidental and clear patterns are emerging. Participation in RNA metabolism is not surprising as bases occurring in RNA are the same or very similar to those in DNA. Other common additional function involves regulation of transcription. This is not unexpected as these proteins bind to specific DNA regions for DNA repair, hence they can also be recruited to regulate transcription. Participation in demethylation and replication of DNA appears logical as well. Some of the multifunctional DNA repair proteins play major roles in many diseases, including cancer. However, their moonlighting might prove a major difficulty in the development of new therapies because it will not be trivial to target a single protein function without affecting its other functions that are not related to the disease.
Collapse
Affiliation(s)
- Vlada Koliadenko
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland
| | - Tomasz Wilanowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland.
| |
Collapse
|
15
|
Al-Shaheri FN, Al-Shami KM, Gamal EH, Mahasneh AA, Ayoub NM. Association of DNA repair gene polymorphisms with colorectal cancer risk and treatment outcomes. Exp Mol Pathol 2019; 113:104364. [PMID: 31881200 DOI: 10.1016/j.yexmp.2019.104364] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/16/2019] [Accepted: 12/24/2019] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is the third most common carcinoma worldwide. Despite the progress in screening and treatment, CRC remains a leading cause of cancer-related mortality. Alterations to normal nucleic acid processing may drive neoplastic transformation of colorectal epithelium. DNA repair machinery performs an essential function in the protection of genome by reducing the number of genetic polymorphisms/variations that may drive carcinogenicity. Four essential DNA repair systems are known which include nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), and double-strand break repair (DSBR). Polymorphisms of DNA repair genes have been shown to influence the risk of cancer development as well as outcomes of treatment. Several studies demonstrated the association between genetic polymorphism of DNA repair genes and increased risk of CRC in different populations. In this review, we have summarized the impact of DNA repair gene polymorphisms on risk of CRC development and treatment outcomes. Advancements of the current understanding for the impact of DNA repair gene polymorphisms on the risk and treatment of CRC may support diagnostic and predictive roles in patients with CRC.
Collapse
Affiliation(s)
- Fawaz N Al-Shaheri
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), ImNeuenheimer Feld 580, 69120 Heidelberg, Germany; Medical Faculty Heidelberg, University of Heidelberg, ImNeuenheimer Feld 672, 69120 Heidelberg, Germany; Faculty of Applied Medical Sciences, Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Kamal M Al-Shami
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, 720 South Donahue Drive, Auburn, Alabama 36849, United States of America; Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Eshrak H Gamal
- Department of Oncology, Collage of Medicine, Bonn University, Germany; Faculty of Applied Medical Sciences, Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Amjad A Mahasneh
- Department of Applied Biological Sciences, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Nehad M Ayoub
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan.
| |
Collapse
|
16
|
Sannai M, Doneddu V, Giri V, Seeholzer S, Nicolas E, Yip SC, Bassi MR, Mancuso P, Cortellino S, Cigliano A, Lurie R, Ding H, Chernoff J, Sobol RW, Yen TJ, Bagella L, Bellacosa A. Modification of the base excision repair enzyme MBD4 by the small ubiquitin-like molecule SUMO1. DNA Repair (Amst) 2019; 82:102687. [PMID: 31476572 PMCID: PMC6785017 DOI: 10.1016/j.dnarep.2019.102687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/21/2019] [Accepted: 08/08/2019] [Indexed: 10/26/2022]
Abstract
The base excision repair DNA N-glycosylase MBD4 (also known as MED1), an interactor of the DNA mismatch repair protein MLH1, plays a central role in the maintenance of genomic stability of CpG sites by removing thymine and uracil from G:T and G:U mismatches, respectively. MBD4 is also involved in DNA damage response and transcriptional regulation. The interaction with other proteins is likely critical for understanding MBD4 functions. To identify novel proteins that interact with MBD4, we used tandem affinity purification (TAP) from HEK-293 cells. The MBD4-TAP fusion and its co-associated proteins were purified sequentially on IgG and calmodulin affinity columns; the final eluate was shown to contain MLH1 by western blotting, and MBD4-associated proteins were identified by mass spectrometry. Bands with molecular weight higher than that expected for MBD4 (˜66 kD) yielded peptides corresponding to MBD4 itself and the small ubiquitin-like molecule-1 (SUMO1), suggesting that MBD4 is sumoylated in vivo. MBD4 sumoylation was validated by co-immunoprecipitation in HEK-293 and MCF7 cells, and by an in vitrosumoylation assay. Sequence and mutation analysis identified three main sumoylation sites: MBD4 is sumoylated preferentially on K137, with additional sumoylation at K215 and K377. Patterns of MBD4 sumoylation were altered, in a DNA damage-specific way, by the anti-metabolite 5-fluorouracil, the alkylating agent N-Methyl-N-nitrosourea and the crosslinking agent cisplatin. MCF7 extract expressing sumoylated MBD4 displays higher thymine glycosylase activity than the unmodified species. Of the 67 MBD4 missense mutations reported in The Cancer Genome Atlas, 14 (20.9%) map near sumoylation sites. These results indicate that MBD4 is sumoylated in vivo in a DNA damage-specific manner, and suggest that sumoylation serves to regulate its repair activity and could be compromised in cancer. This study expands the role played by sumoylation in fine-tuning DNA damage response and repair.
Collapse
Affiliation(s)
- Mara Sannai
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Valentina Doneddu
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA; Department of Biomedical Sciences, University of Sassari, Sassari, 07100, Italy
| | - Veda Giri
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Steven Seeholzer
- Proteomics Core, The Children's Hospital of Philadelphia, Philadelphia PA, 19104, USA
| | - Emmanuelle Nicolas
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Shu-Chin Yip
- Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Maria Rosaria Bassi
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Pietro Mancuso
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Salvatore Cortellino
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Antonio Cigliano
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Rebecca Lurie
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Hua Ding
- Proteomics Core, The Children's Hospital of Philadelphia, Philadelphia PA, 19104, USA
| | - Jonathan Chernoff
- Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Robert W Sobol
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Timothy J Yen
- Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Luigi Bagella
- Department of Biomedical Sciences, University of Sassari, Sassari, 07100, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, 19122, USA
| | - Alfonso Bellacosa
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
| |
Collapse
|
17
|
Vivet-Noguer R, Tarin M, Roman-Roman S, Alsafadi S. Emerging Therapeutic Opportunities Based on Current Knowledge of Uveal Melanoma Biology. Cancers (Basel) 2019; 11:E1019. [PMID: 31330784 PMCID: PMC6678734 DOI: 10.3390/cancers11071019] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/09/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
Uveal Melanoma (UM) is a rare and malignant intraocular tumor with dismal prognosis. Despite the efficient control of the primary tumor by radiation or surgery, up to 50% of patients subsequently develop metastasis, mainly in the liver. Once the tumor has spread from the eye, the treatment is challenging and the median survival is only nine months. UM represents an intriguing model of oncogenesis that is characterized by a relatively homogeneous histopathological architecture and a low burden of genetic alterations, in contrast to other melanomas. UM is driven by recurrent activating mutations in Gαq pathway, which are associated with a second mutation in BRCA1 associated protein 1 (BAP1), splicing factor 3b subunit 1 (SF3B1), or eukaryotic translation initiation factor 1A X-linked (EIF1AX), occurring in an almost mutually exclusive manner. The monosomy of chromosome 3 is also a recurrent feature that is associated with high metastatic risk. These events driving UM oncogenesis have been thoroughly investigated over the last decade. However, no efficient related therapeutic strategies are yet available and the metastatic disease remains mostly incurable. Here, we review current knowledge regarding the molecular biology and the genetics of uveal melanoma and highlight the related therapeutic applications and perspectives.
Collapse
Affiliation(s)
- Raquel Vivet-Noguer
- Uveal Melanoma Translational Group, Department of Translational Research, Institut Curie, PSL Research University, 75248 Paris, France
| | - Malcy Tarin
- Uveal Melanoma Translational Group, Department of Translational Research, Institut Curie, PSL Research University, 75248 Paris, France
| | - Sergio Roman-Roman
- Uveal Melanoma Translational Group, Department of Translational Research, Institut Curie, PSL Research University, 75248 Paris, France
| | - Samar Alsafadi
- Uveal Melanoma Translational Group, Department of Translational Research, Institut Curie, PSL Research University, 75248 Paris, France.
| |
Collapse
|
18
|
Godini R, Fallahi H. Shortening the list of essential genes in the human genome by network analysis. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
19
|
Xu J, Cortellino S, Tricarico R, Chang WC, Scher G, Devarajan K, Slifker M, Moore R, Bassi MR, Caretti E, Clapper M, Cooper H, Bellacosa A. Thymine DNA Glycosylase (TDG) is involved in the pathogenesis of intestinal tumors with reduced APC expression. Oncotarget 2017; 8:89988-89997. [PMID: 29163805 PMCID: PMC5685726 DOI: 10.18632/oncotarget.21219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 08/21/2017] [Indexed: 12/22/2022] Open
Abstract
Thymine DNA Glycosylase (TDG) is a base excision repair enzyme that acts as a thymine and uracil DNA N-glycosylase on G:T and G:U mismatches, thus protecting CpG sites in the genome from mutagenesis by deamination. In addition, TDG has an epigenomic function by removing the novel cytosine derivatives 5-formylcytosine and 5-carboxylcytosine (5caC) generated by Ten-Eleven Translocation (TET) enzymes during active DNA demethylation. We and others previously reported that TDG is essential for mammalian development. However, its involvement in tumor formation is unknown. To study the role of TDG in tumorigenesis, we analyzed the effects of its inactivation in a well-characterized model of tumor predisposition, the ApcMin mouse strain. Mice bearing a conditional Tdgflox allele were crossed with Fabpl::Cre transgenic mice, in the context of the ApcMin mutation, in order to inactivate Tdg in the small intestinal and colonic epithelium. We observed an approximately 2-fold increase in the number of small intestinal adenomas in the test Tdg-mutant ApcMin mice in comparison to control genotypes (p=0.0001). This increase occurred in female mice, and is similar to the known increase in intestinal adenoma formation due to oophorectomy. In the human colorectal cancer (CRC) TCGA database, the subset of patients with TDG and APC expression in the lowest quartile exhibits an excess of female cases. We conclude that TDG inactivation plays a role in intestinal tumorigenesis initiated by mutation/underexpression of APC. Our results also indicate that TDG may be involved in sex-specific protection from CRC.
Collapse
Affiliation(s)
- Jinfei Xu
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Salvatore Cortellino
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Rossella Tricarico
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Wen-Chi Chang
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Gabrielle Scher
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Karthik Devarajan
- Department of Biostatistics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Michael Slifker
- Department of Biostatistics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Robert Moore
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Maria Rosaria Bassi
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Elena Caretti
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Margie Clapper
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Harry Cooper
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Alfonso Bellacosa
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| |
Collapse
|
20
|
Seki M, Nishimura R, Yoshida K, Shimamura T, Shiraishi Y, Sato Y, Kato M, Chiba K, Tanaka H, Hoshino N, Nagae G, Shiozawa Y, Okuno Y, Hosoi H, Tanaka Y, Okita H, Miyachi M, Souzaki R, Taguchi T, Koh K, Hanada R, Kato K, Nomura Y, Akiyama M, Oka A, Igarashi T, Miyano S, Aburatani H, Hayashi Y, Ogawa S, Takita J. Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma. Nat Commun 2015; 6:7557. [PMID: 26138366 PMCID: PMC4506514 DOI: 10.1038/ncomms8557] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 05/20/2015] [Indexed: 01/21/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma in childhood. Here we studied 60 RMSs using whole-exome/-transcriptome sequencing, copy number (CN) and DNA methylome analyses to unravel the genetic/epigenetic basis of RMS. On the basis of methylation patterns, RMS is clustered into four distinct subtypes, which exhibits remarkable correlation with mutation/CN profiles, histological phenotypes and clinical behaviours. A1 and A2 subtypes, especially A1, largely correspond to alveolar histology with frequent PAX3/7 fusions and alterations in cell cycle regulators. In contrast, mostly showing embryonal histology, both E1 and E2 subtypes are characterized by high frequency of CN alterations and/or allelic imbalances, FGFR4/RAS/AKT pathway mutations and PTEN mutations/methylation and in E2, also by p53 inactivation. Despite the better prognosis of embryonal RMS, patients in the E2 are likely to have a poor prognosis. Our results highlight the close relationships of the methylation status and gene mutations with the biological behaviour in RMS.
Collapse
Affiliation(s)
- Masafumi Seki
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Riki Nishimura
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Kenichi Yoshida
- 1] Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan [2] Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Teppei Shimamura
- 1] Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan [2] Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yusuke Sato
- 1] Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan [2] Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Motohiro Kato
- 1] Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan [2] Department of Cell Therapy and Transplantation Medicine, The University of Tokyo, Tokyo 113-8655, Japan [3] Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama 339-8551, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hiroko Tanaka
- Laboratory of Sequence Data Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Noriko Hoshino
- Department of Pediatric Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Genta Nagae
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Yusuke Shiozawa
- 1] Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan [2] Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Yusuke Okuno
- 1] Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan [2] Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Hajime Hosoi
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Yukichi Tanaka
- Department of Pathology, Kanagawa Children's Medical Center, Yokohama 232-8555, Japan
| | - Hajime Okita
- Molecular Pathology Laboratory, Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Mitsuru Miyachi
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Ryota Souzaki
- Department of Pediatric Surgery, Reproductive and Developmental Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Tomoaki Taguchi
- Department of Pediatric Surgery, Reproductive and Developmental Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama 339-8551, Japan
| | - Ryoji Hanada
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama 339-8551, Japan
| | - Keisuke Kato
- Division of Pediatric Hematology and Oncology, Ibaraki Children's Hospital, Mito 311-4145, Japan
| | - Yuko Nomura
- Department of Pediatrics, School of Medicine, Fukuoka University, Fukuoka 814-0180, Japan
| | - Masaharu Akiyama
- Department of Pediatrics, The Jikei University School of Medicine, Tokyo 105-8471, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Takashi Igarashi
- 1] Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan [2] National Center for Child Health and Development, Tokyo 157-8535, Japan
| | - Satoru Miyano
- 1] Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan [2] Laboratory of Sequence Data Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Yasuhide Hayashi
- Department of Hematology/Oncology, Gunma Children's Medical Center, Shibukawa, Gunma, 377-8577, Japan
| | - Seishi Ogawa
- 1] Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan [2] Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| |
Collapse
|
21
|
Bellacosa A, Drohat AC. Role of base excision repair in maintaining the genetic and epigenetic integrity of CpG sites. DNA Repair (Amst) 2015; 32:33-42. [PMID: 26021671 DOI: 10.1016/j.dnarep.2015.04.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cytosine methylation at CpG dinucleotides is a central component of epigenetic regulation in vertebrates, and the base excision repair (BER) pathway is important for maintaining both the genetic stability and the methylation status of CpG sites. This perspective focuses on two enzymes that are of particular importance for the genetic and epigenetic integrity of CpG sites, methyl binding domain 4 (MBD4) and thymine DNA glycosylase (TDG). We discuss their capacity for countering C to T mutations at CpG sites, by initiating base excision repair of G · T mismatches generated by deamination of 5-methylcytosine (5mC). We also consider their role in active DNA demethylation, including pathways that are initiated by oxidation and/or deamination of 5mC.
Collapse
Affiliation(s)
- Alfonso Bellacosa
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, United States.
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, United States.
| |
Collapse
|
22
|
Calcagno DQ, de Arruda Cardoso Smith M, Burbano RR. Cancer type-specific epigenetic changes: gastric cancer. Methods Mol Biol 2015; 1238:79-101. [PMID: 25421656 DOI: 10.1007/978-1-4939-1804-1_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gastric cancer (GC) remains a major cause of mortality despite declining rate in the world. Epigenetic alterations contribute significantly to the development and progression of gastric tumors. Epigenetic refers to the number of modifications of the chromatin structure that affect gene expression without altering the primary sequence of DNA, and these changes lead to transcriptional activation or silencing of the gene. Over the years, the study of epigenetic processes has increased, and novel therapeutic approaches have emerged. This chapter summarizes the main epigenomic mechanisms described recently involved in gastric carcinogenesis, focusing on the roles that aberrant DNA methylation, histone modifications (histone acetylation and methylation), and miRNAs (oncogenic and tumor suppressor function of miRNA) play in the onset and progression of gastric tumors. Clinical implications of these epigenetic alterations in GC are also discussed.
Collapse
Affiliation(s)
- Danielle Queiroz Calcagno
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Rua dos Mundurucus, 4487, Guamá, CEP 66073-000 Belém, PA, Brazil,
| | | | | |
Collapse
|
23
|
Abstract
Mounting evidence has recently underscored the importance of DNA methylation in normal brain functions. DNA methylation machineries are responsible for dynamic regulation of methylation patterns in discrete brain regions. In addition to methylation of cytosines in genomic DNA (5-methylcytosine; 5mC), other forms of modified cytosines, such as 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine, can potentially act as epigenetic marks that regulate gene expression. Importantly, epigenetic modifications require cognate binding proteins to read and translate information into gene expression regulation. Abnormal or incorrect interpretation of DNA methylation patterns can cause devastating consequences, including mental illnesses and neurological disorders. Although DNA methylation was generally considered to be a stable epigenetic mark in post-mitotic cells, recent studies have revealed dynamic DNA modifications in neurons. Such reversibility of 5mC sheds light on potential mechanisms underlying some neurological disorders and suggests a new route to correct aberrant methylation patterns associated with these disorders.
Collapse
Affiliation(s)
- Yi-Lan Weng
- />Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- />Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Ran An
- />Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- />Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Jaehoon Shin
- />Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- />Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Hongjun Song
- />Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- />Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- />Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- />The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Guo-li Ming
- />Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- />Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- />Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- />The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD USA
| |
Collapse
|
24
|
Xu Y, Zhou B, Wu D, Yin Z, Luo D. Baicalin modulates microRNA expression in UVB irradiated mouse skin. J Biomed Res 2013; 26:125-34. [PMID: 23554741 PMCID: PMC3597329 DOI: 10.1016/s1674-8301(12)60022-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 10/25/2011] [Accepted: 11/23/2011] [Indexed: 12/31/2022] Open
Abstract
This study aimed to evaluate the effects of baicalin on ultraviolet radiation B (UVB)-mediated microRNA (miRNA) expression in mouse skin. We determined miRNA expression profiles in UVB irradiated mice, baicalin treated irradiated mice, and untreated mice, and conducted TargetScan and Gene Ontology analyses to predict miRNA targets. Three miRNAs (mmu-miR-125a-5p, mmu-miR-146a, and mmu-miR-141) were downregulated and another three (mmu-miR-188-5p, mmu-miR-223 and mmu-miR-22) were upregulated in UVB irradiated mice compared with untreated mice. Additionally, these miRNAs were predicted to be related to photocarcinogenesis, hypomethylation and apoptosis. Three miRNAs (mmu-miR-378, mmu-miR-199a-3p and mmu-miR-181b) were downregulated and one (mmu-miR-23a) was upregulated in baicalin treated mice compared with UVB irradiated mice, and they were predicted to be related to DNA repair signaling pathway. These deregulated miRNAs are potentially involved in the pathogenesis of photodamage, and may aid treatment and prevention of UVB-induced dermatoses.
Collapse
Affiliation(s)
- Yang Xu
- Department of Dermatology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | | | | | | | | |
Collapse
|
25
|
Calcagno DQ, Gigek CO, Chen ES, Burbano RR, Smith MDAC. DNA and histone methylation in gastric carcinogenesis. World J Gastroenterol 2013; 19:1182-92. [PMID: 23482412 PMCID: PMC3587474 DOI: 10.3748/wjg.v19.i8.1182] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 06/13/2012] [Accepted: 06/28/2012] [Indexed: 02/06/2023] Open
Abstract
Epigenetic alterations contribute significantly to the development and progression of gastric cancer, one of the leading causes of cancer death worldwide. Epigenetics refers to the number of modifications of the chromatin structure that affect gene expression without altering the primary sequence of DNA, and these changes lead to transcriptional activation or silencing of the gene. Over the years, the study of epigenetic processes has increased, and novel therapeutic approaches that target DNA methylation and histone modifications have emerged. A greater understanding of epigenetics and the therapeutic potential of manipulating these processes is necessary for gastric cancer treatment. Here, we review recent research on the effects of aberrant DNA and histone methylation on the onset and progression of gastric tumors and the development of compounds that target enzymes that regulate the epigenome.
Collapse
|
26
|
Abstract
DNA methylation has long been considered a very stable DNA modification in mammals that could only be removed by replication in the absence of remethylation - that is, by mere dilution of this epigenetic mark (so-called passive DNA demethylation). However, in recent years, a significant number of studies have revealed the existence of active processes of DNA demethylation in mammals, with important roles in development and transcriptional regulation, allowing the molecular mechanisms of active DNA demethylation to be unraveled. In this article, we review the recent literature highlighting the prominent role played in active DNA demethylation by base excision repair and especially by TDG.
Collapse
Affiliation(s)
- Shannon R Dalton
- Cancer Biology Program, Epigenetics & Progenitor Cells Program, Fox Chase Cancer Center, PA 19111, USA
| | | |
Collapse
|
27
|
Ko HL, Ren EC. Functional Aspects of PARP1 in DNA Repair and Transcription. Biomolecules 2012; 2:524-48. [PMID: 24970148 PMCID: PMC4030864 DOI: 10.3390/biom2040524] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 10/24/2012] [Accepted: 10/31/2012] [Indexed: 01/08/2023] Open
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) is an ADP-ribosylating enzyme essential for initiating various forms of DNA repair. Inhibiting its enzyme activity with small molecules thus achieves synthetic lethality by preventing unwanted DNA repair in the treatment of cancers. Through enzyme-dependent chromatin remodeling and enzyme-independent motif recognition, PARP1 also plays important roles in regulating gene expression. Besides presenting current findings on how each process is individually controlled by PARP1, we shall discuss how transcription and DNA repair are so intricately linked that disturbance by PARP1 enzymatic inhibition, enzyme hyperactivation in diseases, and viral replication can favor one function while suppressing the other.
Collapse
Affiliation(s)
- Hui Ling Ko
- Singapore Immunology Network, A*STAR, 8A Biomedical Grove, #03-06 Immunos, Singapore 138648, Singapore.
| | - Ee Chee Ren
- Singapore Immunology Network, A*STAR, 8A Biomedical Grove, #03-06 Immunos, Singapore 138648, Singapore.
| |
Collapse
|
28
|
Vasovcak P, Krepelova A, Menigatti M, Puchmajerova A, Skapa P, Augustinakova A, Amann G, Wernstedt A, Jiricny J, Marra G, Wimmer K. Unique mutational profile associated with a loss of TDG expression in the rectal cancer of a patient with a constitutional PMS2 deficiency. DNA Repair (Amst) 2012; 11:616-23. [PMID: 22608206 PMCID: PMC3387372 DOI: 10.1016/j.dnarep.2012.04.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 04/21/2012] [Accepted: 04/24/2012] [Indexed: 12/14/2022]
Abstract
Cells with DNA repair defects have increased genomic instability and are more likely to acquire secondary mutations that bring about cellular transformation. We describe the frequency and spectrum of somatic mutations involving several tumor suppressor genes in the rectal carcinoma of a 13-year-old girl harboring biallelic, germline mutations in the DNA mismatch repair gene PMS2. Apart from microsatellite instability, the tumor DNA contained a number of C:G → T:A or G:C → A:T transitions in CpG dinucleotides, which often result through spontaneous deamination of cytosine or 5-methylcytosine. Four DNA glycosylases, UNG2, SMUG1, MBD4 and TDG, are involved in the repair of these deamination events. We identified a heterozygous missense mutation in TDG, which was associated with TDG protein loss in the tumor. The CpGs mutated in this patient's tumor are generally methylated in normal colonic mucosa. Thus, it is highly likely that loss of TDG contributed to the supermutator phenotype and that most of the point mutations were caused by deamination of 5-methylcytosine to thymine, which remained uncorrected owing to the TDG deficiency. This case provides the first in vivo evidence of the key role of TDG in protecting the human genome against the deleterious effects of 5-methylcytosine deamination.
Collapse
Affiliation(s)
- P Vasovcak
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, V Uvalu 84, 15006 Prague 5, Czech Republic.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Tudek B, Speina E. Oxidatively damaged DNA and its repair in colon carcinogenesis. Mutat Res 2012; 736:82-92. [PMID: 22561673 DOI: 10.1016/j.mrfmmm.2012.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 04/02/2012] [Accepted: 04/16/2012] [Indexed: 12/18/2022]
Abstract
Inflammation, high fat, high red meat and low fiber consumption have for long been known as the most important etiological factors of sporadic colorectal cancers (CRC). Colon cancer originates from neoplastic transformation in a single layer of epithelial cells occupying colonic crypts, in which migration and apoptosis program becomes disrupted. This results in the formation of polyps and metastatic cancers. Mutational program in sporadic cancers involves APC gene, in which mutations occur most abundantly in the early phase of the process. This is followed by mutations in RAS, TP53, and other genes. Progression of carcinogenic process in the colon is accompanied by augmentation of the oxidative stress, which manifests in the increased level of oxidatively damaged DNA both in the colon epithelium, and in blood leukocytes and urine, already at the earliest stages of disease development. Defence mechanisms are deregulated in CRC patients: (i) antioxidative vitamins level in blood plasma declines with the development of disease; (ii) mRNA level of base excision repair enzymes in blood leukocytes of CRC patients is significantly increased; however, excision rate is regulated separately, being increased for 8-oxoGua, while decreased for lipid peroxidation derived ethenoadducts, ɛAde and ɛCyt; (iii) excision rate of ɛAde and ɛCyt in colon tumors is significantly increased in comparison to asymptomatic colon margin, and ethenoadducts level is decreased. This review highlights mechanisms underlying such deregulation, which is the driving force to colon carcinogenesis.
Collapse
Affiliation(s)
- Barbara Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | |
Collapse
|
30
|
Winczura A, Zdżalik D, Tudek B. Damage of DNA and proteins by major lipid peroxidation products in genome stability. Free Radic Res 2012; 46:442-59. [PMID: 22257221 DOI: 10.3109/10715762.2012.658516] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Oxidative stress and lipid peroxidation (LPO) accompanying infections and chronic inflammation may induce several human cancers. LPO products are characterized by carbohydrate chains of different length, reactive aldehyde groups and double bonds, which make these molecules reactive to nucleic acids, proteins and cellular thiols. LPO-derived adducts to DNA bases form etheno-type and propano-type exocyclic rings, which have profound mutagenic potential, and are elevated in several cancer-prone diseases. Adducts of long chain LPO products to DNA bases inhibit transcription. Elimination from DNA of LPO-induced lesions is executed by several repair systems: base excision repair (BER), direct reversal by AlkB family proteins, nucleotide excision repair (NER) and recombination. Modifications of proteins with LPO products may regulate cellular processes like apoptosis, cell signalling and senescence. This review summarizes consequences of LPO products' presence in cell, particularly 4-hydroxy-2-nonenal, in terms of genomic stability.
Collapse
Affiliation(s)
- Alicja Winczura
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 02-106 Warsaw, Poland
| | | | | |
Collapse
|
31
|
Zhou BR, Xu Y, Luo D. Effect of UVB irradiation on microRNA expression in mouse epidermis. Oncol Lett 2012; 3:560-564. [PMID: 22740952 DOI: 10.3892/ol.2012.551] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 12/20/2011] [Indexed: 11/06/2022] Open
Abstract
The aim of this study was to assess the effects of UVB irradiation on miRNA expression in the mouse epidermis. We determined miRNA expression profiles in the epidermis of UVB irradiated mice and untreated mice, and conducted TargetScan and Gene Ontology analyses to predict miRNA targets. Three miRNAs were downregulated and three were upregulated in the epidermis of UVB irradiated mice compared with untreated mice, and were predicted to be associated with photocarcinogenesis, hypomethylation and apoptosis. miRNAs are potentially involved in the pathogenesis of photodamage, and may aid in the treatment and prevention of UVB-induced dermatoses.
Collapse
Affiliation(s)
- Bing-Rong Zhou
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P.R. China
| | | | | |
Collapse
|
32
|
Zhang W, Liu Z, Crombet L, Amaya MF, Liu Y, Zhang X, Kuang W, Ma P, Niu L, Qi C. Crystal structure of the mismatch-specific thymine glycosylase domain of human methyl-CpG-binding protein MBD4. Biochem Biophys Res Commun 2011; 412:425-8. [PMID: 21820404 DOI: 10.1016/j.bbrc.2011.07.091] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 07/21/2011] [Indexed: 10/17/2022]
Abstract
Methyl-CpG (mCpG) binding domain protein 4 (MBD4) is a member of mammalian DNA glycosylase superfamily. It contains an amino-proximal methyl-CpG binding domain (MBD) and a C-terminal mismatch-specific glycosylase domain, which is an important molecule believed to be involved in maintaining of genome stability. Herein, we determined the crystal structure of C-terminal glycosylase domain of human MBD4. And the structural alignments of other helix-hairpin-helix (HhH) DNA glycosylases show that the human MBD4 glycosylase domain has the similar active site and the catalytic mechanisms as others. But the different residues in the N-terminal of domain result in the change of charge distribution on the surface of the protein, which suggest the different roles that may relate some diseases.
Collapse
Affiliation(s)
- Wei Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079, People's Republic of China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Grogan BC, Parker JB, Guminski AF, Stivers JT. Effect of the thymidylate synthase inhibitors on dUTP and TTP pool levels and the activities of DNA repair glycosylases on uracil and 5-fluorouracil in DNA. Biochemistry 2011; 50:618-27. [PMID: 21222484 DOI: 10.1021/bi102046h] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
5-Fluorouracil (5-FU), 5-fluorodeoxyuridine (5-dUrd), and raltitrixed (RTX) are anticancer agents that target thymidylate synthase (TS), thereby blocking the conversion of dUMP into dTMP. In budding yeast, 5-FU promotes a large increase in the dUMP/dTMP ratio leading to massive polymerase-catalyzed incorporation of uracil (U) into genomic DNA, and to a lesser extent 5-FU, which are both excised by yeast uracil DNA glycosylase (UNG), leading to DNA fragmentation and cell death. In contrast, the toxicity of 5-FU and RTX in human and mouse cell lines does not involve UNG, but, instead, other DNA glycosylases that can excise uracil derivatives. To elucidate the basis for these divergent findings in yeast and human cells, we have investigated how these drugs perturb cellular dUTP and TTP pool levels and the relative abilities of three human DNA glycosylases (hUNG2, hSMUG1, and hTDG) to excise various TS drug-induced lesions in DNA. We found that 5-dUrd only modestly increases the dUTP and dTTP pool levels in asynchronous MEF, HeLa, and HT-29 human cell lines when growth occurs in standard culture media. In contrast, treatment of chicken DT40 B cells with 5-dUrd or RTX resulted in large increases in the dUTP/TTP ratio. Surprisingly, even though UNG is the only DNA glycosylase in DT40 cells that can act on U·A base pairs derived from dUTP incorporation, an isogenic ung(-/-) DT40 cell line showed little change in its sensitivity to RTX as compared to control cells. In vitro kinetic analyses of the purified human enzymes show that hUNG2 is the most powerful catalyst for excision of 5-FU and U regardless of whether it is found in base pairs with A or G or present in single-stranded DNA. Fully consistent with the in vitro activity assays, nuclear extracts isolated from human and chicken cell cultures show that hUNG2 is the overwhelming activity for removal of both U and 5-FU, despite its bystander status with respect to drug toxicity in these cell lines. The diverse outcomes of TS inhibition with respect to nucleotide pool levels, the nature of the resulting DNA lesion, and the DNA repair response are discussed.
Collapse
Affiliation(s)
- Breeana C Grogan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
| | | | | | | |
Collapse
|
34
|
Regulation of cell cycle and DNA repair in post-mitotic GABA neurons in psychotic disorders. Neuropharmacology 2010; 60:1232-42. [PMID: 21184762 DOI: 10.1016/j.neuropharm.2010.12.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 11/24/2010] [Accepted: 12/15/2010] [Indexed: 11/24/2022]
Abstract
Disturbances of cell cycle regulation and DNA repair in post-mitotic neurons have been implicated in degenerative and malignant diseases of the human brain. Recent work is now suggesting that abnormal regulation of these functions in GABA cells of the adult hippocampus may also play a role in two neuropsychiatric disorders. In schizophrenia and bipolar disorder, a network of genes involved in the regulation of GAD₆₇, a marker for the functional differentiation of GABA cells, show pronounced changes in expression and include kainate receptor subunits, TGFβ and Wnt signaling pathways, epigenetic factors and transcription factors. One of these genes, cyclin D2, is involved in the regulation of cell cycle and DNA repair and appears to be a pivotal element in linking GAD₆₇ expression with these functional clusters of genes. Dysfunction of post-mitotic GABAergic neurons in the adult hippocampus of patients with psychotic disorders is associated with changes in the expression of genes that are involved in the maintenance of functional and genomic integrity of GABA cells. The nature of these changes is quite different in schizophrenia and bipolar disorder, suggesting that a common cell phenotype (in this case, decreased GAD₆₇ expression) may involve two fundamentally different molecular endophenotypes and reflect unique susceptibility genes involved in the respective disorders. This article is part of a Special Issue entitled 'Trends in neuropharmacology: in memory of Erminio Costa'.
Collapse
|
35
|
Nemec AA, Wallace SS, Sweasy JB. Variant base excision repair proteins: contributors to genomic instability. Semin Cancer Biol 2010; 20:320-8. [PMID: 20955798 DOI: 10.1016/j.semcancer.2010.10.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cells sustain endogenous DNA damage at rates greater than 20,000 DNA lesions per cell per day. These damages occur largely as a result of the inherently unstable nature of DNA and the presence of reactive oxygen species within cells. The base excision repair system removes the majority of DNA lesions resulting from endogenous DNA damage. There are several enzymes that function during base excision repair. Importantly, there are over 100 germline single nucleotide polymorphisms in genes that function in base excision repair and that result in non-synonymous amino acid substitutions in the proteins they encode. Somatic variants of these enzymes are also found in human tumors. Variant repair enzymes catalyze aberrant base excision repair. Aberrant base excision repair combined with continuous endogenous DNA damage over time has the potential to lead to a mutator phenotype. Mutations that arise in key growth control genes, imbalances in chromosome number, chromosomal translocations, and loss of heterozygosity can result in the initiation of human cancer or its progression.
Collapse
Affiliation(s)
- Antonia A Nemec
- Department of Therapeutic Radiology, 15 York Street, New Haven, CT 06510, United States
| | | | | |
Collapse
|
36
|
Steilmann C, Cavalcanti MCO, Bergmann M, Kliesch S, Weidner W, Steger K. Aberrant mRNA expression of chromatin remodelling factors in round spermatid maturation arrest compared with normal human spermatogenesis. Mol Hum Reprod 2010; 16:726-33. [DOI: 10.1093/molehr/gaq054] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
37
|
Li S, Huang Q, Wang L, Lan Y, Zhang X, Yang B, Du P, Hua Z. A convenient spectrometric assay system for intracellular quantitative measurement of DNA glycosylase activity. Acta Biochim Biophys Sin (Shanghai) 2010; 42:381-7. [PMID: 20539937 DOI: 10.1093/abbs/gmq032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cytosine methylation is a vital biology event. However, it is also the source of genomic instability due to deamination of 5'-methylcytosine by spontaneous hydrolysis, which produces thymine and results in G:T mismatches. Thymine DNA glycosylase and methyl-CpG-binding protein 4 are major DNA glycosylases involved in the mismatch repair progress, and their activities have been measured in many related researches. In this study, we developed a convenient spectrometric assay system for specific and quantitative measurement of intracellular DNA glycosylase activity. A G:T mismatch was introduced into the upstream region of firefly luciferase-coding sequence in the pGL3-control plasmid. Only if the G:T mismatches were repaired to G:C, will luciferase be expressed in transfected cells. By measuring luciferase activity, which is simple and convenient, the intracellular DNA glycosylase activity can be determined.
Collapse
Affiliation(s)
- Shiying Li
- Jiangsu Center of Hepatobiliary Diseases and School of Stomatology, Affiliated Stomatological Hospital, Nanjing University, China
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Bertoni C, Rustagi A, Rando TA. Enhanced gene repair mediated by methyl-CpG-modified single-stranded oligonucleotides. Nucleic Acids Res 2010; 37:7468-82. [PMID: 19854937 PMCID: PMC2794159 DOI: 10.1093/nar/gkp757] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Gene editing mediated by oligonucleotides has been shown to induce stable single base alterations in genomic DNA in both prokaryotic and eukaryotic organisms. However, the low frequencies of gene repair have limited its applicability for both basic manipulation of genomic sequences and for the development of therapeutic approaches for genetic disorders. Here, we show that single-stranded oligodeoxynucleotides (ssODNs) containing a methyl-CpG modification and capable of binding to the methyl-CpG binding domain protein 4 (MBD4) are able to induce >10-fold higher levels of gene correction than ssODNs lacking the specific modification. Correction was stably inherited through cell division and was confirmed at the protein, transcript and genomic levels. Downregulation of MBD4 expression using RNAi prevented the enhancement of gene correction efficacy obtained using the methyl-CpG-modified ssODN, demonstrating the specificity of the repair mechanism being recruited. Our data demonstrate that efficient manipulation of genomic targets can be achieved and controlled by the type of ssODN used and by modulation of the repair mechanism involved in the correction process. This new generation of ssODNs represents an important technological advance that is likely to have an impact on multiple applications, especially for gene therapy where permanent correction of the genetic defect has clear advantages over viral and other nonviral approaches currently being tested.
Collapse
Affiliation(s)
- Carmen Bertoni
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | | | | |
Collapse
|
39
|
Li LS, Morales JC, Veigl M, Sedwick D, Greer S, Meyers M, Wagner M, Fishel R, Boothman DA. DNA mismatch repair (MMR)-dependent 5-fluorouracil cytotoxicity and the potential for new therapeutic targets. Br J Pharmacol 2009; 158:679-92. [PMID: 19775280 DOI: 10.1111/j.1476-5381.2009.00423.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The metabolism and efficacy of 5-fluorouracil (FUra) and other fluorinated pyrimidine (FP) derivatives have been intensively investigated for over fifty years. FUra and its antimetabolites can be incorporated at RNA- and DNA-levels, with RNA level incorporation provoking toxic responses in human normal tissue, and DNA-level antimetabolite formation and incorporation believed primarily responsible for tumour-selective responses. Attempts to direct FUra into DNA-level antimetabolites, based on mechanism-of-action studies, have led to gradual improvements in tumour therapy. These include the use of leukovorin to stabilize the inhibitory thymidylate synthase-5-fluoro-2'-deoxyuridine 5' monophoshate (FdUMP)-5,10-methylene tetrahydrofolate (5,10-CH(2)FH(4)) trimeric complex. FUra incorporated into DNA also contributes to antitumour activity in preclinical and clinical studies. This review examines our current state of knowledge regarding the mechanistic aspects of FUra:Gua lesion detection by DNA mismatch repair (MMR) machinery that ultimately results in lethality. MMR-dependent direct cell death signalling or futile cycle responses will be discussed. As 10-30% of sporadic colon and endometrial tumours display MMR defects as a result of human MutL homologue-1 (hMLH1) promoter hypermethylation, we discuss the use and manipulation of the hypomethylating agent, 5-fluorodeoxycytidine (FdCyd), and our ability to manipulate its metabolism using the cytidine or deoxycytidylate (dCMP) deaminase inhibitors, tetrahydrouridine or deoxytetrahydrouridine, respectively, as a method for re-expression of hMLH1 and re-sensitization of tumours to FP therapy.
Collapse
Affiliation(s)
- Long Shan Li
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Kunz C, Focke F, Saito Y, Schuermann D, Lettieri T, Selfridge J, Schär P. Base excision by thymine DNA glycosylase mediates DNA-directed cytotoxicity of 5-fluorouracil. PLoS Biol 2009; 7:e91. [PMID: 19402749 PMCID: PMC2671560 DOI: 10.1371/journal.pbio.1000091] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 03/10/2009] [Indexed: 01/27/2023] Open
Abstract
5-Fluorouracil (5-FU), a chemotherapeutic drug commonly used in cancer treatment, imbalances nucleotide pools, thereby favoring misincorporation of uracil and 5-FU into genomic DNA. The processing of these bases by DNA repair activities was proposed to cause DNA-directed cytotoxicity, but the underlying mechanisms have not been resolved. In this study, we investigated a possible role of thymine DNA glycosylase (TDG), one of four mammalian uracil DNA glycosylases (UDGs), in the cellular response to 5-FU. Using genetic and biochemical tools, we found that inactivation of TDG significantly increases resistance of both mouse and human cancer cells towards 5-FU. We show that excision of DNA-incorporated 5-FU by TDG generates persistent DNA strand breaks, delays S-phase progression, and activates DNA damage signaling, and that the repair of 5-FU–induced DNA strand breaks is more efficient in the absence of TDG. Hence, excision of 5-FU by TDG, but not by other UDGs (UNG2 and SMUG1), prevents efficient downstream processing of the repair intermediate, thereby mediating DNA-directed cytotoxicity. The status of TDG expression in a cancer is therefore likely to determine its response to 5-FU–based chemotherapy. 5-Fluorouracil (5-FU) has been used in clinical cancer therapy for more than four decades. Despite a moderate response rate and a high propensity of tumors to develop resistance to the drug, 5-FU remains a mainstay in the first-line treatment of colorectal cancer in particular. But precisely how 5-FU kills cancerous cells is not well understood. It is known, for example, that 5-FU affects RNA or DNA metabolism. Its DNA-directed cytotoxicity is thought to be based on extensive misincorporation of uracil and 5-FU into cellular DNA, and it has been proposed that the excision of these bases by uracil DNA glycosylases (UDGs) results in destructive DNA fragmentation, which can ultimately lead to cell death. However, the UDG responsible has not been identified. We now show that inactivation of only one of four mammalian UDGs, the thymine DNA glycosylase (TDG) in mouse and human cells is sufficient to confer resistance to 5-FU, whereas overexpression of TDG sensitizes cells to the drug. We provide further experimental evidence to show that excision of 5-FU from DNA by TDG, but not by other UDGs, inhibits efficient downstream processing of the lesion. This leads to an accumulation of DNA repair intermediates, which induce DNA damage signaling and, eventually, cell death. Thus, TDG activity in cells represents an important determinant of the DNA-directed cytotoxicity of 5-FU, an observation that might help us to understand the variable response to 5-FU treatments in cancer. Targeted disruption of thymine DNA glycosylase (TDG) in mouse cells and down-regulation in human cancer cells establishes an important role of this protein in the cellular response to the anticancer drug 5-fluorouracil.
Collapse
Affiliation(s)
- Christophe Kunz
- Institute of Biochemistry and Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Frauke Focke
- Institute of Biochemistry and Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Yusuke Saito
- Institute of Biochemistry and Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - David Schuermann
- Institute of Biochemistry and Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Jim Selfridge
- Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh, Scotland
| | - Primo Schär
- Institute of Biochemistry and Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
41
|
Site-specific regulation of cell cycle and DNA repair in post-mitotic GABA cells in schizophrenic versus bipolars. Proc Natl Acad Sci U S A 2009; 106:11731-6. [PMID: 19564623 DOI: 10.1073/pnas.0903066106] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
GABA cell dysfunction in both schizophrenia (SZ) and bipolar disorder (BD) involves decreased GAD(67) expression, although this change involves fundamentally different networks of genes in the 2 disorders. One gene that is common to these 2 networks is cyclin D2, a key component of cell cycle regulation that shows increased expression in SZ, but decreased expression in BD. Because of the importance of cell cycle regulation in maintaining functional differentiation and DNA repair, the current study has examined the genes involved in the G(1) and G(2) checkpoints to generate new hypotheses regarding the regulation of the GABA cell phenotype in the hippocampus of SZ and BD. The results have demonstrated significant changes in cell cycle regulation in both SZ and BD and these changes include the transcriptional complex (TC) that controls the expression of E2F/DP-1 target genes critical for progression to G(2)/M. The methyl-CpG binding domain protein (MBD4) that is pivotal for DNA repair, is significantly up-regulated in the stratum oriens (SO) of CA3/2 and CA1 in SZs and BDs. However, other genes associated with the TC, and the G(1) and G(2) checkpoints, show complex changes in expression in the SO of CA3/2 and CA1 of both SZs and BDS. Overall, the patterns of expression observed have suggested that the regulation of functional differentiation and/or genomic integrity of hippocampal GABA cells varies according to diagnosis and their location within the trisynaptic pathway.
Collapse
|
42
|
Visnes T, Doseth B, Pettersen HS, Hagen L, Sousa MML, Akbari M, Otterlei M, Kavli B, Slupphaug G, Krokan HE. Uracil in DNA and its processing by different DNA glycosylases. Philos Trans R Soc Lond B Biol Sci 2009; 364:563-8. [PMID: 19008197 DOI: 10.1098/rstb.2008.0186] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Uracil in DNA may result from incorporation of dUMP during replication and from spontaneous or enzymatic deamination of cytosine, resulting in U:A pairs or U:G mismatches, respectively. Uracil generated by activation-induced cytosine deaminase (AID) in B cells is a normal intermediate in adaptive immunity. Five mammalian uracil-DNA glycosylases have been identified; these are mitochondrial UNG1 and nuclear UNG2, both encoded by the UNG gene, and the nuclear proteins SMUG1, TDG and MBD4. Nuclear UNG2 is apparently the sole contributor to the post-replicative repair of U:A lesions and to the removal of uracil from U:G contexts in immunoglobulin genes as part of somatic hypermutation and class-switch recombination processes in adaptive immunity. All uracil-DNA glycosylases apparently contribute to U:G repair in other cells, but they are likely to have different relative significance in proliferating and non-proliferating cells, and in different phases of the cell cycle. There are also some indications that there may be species differences in the function of the uracil-DNA glycosylases.
Collapse
Affiliation(s)
- Torkild Visnes
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7489 Trondheim, Norway
| | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Viana-Pereira M, Almeida I, Sousa S, Mahler-Araújo B, Seruca R, Pimentel J, Reis RM. Analysis of microsatellite instability in medulloblastoma. Neuro Oncol 2009; 11:458-67. [PMID: 19179424 DOI: 10.1215/15228517-2008-115] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Medulloblastoma is the most common malignant brain tumor in children. The presence of microsatellite instability (MSI) in brain tumors, particularly medulloblastomas, has not been properly addressed. The aim of the present study was to evaluate the role of MSI in medulloblastoma carcinogenesis. MSI status was determined in 36 patients using a pentaplex PCR of quasimonomorphic markers (NR27, NR21, NR24, BAT25, and BAT26). Methylation status of mismatch repair (MMR) genes was achieved by methylation-specific multiplex ligation-dependent probe amplification (MLPA). In addition, MutS homolog 6 (MSH6) expression was determined by immunohistochemistry. Mutations of 10 MSI target genes (TCF4, XRCC2, MBD4, MRE11, ATR, MSH3, TGFBR2, RAD50, MSH6, and BAX) were studied by pentaplex PCR followed by analysis with GeneScan 3.7 software. Mutation analysis of hotspot regions of beta-catenin (CTNNB1) and BRAF (v-raf murine sarcoma viral oncogene homolog B1) oncogenes was performed by PCR single-strand conformation polymorphism analysis followed by direct sequencing. Among the 36 tumors, we found four (11%) cases with instability, one with high MSI and three with low MSI. Methylation analysis of MMR genes in cases presenting shifts on the MSI markers revealed mild hypermethylation of MSH6 in 75% of cases, yet MSH6 was expressed in all the tumors. The MSI target genes MBD4 (methyl-CpG binding domain protein 4) and MRE11 (meiotic recombination 11 homolog A) were mutated in two different tumors. No CTNNB1 or BRAF mutations were found. This study is the most comprehensive analysis of MSI in medulloblastomas to date. We observed the presence of MSI together with mutations of MSI target genes in a small fraction of cases, suggesting a new genetic pathway for a role in medulloblastoma development.
Collapse
Affiliation(s)
- Marta Viana-Pereira
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | | | | | | | | | | | | |
Collapse
|
44
|
Howard JH, Frolov A, Tzeng CWD, Stewart A, Midzak A, Majmundar A, Godwin A, Heslin M, Bellacosa A, Arnoletti JP. Epigenetic downregulation of the DNA repair gene MED1/MBD4 in colorectal and ovarian cancer. Cancer Biol Ther 2009; 8:94-100. [PMID: 19127118 DOI: 10.4161/cbt.8.1.7469] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
MED1 is a base excision repair enzyme that interacts with the mismatch repair protein MLH1 and maintains genomic integrity by binding methylated DNA and repairing spontaneous deamination events. MED1 mutations have been associated with microsatellite instability and accelerated colorectal cancer (CRC) tumorigenesis. We propose that promoter methylation may serve as an alternative epigenetic mechanism for MED1 gene suppression during sporadic CRC tumorigenesis. Methylation status of the MED1 promoter was investigated in a panel of ovarian and colorectal cancer cell lines. The MED1 promoter region was sequenced following bisulfite treatment and sequence analysis identified a CpG island within the MED1 promoter which is frequently and preferentially methylated (> or =50%) in ovarian and colorectal cancer cell lines with low/reduced MED1 expression. In vitro reversal of methylation restored MED1 expression. In colorectal cancer patients, when MED1 methylation was present, both tumor and matched mucosa were affected equally (mean frequency of methylation 24%) and there was no correlation between methylation and tumor stage. Patients without history of CRC showed significantly lower frequency of methylation (mean 14%, p < 0.05). Decreased MED1 transcript levels were observed in matched normal mucosa when compared to controls (median fold difference 8.0). Additional decreased expression was seen between mucosa and matched tumor (median fold decrease 4.4). Thus, MED1 promoter methylation and gene silencing occur in sporadic CRC patients and represent an early event in CRC tumorigenesis. Detection of MED1 methylation and gene suppression in normal colon mucosa may contribute to identifying patients at higher risk of developing CRC during screening procedures.
Collapse
Affiliation(s)
- J Harrison Howard
- Department of Surgery at the University of Alabama at Birmingham, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Abstract
Oncogenic tyrosine kinases, such as BCR-ABL, TEL-ABL, TEL-PDGFbetaR, and FLT3-ITD, play a major role in the development of hematopoietic malignancy. They activate many of the same signal transduction pathways. To identify the critical target genes required for transformation in hematopoietic cells, we used a comparative gene expression strategy in which selective small molecules were applied to 32Dcl3 cells that had been transformed to factor-independent growth by these respective oncogenic alleles. We identified inhibitor of DNA binding 1 (Id1), a gene involved in development, cell cycle, and tumorigenesis, as a common target of these oncogenic kinases. These findings were prospectively confirmed in cell lines and primary bone marrow cells engineered to express the respective tyrosine kinase alleles and were also confirmed in vivo in murine models of disease. Moreover, human AML cell lines Molm-14 and K562, which express the FLT3-ITD and BCR-ABL tyrosine kinases, respectively, showed high levels of Id1 expression. Antisense and siRNA based knockdown of Id1-inhibited growth of these cells associated with increased p27(Kip1) expression and increased sensitivity to Trail-induced apoptosis. These findings indicate that Id1 is an important target of constitutively activated tyrosine kinases and may be a therapeutic target for leukemias associated with oncogenic tyrosine kinases.
Collapse
|
46
|
Escobar-Morreale HF, Insenser M, Cortón M, Millán JLS, Peral B. Proteomics and genomics: A hypothesis-free approach to the study of the role of visceral adiposity in the pathogenesis of the polycystic ovary syndrome. Proteomics Clin Appl 2008; 2:444-55. [DOI: 10.1002/prca.200780031] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
47
|
Brieger A, Plotz G, Zeuzem S, Trojan J. Thymosin beta 4 expression and nuclear transport are regulated by hMLH1. Biochem Biophys Res Commun 2007; 364:731-6. [DOI: 10.1016/j.bbrc.2007.10.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Accepted: 10/03/2007] [Indexed: 10/22/2022]
|
48
|
Erdeniz N, Nguyen M, Deschênes SM, Liskay RM. Mutations affecting a putative MutLalpha endonuclease motif impact multiple mismatch repair functions. DNA Repair (Amst) 2007; 6:1463-70. [PMID: 17567544 PMCID: PMC2366940 DOI: 10.1016/j.dnarep.2007.04.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Accepted: 04/16/2007] [Indexed: 12/11/2022]
Abstract
Mutations in DNA mismatch repair (MMR) lead to increased mutation rates and higher recombination between similar, but not identical sequences, as well as resistance to certain DNA methylating agents. Recently, a component of human MMR machinery, MutLalpha, has been shown to display a latent endonuclease activity. The endonuclease active site appears to include a conserved motif, DQHA(X)(2)E(X)(4)E, within the COOH-terminus of human PMS2. Substitution of the glutamic acid residue (E705) abolished the endonuclease activity and mismatch-dependent excision in vitro. Previously, we showed that the PMS2-E705K mutation and the corresponding mutation in Saccharomyces cerevisiae were both recessive loss of function alleles for mutation avoidance in vivo. Here, we show that mutations impacting this endonuclease motif also significantly affect MMR-dependent suppression of homeologous recombination in yeast and responses to S(n)1-type methylating agents in both yeast and mammalian cells. Thus, our in vivo results suggest that the endonuclease activity of MutLalpha is important not only in MMR-dependent mutation avoidance but also for recombination and damage response functions.
Collapse
Affiliation(s)
- Naz Erdeniz
- Department of Molecular and Medical Genetics, Oregon Health & Science University L103, 3181 SW, Sam Jackson Park Road, Portland, OR 97239-3098, United States
| | - Megan Nguyen
- Department of Molecular and Medical Genetics, Oregon Health & Science University L103, 3181 SW, Sam Jackson Park Road, Portland, OR 97239-3098, United States
| | - Suzanne M. Deschênes
- Department of Biology, Sacred Heart University, 5151 Park Ave., Fairfield, CT 06825, United States
| | - R. Michael Liskay
- Department of Molecular and Medical Genetics, Oregon Health & Science University L103, 3181 SW, Sam Jackson Park Road, Portland, OR 97239-3098, United States
| |
Collapse
|
49
|
Sousa MML, Krokan HE, Slupphaug G. DNA-uracil and human pathology. Mol Aspects Med 2007; 28:276-306. [PMID: 17590428 DOI: 10.1016/j.mam.2007.04.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Accepted: 04/26/2007] [Indexed: 01/08/2023]
Abstract
Uracil is usually an inappropriate base in DNA, but it is also a normal intermediate during somatic hypermutation (SHM) and class switch recombination (CSR) in adaptive immunity. In addition, uracil is introduced into retroviral DNA by the host as part of a defence mechanism. The sources of uracil in DNA are spontaneous or enzymatic deamination of cytosine (U:G mispairs) and incorporation of dUTP (U:A pairs). Uracil in DNA is removed by a uracil-DNA glycosylase. The major ones are nuclear UNG2 and mitochondrial UNG1 encoded by the UNG-gene, and SMUG1 that also removes oxidized pyrimidines, e.g. 5-hydroxymethyluracil. The other ones are TDG that removes U and T from mismatches, and MBD4 that removes U from CpG contexts. UNG2 is found in replication foci during the S-phase and has a distinct role in repair of U:A pairs, but it is also important in U:G repair, a function shared with SMUG1. SHM is initiated by activation-induced cytosine deaminase (AID), followed by removal of U by UNG2. Humans lacking UNG2 suffer from recurrent infections and lymphoid hyperplasia, and have skewed SHM and defective CSR, resulting in elevated IgM and strongly reduced IgG, IgA and IgE. UNG-defective mice also develop B-cell lymphoma late in life. In the defence against retrovirus, e.g. HIV-1, high concentrations of dUTP in the target cells promotes misincorporation of dUMP-, and host cell APOBEC proteins may promote deamination of cytosine in the viral DNA. This facilitates degradation of viral DNA by UNG2 and AP-endonuclease. However, viral proteins Vif and Vpr counteract this defense by mechanisms that are now being revealed. In conclusion, uracil in DNA is both a mutagenic burden and a tool to modify DNA for diversity or degradation.
Collapse
Affiliation(s)
- Mirta M L Sousa
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7006 Trondheim, Norway
| | | | | |
Collapse
|
50
|
Sansom OJ, Maddison K, Clarke AR. Mechanisms of disease: methyl-binding domain proteins as potential therapeutic targets in cancer. ACTA ACUST UNITED AC 2007; 4:305-15. [PMID: 17464338 DOI: 10.1038/ncponc0812] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Accepted: 11/02/2006] [Indexed: 12/22/2022]
Abstract
The methyl-CpG-binding domain (MBD) proteins 'read' and interpret the methylation moieties on DNA, and thus are critical mediators of many epigenetic processes. Currently, the MBD family comprises five members; MBD1, MBD2, MBD3, MBD4 and MeCP2. Although not a 'classical' MBD protein, Kaiso also mediates transcriptional repression by using zinc finger domains to bind its targets. Since DNA hypermethylation is a well-recognized mechanism underlying gene silencing events in both tumorigenesis and drug resistance, it is likely that the MBD proteins may be important modulators of tumorigenesis. We review the recent work addressing this possibility, and discuss several of the MBD proteins as potentially excellent novel therapeutic targets.
Collapse
Affiliation(s)
- Owen J Sansom
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | | | | |
Collapse
|