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Baljinnyam T, Conrad JW, Sowers ML, Chang-Gu B, Herring JL, Hackfeld LC, Zhang K, Sowers LC. Characterization of a Novel Thermostable DNA Lyase Used To Prepare DNA for Next-Generation Sequencing. Chem Res Toxicol 2023; 36:162-176. [PMID: 36647573 PMCID: PMC9945173 DOI: 10.1021/acs.chemrestox.2c00172] [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] [Indexed: 01/18/2023]
Abstract
Recently, we constructed a hybrid thymine DNA glycosylase (hyTDG) by linking a 29-amino acid sequence from the human thymine DNA glycosylase with the catalytic domain of DNA mismatch glycosylase (MIG) from M. thermoautotrophicum, increasing the overall activity of the glycosylase. Previously, it was shown that a tyrosine to lysine (Y126K) mutation in the catalytic site of MIG could convert the glycosylase activity to a lyase activity. We made the corresponding mutation to our hyTDG to create a hyTDG-lyase (Y163K). Here, we report that the hybrid mutant has robust lyase activity, has activity over a broad temperature range, and is active under multiple buffer conditions. The hyTDG-lyase cleaves an abasic site similar to endonuclease III (Endo III). In the presence of β-mercaptoethanol (β-ME), the abasic site unsaturated aldehyde forms a β-ME adduct. The hyTDG-lyase maintains its preference for cleaving opposite G, as with the hyTDG glycosylase, and the hyTDG-lyase and hyTDG glycosylase can function in tandem to cleave T:G mismatches. The hyTDG-lyase described here should be a valuable tool in studies examining DNA damage and repair. Future studies will utilize these enzymes to quantify T:G mispairs in cells, tissues, and genomic DNA using next-generation sequencing.
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Affiliation(s)
- Tuvshintugs Baljinnyam
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - James W Conrad
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Mark L Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States.,MD-PhD Combined Degree Program University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Bruce Chang-Gu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States.,MD-PhD Combined Degree Program University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Jason L Herring
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Linda C Hackfeld
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Lawrence C Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States.,Department of Internal Medicine, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
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Zhang Y, Wei WB, Zhao J, Xu X, Wang F. Spectrum and tissue distribution of RB1 pathogenic alleles in mosaic retinoblastoma patients. Ophthalmic Genet 2022; 43:795-805. [PMID: 35938543 DOI: 10.1080/13816810.2022.2098985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
To characterize the spectrum of mosaic RB1 pathogenic alleles and map the distribution of mutant cells in available tissues from mosaic patients. Next-generation sequencing was performed on blood samples from 263 retinoblastoma families to identify mosaic RB1 variant alleles. A variety of available tissues were sampled to determine tissue distribution and fraction of mutant cells in five mosaic patients who consented to participate in mosaic pathogenic allele research. Twelve identified mosaic RB1 variants were all "null" pathogenic alleles and displayed reduced expressivity. The use of next-generation deep sequencing increased the sensitivity of mosaicism detection to 0.03% in the case of tissue DNA. In the five mosaic participants, we observed coherent but uneven, bilateral asymmetrical distribution of mutant cells across various tissues. They all carried early-embryonic mosaic pathogenic alleles and had significantly higher variant fractions in blood than in other tissues. Variant fractions of ipsilateral tissue samples were not concordant higher or lower compared with the contralateral side. Only ipsilateral conjunctival and oral epithelial cells showed concordance in mosaicism levels. No associations were observed between the laterality of affected eyes and variant fractions of any tissue type. NGS allows the detection of low-level mosaicism. Mosaic RB1 pathogenic alleles are prone to occur at very early stages of human embryonic development. With respect to genetic counseling, risk prediction should take into account unrecognized mosaicism. The underlying tissue distribution patterns of mosaic RB1 variant alleles remain to be determined.
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Affiliation(s)
- Yan Zhang
- Department of Ophthalmology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Wen-Bin Wei
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Junyang Zhao
- Department of Ophthalmology, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xiaolin Xu
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Fufeng Wang
- Nanjing Geneseeq Technology Inc, Nanjing, China
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3
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Yao Y, Gu X, Xu X, Ge S, Jia R. Novel insights into RB1 mutation. Cancer Lett 2022; 547:215870. [PMID: 35964818 DOI: 10.1016/j.canlet.2022.215870] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 01/09/2023]
Abstract
Since the discovery of the retinoblastoma susceptibility gene (RB1) decades ago, RB1 has been regarded as a prototype tumor suppressor gene providing a paradigm for tumor genetic research. Constant research has updated the understanding of RB1-related pathways and their impact on tumor and nontumor diseases. Mutation of RB1 gene has been observed in multiple types of malignant tumors including prostate cancer, lung cancer, breast cancer, and almost every familial and sporadic case of retinoblastoma. Even if well-known and long-investigated, the application potential of RB1 mutation has not been fully tapped. In this review, we focus on the mechanism underlying RB1 mutation during oncogenesis. Therapeutically, we have further discussed potential clinical strategies by targeting RB1-mutated cancers. The unsolved problems and prospects of RB1 mutation are also discussed.
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Affiliation(s)
- Yiran Yao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Xiaofang Xu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
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4
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Deisseroth CA, Lerma VC, Magyar CL, Pfliger JM, Nayak A, Bliss ND, LeMaire AW, Narayanan V, Balak C, Zanni G, Valente EM, Bertini E, Benke PJ, Wangler MF, Chao HT. An Integrated Phenotypic and Genotypic Approach Reveals a High-Risk Subtype Association for EBF3 Missense Variants Affecting the Zinc Finger Domain. Ann Neurol 2022; 92:138-153. [PMID: 35340043 DOI: 10.1002/ana.26359] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/28/2022] [Accepted: 03/20/2022] [Indexed: 11/10/2022]
Abstract
OBJECTIVE Collier/Olf/EBF (COE) transcription factors have distinct expression patterns in the developing and mature nervous system. To date, a neurological disease association has been conclusively established for only the Early B-cell Factor-3 (EBF3) COE family member through the identification of heterozygous loss-of-function variants in individuals with autism spectrum/neurodevelopmental disorders (NDD). Here, we identify a symptom severity risk association with missense variants primarily disrupting the zinc finger domain (ZNF) in EBF3-related NDD. METHODS A phenotypic assessment of 41 individuals was combined with a literature meta-analysis for a total of 83 individuals diagnosed with EBF3-related NDD. Quantitative diagnostic phenotypic and symptom severity scales were developed to compare EBF3 variant type and location to identify genotype-phenotype correlations. To stratify the effects of EBF3 variants disrupting either the DNA-binding domain (DBD) or the ZNF, we used in vivo fruit fly UAS-GAL4 expression and in vitro luciferase assays. RESULTS We show that patient symptom severity correlates with EBF3 missense variants perturbing the ZNF, which is a key protein domain required for stabilizing the interaction between EBF3 and the target DNA sequence. We found that ZNF-associated variants failed to restore viability in the fruit fly and impaired transcriptional activation. However, the recurrent variant EBF3 p.Arg209Trp in the DBD is capable of partially rescuing viability in the fly and preserved transcriptional activation. INTERPRETATION We describe a symptom severity risk association with ZNF perturbations and EBF3 loss-of-function in the largest reported cohort to date of EBF3-related NDD patients. This analysis should have potential predictive clinical value for newly identified patients with EBF3 gene variants. ANN NEUROL 2022;92:138-153.
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Affiliation(s)
- Cole A Deisseroth
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Vanesa C Lerma
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Christina L Magyar
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX, USA
| | - Jessica Mae Pfliger
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Development, Disease Models, and Therapeutics Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Aarushi Nayak
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Nathan D Bliss
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Ashley W LeMaire
- Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Christopher Balak
- Biomedical Sciences Graduate Program, University of California at San Diego, San Diego, CA, USA
| | - Ginevra Zanni
- Department of Neurosciences, Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu Children's Research Hospital IRCCS, Rome, Italy
| | - Enza Maria Valente
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy
| | - Enrico Bertini
- Department of Neurosciences, Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu Children's Research Hospital IRCCS, Rome, Italy
| | - Paul J Benke
- Joe DiMaggio Children's Hospital, Hollywood, FL, USA
| | - Michael F Wangler
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hsiao-Tuan Chao
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX, USA
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5
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Hsu CW, Sowers ML, Baljinnyam T, Herring JL, Hackfeld LC, Tang H, Zhang K, Sowers LC. Measurement of deaminated cytosine adducts in DNA using a novel hybrid thymine DNA glycosylase. J Biol Chem 2022; 298:101638. [PMID: 35085553 PMCID: PMC8861164 DOI: 10.1016/j.jbc.2022.101638] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 01/16/2023] Open
Abstract
The hydrolytic deamination of cytosine and 5-methylcytosine drives many of the transition mutations observed in human cancer. The deamination-induced mutagenic intermediates include either uracil or thymine adducts mispaired with guanine. While a substantial array of methods exist to measure other types of DNA adducts, the cytosine deamination adducts pose unusual analytical problems, and adequate methods to measure them have not yet been developed. We describe here a novel hybrid thymine DNA glycosylase (TDG) that is comprised of a 29-amino acid sequence from human TDG linked to the catalytic domain of a thymine glycosylase found in an archaeal thermophilic bacterium. Using defined-sequence oligonucleotides, we show that hybrid TDG has robust mispair-selective activity against deaminated U:G and T:G mispairs. We have further developed a method for separating glycosylase-released free bases from oligonucleotides and DNA followed by GC-MS/MS quantification. Using this approach, we have measured for the first time the levels of total uracil, U:G, and T:G pairs in calf thymus DNA. The method presented here will allow the measurement of the formation, persistence, and repair of a biologically important class of deaminated cytosine adducts.
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Affiliation(s)
- Chia Wei Hsu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA; MD-PhD Combined Degree Program, University of Texas Medical Branch, Galveston, Texas, USA
| | - Mark L Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA; MD-PhD Combined Degree Program, University of Texas Medical Branch, Galveston, Texas, USA
| | - Tuvshintugs Baljinnyam
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jason L Herring
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Linda C Hackfeld
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Hui Tang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Lawrence C Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA; Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA.
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6
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Ye W, Siwko S, Tsai RYL. Sex and Race-Related DNA Methylation Changes in Hepatocellular Carcinoma. Int J Mol Sci 2021; 22:ijms22083820. [PMID: 33917049 PMCID: PMC8067720 DOI: 10.3390/ijms22083820] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the sixth most common cancer and fourth leading cause of cancer-related death worldwide. The number of HCC cases continues to rise despite advances in screening and therapeutic inventions. More importantly, HCC poses two major health disparity issues. First, HCC occurs more commonly in men than women. Second, with the global increase in non-alcoholic fatty liver diseases (NAFLD), it has also become evident that HCC is more prevalent in some races and/or ethnic groups compared to others, depending on its predisposing etiology. Most studies on HCC in the past have been focused on genetic factors as the driving force for HCC development, and the results revealed that genetic mutations associated with HCC are often heterogeneous and involve multiple pathogenic pathways. An emerging new research field is epigenetics, in which gene expression is modified without altering DNA sequences. In this article, we focus on reviewing current knowledge on HCC-related DNA methylation changes that show disparities among different sexes or different racial/ethnic groups, in an effort to establish a point of departure for resolving the broader issue of health disparities in gastrointestinal malignancies using cutting-edge epigenetic approaches.
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7
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Cytosine Methylation Affects the Mutability of Neighboring Nucleotides in Germline and Soma. Genetics 2020; 214:809-823. [PMID: 32079595 DOI: 10.1534/genetics.120.303028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/12/2020] [Indexed: 02/07/2023] Open
Abstract
Methylated cytosines deaminate at higher rates than unmethylated cytosines, and the lesions they produce are repaired less efficiently. As a result, methylated cytosines are mutational hotspots. Here, combining rare polymorphism and base-resolution methylation data in humans, Arabidopsis thaliana, and rice (Oryza sativa), we present evidence that methylation state affects mutation dynamics not only at the focal cytosine but also at neighboring nucleotides. In humans, contrary to prior suggestions, we find that nucleotides in the close vicinity (±3 bp) of methylated cytosines mutate less frequently. Reduced mutability around methylated CpGs is also observed in cancer genomes, considering single nucleotide variants alongside tissue-of-origin-matched methylation data. In contrast, methylation is associated with increased neighborhood mutation risk in A. thaliana and rice. The difference in neighborhood mutation risk is less pronounced further away from the focal CpG and modulated by regional GC content. Our results are consistent with a model where altered risk at neighboring bases is linked to lesion formation at the focal CpG and subsequent long-patch repair. Our findings indicate that cytosine methylation has a broader mutational footprint than is commonly assumed.
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Mayorga L, Salassa BN, Marzese DM, Loos MA, Eiroa HD, Lubieniecki F, García Samartino C, Romano PS, Roqué M. Mitochondrial stress triggers a pro-survival response through epigenetic modifications of nuclear DNA. Cell Mol Life Sci 2019; 76:1397-1417. [PMID: 30673822 PMCID: PMC11105675 DOI: 10.1007/s00018-019-03008-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/19/2018] [Accepted: 01/08/2019] [Indexed: 12/20/2022]
Abstract
Mitochondrial dysfunction represents an important cellular stressor and when intense and persistent cells must unleash an adaptive response to prevent their extinction. Furthermore, mitochondria can induce nuclear transcriptional changes and DNA methylation can modulate cellular responses to stress. We hypothesized that mitochondrial dysfunction could trigger an epigenetically mediated adaptive response through a distinct DNA methylation patterning. We studied cellular stress responses (i.e., apoptosis and autophagy) in mitochondrial dysfunction models. In addition, we explored nuclear DNA methylation in response to this stressor and its relevance in cell survival. Experiments in cultured human myoblasts revealed that intense mitochondrial dysfunction triggered a methylation-dependent pro-survival response. Assays done on mitochondrial disease patient tissues showed increased autophagy and enhanced DNA methylation of tumor suppressor genes and pathways involved in cell survival regulation. In conclusion, mitochondrial dysfunction leads to a "pro-survival" adaptive state that seems to be triggered by the differential methylation of nuclear genes.
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Affiliation(s)
- Lía Mayorga
- Instituto de Histología y Embriología de Mendoza (IHEM, Universidad Nacional de Cuyo, CONICET)-Centro Universitario UNCuyo, 5500, Mendoza, Argentina.
| | - Betiana N Salassa
- Instituto de Histología y Embriología de Mendoza (IHEM, Universidad Nacional de Cuyo, CONICET)-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
- Facultad de Odontología, Univeridad Nacional de Cuyo- Centro Universitario UNCuyo, 5500, Mendoza, Argentina
| | - Diego M Marzese
- John Wayne Cancer Institute, 2200 Santa Monica Boulevard, Santa Monica, CA, 90404, USA
| | - Mariana A Loos
- Hospital de Pediatría J.P. Garrahan, Combate de los Pozos 1881, 1245, Buenos Aires, Argentina
| | - Hernán D Eiroa
- Hospital de Pediatría J.P. Garrahan, Combate de los Pozos 1881, 1245, Buenos Aires, Argentina
| | - Fabiana Lubieniecki
- Hospital de Pediatría J.P. Garrahan, Combate de los Pozos 1881, 1245, Buenos Aires, Argentina
| | - Clara García Samartino
- Facultad de Ciencias Médicas, Universidad Nacional de Cuyo-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
| | - Patricia S Romano
- Instituto de Histología y Embriología de Mendoza (IHEM, Universidad Nacional de Cuyo, CONICET)-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de Cuyo-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
| | - María Roqué
- Instituto de Histología y Embriología de Mendoza (IHEM, Universidad Nacional de Cuyo, CONICET)-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
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9
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Ho TN, Paul GV, Chen YH, Hsu T. Heat stress upregulates G-T mismatch binding activities in zebrafish (Danio rerio) embryos preexposed and nonexposed to a sublethal level of cadmium (Cd). CHEMOSPHERE 2019; 218:179-188. [PMID: 30471498 DOI: 10.1016/j.chemosphere.2018.11.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/02/2018] [Accepted: 11/04/2018] [Indexed: 05/20/2023]
Abstract
G-T mispair frequently appears in eukaryotic DNA due to the spontaneous deamination of 5-methylcytosine paired with guanine and is therefore an important target for DNA mismatch repair (MMR). Our earlier studies showed the downregulation of G-T binding activities in cadmium (Cd)-exposed (Danio rerio) embryos. Since elevation of water temperature was reported to increase Cd toxicity in zebrafish, this study explored whether heat stress affected zebrafish mismatch binding capacity in the absence or presence of Cd. Heat stress (37 °C for 30 min) induced heat shock protein 70 mRNA expression in embryos at 10 and 24 h post fertilization (hpf). Heat stress weakly upregulated normal G-T sensing machinery and inhibited G-T recognition activity in embryos preexposed to 3 μM Cd for 9 h. Either heat shock or a 23-h Cd treatment alone caused a 1.7-fold stimulation of G-T binding capacity in 24 hpf embryos and heat stress of Cd-preexposed embryos further enhanced G-T binding activity to 2.5 fold of control. Normal and Cd-downregulated loop binding activities in 10 and 24 hpf embryos were almost unreactive to heat shock. Heat stress-upregulated G-T sensing in nonexposed, but not in Cd-preexposed, 24 hpf embryos correlated with stronger gene activities encoding MMR-linked mismatch detecting factors MutS homolog 2 and 6 plus a higher DNA binding activity of the transcription factor Sp1 that regulates msh2/msh6 expression. Our results suggested the importance of heat shock response in facilitating the correction of G-T mismatch in developing zebrafish even under Cd exposure.
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Affiliation(s)
- Tsung-Nan Ho
- Department of Bioscience and Biotechnology and Center of Excellence for the Oceans, National Taiwan Ocean University, No.2, Pei-Ning Rd. Keelung, 20224, Taiwan, Republic of China
| | - Ganjai Vikram Paul
- Department of Bioscience and Biotechnology and Center of Excellence for the Oceans, National Taiwan Ocean University, No.2, Pei-Ning Rd. Keelung, 20224, Taiwan, Republic of China
| | - Yen-Hung Chen
- Department of Bioscience and Biotechnology and Center of Excellence for the Oceans, National Taiwan Ocean University, No.2, Pei-Ning Rd. Keelung, 20224, Taiwan, Republic of China
| | - Todd Hsu
- Department of Bioscience and Biotechnology and Center of Excellence for the Oceans, National Taiwan Ocean University, No.2, Pei-Ning Rd. Keelung, 20224, Taiwan, Republic of China.
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10
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Venkatesh T, Shetty A, Chakraborti S, Suresh PS. PTPH1 immunohistochemical expression and promoter methylation in breast cancer patients from India: A retrospective study. J Cell Physiol 2018; 234:1071-1079. [DOI: 10.1002/jcp.27211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/12/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Thejaswini Venkatesh
- Department of Biochemistry and Molecular Biology Central University of Kerala, Paddanakkad Campus Kasargod Kerala India
| | - Abhishek Shetty
- Department of Biosciences Mangalore University Mangalore Karnataka India
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11
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Diez-Fernandez C, Rüfenacht V, Gemperle C, Fingerhut R, Häberle J. Mutations and common variants in the human arginase 1 (ARG1
) gene: Impact on patients, diagnostics, and protein structure considerations. Hum Mutat 2018; 39:1029-1050. [DOI: 10.1002/humu.23545] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/20/2018] [Accepted: 04/25/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Carmen Diez-Fernandez
- University Children's Hospital Zurich; Division of Metabolism and Children's Research Center; Zurich Switzerland
| | - Véronique Rüfenacht
- University Children's Hospital Zurich; Division of Metabolism and Children's Research Center; Zurich Switzerland
| | - Corinne Gemperle
- University Children's Hospital Zurich; Division of Metabolism and Children's Research Center; Zurich Switzerland
| | - Ralph Fingerhut
- University Children's Hospital Zurich; Division of Metabolism and Children's Research Center; Zurich Switzerland
| | - Johannes Häberle
- University Children's Hospital Zurich; Division of Metabolism and Children's Research Center; Zurich Switzerland
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12
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Chowdhury K, Kumar S, Sharma T, Sharma A, Bhagat M, Kamai A, Ford BM, Asthana S, Mandal CC. Presence of a consensus DNA motif at nearby DNA sequence of the mutation susceptible CG nucleotides. Gene 2017; 639:85-95. [PMID: 28986316 DOI: 10.1016/j.gene.2017.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 08/07/2017] [Accepted: 10/02/2017] [Indexed: 12/18/2022]
Abstract
Complexity in tissues affected by cancer arises from somatic mutations and epigenetic modifications in the genome. The mutation susceptible hotspots present within the genome indicate a non-random nature and/or a position specific selection of mutation. An association exists between the occurrence of mutations and epigenetic DNA methylation. This study is primarily aimed at determining mutation status, and identifying a signature for predicting mutation prone zones of tumor suppressor (TS) genes. Nearby sequences from the top five positions having a higher mutation frequency in each gene of 42 TS genes were selected from a cosmic database and were considered as mutation prone zones. The conserved motifs present in the mutation prone DNA fragments were identified. Molecular docking studies were done to determine putative interactions between the identified conserved motifs and enzyme methyltransferase DNMT1. Collective analysis of 42 TS genes found GC as the most commonly replaced and AT as the most commonly formed residues after mutation. Analysis of the top 5 mutated positions of each gene (210 DNA segments for 42 TS genes) identified that CG nucleotides of the amino acid codons (e.g., Arginine) are most susceptible to mutation, and found a consensus DNA "T/AGC/GAGGA/TG" sequence present in these mutation prone DNA segments. Similar to TS genes, analysis of 54 oncogenes not only found CG nucleotides of the amino acid Arg as the most susceptible to mutation, but also identified the presence of similar consensus DNA motifs in the mutation prone DNA fragments (270 DNA segments for 54 oncogenes) of oncogenes. Docking studies depicted that, upon binding of DNMT1 methylates to this consensus DNA motif (C residues of CpG islands), mutation was likely to occur. Thus, this study proposes that DNMT1 mediated methylation in chromosomal DNA may decrease if a foreign DNA segment containing this consensus sequence along with CG nucleotides is exogenously introduced to dividing cancer cells.
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Affiliation(s)
- Kaushik Chowdhury
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Suresh Kumar
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Tanu Sharma
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Ankit Sharma
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Meenakshi Bhagat
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Asangla Kamai
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Bridget M Ford
- Department of Biology, University of the Incarnate Word, San Antonio 78209, TX, USA
| | - Shailendra Asthana
- Drug Discovery Research Centre, Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India.
| | - Chandi C Mandal
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, Rajasthan, India.
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Diez-Fernandez C, Rüfenacht V, Häberle J. Mutations in the Human Argininosuccinate Synthetase (ASS1) Gene, Impact on Patients, Common Changes, and Structural Considerations. Hum Mutat 2017; 38:471-484. [DOI: 10.1002/humu.23184] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/14/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Carmen Diez-Fernandez
- Division of Metabolism; University Children´s Hospital and Children's Research Center; Zurich Switzerland
| | - Véronique Rüfenacht
- Division of Metabolism; University Children´s Hospital and Children's Research Center; Zurich Switzerland
| | - Johannes Häberle
- Division of Metabolism; University Children´s Hospital and Children's Research Center; Zurich Switzerland
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14
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Aggarwala V, Ganguly A, Voight BF. De novo mutational profile in RB1 clarified using a mutation rate modeling algorithm. BMC Genomics 2017; 18:155. [PMID: 28193182 PMCID: PMC5307739 DOI: 10.1186/s12864-017-3522-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/27/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Studies of de novo mutations offer great promise to improve our understanding of human disease. After a causal gene has been identified, it is natural to hypothesize that disease relevant mutations accumulate within a sub-sequence of the gene - for example, an exon, a protein domain, or at CpG sites. These assessments are typically qualitative, because we lack methodology to assess the statistical significance of sub-gene mutational burden ultimately to infer disease-relevant biology. METHODS To address this issue, we present a generalized algorithm to grade the significance of de novo mutational burden within a gene ascertained from affected probands, based on our model for mutation rate informed by local sequence context. RESULTS We applied our approach to 268 newly identified de novo germline mutations by re-sequencing the coding exons and flanking intronic regions of RB1 in 642 sporadic, bilateral probands affected with retinoblastoma (RB). We confirm enrichment of loss-of-function mutations, but demonstrate that previously noted 'hotspots' of nonsense mutations in RB1 are compatible with the elevated mutation rates expected at CpG sites, refuting a RB specific pathogenic mechanism. Our approach demonstrates an enrichment of splice-site donor mutations of exon 6 and 12 but depletion at exon 5, indicative of previously unappreciated heterogeneity in penetrance within this class of substitution. We demonstrate the enrichment of missense mutations to the pocket domain of RB1, which contains the known Arg661Trp low-penetrance mutation. CONCLUSION Our approach is generalizable to any phenotype, and affirms the importance of statistical interpretation of de novo mutations found in human genomes.
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Affiliation(s)
- Varun Aggarwala
- Genomics and Computational Biology Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Arupa Ganguly
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Perelman School of Medicine, University of Pennsylvania, 415 Anatomy Chemistry Building, 3620 Hamilton Walk, Philadelphia, PA 19104 USA
| | - Benjamin F. Voight
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Perelman School of Medicine, 10–126 Smilow Center for Translational Research, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104 USA
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15
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Chao HT, Davids M, Burke E, Pappas JG, Rosenfeld JA, McCarty AJ, Davis T, Wolfe L, Toro C, Tifft C, Xia F, Stong N, Johnson TK, Warr CG, Yamamoto S, Adams DR, Markello TC, Gahl WA, Bellen HJ, Wangler MF, Malicdan MCV, Adams DR, Adams CJ, Alejandro ME, Allard P, Ashley EA, Bacino CA, Balasubramanyam A, Barseghyan H, Beggs AH, Bellen HJ, Bernstein JA, Bick DP, Birch CL, Boone BE, Briere LC, Brown DM, Brush M, Burrage LC, Chao KR, Clark GD, Cogan JD, Cooper CM, Craigen WJ, Davids M, Dayal JG, Dell'Angelica EC, Dhar SU, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Draper DD, Dries AM, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fisher PG, Frisby TS, Frost K, Gahl WA, Gartner V, Godfrey RA, Goheen M, Golas GA, Goldstein DB, Gordon M“GG, Gould SE, Gourdine JPF, Graham BH, Groden CA, Gropman AL, Hackbarth ME, Haendel M, Hamid R, Hanchard NA, Handley LH, Hardee I, Herzog MR, Holm IA, Howerton EM, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Koehler AE, Koeller DM, Kohane IS, Kohler JN, Krasnewich DM, Krieg EL, Krier JB, Kyle JE, Lalani SR, Latham L, Latour YL, Lau CC, Lazar J, Lee BH, Lee H, Lee PR, Levy SE, Levy DJ, Lewis RA, Liebendorder AP, Lincoln SA, Loomis CR, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Mashid AS, Mazur P, McCarty AJ, McConkie-Rosell A, McCray AT, Metz TO, Might M, Moretti PM, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Ramoni RB, Rodan LH, Sadozai S, Schaffer KE, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Silverman EK, Sinsheimer JS, Soldatos AG, Spillmann RC, Splinter K, Stoler JM, Stong N, Strong KA, Sullivan JA, Sweetser DA, Thomas SP, Tift CJ, Tolman NJ, Toro C, Tran AA, Valivullah ZM, Vilain E, Waggott DM, Wahl CE, Walley NM, Walsh CA, Wangler MF, Warburton M, Ward PA, Waters KM, Webb-Robertson BJM, Weech AA, Westerfield M, Wheeler MT, Wise AL, Worthe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zornio PA. A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3. Am J Hum Genet 2017; 100:128-137. [PMID: 28017372 PMCID: PMC5223093 DOI: 10.1016/j.ajhg.2016.11.018] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
Early B cell factor 3 (EBF3) is a member of the highly evolutionarily conserved Collier/Olf/EBF (COE) family of transcription factors. Prior studies on invertebrate and vertebrate animals have shown that EBF3 homologs are essential for survival and that loss-of-function mutations are associated with a range of nervous system developmental defects, including perturbation of neuronal development and migration. Interestingly, aristaless-related homeobox (ARX), a homeobox-containing transcription factor critical for the regulation of nervous system development, transcriptionally represses EBF3 expression. However, human neurodevelopmental disorders related to EBF3 have not been reported. Here, we describe three individuals who are affected by global developmental delay, intellectual disability, and expressive speech disorder and carry de novo variants in EBF3. Associated features seen in these individuals include congenital hypotonia, structural CNS malformations, ataxia, and genitourinary abnormalities. The de novo variants affect a single conserved residue in a zinc finger motif crucial for DNA binding and are deleterious in a fly model. Our findings indicate that mutations in EBF3 cause a genetic neurodevelopmental syndrome and suggest that loss of EBF3 function might mediate a subset of neurologic phenotypes shared by ARX-related disorders, including intellectual disability, abnormal genitalia, and structural CNS malformations.
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Hsu CW, Sowers ML, Hsu W, Eyzaguirre E, Qiu S, Chao C, Mouton CP, Fofanov Y, Singh P, Sowers LC. How does inflammation drive mutagenesis in colorectal cancer? TRENDS IN CANCER RESEARCH 2017; 12:111-132. [PMID: 30147278 PMCID: PMC6107301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Colorectal cancer (CRC) is a major health challenge worldwide. Factors thought to be important in CRC etiology include diet, microbiome, exercise, obesity, a history of colon inflammation and family history. Interventions, including the use of non-steroidal anti-Inflammatory drugs (NSAIDs) and anti-inflammatory agents, have been shown to decrease incidence in some settings. However, our current understanding of the mechanistic details that drive CRC are insufficient to sort out the complex and interacting factors responsible for cancer-initiating events. It has been known for some time that the development of CRC involves mutations in key genes such as p53 and APC, and the sequence in which these mutations occur can determine tumor presentation. Observed recurrent mutations are dominated by C to T transitions at CpG sites, implicating the deamination of 5-methylcytosine (5mC) as a key initiating event in cancer-driving mutations. While it has been widely assumed that inflammation-mediated oxidation drives mutations in CRC, oxidative damage to DNA induces primarily G to T transversions, not C to T transitions. In this review, we discuss this unresolved conundrum, and specifically, we elucidate how the known nucleotide excision repair (NER) and base excision repair (BER) pathways, which are partially redundant and potentially competing, might provide a critical link between oxidative DNA damage and C to T mutations. Studies using recently developed next-generation DNA sequencing technologies have revealed the genetic heterogeneity in human tissues including tumors, as well as the presence of DNA damage. The capacity to follow DNA damage, repair and mutagenesis in human tissues using these emerging technologies could provide a mechanistic basis for understanding the role of oxidative damage in CRC tumor initiation. The application of these technologies could identify mechanism-based biomarkers useful in earlier diagnosis and aid in the development of cancer prevention strategies.
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Affiliation(s)
- Chia Wei Hsu
- MD/PhD program, University of Texas Medical Branch, Galveston, Texas
| | - Mark L Sowers
- MD/PhD program, University of Texas Medical Branch, Galveston, Texas
| | - Willie Hsu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas
| | - Eduardo Eyzaguirre
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Suimin Qiu
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Celia Chao
- Department of Surgery, University of Texas Medical Branch, Galveston, Texas
| | - Charles P Mouton
- Department of Family Medicine, University of Texas Medical Branch, Galveston, Texas
| | - Yuri Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas
| | - Pomila Singh
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas
| | - Lawrence C Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA
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17
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Singh J, Mishra A, Pandian AJ, Mallipatna AC, Khetan V, Sripriya S, Kapoor S, Agarwal S, Sankaran S, Katragadda S, Veeramachaneni V, Hariharan R, Subramanian K, Mannan AU. Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort. Mol Vis 2016; 22:1036-47. [PMID: 27582626 PMCID: PMC4985049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/14/2016] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Retinoblastoma (Rb) is the most common primary intraocular cancer of childhood and one of the major causes of blindness in children. India has the highest number of patients with Rb in the world. Mutations in the RB1 gene are the primary cause of Rb, and heterogeneous mutations are distributed throughout the entire length of the gene. Therefore, genetic testing requires screening of the entire gene, which by conventional sequencing is time consuming and expensive. METHODS In this study, we screened the RB1 gene in the DNA isolated from blood or saliva samples of 50 unrelated patients with Rb using the TruSight Cancer panel. Next-generation sequencing (NGS) was done on the Illumina MiSeq platform. Genetic variations were identified using the Strand NGS software and interpreted using the StrandOmics platform. RESULTS We were able to detect germline pathogenic mutations in 66% (33/50) of the cases, 12 of which were novel. We were able to detect all types of mutations, including missense, nonsense, splice site, indel, and structural variants. When we considered bilateral Rb cases only, the mutation detection rate increased to 100% (22/22). In unilateral Rb cases, the mutation detection rate was 30% (6/20). CONCLUSIONS Our study suggests that NGS-based approaches increase the sensitivity of mutation detection in the RB1 gene, making it fast and cost-effective compared to the conventional tests performed in a reflex-testing mode.
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Affiliation(s)
- Jaya Singh
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | - Avshesh Mishra
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | | | - Ashwin C. Mallipatna
- Department of Pediatric Ophthalmology and Strabismology, Narayana Nethralaya, Bangalore, India
| | - Vikas Khetan
- Department of Vitreo Retina, Sankara Nethralaya, Chennai, India
| | - S. Sripriya
- Sankara Nethralaya ONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, India
| | - Suman Kapoor
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | - Smita Agarwal
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | - Satish Sankaran
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | - Shanmukh Katragadda
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | - Vamsi Veeramachaneni
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | - Ramesh Hariharan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India,Department of Computer Science and Automation, Indian Institute of Science, Bangalore, India
| | | | - Ashraf U. Mannan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
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18
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Sagi M, Frenkel A, Eilat A, Weinberg N, Frenkel S, Pe'er J, Abeliovich D, Lerer I. Genetic screening in patients with Retinoblastoma in Israel. Fam Cancer 2016; 14:471-80. [PMID: 25754945 DOI: 10.1007/s10689-015-9794-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Retinoblastoma (Rb) is a childhood tumor (~1 in 20,000 live births) developing in the retina due to mutations in the RB1 gene. Identification of the oncogenic mutations in the RB1 gene is important for the clinical management and for genetic counseling to families with a child or a parent affected with the tumor. Here we present our experience in detecting the pathogenic mutations in blood samples, from 150 unrelated Rb patients and highlight the relevant counseling issues. Mutation screening in the RB1 gene was based on Sanger sequencing, mosaicism of recurrent CpG transition mutations was detected by allele specific PCR and multiplex ligation dependent probe amplification for detecting of large deletions/duplications. The overall detection rate of mutations in our cohort was 55% (82/150). In the familial cases it was 100% (17/17), in bilateral and unilateral-multifocal sporadic cases 91% (50/55), and in the unilateral sporadic cases 19% (15/78). Nonsense mutations and small deletions or insertions that results in transcripts with premature termination codons that are subject to nonsense mediated decay were the most frequent, detected in 50/82 (61%) of the patients. The rest were large deletions detected in 14/82 (17%), splice site mutations detected in 11/82 (13%), missense mutations in four patients and mutations in the promoter sequence in three patients. Mutation mosaicism ranging from 10 to 30% was detected by allele specific PCR in ten patients, 9% (5/55) of patients with bilateral tumor and 33% (5/15) of the patients with unilateral tumor. In three patients rare variants were detected as the only finding which was also detected in other healthy family members. Allele specific amplification of recurrent mutations raises in our cohort the identification rate from 82 to 91% in the sporadic bilateral cases and from 13 to 19% in the unilateral sporadic cases. Most mosaic cases could not be identified by Sanger sequencing and therefore screening for recurrent CpG transition mutations by allele specific amplification is of utmost importance. Molecular screening is important for the genetic counseling regarding the risk for tumor development and the relevance for prenatal diagnosis but in several families is accompanied by detecting rare variants that might be rare polymorphisms or low penetrant mutations.
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Affiliation(s)
- Michal Sagi
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Kiryat Hadassah, POB 12000, 91120, Jerusalem, Israel
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19
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Inauen C, Rüfenacht V, Pandey AV, Hu L, Blom H, Nuoffer JM, Häberle J. Effect of Cysteamine on Mutant ASL Proteins with Cysteine for Arginine Substitutions. Mol Diagn Ther 2016; 20:125-33. [DOI: 10.1007/s40291-015-0182-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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20
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Sankar S, Upadhyay M, Ramamurthy M, Vadivel K, Sagadevan K, Nandagopal B, Vivekanandan P, Sridharan G. Novel Insights on Hantavirus Evolution: The Dichotomy in Evolutionary Pressures Acting on Different Hantavirus Segments. PLoS One 2015; 10:e0133407. [PMID: 26193652 PMCID: PMC4508033 DOI: 10.1371/journal.pone.0133407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/26/2015] [Indexed: 01/01/2023] Open
Abstract
Background Hantaviruses are important emerging zoonotic pathogens. The current understanding of hantavirus evolution is complicated by the lack of consensus on co-divergence of hantaviruses with their animal hosts. In addition, hantaviruses have long-term associations with their reservoir hosts. Analyzing the relative abundance of dinucleotides may shed new light on hantavirus evolution. We studied the relative abundance of dinucleotides and the evolutionary pressures shaping different hantavirus segments. Methods A total of 118 sequences were analyzed; this includes 51 sequences of the S segment, 43 sequences of the M segment and 23 sequences of the L segment. The relative abundance of dinucleotides, effective codon number (ENC), codon usage biases were analyzed. Standard methods were used to investigate the relative roles of mutational pressure and translational selection on the three hantavirus segments. Results All three segments of hantaviruses are CpG depleted. Mutational pressure is the predominant evolutionary force leading to CpG depletion among hantaviruses. Interestingly, the S segment of hantaviruses is GpU depleted and in contrast to CpG depletion, the depletion of GpU dinucleotides from the S segment is driven by translational selection. Our findings also suggest that mutational pressure is the primary evolutionary pressure acting on the S and the M segments of hantaviruses. While translational selection plays a key role in shaping the evolution of the L segment. Our findings highlight how different evolutionary pressures may contribute disproportionally to the evolution of the three hantavirus segments. These findings provide new insights on the current understanding of hantavirus evolution. Conclusions There is a dichotomy among evolutionary pressures shaping a) the relative abundance of different dinucleotides in hantavirus genomes b) the evolution of the three hantavirus segments.
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Affiliation(s)
- Sathish Sankar
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India
| | - Mohita Upadhyay
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, 110 016, India
| | - Mageshbabu Ramamurthy
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India
| | - Kumaran Vadivel
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India
| | - Kalaiselvan Sagadevan
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India
| | - Balaji Nandagopal
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, 110 016, India
- * E-mail:
| | - Gopalan Sridharan
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India
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21
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Overrepresentation of missense mutations in mild hemophilia A patients from Belgium: founder effect or independent occurrence? Thromb Res 2015; 135:1057-63. [DOI: 10.1016/j.thromres.2015.03.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/26/2015] [Accepted: 03/08/2015] [Indexed: 11/30/2022]
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22
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O'Brown NM, Summers BR, Jones FC, Brady SD, Kingsley DM. A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA. eLife 2015; 4:e05290. [PMID: 25629660 PMCID: PMC4384742 DOI: 10.7554/elife.05290] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/26/2015] [Indexed: 12/15/2022] Open
Abstract
Armor plate changes in sticklebacks are a classic example of repeated adaptive
evolution. Previous studies identified ectodysplasin (EDA) gene as
the major locus controlling recurrent plate loss in freshwater fish, though the
causative DNA alterations were not known. Here we show that freshwater
EDA alleles have cis-acting regulatory changes
that reduce expression in developing plates and spines. An identical T → G
base pair change is found in EDA enhancers of divergent low-plated
fish. Recreation of the T → G change in a marine enhancer strongly reduces
expression in posterior armor plates. Bead implantation and cell culture experiments
show that Wnt signaling strongly activates the marine EDA enhancer,
and the freshwater T → G change reduces Wnt responsiveness. Thus parallel
evolution of low-plated sticklebacks has occurred through a shared DNA regulatory
change, which reduces the sensitivity of an EDA enhancer to Wnt
signaling, and alters expression in developing armor plates while preserving
expression in other tissues. DOI:http://dx.doi.org/10.7554/eLife.05290.001 Stickleback fish develop bony plates on their surface to protect themselves from
predators. The extent and pattern of their bony armor depends on their habitat:
marine sticklebacks are typically covered from head to tail with bony plates, but
freshwater sticklebacks retain only a few plates on their sides. One gene that promotes the formation of the bony plates is called
ectodysplasin (EDA). This encodes a signaling
protein that is important for the development of the skeleton, skin and many other
tissues. Variations in the sequence of this gene are shared among different
stickleback populations worldwide. However, it has not been clear which genetic
changes can explain how lightly armored freshwater sticklebacks could have evolved
from their well-armored marine ancestors on several separate occasions. Here, O'Brown et al. studied EDA in marine and groups of
freshwater sticklebacks that have evolved in different locations around the world.
The experiments show that the level of expression of EDA in the
developing plates and spines is lower in the freshwater fish. O'Brown et al.
thought this could be due to genetic changes in regions of EDA that
lie outside the region that encodes the protein, so called ‘regulatory
elements’. Indeed, further experiments found that all freshwater fish have a small change in the
DNA of a regulatory element that switches on the gene in plate-forming regions of the
body. When this change was introduced into marine sticklebacks, the fish had lower
levels of gene expression in these plate-forming regions. These findings demonstrate that lightly armored sticklebacks have evolved multiple
times from their well-armored marine ancestors through the same small change in their
DNA that alters the expression of the EDA gene. The next challenge
will be to understand why this particular small change in DNA appears to be favored
over all the other changes that could occur in the regulatory element, and to see if
factors that act through this regulatory switch also modify armor structures in
natural populations. DOI:http://dx.doi.org/10.7554/eLife.05290.002
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Affiliation(s)
- Natasha M O'Brown
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States
| | - Brian R Summers
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States
| | - Felicity C Jones
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States
| | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States
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Monochorionic-monoamniotic twins discordant for VATER association. J Perinatol 2014; 34:645-6. [PMID: 25073497 DOI: 10.1038/jp.2014.61] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/13/2014] [Indexed: 11/08/2022]
Abstract
We describe a monozygotic twin discordant for VATER association with single dysplastic kidney and cloacal anomaly, who had no pulmonary hypoplasia. This twin probably had little or no urine output in utero, but still had normal lung development due to production of adequate amniotic fluid by the healthy twin preventing pulmonary hypoplasia. The discordance between monozygotic twins for VATER association indicates that factors other than inherited genetic ones may have a role in the causation of this association.
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24
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Dommering CJ, Mol BM, Moll AC, Burton M, Cloos J, Dorsman JC, Meijers-Heijboer H, van der Hout AH. RB1 mutation spectrum in a comprehensive nationwide cohort of retinoblastoma patients. J Med Genet 2014; 51:366-74. [PMID: 24688104 DOI: 10.1136/jmedgenet-2014-102264] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Retinoblastoma (Rb) is a childhood cancer of the retina, commonly initiated by biallelic inactivation of the RB1 gene. Knowledge of the presence of a heritable RB1 mutation can help in risk management and reproductive decision making. We report here on RB1 mutation scanning in a unique nationwide cohort of Rb patients from the Netherlands. METHODS From the 1173 Rb patients registered in the Dutch National Retinoblastoma Register until January 2013, 529 patients from 433 unrelated families could be included. RB1 mutation scanning was performed with different detection methods, depending on the time period. RESULTS Our mutation detection methods revealed RB1 mutations in 92% of bilateral and/or familial Rb patients and in 10% of non-familial unilateral cases. Overall an RB1 germline mutation was detected in 187 (43%) of 433 Rb families, including 33 novel mutations. The distribution of the type of mutation was 37% nonsense, 20% frameshift, 21% splice, 9% large indel, 5% missense, 7% chromosomal deletions and 1% promoter. Ten per cent of patients were mosaic for the RB1 mutation. Six three-generation families with incomplete penetrance RB1 mutations were found. We found evidence that two variants, previously described as pathogenic RB1 mutations, are likely to be neutral variants. CONCLUSIONS The frequency of the type of mutations in the RB1 gene in our unbiased national cohort is the same as the mutation spectrum described worldwide. Furthermore, our RB1 mutation detection regimen achieves a high scanning sensitivity.
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Affiliation(s)
- Charlotte J Dommering
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Berber M Mol
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Annette C Moll
- Department of Ophthalmology, VU University Medical Center, Amsterdam, The Netherlands
| | - Margaret Burton
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jacqueline Cloos
- Department of Hematology, VU University Medical Center, Amsterdam, The Netherlands Department of Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Josephine C Dorsman
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Annemarie H van der Hout
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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25
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Ma X, Wang YW, Zhang MQ, Gazdar AF. DNA methylation data analysis and its application to cancer research. Epigenomics 2013; 5:301-16. [PMID: 23750645 DOI: 10.2217/epi.13.26] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
With the rapid development of genome-wide high-throughput technologies, including expression arrays, SNP arrays and next-generation sequencing platforms, enormous amounts of molecular data have been generated and deposited in the public domain. The application of computational approaches is required to yield biological insights from this enormous, ever-growing resource. A particularly interesting subset of these resources is related to epigenetic regulation, with DNA methylation being the most abundant data type. In this paper, we will focus on the analysis of DNA methylation data and its application to cancer studies. We first briefly review the molecular techniques that generate such data, much of which has been obtained with the use of the most recent version of Infinium HumanMethylation450 BeadChip(®) technology (Illumina, CA, USA). We describe the coverage of the methylome by this technique. Several examples of data mining are provided. However, it should be understood that reliance on a single aspect of epigenetics has its limitations. In the not too distant future, these defects may be rectified, providing scientists with previously unavailable opportunities to explore in detail the role of epigenetics in cancer and other disease states.
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Affiliation(s)
- Xiaotu Ma
- Department of Molecular & Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA
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26
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Shull AY, Clendenning ML, Ghoshal-Gupta S, Farrell CL, Vangapandu HV, Dudas L, Wilkerson BJ, Buckhaults PJ. Somatic mutations, allele loss, and DNA methylation of the Cub and Sushi Multiple Domains 1 (CSMD1) gene reveals association with early age of diagnosis in colorectal cancer patients. PLoS One 2013; 8:e58731. [PMID: 23505554 PMCID: PMC3591376 DOI: 10.1371/journal.pone.0058731] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 02/05/2013] [Indexed: 01/01/2023] Open
Abstract
Background The Cub and Sushi Multiple Domains 1 (CSMD1) gene, located on the short arm of chromosome 8, codes for a type I transmembrane protein whose function is currently unknown. CSMD1 expression is frequently lost in many epithelial cancers. Our goal was to characterize the relationships between CSMD1 somatic mutations, allele imbalance, DNA methylation, and the clinical characteristics in colorectal cancer patients. Methods We sequenced the CSMD1 coding regions in 54 colorectal tumors using the 454FLX pyrosequencing platform to interrogate 72 amplicons covering the entire coding sequence. We used heterozygous SNP allele ratios at multiple CSMD1 loci to determine allelic balance and infer loss of heterozygosity. Finally, we performed methylation-specific PCR on 76 colorectal tumors to determine DNA methylation status for CSMD1 and known methylation targets ALX4, RUNX3, NEUROG1, and CDKN2A. Results Using 454FLX sequencing and confirming with Sanger sequencing, 16 CSMD1 somatic mutations were identified in 6 of the 54 colorectal tumors (11%). The nonsynonymous to synonymous mutation ratio of the 16 somatic mutations was 15∶1, a ratio significantly higher than the expected 2∶1 ratio (p = 0.014). This ratio indicates a presence of positive selection for mutations in the CSMD1 protein sequence. CSMD1 allelic imbalance was present in 19 of 37 informative cases (56%). Patients with allelic imbalance and CSMD1 mutations were significantly younger (average age, 41 years) than those without somatic mutations (average age, 68 years). The majority of tumors were methylated at one or more CpG loci within the CSMD1 coding sequence, and CSMD1 methylation significantly correlated with two known methylation targets ALX4 and RUNX3. C:G>T:A substitutions were significantly overrepresented (47%), suggesting extensive cytosine methylation predisposing to somatic mutations. Conclusions Deep amplicon sequencing and methylation-specific PCR reveal that CSMD1 alterations can correlate with earlier clinical presentation in colorectal tumors, thus further implicating CSMD1 as a tumor suppressor gene.
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Affiliation(s)
- Austin Y. Shull
- Georgia Health Sciences University Cancer Center, Georgia Health Sciences University, Augusta, Georgia, United States of America
- Department of Biochemistry and Cancer Biology, Georgia Health Sciences University, Augusta, Georgia, United States of America
| | - Megan L. Clendenning
- Georgia Health Sciences University Cancer Center, Georgia Health Sciences University, Augusta, Georgia, United States of America
| | - Sampa Ghoshal-Gupta
- Georgia Health Sciences University Cancer Center, Georgia Health Sciences University, Augusta, Georgia, United States of America
| | - Christopher L. Farrell
- Department of Pharmaceutical and Administrative Sciences, Presbyterian College School of Pharmacy, Clinton, South Carolina, United States of America
| | - Hima V. Vangapandu
- Graduate School of Biomedical Sciences, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Larry Dudas
- Northeast Georgia Medical Center, Department of Internal Medicine, Gainesville, Georgia, United States of America
| | - Brent J. Wilkerson
- Department of Otolaryngology-Head and Neck Surgery, University of California Davis Medical Center, Sacramento, California, United States of America
| | - Phillip J. Buckhaults
- Georgia Health Sciences University Cancer Center, Georgia Health Sciences University, Augusta, Georgia, United States of America
- Department of Biochemistry and Cancer Biology, Georgia Health Sciences University, Augusta, Georgia, United States of America
- * E-mail:
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Lee TC, Gombos DS, Harbour JW, Mansfield NC, Murphree AL. Retinoblastoma. Retina 2013. [DOI: 10.1016/b978-1-4557-0737-9.00128-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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Dommering CJ, Marees T, van der Hout AH, Imhof SM, Meijers-Heijboer H, Ringens PJ, van Leeuwen FE, Moll AC. RB1 mutations and second primary malignancies after hereditary retinoblastoma. Fam Cancer 2012; 11:225-33. [PMID: 22205104 PMCID: PMC3365233 DOI: 10.1007/s10689-011-9505-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Survivors of hereditary retinoblastoma have a high risk of second primary malignancies, but it has not been investigated whether specific RB1 germline mutations are associated with greater risk of second primary malignancies in a large cohort. We conducted a retrospective cohort study of 199 survivors of hereditary retinoblastoma with a documented RB1 germline mutation diagnosed between 1905 and 2005. In total, 44 hereditary retinoblastoma survivors developed a second primary malignancy after a median follow-up of 30.2 years (range 1.33-76.0). A significantly increased risk of second primary malignancy was observed among carriers of one of the 11 recurrent CGA>TGA nonsense RB1 mutations (hazard ratio (HR) = 3.53; [95% confidence interval (CI) = 1.82-6.84]; P = .000), and there was a significantly lower risk for subjects with a low penetrance mutation (HR = .19; [95% CI = .05-.81]; P = .025). Our findings suggest a genotype-phenotype correlation for second primary cancers of retinoblastoma survivors and may impact on long-term surveillance protocols of patients with hereditary retinoblastoma, if confirmed by future studies.
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Affiliation(s)
- Charlotte J Dommering
- Department of Clinical Genetics, VU University Medical Center, PO Box 7057, 1007 MB, Amsterdam, The Netherlands.
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29
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[Molecular study of retinoblastoma in the Algerian population. Screening of Rb gene in constitutional and tumoral level]. Bull Cancer 2012; 99:127-35. [PMID: 22265791 DOI: 10.1684/bdc.2011.1529] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Inactivation of both alleles of the RB1 gene during normal retinal development initiates the formation of a retinoblastoma (RB) tumor. RB1 screening remains difficult, most of the alterations being unique and randomly distributed throughout the entire coding sequence. In this report, we present the results of a constitutionnal and tumoral RB1 analysis in Algerian population. The detection of RB1 gene deletion or mutation was performed by high performance liquid chromatography (HPLC) and sequence analyses in 21 patients. Germline abnormalities were found in 2/21 patients of sporadic unilateral retinoblastoma. The spectrum of germline and tumoral alterations included: three nonsense mutations; one mutation affecting splice site; one deletion and two polymorphisms. In general, for the 21 patients with no family history of the disease, we have identified mutations in germinal level in two of them showing that it is a transmissible form of retinoblastoma in these two cases known to be sporadic. A total of two mutations have not been previously reported.
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30
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Lagarde WH, Blackwelder AJ, Minges JT, Hnat AT, French FS, Wilson EM. Androgen receptor exon 1 mutation causes androgen insensitivity by creating phosphorylation site and inhibiting melanoma antigen-A11 activation of NH2- and carboxyl-terminal interaction-dependent transactivation. J Biol Chem 2012; 287:10905-15. [PMID: 22334658 DOI: 10.1074/jbc.m111.336081] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Naturally occurring germ line mutations in the X-linked human androgen receptor (AR) gene cause incomplete masculinization of the external genitalia by disrupting AR function in males with androgen insensitivity syndrome. Almost all AR missense mutations that cause androgen insensitivity syndrome are located in the highly structured DNA and ligand binding domains. In this report we investigate the functional defect associated with an AR exon 1 missense mutation, R405S, that caused partial androgen insensitivity. The 46,XX heterozygous maternal carrier had a wild-type Arg-405 CGC allele but transmitted an AGC mutant allele coding for Ser-405. At birth, the 46,XY proband had a bifid scrotum, hypospadias, and micropenis consistent with clinical stage 3 partial androgen insensitivity. Androgen-dependent transcriptional activity of AR-R405S expressed in CV1 cells was less than wild-type AR and refractory in androgen-dependent AR NH(2)- and carboxyl interaction transcription assays that depend on the coregulator effects of melanoma antigen-A11. This mutation created a Ser-405 phosphorylation site evident by the gel migration of an AR-R405S NH(2)-terminal fragment as a double band that converted to the wild-type single band after treatment with λ-phosphatase. Detrimental effects of the R405S mutation were related to the proximity of the AR WXXLF motif (433)WHTLF(437) required for melanoma antigen-A11 and p300 to stimulate transcriptional activity associated with the AR NH(2)- and carboxyl-terminal interaction. We conclude that the coregulator effects of melanoma antigen-A11 on the AR NH(2)- and carboxyl-terminal interaction amplify the androgen-dependent transcriptional response to p300 required for normal human male sex development in utero.
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Affiliation(s)
- William H Lagarde
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina 27599-7500, USA
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31
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The impact of the organism on its descendants. GENETICS RESEARCH INTERNATIONAL 2011; 2012:640612. [PMID: 22567396 PMCID: PMC3335618 DOI: 10.1155/2012/640612] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 09/30/2011] [Accepted: 10/24/2011] [Indexed: 11/18/2022]
Abstract
Historically, evolutionary biologists have taken the view that an understanding of development is irrelevant to theories of evolution. However, the integration of several disciplines in recent years suggests that this position is wrong. The capacity of the organism to adapt to challenges from the environment can set up conditions that affect the subsequent evolution of its descendants. Moreover, molecular events arising from epigenetic processes can be transmitted from one generation to the next and influence genetic mutation. This in turn can facilitate evolution in the conditions in which epigenetic change was first initiated.
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Cooper DN, Bacolla A, Férec C, Vasquez KM, Kehrer-Sawatzki H, Chen JM. On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease. Hum Mutat 2011; 32:1075-99. [PMID: 21853507 PMCID: PMC3177966 DOI: 10.1002/humu.21557] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Accepted: 06/17/2011] [Indexed: 12/21/2022]
Abstract
Different types of human gene mutation may vary in size, from structural variants (SVs) to single base-pair substitutions, but what they all have in common is that their nature, size and location are often determined either by specific characteristics of the local DNA sequence environment or by higher order features of the genomic architecture. The human genome is now recognized to contain "pervasive architectural flaws" in that certain DNA sequences are inherently mutation prone by virtue of their base composition, sequence repetitivity and/or epigenetic modification. Here, we explore how the nature, location and frequency of different types of mutation causing inherited disease are shaped in large part, and often in remarkably predictable ways, by the local DNA sequence environment. The mutability of a given gene or genomic region may also be influenced indirectly by a variety of noncanonical (non-B) secondary structures whose formation is facilitated by the underlying DNA sequence. Since these non-B DNA structures can interfere with subsequent DNA replication and repair and may serve to increase mutation frequencies in generalized fashion (i.e., both in the context of subtle mutations and SVs), they have the potential to serve as a unifying concept in studies of mutational mechanisms underlying human inherited disease.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom.
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Liu Q, Su S, Blackwelder AJ, Minges JT, Wilson EM. Gain in transcriptional activity by primate-specific coevolution of melanoma antigen-A11 and its interaction site in androgen receptor. J Biol Chem 2011; 286:29951-63. [PMID: 21730049 DOI: 10.1074/jbc.m111.244715] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Male sex development and growth occur in response to high affinity androgen binding to the androgen receptor (AR). In contrast to complete amino acid sequence conservation in the AR DNA and ligand binding domains among mammals, a primate-specific difference in the AR NH(2)-terminal region that regulates the NH(2)- and carboxyl-terminal (N/C) interaction enables direct binding to melanoma antigen-A11 (MAGE-11), an AR coregulator that is also primate-specific. Human, mouse, and rat AR share the same NH(2)-terminal (23)FQNLF(27) sequence that mediates the androgen-dependent N/C interaction. However, the mouse and rat AR FXXLF motif is flanked by Ala(33) that evolved to Val(33) in primates. Human AR Val(33) was required to interact directly with MAGE-11 and for the inhibitory effect of the AR N/C interaction on activation function 2 that was relieved by MAGE-11. The functional importance of MAGE-11 was indicated by decreased human AR regulation of an androgen-dependent endogenous gene using lentivirus short hairpin RNAs and by the greater transcriptional strength of human compared with mouse AR. MAGE-11 increased progesterone and glucocorticoid receptor activity independently of binding an FXXLF motif by interacting with p300 and p160 coactivators. We conclude that the coevolution of the AR NH(2)-terminal sequence and MAGE-11 expression among primates provides increased regulatory control over activation domain dominance. Primate-specific expression of MAGE-11 results in greater steroid receptor transcriptional activity through direct interactions with the human AR FXXLF motif region and indirectly through steroid receptor-associated p300 and p160 coactivators.
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Affiliation(s)
- Qiang Liu
- Laboratories for Reproductive Biology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7500, USA
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Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides. Hum Genomics 2011; 4:406-10. [PMID: 20846930 PMCID: PMC3525222 DOI: 10.1186/1479-7364-4-6-406] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The cytosine-guanine (CpG) dinucleotide has long been known to be a hotspot for pathological mutation in the human genome. This hypermutability is related to its role as the major site of cytosine methylation with the attendant risk of spontaneous deamination of 5-methylcytosine (5mC) to yield thymine. Cytosine methylation, however, also occurs in the context of CpNpG sites in the human genome, an unsurprising finding since the intrinsic symmetry of CpNpG renders it capable of supporting a semi-conservative model of replication of the methylation pattern. Recently, it has become clear that significant DNA methylation occurs in a CpHpG context (where H = A, C or T) in a variety of human somatic tissues. If we assume that CpHpG methylation also occurs in the germline, and that 5mC deamination can occur within a CpHpG context, then we might surmise that methylated CpHpG sites could also constitute mutation hotspots causing human genetic disease. To test this postulate, 54,625 missense and nonsense mutations from 2,113 genes causing inherited disease were retrieved from the Human Gene Mutation Database (http://www.hgmd.org). Some 18.2 per cent of these pathological lesions were found to be C → T and G → A transitions located in CpG dinucleotides (compatible with a model of methylation-mediated deamination of 5mC), an approximately ten-fold higher proportion than would have been expected by chance alone. The corresponding proportion for the CpHpG trinucleotide was 9.9 per cent, an approximately two-fold higher proportion than would have been expected by chance. We therefore estimate that ∼5 per cent of missense/nonsense mutations causing human inherited disease may be attributable to methylation-mediated deamination of 5mC within a CpHpG context.
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Direct electrochemical detection of DNA methylation for retinoblastoma and CpG fragments using a nanocarbon film. Anal Biochem 2010; 405:59-66. [DOI: 10.1016/j.ab.2010.06.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 05/13/2010] [Accepted: 06/02/2010] [Indexed: 11/18/2022]
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de Lima ELS, da Silva VC, da Silva HDA, Bezerra AM, de Morais VLL, de Morais AL, Cruz RV, Barros MHM, Hassan R, de Freitas AC, Muniz MTC. MTR polymorphic variant A2756G and retinoblastoma risk in Brazilian children. Pediatr Blood Cancer 2010; 54:904-8. [PMID: 20310006 DOI: 10.1002/pbc.22472] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
BACKGROUND Polymorphisms in the genes of folate and methionine metabolism enzymes have been associated with some forms of cancer by affecting DNA synthesis, repair, and methylation. PROCEDURE A case-control study of 72 retinoblastoma cases and 98 cancer-free children controls was performed to investigate whether the polymorphisms of the methylenetetrahydrofolate reductase (MTHFR C677T and A1298C), methionine synthase (MTR A2756G), carrier of reduced folate 1 (RFC-1 A80G) and thymidylate synthase (TYMS 2R > 3R) altered the risk for retinoblastoma. RESULTS MTR A2756G AG plus GG genotype frequencies were higher in patients than in controls (45% vs. 26%, P = 0.03). Individual carriers of the variant allele G had a 2.02 (95% CI: 1.05-3.92)-fold increased risk for retinoblastoma. In contrast, no association was observed with respect to MTHFR C677T and A1298C, RFC A80G, and TYMS polymorphisms. CONCLUSIONS This study presents evidence for an association between the MTR A2756G polymorphism and retinoblastoma susceptibility in a Northeast population from Brazil.
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Affiliation(s)
- Elker Lene Santos de Lima
- Laboratório de Biologia Molecular, Centro de Oncohematologia Pediátrica (CEONHPE), Hospital Universitário Oswaldo Cruz, Universidade de Pernambuco, Recife, PE, Brazil
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Rushlow D, Piovesan B, Zhang K, Prigoda-Lee NL, Marchong MN, Clark RD, Gallie BL. Detection of mosaic RB1 mutations in families with retinoblastoma. Hum Mutat 2009; 30:842-51. [PMID: 19280657 DOI: 10.1002/humu.20940] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The RB1 gene mutation detection rate in 1,020 retinoblastoma families was increased by the use of highly sensitive allele specific-PCR (AS-PCR) to detect low-level mosaicism for 11 recurrent RB1 CGA>TGA nonsense mutations. For bilaterally affected probands, AS-PCR increased the RB1 mutation detection sensitivity from 92.6% to 94.8%. Both RB1 oncogenic changes were detected in 92.7% of sporadic unilateral tumors (357/385); 14.6% (52/357) of unilateral probands with both tumor mutations identified carried one of the tumor mutations in blood. Mosaicism was evident in 5.5% of bilateral probands (23 of 421), in 3.8% of unilateral probands (22 of 572), and in one unaffected mother of a unilateral proband. Half of the mosaic mutations were only detectable by AS-PCR for the 11 recurrent CGA>TGA mutations, and not by standard sequencing. This suggests that significant numbers of low-level mosaics with other classes of RB1 mutations remain unidentified by current technology. We show that the use of linkage analysis in a two-generation retinoblastoma family resulted in the erroneous conclusion that a child carried the parental mutation, because the founder parent was mosaic for the RB1 mutation. Of 142 unaffected parental pairs tested, only one unaffected parent of a proband (0.7%) showed somatic mosaicism for the proband's mutation, in contrast to an overall 4.5% somatic mosaicism rate for retinoblastoma probands, suggesting that mosaicism for an RB1 mutation is highly likely to manifest as retinoblastoma.
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Affiliation(s)
- Diane Rushlow
- Retinoblastoma Solutions, Toronto Western Hospital, Toronto, Ontario, Canada
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Sadikovic B, Al-Romaih K, Squire J, Zielenska M. Cause and consequences of genetic and epigenetic alterations in human cancer. Curr Genomics 2008; 9:394-408. [PMID: 19506729 PMCID: PMC2691666 DOI: 10.2174/138920208785699580] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 05/06/2008] [Accepted: 05/08/2008] [Indexed: 12/16/2022] Open
Abstract
Both genetic and epigenetic changes contribute to development of human cancer. Oncogenomics has primarily focused on understanding the genetic basis of neoplasia, with less emphasis being placed on the role of epigenetics in tumourigenesis. Genomic alterations in cancer vary between the different types and stages, tissues and individuals. Moreover, genomic change ranges from single nucleotide mutations to gross chromosomal aneuploidy; which may or may not be associated with underlying genomic instability. Collectively, genomic alterations result in widespread deregulation of gene expression profiles and the disruption of signalling networks that control proliferation and cellular functions. In addition to changes in DNA and chromosomes, it has become evident that oncogenomic processes can be profoundly influenced by epigenetic mechanisms. DNA methylation is one of the key epigenetic factors involved in regulation of gene expression and genomic stability, and is biologically necessary for the maintenance of many cellular functions. While there has been considerable progress in understanding the impact of genetic and epigenetic mechanisms in tumourigenesis, there has been little consideration of the importance of the interplay between these two processes. In this review we summarize current understanding of the role of genetic and epigenetic alterations in human cancer. In addition we consider the associated interactions of genetic and epigenetic processes in tumour onset and progression. Furthermore, we provide a model of tumourigenesis that addresses the combined impact of both epigenetic and genetic alterations in cancer cells.
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Affiliation(s)
- B Sadikovic
- Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Canada
- The Ontario Cancer Institute, Princess Margaret Hospital, Toronto, Canada
| | - K Al-Romaih
- The Ontario Cancer Institute, Princess Margaret Hospital, Toronto, Canada
| | - J.A Squire
- The Ontario Cancer Institute, Princess Margaret Hospital, Toronto, Canada
| | - M Zielenska
- Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Canada
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Gorlov IP, Gorlova OY, Amos CI. Relative effects of mutability and selection on single nucleotide polymorphisms in transcribed regions of the human genome. BMC Genomics 2008; 9:292. [PMID: 18559102 PMCID: PMC2442617 DOI: 10.1186/1471-2164-9-292] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Accepted: 06/17/2008] [Indexed: 11/10/2022] Open
Abstract
MOTIVATION Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in humans. However, the factors that affect SNP density are poorly understood. The goal of this study was to estimate the relative effects of mutability and selection on SNP density in transcribed regions of human genes. It is important for prediction of the regions that harbor functional polymorphisms. RESULTS We used frequency-validated SNPs resulting from single-nucleotide substitutions. SNPs were subdivided into five functional categories: (i) 5' untranslated region (UTR) SNPs, (ii) 3' UTR SNPs, (iii) synonymous SNPs, (iv) SNPs producing conservative missense mutations, and (v) SNPs producing radical missense mutations. Each of these categories was further subdivided into nine mutational categories on the basis of the single-nucleotide substitution type. Thus, 45 functional/mutational categories were analyzed. The relative mutation rate in each mutational category was estimated on the basis of published data. The proportion of segregating sites (PSSs) for each functional/mutational category was estimated by dividing the observed number of SNPs by the number of potential sites in the genome for a given functional/mutational category. By analyzing each functional group separately, we found significant positive correlations between PSSs and relative mutation rates (Spearman's correlation coefficient, at least r = 0.96, df = 9, P < 0.001). We adjusted the PSSs for the mutation rate and found that the functional category had a significant effect on SNP density (F = 5.9, df = 4, P = 0.001), suggesting that selection affects SNP density in transcribed regions of the genome. We used analyses of variance and covariance to estimate the relative effects of selection (functional category) and mutability (relative mutation rate) on the PSSs and found that approximately 87% of variation in PSS was due to variation in the mutation rate and approximately 13% was due to selection, suggesting that the probability that a site located in a transcribed region of a gene is polymorphic mostly depends on the mutability of the site.
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Affiliation(s)
- Ivan P Gorlov
- Department of Epidemiology, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA.
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Epigenetic drivers and genetic passengers on the road to cancer. Mutat Res 2008; 642:1-13. [PMID: 18471836 DOI: 10.1016/j.mrfmmm.2008.03.002] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Revised: 02/29/2008] [Accepted: 03/19/2008] [Indexed: 12/31/2022]
Abstract
Cancer is traditionally viewed as a primarily genetic disorder, however it is now becoming accepted that cancer is also a consequence of abnormal epigenetic events. Genetic changes and aneuploidy are associated with alterations in DNA sequence, and they are a hallmark of the malignant process. Epigenetic alterations are universally present in human cancer and result in heritable changes in gene expression and chromatin structure over many cell generations without changes in DNA sequence, leading to functional consequences equivalent to those induced by genetic alterations. Importantly, intriguing evidence emerged suggesting that epigenetic changes may precede and provoke genetic changes. In this scenario, epigenetic events are primary events while genetic changes (such as mutations) may simply be a consequence of disrupted epigenetic states. This fact may explain why many genetic screens proved to be limited with regard to cancer causality and pathogenesis. Aberrant epigenetic events affect multiple genes and cellular pathways in a non-random fashion and this can predispose to induction and accumulation of genetic changes in the course of tumour initiation and progression. These considerations are critical for a better understanding of tumourigenesis and molecular events underlying the acquisition of drug resistance, as well as development of novel strategies for cancer therapy and prevention.
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Tanaka K, Tainaka K, Umemoto T, Nomura A, Okamoto A. An osmium-DNA interstrand complex: application to facile DNA methylation analysis. J Am Chem Soc 2007; 129:14511-7. [PMID: 17963391 DOI: 10.1021/ja076140r] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleic acids often acquire new functions by forming a variety of complexes with metal ions. Osmium, in an oxidized state, also reacts with C5-methylated pyrimidines. However, control of the sequence specificity of osmium complexation with DNA is still immature, and the value of the resulting complexes is unknown. We have designed a bipyridine-attached adenine derivative for sequence-specific osmium complexation. Sequence-specific osmium complexation was achieved by hybridization of a short DNA molecule containing this functional nucleotide to a target DNA sequence and resulted in the formation of a cross-linked structure. The interstrand cross-link clearly distinguished methylated cytosines from unmethylated cytosines and was used to quantify the degree of methylation at a specific cytosine in the genome.
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Affiliation(s)
- Kazuo Tanaka
- Frontier Research System, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-1098, Japan
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Cheung LWT, Lee YF, Ng TW, Ching WK, Khoo US, Ng MKP, Wong AST. CpG/CpNpG motifs in the coding region are preferred sites for mutagenesis in the breast cancer susceptibility genes. FEBS Lett 2007; 581:4668-74. [PMID: 17826769 DOI: 10.1016/j.febslet.2007.08.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Revised: 08/21/2007] [Accepted: 08/26/2007] [Indexed: 10/22/2022]
Abstract
The range of BRCA1/BRCA2 gene mutations is diverse and the mechanism accounting for this heterogeneity is obscure. To gain insight into the endogenous mutational mechanisms involved, we evaluated the association of specific sequences (i.e. CpG/CpNpG motifs, homonucleotides, short repeats) and mutations within the genes. We classified 1337 published mutations in BRCA1 (1765 BRCA2 mutations) for each specific sequence, and employed computer simulation combined with mathematical calculations to estimate the true underlying tendency of mutation occurrence. Interestingly, we found no mutational bias to homonucleotides and repeats in deletions/insertions and substitutions but striking bias to CpG/CpNpG in substitutions in both genes. This suggests that methylation-dependent DNA alterations would be a major mechanism for mutagenesis.
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Affiliation(s)
- Lydia W T Cheung
- School of Biological Sciences, University of Hong Kong, Hong Kong
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Zhang W, Bouffard GG, Wallace SS, Bond JP. Estimation of DNA sequence context-dependent mutation rates using primate genomic sequences. J Mol Evol 2007; 65:207-14. [PMID: 17676366 DOI: 10.1007/s00239-007-9000-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Accepted: 11/30/2006] [Indexed: 10/23/2022]
Abstract
It is understood that DNA and amino acid substitution rates are highly sequence context-dependent, e.g., C --> T substitutions in vertebrates may occur much more frequently at CpG sites and that cysteine substitution rates may depend on support of the context for participation in a disulfide bond. Furthermore, many applications rely on quantitative models of nucleotide or amino acid substitution, including phylogenetic inference and identification of amino acid sequence positions involved in functional specificity. We describe quantification of the context dependence of nucleotide substitution rates using baboon, chimpanzee, and human genomic sequence data generated by the NISC Comparative Sequencing Program. Relative mutation rates are reported for the 96 classes of mutations of the form 5' alphabetagamma 3' --> 5' alphadeltagamma 3', where alpha, beta, gamma, and delta are nucleotides and beta not equal delta, based on maximum likelihood calculations. Our results confirm that C --> T substitutions are enhanced at CpG sites compared with other transitions, relatively independent of the identity of the preceding nucleotide. While, as expected, transitions generally occur more frequently than transversions, we find that the most frequent transversions involve the C at CpG sites (CpG transversions) and that their rate is comparable to the rate of transitions at non-CpG sites. A four-class model of the rates of context-dependent evolution of primate DNA sequences, CpG transitions > non-CpG transitions approximately CpG transversions > non-CpG transversions, captures qualitative features of the mutation spectrum. We find that despite qualitative similarity of mutation rates among different genomic regions, there are statistically significant differences.
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Affiliation(s)
- Wei Zhang
- Department of Medicine, University of Chicago, 515 CLSC, Chicago, IL 60637, USA
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Abstract
Cytosine methylation is a common form of post-replicative DNA modification seen in both bacteria and eukaryotes. Modified cytosines have long been known to act as hotspots for mutations due to the high rate of spontaneous deamination of this base to thymine, resulting in a G/T mismatch. This will be fixed as a C-->T transition after replication if not repaired by the base excision repair (BER) pathway or specific repair enzymes dedicated to this purpose. This hypermutability has led to depletion of the target dinucleotide CpG outside of special CpG islands in mammals, which are normally unmethylated. We review the importance of C-->T transitions at non-island CpGs in human disease: When these occur in the germline, they are a common cause of inherited diseases such as epidermolysis bullosa and mucopolysaccharidosis, while in the soma they are frequently found in the genes for tumor suppressors such as p53 and the retinoblastoma protein, causing cancer. We also examine the specific repair enzymes involved, namely the endonuclease Vsr in Escherichia coli and two members of the uracil DNA glycosylase (UDG) superfamily in mammals, TDG and MBD4. Repair brings its own problems, since it will require remethylation of the replacement cytosine, presumably coupling repair to methylation by either the maintenance methylase Dnmt1 or a de novo enzyme such as Dnmt3a. Uncoupling of methylation from repair may be one way to remove methylation from DNA. We also look at the possible role of specific cytosine deaminases such as Aid and Apobec in accelerating deamination of methylcytosine and consequent DNA demethylation.
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Affiliation(s)
- C P Walsh
- Centre for Molecular Biosciences, School of Biomedical Sciences, University of Ulster, Northern Ireland
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Murphree AL, Samuel MA, Harbour JW, Mansfield NC. Retinoblastoma. Retina 2006. [DOI: 10.1016/b978-0-323-02598-0.50028-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Valverde JR, Alonso J, Palacios I, Pestaña Á. RB1 gene mutation up-date, a meta-analysis based on 932 reported mutations available in a searchable database. BMC Genet 2005; 6:53. [PMID: 16269091 PMCID: PMC1298292 DOI: 10.1186/1471-2156-6-53] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Accepted: 11/04/2005] [Indexed: 11/16/2022] Open
Abstract
Background Retinoblastoma, a prototype of hereditary cancer, is the most common intraocular tumour in children and potential cause of blindness from therapeutic eye ablation, second tumours in germ line carrier's survivors, and even death when left untreated. The molecular scanning of RB1 in search of germ line mutations lead to the publication of more than 900 mutations whose knowledge is important for genetic counselling and the characterization of phenotypic-genotypic relationships. Results A searchable database (RBGMdb) has been constructed with 932 published RB1 mutations. The spectrum of these mutations has been analyzed with the following results: 1) the retinoblastoma protein is frequently inactivated by deletions and nonsense mutations while missense mutations are the main inactivating event in most genetic diseases. 2) Near 40% of RB1 gene mutations are recurrent and gather in sixteen hot points, including twelve nonsense, two missense and three splicing mutations. The remainder mutations are scattered along RB1, being most frequent in exons 9, 10, 14, 17, 18, 20, and 23. 3) The analysis of RB1 mutations by country of origin of the patients identifies two groups in which the incidence of nonsense and splicing mutations show differences extremely significant, and suggest the involvement of predisposing ethnic backgrounds. 4) A significant association between late age at diagnosis and splicing mutations in bilateral retinoblastoma patients suggests the occurrence of a delayed-onset genotype. 5) Most of the reported mutations in low-penetrance families fall in three groups: a) Mutations in regulatory sequences at the promoter resulting in low expression of a normal Rb; b) Missense and in-frame deletions affecting non-essential sequence motifs which result in a partial inactivation of Rb functions; c) Splicing mutations leading to the reduction of normal mRNA splicing or to alternative splicing involving either true oncogenic or defective (weak) alleles. Conclusion The analysis of RB1 gene mutations logged in the RBGMdb has shown relevant phenotype-genotype relationships and provided working hypothesis to ascertain mechanisms linking certain mutations to ethnicity, delayed onset of the disease and low-penetrance. Gene profiling of tumors will help to clarify the genetic background linked to ethnicity and variable expressivity or delayed onset phenotypes.
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Affiliation(s)
- José R Valverde
- Servicio de Informática. Centro Nacional de Biotecnología, CSIC. Campus de Cantoblanco. 28049-Madrid, Spain
| | - Javier Alonso
- Oncolab. Deparatamento de Biología Molecular y Celular del Cáncer. Instituto de Investigaciones Biomédicas "A. Sols", CSIC-UAM. 28029 Madrid, Spain
| | - Itziar Palacios
- Oncolab. Deparatamento de Biología Molecular y Celular del Cáncer. Instituto de Investigaciones Biomédicas "A. Sols", CSIC-UAM. 28029 Madrid, Spain
| | - Ángel Pestaña
- Oncolab. Deparatamento de Biología Molecular y Celular del Cáncer. Instituto de Investigaciones Biomédicas "A. Sols", CSIC-UAM. 28029 Madrid, Spain
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Orjuela MA, Titievsky L, Liu X, Ramirez-Ortiz M, Ponce-Castaneda V, Lecona E, Molina E, Beaverson K, Abramson DH, Mueller NE. Fruit and Vegetable Intake during Pregnancy and Risk for Development of Sporadic Retinoblastoma. Cancer Epidemiol Biomarkers Prev 2005; 14:1433-40. [PMID: 15941952 DOI: 10.1158/1055-9965.epi-04-0427] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE Little is known about the causes of sporadic (noninherited) retinoblastoma. Rates seem to be somewhat higher among poorer populations in Mexico. Fruits and vegetables are important sources of carotenoids and folate. We examined whether decreased gestational maternal intake of fruits and vegetables may contribute to development of sporadic retinoblastoma. METHODS At the Instituto Nacional de Pediatria in Mexico City, we conducted a hospital-based case-control study to evaluate prenatal maternal diet. We examined dietary intake of fruits and vegetables of mothers of 101 children with retinoblastoma and 172 control children using a dietary recall questionnaire and published food nutrient content tables. RESULTS The reported number of mean daily servings of fruits and vegetables was lower among case mothers when compared with control mothers [vegetables: 2.28 in controls, 1.75 in cases (P < 0.01); fruits: 2.13 in controls, 1.59 in cases (P = 0.07)]. Mean daily maternal folate intake from both vegetables and fruits was higher in controls (103 microg) than in cases (48 microg; P < 0.05). Risk for having a child with retinoblastoma was increased for mothers consuming fewer than 2 daily servings of vegetables [odds ratios (OR), 3.4; 95% confidence interval (95% CI), 2.0-6.0] or with a low intake of folate (OR, 3.9; 95% CI, 2.1, 7.3), or lutein/zeaxanthin (OR, 2.6; 95% CI, 1.5-4.6) derived from fruits and vegetables. CONCLUSIONS Decreased intake of vegetables and fruits during pregnancy and the consequent decreased intake of nutrients such as folate and lutein/zeaxanthin, necessary for DNA methylation, synthesis, and retinal function, may increase risk for having a child with sporadic retinoblastoma.
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Affiliation(s)
- Manuela A Orjuela
- Department of Pediatrics, Mailman School of Public Health at Columbia University, Room B106, 60 Haven Avenue, New York, New York 10032, USA.
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Karpinets TV, Foy BD. Tumorigenesis: the adaptation of mammalian cells to sustained stress environment by epigenetic alterations and succeeding matched mutations. Carcinogenesis 2005; 26:1323-34. [PMID: 15802302 DOI: 10.1093/carcin/bgi079] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Recent studies indicate that during tumorigenic transformations, cells may generate mutations by themselves as a result of error-prone cell division with participation of error-prone polymerases and aberrant mitosis. These mechanisms may be activated in cells by continuing proliferative and survival signaling in a sustained stress environment (SSE). The paper hypothesizes that long-term exposure to this signaling epigenetically reprograms the genome of some cells and, in addition, leads to their senescence. The epigenetic reprogramming results in: (i) hypermethylation of tumor-suppressor genes involved in the onset of cell-cycle arrest, apoptosis and DNA repair; (ii) hypomethylation of proto-oncogenes associated with persistent proliferative activity; and (iii) the global demethylation of the genome and activation of DNA repeats. These epigenetic changes in the proliferating cells associate with their replicative senescence and allow the reprogrammed senescent cells to overcome the cell-cycle arrest and to activate error-prone replications. It is hypothesized that the generation of mutations in the error-prone replications of the epigenetically reprogrammed cells is not random. The mutations match epigenetic alterations in the cellular genome, namely gain of function mutations in the case of hypomethylation and loss of functions in the case of hypermethylation. In addition, continuing proliferation of the cells imposed by signaling in SSE speeds up the natural selection of the mutant cells favoring the survival of the cells with mutations that are beneficial in the environment. In this way, a stress-induced replication of the cells epigenetically reprograms their genome for quick adaptation to stressful environments providing an increased rate of mutations, epigenetic tags to beneficial mutations and quick selection process. In combination, these processes drive the origin of the transformed mammalian cells, cancer development and progression. Support from genomic, biochemical and medical studies for the proposed hypothesis, and its implementations are discussed.
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Affiliation(s)
- Tatiana V Karpinets
- Department of Plant Sciences, University of Tennessee, 2431 Center Drive Knoxville, TN 37996-4500, USA.
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Choy KW, Lee TC, Cheung KF, Fan DSP, Lo KW, Beaverson KL, Abramson DH, Lam DSC, Yu CBO, Pang CP. Clinical implications of promoter hypermethylation in RASSF1A and MGMT in retinoblastoma. Neoplasia 2005; 7:200-6. [PMID: 15799820 PMCID: PMC1501141 DOI: 10.1593/neo.04565] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2004] [Revised: 10/15/2004] [Accepted: 10/18/2004] [Indexed: 11/18/2022]
Abstract
We investigated the epigenetic silencing and genetic changes of the RAS-associated domain family 1A (RASSF1A) gene and the O6-methylguanine-DNA methyltransferase (MGMT) gene in retinoblastoma. We extracted DNA from microdissected tumor and normal retina tissues of the same patient in 68 retinoblastoma cases. Promoter methylation in RASSF1A and MGMT was analyzed by methylation-specific PCR, RASSF1A sequence alterations in all coding exons by direct DNA sequencing, and RASSF1A expression by RT-PCR. Cell cycle staging was analyzed by flow cytometry. We detected RASSF1A promoter hypermethylation in 82% of retinoblastoma, in tumor tissues only but not in adjacent normal retinal tissue cells. There was no expression of RASSF1A transcripts in all hypermethylated samples, but RASSF1A transcripts were restored after 5-aza-2'-deoxycytidine treatment with no changes in cell cycle or apoptosis. No mutation in the RASSF1A sequence was found. MGMT hypermethylation was present in 15% of the retinoblastoma samples, and the absence of MGMT hypermethylation was associated (P = .002) with retinoblastoma at advanced Reese-Ellsworth tumor stage. Our results revealed a high RASSF1A hypermethylation frequency in retinoblastoma. The correlation of MGMT inactivation by promoter hypermethylation with lower-stage diseases indicated that MGMT hypermethylation provides useful prognostic information. Epigenetic mechanism plays an important role in the progression of retinoblastoma.
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Affiliation(s)
- Kwong Wai Choy
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong Eye Hospital, Kowloon, Hong Kong, China.
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Dalamón V, Surace E, Giliberto F, Ferreiro V, Fernandez C, Szijan I. Detection of germline mutations in argentine retinoblastoma patients: low and full penetrance retinoblastoma caused by the same germline truncating mutation. BMB Rep 2004; 37:246-53. [PMID: 15469703 DOI: 10.5483/bmbrep.2004.37.2.246] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Constitutional RB1 gene mutations were studied in a series of 21 families with unilateral and bilateral retinoblastoma patients. Peripheral blood lymphocytes were analyzed by "exon by exon" PCR-heteroduplex and sequencing. Mutations were identified in 6 (29%) of the patients. One mutation corresponded to an intronic polymorphism in g.174351T > A. The other five mutations resulted C to T exonic transitions, four were CGA sequences (g.65386, g.150037 in two patients, and g.162237), creating stop codons and presumably truncated proteins. The fifth one was new and resulted in alanine to valine substitution (g.73774). Two patients had the same the germline truncated mutation (g.150037C > T), one with a familial bilateral early onset retinoblastoma and one with a sporadic unilateral late onset retinoblastoma. The later type has not been previously described. This finding is discussed in the genotype/phenotype correlation context. Additionally, a single nucleotide change was found in six studied samples, where a C to T homozygous transversion was identified in intron 26 (IVS26 + 28). It is worthy the non concordance of the nucleotide with the published sequence. This analysis proved to be a useful method for the detection of mutations in the RB1 gene, and contributed to the adequate genetic counseling to patients and relatives.
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Affiliation(s)
- Viviana Dalamón
- Catedra de Genetica y Biologia Molecular, Facultad de Farmacia y Bioquimica, Universidad de Buenos Aires, Argentina.
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