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Eaaswarkhanth M, dos Santos ALC, Gokcumen O, Al-Mulla F, Thanaraj TA. Genome-Wide Selection Scan in an Arabian Peninsula Population Identifies a TNKS Haplotype Linked to Metabolic Traits and Hypertension. Genome Biol Evol 2020; 12:77-87. [PMID: 32068798 PMCID: PMC7093833 DOI: 10.1093/gbe/evaa033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2020] [Indexed: 12/12/2022] Open
Abstract
Despite the extreme and varying environmental conditions prevalent in the Arabian Peninsula, it has experienced several waves of human migrations following the out-of-Africa diaspora. Eventually, the inhabitants of the peninsula region adapted to the hot and dry environment. The adaptation and natural selection that shaped the extant human populations of the Arabian Peninsula region have been scarcely studied. In an attempt to explore natural selection in the region, we analyzed 662,750 variants in 583 Kuwaiti individuals. We searched for regions in the genome that display signatures of positive selection in the Kuwaiti population using an integrative approach in a conservative manner. We highlight a haplotype overlapping TNKS that showed strong signals of positive selection based on the results of the multiple selection tests conducted (integrated Haplotype Score, Cross Population Extended Haplotype Homozygosity, Population Branch Statistics, and log-likelihood ratio scores). Notably, the TNKS haplotype under selection potentially conferred a fitness advantage to the Kuwaiti ancestors for surviving in the harsh environment while posing a major health risk to present-day Kuwaitis.
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Affiliation(s)
| | - Andre Luiz Campelo dos Santos
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo
- Department of Archeology, Federal University of Pernambuco, Recife, Brazil
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
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Wan S, Wan F, Wan P, Wan J, He X, Liu F, Yang G. The relation of microsatellite instability to expression of hTERT in human gastric carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:2257-2263. [PMID: 31934049 PMCID: PMC6949629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/19/2019] [Indexed: 06/10/2023]
Abstract
OBJECTIVE To investigate the role of microsatellite instability (MSI) in the pathogenesis of gastric carcinoma and its relationship with the expression of hTERT gene. METHODS 75 cases of gastric carcinoma and paired normal control tissues were included in this study. MSI of BAT-25, BAT-26, D5S346, D17S250 and D2S1235 were detected by PCR, native polyacrylamide gel electrophoresis, and silver staining while the expression of hTERT was localized by immunohistochemistry at the same time. RESULTS MSI positive rates of BAT-25, BAT-26, D5S346, D17S250 and D2S123 were 14.7%, 12.00%, 26.67%, 16% and 21.3%. MSI was obviously related with lymph node metastasis and pathologic stages respectively (P<0.05), but not with age, gender, histologic type, or infiltration depth (P>0.05). hTERT was not expressed in normal gastric mucosa, but in intestinal metaplasia, dysplasia, and gastric carcinoma. The positive rate of hTERT was 76% (57/75) in 75 cases of gastric carcinoma tissues. The expression of hTERT was obviously related to histological type (P<0.05), but not to age, gender, lymph node metastasis, depth of invasion, or staging, respectively (P>0.05). The positive rate was higher in poorly differentiated cases than in moderately and well differentiated cases (P<0.05). MSI accounted for 28.1% of 57 hTERT positive cases while MSI accounted for 72.2% in 18 hTERT negative cases. Spearman rank correlation analysis showed that MSI was negatively related to hTERT expression (r=0.387, P=0.001). CONCLUSION MSI may play an important role in the pathogenesis and progression of gastric carcinoma by affecting the expression of TERT gene.
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Affiliation(s)
- Shunmei Wan
- Department of Gastroenterology, San Ai Tang HospitalLanzhou, Gansu, China
| | - Furong Wan
- Rehabilitation Central Hospital of GansuLanzhou, Gansu, China
| | - Pingxin Wan
- Traditional Chinese Medicine Hospital of Jingyuan CountyBaiyin, Gansu, China
| | - Jianxin Wan
- Gansu Medical CollegePingliang, Gansu, China
| | - Xiaoxia He
- Department of Gastroenterology and Oncology, The Second People’s Hospital of LanzhouLanzhou, Gansu, China
| | - Fuxia Liu
- Department of Gastroenterology, San Ai Tang HospitalLanzhou, Gansu, China
| | - Guorong Yang
- Department of Pathology, San Ai Tang HospitalLanzhou, Gansu, China
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Kim N, Choi S, Kim SM, Lee AC, Im K, Park HS, Kim JA, Kim K, Kim I, Chang YH, Lee DS. Monozygotic twins with shared de novo GATA2 mutation but dissimilar phenotypes due to differential promoter methylation. Leuk Lymphoma 2019; 60:1053-1061. [PMID: 30714451 DOI: 10.1080/10428194.2018.1516039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A revised WHO classification of hematopoietic neoplasm introduced the new category 'Myeloid Neoplasms with Germline Predisposition', reflecting the growing importance of genetic testing for myeloid neoplasms. Here, we investigated monozygotic twins with the same de novo mutation in GATA2 but different phenotypes. The patient suffering a bleeding tendency was diagnosed with myelodysplastic syndrome (MDS), and her monozygotic twin showed dysmegakaryopoietic features in the bone marrow. Targeted sequencing revealed the same germline mutation in GATA2, c.1192C > T, in both sisters and different somatic mutations in 14 genes between the sisters. The GATA2 mutation was absent in both parents, and their hemograms were normal. The methylation profile of the GATA2 promoter region was different between the twins, showing denser promoter methylation in the patient, correlated with MDS. Thus, we concluded that the twins had acquired a de novo GATA2 mutation but showed different phenotypes, possibly due to the critical role of epigenetic changes.
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Affiliation(s)
- Namhee Kim
- a Department of Laboratory Medicine , Seoul National University College of Medicine , Seoul , Republic of Korea
| | - Seongmin Choi
- b Division of Clinical Bioinformatics Biomedical Research Institute , Seoul National University Hospital , Seoul , Republic of Korea
| | - Sung-Min Kim
- c Cancer Research Institute, Seoul National University College of Medicine , Seoul , Republic of Korea
| | - Amos Chungwon Lee
- d Interdisciplinary program of Bioengineering , Seoul National University , Seoul , Republic of Korea
| | - Kyongok Im
- c Cancer Research Institute, Seoul National University College of Medicine , Seoul , Republic of Korea
| | - Hee Sue Park
- a Department of Laboratory Medicine , Seoul National University College of Medicine , Seoul , Republic of Korea
| | - Jung-Ah Kim
- a Department of Laboratory Medicine , Seoul National University College of Medicine , Seoul , Republic of Korea
| | - Kwangsoo Kim
- b Division of Clinical Bioinformatics Biomedical Research Institute , Seoul National University Hospital , Seoul , Republic of Korea
| | - Inho Kim
- e Department of Internal Medicine , Seoul National University College of Medicine , Seoul , Republic of Korea
| | - Yoon Hwan Chang
- f Department of Laboratory Medicine , Korea Cancer Center Hospital , Seoul , Republic of Korea
| | - Dong Soon Lee
- a Department of Laboratory Medicine , Seoul National University College of Medicine , Seoul , Republic of Korea.,c Cancer Research Institute, Seoul National University College of Medicine , Seoul , Republic of Korea
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Joyce BT, Zheng Y, Nannini D, Zhang Z, Liu L, Gao T, Kocherginsky M, Murphy R, Yang H, Achenbach CJ, Roberts LR, Hoxha M, Shen J, Vokonas P, Schwartz J, Baccarelli A, Hou L. DNA Methylation of Telomere-Related Genes and Cancer Risk. Cancer Prev Res (Phila) 2018; 11:511-522. [PMID: 29895583 DOI: 10.1158/1940-6207.capr-17-0413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/03/2018] [Accepted: 05/22/2018] [Indexed: 01/09/2023]
Abstract
Researchers hypothesized that telomere shortening facilitates carcinogenesis. Previous studies found inconsistent associations between blood leukocyte telomere length (LTL) and cancer. Epigenetic reprogramming of telomere maintenance mechanisms may help explain this inconsistency. We examined associations between DNA methylation in telomere-related genes (TRG) and cancer. We analyzed 475 participants providing 889 samples 1 to 3 times (median follow-up, 10.1 years) from 1999 to 2013 in the Normative Aging Study. All participants were cancer-free at each visit and blood leukocytes profiled using the Illumina 450K array. Of 121 participants who developed cancer, 34 had prostate cancer, 10 melanoma, 34 unknown skin malignancies, and 43 another cancer. We examined 2,651 CpGs from 80 TRGs and applied a combination of Cox and mixed models to identify CpGs prospectively associated with cancer (at FDR < 0.05). We also explored trajectories of DNA methylation, logistic regression stratified by time to diagnosis/censoring, and cross-sectional models of LTL at first blood draw. We identified 30 CpGs on 23 TRGs whose methylation was positively associated with cancer incidence (β = 1.0-6.93) and one protective CpG in MAD1L1 (β = -0.65), of which 87% were located in TRG promoters. Methylation trajectories of 21 CpGs increased in cancer cases relative to controls; at 4 to 8 years prediagnosis/censoring, 17 CpGs were positively associated with cancer. Three CpGs were cross-sectionally associated with LTL. TRG methylation may be a mechanism through which LTL dynamics reflect cancer risk. Future research should confirm these findings and explore potential mechanisms underlying these findings, including telomere maintenance and DNA repair dysfunction. Cancer Prev Res; 11(8); 511-22. ©2018 AACR.
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Affiliation(s)
- Brian T Joyce
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| | - Yinan Zheng
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Drew Nannini
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Zhou Zhang
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lei Liu
- Division of Biostatistics, Washington University in St. Louis, St. Louis, Missouri
| | - Tao Gao
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Masha Kocherginsky
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Robert Murphy
- Center for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Hushan Yang
- Division of Population Science, Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Chad J Achenbach
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Mirjam Hoxha
- Molecular Epidemiology and Environmental Epigenetics Laboratory, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Jincheng Shen
- Department of Population Health Sciences, University of Utah School of Medicine, Salt Lake City, Utah
| | - Pantel Vokonas
- VA Normative Aging Study, VA Boston Healthcare System, Boston, Massachusetts.,Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Joel Schwartz
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts
| | - Andrea Baccarelli
- Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York, New York
| | - Lifang Hou
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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Integrated analysis of promoter methylation and expression of telomere related genes in breast cancer. Oncotarget 2018; 8:25442-25454. [PMID: 28424414 PMCID: PMC5421942 DOI: 10.18632/oncotarget.16036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/07/2017] [Indexed: 11/25/2022] Open
Abstract
Telomeres at the ends of eukaryotic chromosomes play a critical role in tumorgenesis. Using microfluidic PCR and next-generation bisulfite sequencing technology, we investigated the promoter methylation of 29 telomere related genes in paired tumor and normal tissues from 184 breast cancer patients. The expression of significantly differentially methylated genes was quantified using qPCR method.We observed that the average methylation level of the 29 telomere related genes was significant higher in tumor than that in normal tissues (P = 4.30E-21). A total of 4 genes (RAD50, RTEL, TERC and TRF1) showed significant hyper-methylation in breast tumor tissues. RAD51D showed significant methylation difference among the four breast cancer subtypes. The methylation of TERC showed significant association with ER status of breast cancer. The expression profiles of the 4 hyper-methylated genes showed significantly reduced expression in tumor tissues. The integration analysis of methylation and expression of these 4 genes showed a good performance in breast cancer prediction (AUC = 0.947).Our results revealed the methylation pattern of telomere related genes in breast cancer and suggested a novel 4-gene panel might be a valuable biomarker for breast cancer diagnosis.
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Gao J, Roy S, Tong L, Argos M, Jasmine F, Rahaman R, Rakibuz-Zaman M, Parvez F, Ahmed A, Hore SK, Sarwar G, Slavkovich V, Yunus M, Rahman M, Baron JA, Graziano JH, Ahsan H, Pierce BL. Arsenic exposure, telomere length, and expression of telomere-related genes among Bangladeshi individuals. ENVIRONMENTAL RESEARCH 2015; 136:462-9. [PMID: 25460668 PMCID: PMC4264833 DOI: 10.1016/j.envres.2014.09.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/11/2014] [Accepted: 09/22/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND Inorganic arsenic is a carcinogen whose mode of action may involve telomere dysfunction. Recent epidemiological studies suggest that chronic arsenic exposure is associated with longer telomeres and altered expression of telomere-related genes in peripheral blood. In this study, we evaluated the association of urinary arsenic concentration with expression of telomere-related genes and telomere length in Bangladeshi individuals with a wide range of arsenic exposure through naturally contaminated drinking water. METHODS We used linear regression models to estimate associations between urinary arsenic and array-based expression measures for 69 telomere related genes using mononuclear cell RNA samples from 1799 individuals. Association between arsenic exposure and a qPCR-based telomere length measure was assessed among 167 individuals. RESULTS Urinary arsenic was positively associated with expression of WRN, and negatively associated with TERF2, DKC1, TERF2IP and OBFC1 (all P<0.00035, Bonferroni-corrected threshold). We detected interaction between urinary arsenic and arsenic metabolism efficiency in relation to expression of WRN (P for interaction =0.00008). In addition, we observed that very high arsenic exposure was associated with longer telomeres compared to very low exposure (P=0.02). DISCUSSION Our findings suggest that arsenic's carcinogenic mode of action may involve alteration of telomere maintenance and/or telomere damage. This study extends our knowledge regarding the effect of arsenic on telomere length and expression of telomere-related genes.
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Affiliation(s)
- Jianjun Gao
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Shantanu Roy
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Lin Tong
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Maria Argos
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Farzana Jasmine
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Ronald Rahaman
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | | | - Faruque Parvez
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | | | - Samar K Hore
- International Center for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Vesna Slavkovich
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Mohammad Yunus
- International Center for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - John A Baron
- University of North Carolina, Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27514, USA
| | - Joseph H Graziano
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Habibul Ahsan
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA; Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA; Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Brandon L Pierce
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA; Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA.
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Mirabello L, Chung CC, Yeager M, Savage SA. Characterization of population-based variation and putative functional elements for the multiple-cancer susceptibility loci at 5p15.33. F1000Res 2014; 3:231. [PMID: 26664699 PMCID: PMC4654438 DOI: 10.12688/f1000research.5186.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/15/2014] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND TERT encodes the telomerase reverse transcriptase, which is responsible for maintaining telomere ends by addition of (TTAGGG) n nucleotide repeats at the telomere. Recent genome-wide association studies have found common genetic variants at the TERT-CLPTM1L locus (5p15.33) associated with an increased risk of several cancers. RESULTS Data were acquired for 1627 variants in 1092 unrelated individuals from 14 populations within the 1000 Genomes Project. We assessed the population genetics of the 5p15.33 region, including recombination hotspots, diversity, heterozygosity, differentiation among populations, and potential functional impacts. There were significantly lower polymorphism rates, divergence, and heterozygosity for the coding variants, particularly for non-synonymous sites, compared with non-coding and silent changes. Many of the cancer-associated SNPs had differing genotype frequencies among ancestral groups and were associated with potential regulatory changes. CONCLUSIONS Surrogate SNPs in linkage disequilibrium with the majority of cancer-associated SNPs were functional variants with a likely role in regulation of TERT and/or CLPTM1L. Our findings highlight several SNPs that future studies should prioritize for evaluation of functional consequences.
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Affiliation(s)
- Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute,National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Charles C. Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute,National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research, Inc., Frederick, MD 20877, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute,National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
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Reichert S, Rojas ER, Zahn S, Robin JP, Criscuolo F, Massemin S. Maternal telomere length inheritance in the king penguin. Heredity (Edinb) 2014; 114:10-6. [PMID: 25052413 DOI: 10.1038/hdy.2014.60] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 04/24/2014] [Accepted: 05/07/2014] [Indexed: 01/07/2023] Open
Abstract
Telomeres are emerging as a biomarker for ageing and survival, and are likely important in shaping life-history trade-offs. In particular, telomere length with which one starts in life has been linked to lifelong survival, suggesting that early telomere dynamics are somehow related to life-history trajectories. This result highlights the importance of determining the extent to which telomere length is inherited, as a crucial factor determining early life telomere length. Given the scarcity of species for which telomere length inheritance has been studied, it is pressing to assess the generality of telomere length inheritance patterns. Further, information on how this pattern changes over the course of growth in individuals living under natural conditions should provide some insight on the extent to which environmental constraints also shape telomere dynamics. To fill this gap partly, we followed telomere inheritance in a population of king penguins (Aptenodytes patagonicus). We tested for paternal and maternal influence on chick initial telomere length (10 days old after hatching), and how these relationships changed with chick age (at 70, 200 and 300 days old). Based on a correlative approach, offspring telomere length was positively associated with maternal telomere length early in life (at 10 days old). However, this relationship was not significant at older ages. These data suggest that telomere length in birds is maternally inherited. Nonetheless, the influence of environmental conditions during growth remained an important factor shaping telomere length, as the maternal link disappeared with chicks' age.
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Affiliation(s)
- S Reichert
- 1] Département Ecologie, Physiologie et Ethologie, Institut Pluridisciplinaire Hubert Curien, Université de Strasbourg, Strasbourg, France [2] CNRS, UMR 7178, Strasbourg, France
| | - E R Rojas
- 1] Département Ecologie, Physiologie et Ethologie, Institut Pluridisciplinaire Hubert Curien, Université de Strasbourg, Strasbourg, France [2] CNRS, UMR 7178, Strasbourg, France
| | - S Zahn
- 1] Département Ecologie, Physiologie et Ethologie, Institut Pluridisciplinaire Hubert Curien, Université de Strasbourg, Strasbourg, France [2] CNRS, UMR 7178, Strasbourg, France
| | - J-P Robin
- 1] Département Ecologie, Physiologie et Ethologie, Institut Pluridisciplinaire Hubert Curien, Université de Strasbourg, Strasbourg, France [2] CNRS, UMR 7178, Strasbourg, France
| | - F Criscuolo
- 1] Département Ecologie, Physiologie et Ethologie, Institut Pluridisciplinaire Hubert Curien, Université de Strasbourg, Strasbourg, France [2] CNRS, UMR 7178, Strasbourg, France
| | - S Massemin
- 1] Département Ecologie, Physiologie et Ethologie, Institut Pluridisciplinaire Hubert Curien, Université de Strasbourg, Strasbourg, France [2] CNRS, UMR 7178, Strasbourg, France
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Rawal HC, Singh NK, Sharma TR. Conservation, Divergence, and Genome-Wide Distribution of PAL and POX A Gene Families in Plants. Int J Genomics 2013; 2013:678969. [PMID: 23671845 PMCID: PMC3647544 DOI: 10.1155/2013/678969] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 01/04/2013] [Accepted: 01/11/2013] [Indexed: 01/03/2023] Open
Abstract
Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL) and peroxidase A (POX A) enzymes in nine plant species representing very diverse groups like legumes (Glycine max and Medicago truncatula), fruits (Vitis vinifera), cereals (Sorghum bicolor, Zea mays, and Oryza sativa), trees (Populus trichocarpa), and model dicot (Arabidopsis thaliana) and monocot (Brachypodium distachyon) species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future.
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Affiliation(s)
| | | | - T. R. Sharma
- Genoinformatics Laboratory, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Pusa Campus, New Delhi 110 012, India
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Yanowsky K, Barroso A, Osorio A, Urioste M, Benitez J, Martinez-Delgado B. Mutational analysis of telomere genes in BRCA1/2-negative breast cancer families with very short telomeres. Breast Cancer Res Treat 2012; 134:1337-43. [PMID: 22752289 DOI: 10.1007/s10549-012-2141-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 06/12/2012] [Indexed: 11/26/2022]
Abstract
A majority of the familial breast cancer cases are not explained by mutations in the best-known high susceptibility genes BRCA1 and BRCA2. Since there is a link between DNA repair and telomere maintenance mechanisms, we have investigated for the first time the role of telomere genes in breast cancer predisposition. By a combination of DHPLC and direct sequencing, we screened for sequence variation in 14 telomere-related genes which included telomerase and shelterin complexes in index cases from 50 BRCA1/2-negative families previously characterized to have very short telomere length in peripheral blood leukocytes. Clear pathogenic changes were not detected in any of the genes analyzed. Most of the changes were non-coding variants and only nine corresponded to coding variants located in TPP1, TINF2, NHP2, TNKS, and RAD54B genes; although only two corresponded to coding missense changes leading to aminoacid changes in genes NHP2 and RAD54B. However, functional prediction analysis and control population studies of both variants ruled out its possible pathogenic role. Our results discard a major contribution of telomere-specific genes in hereditary breast cancer.
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Affiliation(s)
- Kira Yanowsky
- Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro 3, 28029 Madrid, Spain
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