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Hameed A, Mehmood MA, Shahid M, Fatma S, Khan A, Ali S. Prospects for potato genome editing to engineer resistance against viruses and cold-induced sweetening. GM CROPS & FOOD 2020; 11:185-205. [PMID: 31280681 DOI: 10.1080/21645698.2019.1631115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Crop improvement through transgenic technologies is commonly tagged with GMO (genetically-modified-organisms) where the presence of transgene becomes a big question for the society and the legislation authorities. However, new plant breeding techniques like CRISPR/Cas9 system [clustered regularly interspaced palindromic repeats (CRISPR)-associated 9] can overcome these limitations through transgene-free products. Potato (Solanum tuberosum L.) being a major food crop has the potential to feed the rising world population. Unfortunately, the cultivated potato suffers considerable production losses due to several pre- and post-harvest stresses such as plant viruses (majorly RNA viruses) and cold-induced sweetening (CIS; the conversion of sucrose to glucose and fructose inside cell vacuole). A number of strategies, ranging from crop breeding to genetic engineering, have been employed so far in potato for trait improvement. Recently, new breeding techniques have been utilized to knock-out potato genes/factors like eukaryotic translation initiation factors [elF4E and isoform elF(iso)4E)], that interact with viruses to assist viral infection, and vacuolar invertase, a core enzyme in CIS. In this context, CRISPR technology is predicted to reduce the cost of potato production and is likely to pass through the regulatory process being marker and transgene-free. The current review summarizes the potential application of the CRISPR/Cas9 system for traits improvement in potato. Moreover, the prospects for engineering resistance against potato fungal pathogens and current limitations/challenges are discussed.
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Affiliation(s)
- Amir Hameed
- Department of Plant Biotechnology, Akhuwat Faisalabad Institute of Research Science and Technology , Faisalabad, Pakistan
| | - Muhammad Aamer Mehmood
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad , Faisalabad, Pakistan
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad , Faisalabad, Pakistan
| | - Shabih Fatma
- National Institute for Biotechnology and Genetic Engineering (NIBGE) , Faisalabad, Pakistan
| | - Aysha Khan
- Department of Plant Biotechnology, Akhuwat Faisalabad Institute of Research Science and Technology , Faisalabad, Pakistan
| | - Sumbal Ali
- Department of Plant Biotechnology, Akhuwat Faisalabad Institute of Research Science and Technology , Faisalabad, Pakistan
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Llanos AAM, Warner WA, Luciani S, Lee TY, Bajracharya S, Slovacek S, Roach V, Lamont-Greene M. Gynecologic cancer mortality in Trinidad and Tobago and comparisons of mortality-to-incidence rate ratios across global regions. Cancer Causes Control 2017; 28:1251-1263. [PMID: 28917021 PMCID: PMC5909810 DOI: 10.1007/s10552-017-0961-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 09/08/2017] [Indexed: 12/30/2022]
Abstract
PURPOSE To examine the factors associated with gynecologic cancer mortality risks, to estimate the mortality-to-incidence rate ratios (MIR) in Trinidad and Tobago (TT), and to compare the MIRs to those of select countries. METHODS Data on 3,915 incident gynecologic cancers reported to the National Cancer Registry of TT from 1 January 1995 to 31 December 2009 were analyzed using proportional hazards models to determine factors associated with mortality. MIRs for cervical, endometrial, and ovarian cancers were calculated using cancer registry data (TT), GLOBOCAN 2012 incidence data, and WHO Mortality Database 2012 data (WHO regions and select countries). RESULTS Among the 3,915 incident gynecologic cancers diagnosed in TT during the study period, 1,795 (45.8%) were cervical, 1,259 (32.2%) were endometrial, and 861 (22.0%) were ovarian cancers. Older age, African ancestry, geographic residence, tumor stage, and treatment non-receipt were associated with increased gynecologic cancer mortality in TT. Compared to GLOBOCAN 2012 data, TT MIR estimates for cervical (0.49 vs. 0.53), endometrial (0.61 vs. 0.65), and ovarian cancers (0.32 vs. 0.48) were elevated. While the Caribbean region had intermediate gynecologic cancer MIRs, MIRs in TT were among the highest of the countries examined in the Caribbean region. CONCLUSIONS Given its status as a high-income economy, the relatively high gynecologic cancer MIRs observed in TT are striking. These findings highlight the urgent need for improved cancer surveillance, screening, and treatment for these (and other) cancers in this Caribbean nation.
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Affiliation(s)
- Adana A M Llanos
- Department of Epidemiology, Rutgers School of Public Health and Division of Population Science, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA.
- Department of Epidemiology, Rutgers School of Public Health, 683 Hoes Lane West, Room 211, Piscataway, NJ, 08854, USA.
| | - Wayne A Warner
- Oncology Division, Department of Cell Biology and Physiology, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Silvana Luciani
- Cancer Prevention and Control, Pan American Health Organization, Washington, DC, USA
| | - Tammy Y Lee
- Division of Applied and Advanced Studies in Education, California State University, Los Angeles, CA, USA
| | - Smriti Bajracharya
- Center for Public Health Systems Science, George Warren Brown School of Social Work, Washington University, St. Louis, MO, USA
| | - Simeon Slovacek
- Division of Applied and Advanced Studies in Education, California State University, Los Angeles, CA, USA
| | - Veronica Roach
- Dr. Elizabeth Quamina Cancer Registry, Eric Williams Medical Sciences Complex, Mt. Hope, Trinidad and Tobago
| | - Marjorie Lamont-Greene
- Dr. Elizabeth Quamina Cancer Registry, Eric Williams Medical Sciences Complex, Mt. Hope, Trinidad and Tobago
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Spectrum of genetic variants of BRCA1 and BRCA2 in a German single center study. Arch Gynecol Obstet 2017; 295:1227-1238. [PMID: 28324225 DOI: 10.1007/s00404-017-4330-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/10/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Determination of mutation status of BRCA1 and BRCA2 has become part of the clinical routine. However, the spectrum of genetic variants differs between populations. The aim of this study was to deliver a comprehensive description of all detected variants. METHODS In families fulfilling one of the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC) criteria for genetic testing, one affected was chosen for analysis. DNA of blood lymphocytes was amplified by PCR and prescreened by DHPLC. Aberrant fragments were sequenced. All coding exons and splice sites of BRCA1 and BRCA2 were analyzed. Screening for large rearrangements in both genes was performed by MLPA. RESULTS Of 523 index patients, 121 (23.1%) were found to carry a pathogenic or likely pathogenic (class 4/5) mutation. A variant of unknown significance (VUS) was detected in 73/523 patients (13.9%). Two mutations p.Gln1756Profs*74 and p.Cys61Gly comprised 42.3% (n = 33/78) of all detected pathogenic mutations in BRCA1. Most of the other mutations were unique mutations. The most frequently detected mutation in BRCA2 was p.Val1283Lys (13.9%; n = 6/43). Altogether, 101 different neutral genetic variants were counted in BRCA1 (n = 35) and in BRCA2 (n = 66). CONCLUSION The two most frequently detected mutations are founder mutations in Poland and Czech Republic. More similarities seem to be shared with our direct neighbor countries compared to other European countries. For comparison of the extended genotype, a shared database is needed.
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Warner WA, Morrison RL, Lee TY, Williams TM, Ramnarine S, Roach V, Slovacek S, Maharaj R, Bascombe N, Bondy ML, Ellis MJ, Toriola AT, Roach A, Llanos AAM. Associations among ancestry, geography and breast cancer incidence, mortality, and survival in Trinidad and Tobago. Cancer Med 2015; 4:1742-53. [PMID: 26338451 PMCID: PMC4674001 DOI: 10.1002/cam4.503] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED Breast cancer (BC) is the most common newly diagnosed cancer among women in Trinidad and Tobago (TT) and BC mortality rates are among the highest in the world. Globally, racial/ethnic trends in BC incidence, mortality and survival have been reported. However, such investigations have not been conducted in TT, which has been noted for its rich diversity. In this study, we investigated associations among ancestry, geography and BC incidence, mortality and survival in TT. Data on 3767 incident BC cases, reported to the National Cancer Registry of TT, from 1995 to 2007, were analyzed in this study. Women of African ancestry had significantly higher BC incidence and mortality rates ( INCIDENCE 66.96; MORTALITY 30.82 per 100,000) compared to women of East Indian ( INCIDENCE 41.04, MORTALITY: 14.19 per 100,000) or mixed ancestry ( INCIDENCE 36.72, MORTALITY: 13.80 per 100,000). Geographically, women residing in the North West Regional Health Authority (RHA) catchment area followed by the North Central RHA exhibited the highest incidence and mortality rates. Notable ancestral differences in survival were also observed. Women of East Indian and mixed ancestry experienced significantly longer survival than those of African ancestry. Differences in survival by geography were not observed. In TT, ancestry and geographical residence seem to be strong predictors of BC incidence and mortality rates. Additionally, disparities in survival by ancestry were found. These data should be considered in the design and implementation of strategies to reduce BC incidence and mortality rates in TT.
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Affiliation(s)
- Wayne A Warner
- Oncology Division, Washington University School of Medicine, St. Louis, Missouri.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Robert L Morrison
- Oncology Division, Washington University School of Medicine, St. Louis, Missouri
| | - Tammy Y Lee
- California State University, Los Angeles, California
| | | | - Shelina Ramnarine
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Veronica Roach
- Dr. Elizabeth Quamina Cancer Registry, Eric Williams Medical Sciences Complex, Mt. Hope, Trinidad and Tobago
| | | | - Ravi Maharaj
- Department of Clinical Surgical Sciences, Faculty of Medical Sciences, University of the West Indies, Trinidad and Tobago
| | - Nigel Bascombe
- Department of Clinical Surgical Sciences, Faculty of Medical Sciences, University of the West Indies, Trinidad and Tobago
| | - Melissa L Bondy
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Adetunji T Toriola
- Department of Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Allana Roach
- Public Health and Primary Care Unit, Department of Paraclinical Sciences, Faculty of Medical Sciences, University of the West Indies, Trinidad and Tobago
| | - Adana A M Llanos
- Rutgers School of Public Health and Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
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JIANG HUA, CHEN JIA, SHAN XINJI, LI YING, HE JIANGUO, YANG BEIBEI. Prevalence and range of GJB2 and SLC26A4 mutations in patients with autosomal recessive non-syndromic hearing loss. Mol Med Rep 2014; 10:379-86. [DOI: 10.3892/mmr.2014.2148] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/13/2014] [Indexed: 11/05/2022] Open
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Maxwell KN, Nathanson KL. Common breast cancer risk variants in the post-COGS era: a comprehensive review. Breast Cancer Res 2013; 15:212. [PMID: 24359602 PMCID: PMC3978855 DOI: 10.1186/bcr3591] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Breast cancer has a strong heritable component, with approximately 15% of cases exhibiting a family history of the disease. Mutations in genes such as BRCA1, BRCA2 and TP53 lead to autosomal dominant inherited cancer susceptibility and confer a high lifetime risk of breast cancers. Identification of mutations in these genes through clinical genetic testing enables patients to undergo screening and prevention strategies, some of which provide overall survival benefit. In addition, a number of mutant alleles have been identified in genes such as CHEK2, PALB2, ATM and BRIP1, which often display incomplete penetrance and confer moderate lifetime risks of breast cancer. Studies are underway to determine how to use the identification of mutations in these genes to guide clinical practice. Altogether, however, mutations in high and moderate penetrance genes probably account for approximately 25% of familial breast cancer risk; the remainder may be due to mutations in as yet unidentified genes or lower penetrance variants. Common low penetrance alleles, which have been mainly identified through genome-wide association studies (GWAS), are generally present at 10 to 50% population frequencies and confer less than 1.5-fold increases in breast cancer risk. A number of single nucleotide polymorphisms (SNPs) have been identified and risk associations extensively replicated in populations of European ancestry, the number of which has substantially increased as a result of GWAS performed by the Collaborative Oncological Gene–environment Study consortium. It is now estimated that 28% of familial breast cancer risk is explained by common breast cancer susceptibility loci. In some cases, SNP associations may be specific to different subsets of women with breast cancer, as defined by ethnicity or estrogen receptor status. Although not yet clinically established, it is hoped that identification of common risk variants may eventually allow identification of women at higher risk of breast cancer and enable implementation of breast cancer screening, prevention or treatment strategies that provide clinical benefit.
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Falck E, Klinga-Levan K. Expression patterns of Phf5a/PHF5A and Gja1/GJA1 in rat and human endometrial cancer. Cancer Cell Int 2013; 13:43. [PMID: 23675859 PMCID: PMC3660210 DOI: 10.1186/1475-2867-13-43] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/23/2013] [Indexed: 12/31/2022] Open
Abstract
Endometrial adenocarcinoma is the most frequently diagnosed cancer of the female genital tract in the western world. Studies of complex diseases can be difficult to perform on human tumor samples due to the high genetic heterogeneity in human. The use of rat models is preferable since rat has similarities in pathogenesis and histopathological properties to that of human. A genomic region including the highly conserved Phf5a gene associated to development of EAC has previously been identified in an association study. PHF5A has been suggested to acts as a transcription factor or cofactor in the up regulation of expression of Gja1 gene in the presence of estrogen. It has earlier been shown that the Phf5a gene is down regulated in rat EAC derived cell lines by means of expression microarrays. We analyzed the expression of Phf5a and Gja1 by qPCR, and potential relations between the two genes in EAC tumors and non-malignant cell lines derived from the BDII rat model. In addition, the expression pattern of these genes was compared in rat and human EAC tumor samples. Changes in expression for Phf5a/PHF5A were found in tumors from both rat and human even though the observed pattern was not completely consistent between the two species. By separating rat EAC cell lines according to the genetic background, a significant lower expression of Phf5a in one of the two cross backgrounds was revealed, but not for the other. In contrast to other studies, Phf5a/PHF5A regulation of Gja1/GJA1 was not revealed in this study.
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Affiliation(s)
- Eva Falck
- Systems Biology Research Centre - Tumor biology, School of Life Sciences, University of Skövde, Skövde SE-54128, Sweden.
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Sagong B, Baek JI, Oh SK, Na KJ, Bae JW, Choi SY, Jeong JY, Choi JY, Lee SH, Lee KY, Kim UK. A rapid method for simultaneous screening of multi-gene mutations associated with hearing loss in the Korean population. PLoS One 2013; 8:e57237. [PMID: 23469187 PMCID: PMC3585873 DOI: 10.1371/journal.pone.0057237] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 01/18/2013] [Indexed: 12/20/2022] Open
Abstract
Hearing loss (HL) is a congenital disease with a high prevalence, and patients with hearing loss need early diagnosis for treatment and prevention. The GJB2, MT-RNR1, and SLC26A4 genes have been reported as common causative genes of hearing loss in the Korean population and some mutations of these genes are the most common mutations associated with hearing loss. Accordingly, we developed a method for the simultaneous detection of seven mutations (c.235delC of GJB2, c.439A>G, c.919-2A>G, c.1149+3A>G, c.1229C>T, c.2168A>G of SLC26A4, and m.1555A>G of the MT-RNR1 gene) using multiplex SNaPshot minisequencing to enable rapid diagnosis of hereditary hearing loss. This method was confirmed in patients with hearing loss and used for genetic diagnosis of controls with normal hearing and neonates. We found that 4.06% of individuals with normal hearing and 4.32% of neonates were heterozygous carriers. In addition, we detected that an individual is heterozygous for two different mutations of GJB2 and SLC26A4 gene, respectively and one normal hearing showing the heteroplasmy of m.1555A>G. These genotypes corresponded to those determined by direct sequencing. Overall, we successfully developed a robust and cost-effective diagnosis method that detects common causative mutations of hearing loss in the Korean population. This method will be possible to detect up to 40% causative mutations associated with prelingual HL in the Korean population and serve as a useful genetic technique for diagnosis of hearing loss for patients, carriers, neonates, and fetuses.
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Affiliation(s)
- Borum Sagong
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
| | - Jeong-In Baek
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
| | - Se-Kyung Oh
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
| | - Kyung Jin Na
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Kyungpook National University, Daegu, South Korea
| | - Jae Woong Bae
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
| | - Soo Young Choi
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ji Yun Jeong
- Department of Endocrinology and Metabolism, Kyungpook National University Hospital, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Jae Young Choi
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, South Korea
| | - Sang-Heun Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Kyungpook National University, Daegu, South Korea
| | - Kyu-Yup Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Kyungpook National University, Daegu, South Korea
- * E-mail: (KYL); (UKK)
| | - Un-Kyung Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
- * E-mail: (KYL); (UKK)
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