1
|
Walker CJ, Goodfellow PJ. Traditional Approaches to Molecular Genetic Analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 943:99-118. [DOI: 10.1007/978-3-319-43139-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
2
|
Xu J, Qian Y, Ye M, Fu Z, Jia X, Li W, Xu P, Lv M, Huang L, Wang L, Ruan H, Lv J. Distinct expression profile of lncRNA in endometrial carcinoma. Oncol Rep 2016; 36:3405-3412. [PMID: 27748922 DOI: 10.3892/or.2016.5173] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 09/12/2016] [Indexed: 11/05/2022] Open
Abstract
Endometrial carcinoma (EC) is the most common malignancy in women. Dispite its prevalence, the prognosis of endometrial carcinoma still relies on conventional histological type, grade and invasion information. Its morbidity is still increasing and the outcome is very poor. To the best of our knowledge, hormonal imbalance and/or molecular genetic alterations are the main cause of EC. However, the alterations of lncRNAs which accounts for approximately 4/5 of human transcripts are still poorly understood. In the present study, using the RiboArray™ Custom Array, we studied the expression profiles of lncRNA in EC as compared to normal endometrium (NE) to find potential core lncRNAs for the diagnosis of EC. We found the potential core lncRNA by GO, KEGG, lncRNA and mRNA co-expression network. The potential functional lncRNAs were further detected by qPCR to validate the microarray results. A total of 172 lncRNAs and 188 mRNAs were found to be differentially expressed between type Ⅰ EC and the NE samples (fold change >1.5). qPCR validation showed good consistency with the microarray data. GO, pathway analysis, the lncRNA and mRNA co-expression network as well as the TCGA data revealed that 6 lncRNAs (KIAA0087, RP11-501O2, FAM212B-AS1, LOC102723552, RP11-140I24 and RP11-600K151) may be the core regulators of endometrial carcinogenesis. The potential core lncRNAs revealed by the mRNA and lncRNA co-expression network might be helpful to explore potential early diagnostic and therapeutic targets for EC.
Collapse
Affiliation(s)
- Juan Xu
- Department of Obstetrics and Gynecology, Affiliated Obstetrics and Gynecology Hospital, Nanjing Medical University, Nanjing 210004, P.R. China
| | - Yujia Qian
- Department of Obstetrics and Gynecology, Affiliated Obstetrics and Gynecology Hospital, Nanjing Medical University, Nanjing 210004, P.R. China
| | - Min Ye
- Department of Breast Surgery, Affiliated Obstetrics and Gynecology Hospital, Nanjing Medical University, Nanjing 210004, P.R. China
| | - Ziyi Fu
- Nanjing Maternity and Child Health Medical Institute, Affiliated Obstetrics and Gynecology Hospital, Nanjing Medical University, Nanjing 210004, P.R. China
| | - Xuemei Jia
- Department of Obstetrics and Gynecology, Affiliated Obstetrics and Gynecology Hospital, Nanjing Medical University, Nanjing 210004, P.R. China
| | - Wenqu Li
- Department of Obstetrics and Gynecology, Affiliated Obstetrics and Gynecology Hospital, Nanjing Medical University, Nanjing 210004, P.R. China
| | - Pengfei Xu
- Nanjing Maternity and Child Health Medical Institute, Affiliated Obstetrics and Gynecology Hospital, Nanjing Medical University, Nanjing 210004, P.R. China
| | - Mingming Lv
- Department of Breast Surgery, Affiliated Obstetrics and Gynecology Hospital, Nanjing Medical University, Nanjing 210004, P.R. China
| | - Lei Huang
- First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Luyu Wang
- Department of Breast Surgery, Affiliated Obstetrics and Gynecology Hospital, Nanjing Medical University, Nanjing 210004, P.R. China
| | - Hongjie Ruan
- Department of Obstetrics and Gynecology, Affiliated Obstetrics and Gynecology Hospital, Nanjing Medical University, Nanjing 210004, P.R. China
| | - Juan Lv
- Department of Obstetrics and Gynecology, Affiliated Obstetrics and Gynecology Hospital, Nanjing Medical University, Nanjing 210004, P.R. China
| |
Collapse
|
3
|
Drost M, Koppejan H, de Wind N. Inactivation of DNA mismatch repair by variants of uncertain significance in the PMS2 gene. Hum Mutat 2013; 34:1477-80. [PMID: 24027009 DOI: 10.1002/humu.22426] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 08/05/2013] [Indexed: 01/14/2023]
Abstract
Lynch syndrome (LS) is a common cancer predisposition caused by an inactivating mutation in one of four DNA mismatch repair (MMR) genes. Frequently a variant of uncertain significance (VUS), rather than an obviously pathogenic mutation, is identified in one of these genes. The inability to define pathogenicity of such variants precludes targeted healthcare. Here, we have modified a cell-free assay to test VUS in the MMR gene PMS2 for functional activity. We have analyzed nearly all VUS in PMS2 found thus far and describe loss of MMR activity for five, suggesting the applicability of the assay for diagnosis of LS.
Collapse
Affiliation(s)
- Mark Drost
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | |
Collapse
|
4
|
Niessen RC, Kleibeuker JH, Westers H, Jager POJ, Rozeveld D, Bos KK, Boersma-van Ek W, Hollema H, Sijmons RH, Hofstra RMW. PMS2 involvement in patients suspected of Lynch syndrome. Genes Chromosomes Cancer 2009; 48:322-9. [PMID: 19132747 DOI: 10.1002/gcc.20642] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
It is well-established that germline mutations in the mismatch repair genes MLH1, MSH2, and MSH6 cause Lynch syndrome. However, mutations in these three genes do not account for all Lynch syndrome (suspected) families. Recently, it was shown that germline mutations in another mismatch repair gene, PMS2, play a far more important role in Lynch syndrome than initially thought. To explore this further, we determined the prevalence of pathogenic germline PMS2 mutations in a series of Lynch syndrome-suspected patients. Ninety-seven patients who had early-onset microsatellite instable colorectal or endometrial cancer, or multiple Lynch syndrome-associated tumors and/or were from an Amsterdam Criteria II-positive family were selected for this study. These patients carried no pathogenic germline mutation in MLH1, MSH2, or MSH6. When available, tumors were investigated for immunohistochemical staining (IHC) for PMS2. PMS2 was screened in all patients by exon-by-exon sequencing. We identified four patients with a pathogenic PMS2 mutation (4%) among the 97 patients we selected. IHC of PMS2 was informative in one of the mutation carriers, and in this case, the tumor showed loss of PMS2 expression. In conclusion, our study confirms the finding of previous studies that PMS2 is more frequently involved in Lynch syndrome than originally expected.
Collapse
Affiliation(s)
- Renée C Niessen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Karlan BY, Berchuck A, Mutch D. The Role of Genetic Testing for Cancer Susceptibility in Gynecologic Practice. Obstet Gynecol 2007; 110:155-67. [PMID: 17601911 DOI: 10.1097/01.aog.0000269050.79143.84] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Genetic counseling and testing for inherited disorders are part of every obstetrician-gynecologist's practice. Family history, ethnicity, and race are routinely evaluated as a part of the prenatal assessment. The discovery of genes responsible for inherited cancer susceptibility and the wide availability of clinical genetic testing for mutations in these genes have made similar assessments an integral part of gynecologic practice as well. The indications for genetic testing for mutations in BRCA1, BRCA2, and the mismatch repair genes responsible for the hereditary nonpolyposis colon cancer (HNPCC) syndrome need to be individualized. As in obstetrics, genetic counseling can provide critical assessment of the family history to help determine the likelihood of an inherited cancer susceptibility syndrome and the appropriateness of genetic testing. The subsequent clinical recommendations for mutation carriers need to take into account the patient's age, desire for future childbearing, and other medical history when prescribing screening interventions or prophylactic surgery. Practical applications of genetic testing for cancer susceptibility have the ability to reduce the burden of hereditary cancers by saving lives, decreasing medical morbidities, and reducing psychological stress.
Collapse
Affiliation(s)
- Beth Y Karlan
- Women's Cancer Research Institute, Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of Los Angeles, Los Angeles, California 90048, USA.
| | | | | |
Collapse
|
6
|
Hayward BE, De Vos M, Valleley EMA, Charlton RS, Taylor GR, Sheridan E, Bonthron DT. Extensive gene conversion at the PMS2 DNA mismatch repair locus. Hum Mutat 2007; 28:424-30. [PMID: 17253626 DOI: 10.1002/humu.20457] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Mutations of the PMS2 DNA repair gene predispose to a characteristic range of malignancies, with either childhood onset (when both alleles are mutated) or a partially penetrant adult onset (if heterozygous). These mutations have been difficult to detect, due to interference from a family of pseudogenes located on chromosome 7. One of these, the PMS2CL pseudogene, lies within a 100-kb inverted duplication (inv dup), 700 kb centromeric to PMS2 itself on 7p22. Here, we show that the reference genomic sequences cannot be relied upon to distinguish PMS2 from PMS2CL, because of sequence transfer between the two loci. The 7p22 inv dup occurred prior to the divergence of modern ape species (15 million years ago [Mya]), but has undergone extensive sequence homogenization. This process appears to be ongoing, since there is considerable allelic diversity within the duplicated region, much of it derived from sequence exchange between PMS2 and PMS2CL. This sequence diversity can result in both false-positive and false-negative mutation analysis at this locus. Great caution is still needed in the design and interpretation of PMS2 mutation screens.
Collapse
Affiliation(s)
- Bruce E Hayward
- Leeds Institute of Molecular Medicine, University of Leeds and Yorkshire Regional Genetics Service, St James's University Hospital, Leeds, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
7
|
Thompson E, Meldrum CJ, Crooks R, McPhillips M, Thomas L, Spigelman AD, Scott RJ. Hereditary non-polyposis colorectal cancer and the role of hPMS2 and hEXO1 mutations. Clin Genet 2004; 65:215-25. [PMID: 14756672 DOI: 10.1111/j.1399-0004.2004.00214.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hereditary non-polyposis colorectal cancer (HNPCC) is an autosomal dominant, inherited condition that is characterized primarily by the development of early-onset colorectal cancer and a number of other epithelial malignancies. The underlying genetic basis of the disease is associated with a breakdown of DNA-mismatch repair. There are many genes involved in DNA-mismatch repair, and five of them have been implicated in HNPCC. Two of the genes (hMSH2 and hMLH1) account for the majority of HNPCC families (approximately 60%), and it is not known what the exact contributions of the remaining three genes (hPMS1, hPMS2, and hMSH6) are in relation to this condition. In addition, a sixth gene (hEXO1) has been associated with a disease phenotype that is consistent with HNPCC. Current estimates suggest that all four of these genes, combined, may account for up to 5% of families. In this report, we examine the contribution of hPMS2 and hEXO1 to a well-defined set of families that fulfill the diagnostic criteria for HNPCC. The genes, hPMS2 and hEXO1, were studied by denaturing high performance liquid chromatography (DHPLC) analysis in 21 families that have previously been determined not to have mutations in hMSH2 or hMLH1. hPMS2 accounts for a small proportion of HNPCC families, and none were deemed to be associated with hEXO1. Mutations in hPMS2 appear to account for a small proportion of families adhering to the Amsterdam II criteria, whereas hEXO1 does not appear to be associated with HNPCC.
Collapse
Affiliation(s)
- E Thompson
- Discipline of Medical Genetics, Faculty of Health, University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
| | | | | | | | | | | | | |
Collapse
|
8
|
|
9
|
De Vos M, Hayward BE, Picton S, Sheridan E, Bonthron DT. Novel PMS2 pseudogenes can conceal recessive mutations causing a distinctive childhood cancer syndrome. Am J Hum Genet 2004; 74:954-64. [PMID: 15077197 PMCID: PMC1181988 DOI: 10.1086/420796] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2004] [Accepted: 02/10/2004] [Indexed: 12/29/2022] Open
Abstract
We investigated a family with an autosomal recessive syndrome of cafe-au-lait patches and childhood malignancy, notably supratentorial primitive neuroectodermal tumor. There was no cancer predisposition in heterozygotes; nor was there bowel cancer in any individual. However, autozygosity mapping indicated linkage to a region of 7p22 surrounding the PMS2 mismatch-repair gene. Sequencing of genomic PCR products initially failed to identify a PMS2 mutation. Genome searches then revealed a previously unrecognized PMS2 pseudogene, corresponding to exons 9-15, within a 100-kb inverted duplication situated 600 kb centromeric from PMS2 itself. This information allowed a redesigned sequence analysis, identifying a homozygous mutation (R802X) in PMS2 exon 14. Furthermore, in the family with Turcot syndrome, in which the first inherited PMS2 mutation (R134X) was described, a further truncating mutation was identified on the other allele, in exon 13. Further whole-genome analysis shows that the complexity of PMS2 pseudogenes is greater than appreciated and may have hindered previous mutation studies. Several previously reported PMS2 polymorphisms are, in fact, pseudogene sequence variants. Although PMS2 mutations may be rare in colorectal cancer, they appear, for the most part, to behave as recessive traits. For technical reasons, their involvement in childhood cancer, particularly in primitive neuroectodermal tumor, may have been underestimated.
Collapse
Affiliation(s)
- Michel De Vos
- Molecular Medicine Unit, University of Leeds, and Departments of Paediatric Oncology and Clinical Genetics, St. James’s University Hospital, Leeds, United Kingdom
| | - Bruce E. Hayward
- Molecular Medicine Unit, University of Leeds, and Departments of Paediatric Oncology and Clinical Genetics, St. James’s University Hospital, Leeds, United Kingdom
| | - Susan Picton
- Molecular Medicine Unit, University of Leeds, and Departments of Paediatric Oncology and Clinical Genetics, St. James’s University Hospital, Leeds, United Kingdom
| | - Eamonn Sheridan
- Molecular Medicine Unit, University of Leeds, and Departments of Paediatric Oncology and Clinical Genetics, St. James’s University Hospital, Leeds, United Kingdom
| | - David T. Bonthron
- Molecular Medicine Unit, University of Leeds, and Departments of Paediatric Oncology and Clinical Genetics, St. James’s University Hospital, Leeds, United Kingdom
| |
Collapse
|