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Splicing-Disrupting Mutations in Inherited Predisposition to Solid Pediatric Cancer. Cancers (Basel) 2022; 14:cancers14235967. [PMID: 36497448 PMCID: PMC9739414 DOI: 10.3390/cancers14235967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/09/2022] Open
Abstract
The prevalence of hereditary cancer in children was estimated to be very low until recent studies suggested that at least 10% of pediatric cancer patients carry a germline mutation in a cancer predisposition gene. A significant proportion of pathogenic variants associated with an increased risk of hereditary cancer are variants affecting splicing. RNA splicing is an essential process involved in different cellular processes such as proliferation, survival, and differentiation, and alterations in this pathway have been implicated in many human cancers. Hereditary cancer genes are highly susceptible to splicing mutations, and among them there are several genes that may contribute to pediatric solid tumors when mutated in the germline. In this review, we have focused on the analysis of germline splicing-disrupting mutations found in pediatric solid tumors, as the discovery of pathogenic splice variants in pediatric cancer is a growing field for the development of personalized therapies. Therapies developed to correct aberrant splicing in cancer are also discussed as well as the options to improve the diagnostic yield based on the increase in the knowledge in splicing.
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Fitzpatrick MJ, Boiocchi L, Fathi AT, Brunner AM, Hasserjian RP, Nardi V. Correlation of p53 immunohistochemistry with
TP53
mutational status and overall survival in newly diagnosed acute myeloid leukemia. Histopathology 2022; 81:496-510. [DOI: 10.1111/his.14726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/28/2022] [Accepted: 07/10/2022] [Indexed: 11/26/2022]
Affiliation(s)
| | - Leonardo Boiocchi
- Department of Pathology and Laboratory Medicine Memorial Sloan Kettering Cancer Center New York NY USA
| | - Amir T. Fathi
- Department of Hematology/Oncology Massachusetts General Hospital Boston MA USA
| | - Andrew M. Brunner
- Department of Hematology/Oncology Massachusetts General Hospital Boston MA USA
| | | | - Valentina Nardi
- Department of Pathology Massachusetts General Hospital Boston MA USA
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de Andrade KC, Frone MN, Wegman-Ostrosky T, Khincha PP, Kim J, Amadou A, Santiago KM, Fortes FP, Lemonnier N, Mirabello L, Stewart DR, Hainaut P, Kowalski LP, Savage SA, Achatz MI. Variable population prevalence estimates of germline TP53 variants: A gnomAD-based analysis. Hum Mutat 2018; 40:97-105. [PMID: 30352134 DOI: 10.1002/humu.23673] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 10/09/2018] [Accepted: 10/20/2018] [Indexed: 12/27/2022]
Abstract
Reports of variable cancer penetrance in Li-Fraumeni syndrome (LFS) have raised questions regarding the prevalence of pathogenic germline TP53 variants. We previously reported higher-than-expected population prevalence estimates in sequencing databases composed of individuals unselected for cancer history. This study aimed to expand and further evaluate the prevalence of pathogenic and likely pathogenic germline TP53 variants in the gnomAD dataset (version r2.0.2, n = 138,632). Variants were selected and classified based on our previously published algorithm and compared with alternative estimates based on three different classification databases: ClinVar, HGMD, and the UMD_TP53 database. Conservative prevalence estimates of pathogenic and likely pathogenic TP53 variants were within the range of one carrier in 3,555-5,476 individuals. Less stringent classification increased the approximate prevalence to one carrier in every 400-865 individuals, mainly due to the inclusion of the controvertible p.N235S, p.V31I, and p.R290H variants. This study shows a higher-than-expected population prevalence of pathogenic and likely pathogenic germline TP53 variants even with the most conservative estimates. However, these estimates may not necessarily reflect the prevalence of the classical LFS phenotype, which is based upon family history of cancer. Comprehensive approaches are needed to better understand the interplay of germline TP53 variant classification, prevalence estimates, cancer penetrance, and LFS-associated phenotype.
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Affiliation(s)
- Kelvin C de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland.,International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Megan N Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Talia Wegman-Ostrosky
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland.,Division of Research, National Cancer Institute, Mexico City, Mexico
| | - Payal P Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Amina Amadou
- Institute for Advanced Biosciences, Inserm U 1209 CNRS UMR 5309 Université Grenoble Alpes, Site Santé, Allée des Alpes, La Tronche, France
| | - Karina M Santiago
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Fernanda P Fortes
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Nathanaël Lemonnier
- Institute for Advanced Biosciences, Inserm U 1209 CNRS UMR 5309 Université Grenoble Alpes, Site Santé, Allée des Alpes, La Tronche, France
| | - Lisa Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Pierre Hainaut
- Institute for Advanced Biosciences, Inserm U 1209 CNRS UMR 5309 Université Grenoble Alpes, Site Santé, Allée des Alpes, La Tronche, France
| | - Luiz P Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, AC Camargo Cancer Center, São Paulo, Brazil
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Maria I Achatz
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland.,Centro de Oncologia, Sírio-Libanês Hospital, São Paulo, Brazil
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de Andrade KC, Mirabello L, Stewart DR, Karlins E, Koster R, Wang M, Gapstur SM, Gaudet MM, Freedman ND, Landi MT, Lemonnier N, Hainaut P, Savage SA, Achatz MI. Higher-than-expected population prevalence of potentially pathogenic germline TP53 variants in individuals unselected for cancer history. Hum Mutat 2017; 38:1723-1730. [PMID: 28861920 DOI: 10.1002/humu.23320] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/19/2017] [Accepted: 08/28/2017] [Indexed: 01/09/2023]
Abstract
Li-Fraumeni syndrome (LFS) is an autosomal-dominant cancer predisposition disorder associated with pathogenic germline variants in TP53, with a high penetrance over an individual's lifetime. The actual population prevalence of pathogenic germline TP53 mutations is still unclear, most likely due to biased selection of cancer affected families. The aim of this study was to estimate the population prevalence of potentially pathogenic TP53 exonic variants in three sequencing databases, totaling 63,983 unrelated individuals. Potential pathogenicity was defined using an original algorithm combining bioinformatic prediction tools, suggested clinical significance, and functional data. We identified 34 different potentially pathogenic TP53 variants in 131 out of 63,983 individuals (0.2%). Twenty-eight (82%) of these variants fell within the DNA-binding domain of TP53, with an enrichment for specific variants that were not previously identified as LFS mutation hotspots, such as the p.R290H and p.N235S variants. Our findings reveal that the population prevalence of potentially pathogenic TP53 variants may be up to 10 times higher than previously estimated from family-based studies. These results point to the need for further studies aimed at evaluating cancer penetrance modifiers as well as the risk associated between cancer and rare TP53 variants.
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Affiliation(s)
- Kelvin César de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA.,International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Lisa Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Eric Karlins
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research Inc., Department of Health and Human Services, Bethesda, Maryland, USA
| | - Roelof Koster
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research Inc., Department of Health and Human Services, Bethesda, Maryland, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Mia M Gaudet
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Neal D Freedman
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Maria Teresa Landi
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Nathanaël Lemonnier
- Institute for Advanced Biosciences, Inserm U 1209 CNRS UMR 5309, Université Grenoble Alpes, Allée des Alpes, La Tronche, France
| | - Pierre Hainaut
- Institute for Advanced Biosciences, Inserm U 1209 CNRS UMR 5309, Université Grenoble Alpes, Allée des Alpes, La Tronche, France
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Maria Isabel Achatz
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
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Yurgelun MB, Masciari S, Joshi VA, Mercado RC, Lindor NM, Gallinger S, Hopper JL, Jenkins MA, Buchanan DD, Newcomb PA, Potter JD, Haile RW, Kucherlapati R, Syngal S. Germline TP53 Mutations in Patients With Early-Onset Colorectal Cancer in the Colon Cancer Family Registry. JAMA Oncol 2016; 1:214-21. [PMID: 26086041 DOI: 10.1001/jamaoncol.2015.0197] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
IMPORTANCE Li-Fraumeni syndrome, usually characterized by germline TP53 mutations, is associated with markedly elevated lifetime risks of multiple cancers, and has been linked to an increased risk of early-onset colorectal cancer. OBJECTIVE To examine the frequency of germline TP53 alterations in patients with early-onset colorectal cancer. DESIGN, SETTING, AND PARTICIPANTS This was a multicenter cross-sectional cohort study of individuals recruited to the Colon Cancer Family Registry (CCFR) from 1998 through 2007 (genetic testing data updated as of January 2015). Both population-based and clinic-based patients in the United States, Canada, Australia, and New Zealand were recruited to the CCFR. Demographic information, clinical history, and family history data were obtained at enrollment. Biospecimens were collected from consenting probands and families, including microsatellite instability and DNA mismatch repair immunohistochemistry results. A total of a 510 individuals diagnosed as having colorectal cancer at age 40 years or younger and lacking a known hereditary cancer syndrome were identified from the CCFR as being potentially eligible. Fifty-three participants were excluded owing to subsequent identification of germline mutations in DNA mismatch repair genes (n = 47) or biallelic MUTYH mutations (n = 6). INTERVENTIONS Germline sequencing of the TP53 gene was performed. Identified TP53 alterations were assessed for pathogenicity using literature and international mutation database searches and in silico prediction models. MAIN OUTCOMES AND MEASURES Frequency of nonsynonymous germline TP53 alterations. RESULTS Among 457 eligible participants (314, population-based; 143, clinic-based; median age at diagnosis, 36 years [range, 15-40 years]), 6 (1.3%; 95% CI, 0.5%-2.8%) carried germline missense TP53 alterations, none of whom met clinical criteria for Li-Fraumeni syndrome. Four of the identified TP53 alterations have been previously described in the literature in probands with clinical features of Li-Fraumeni syndrome, and 2 were novel alterations. CONCLUSIONS AND RELEVANCE In a large cohort of patients with early-onset colorectal cancer, germline TP53 mutations were detected at a frequency comparable with the published prevalence of germline APC mutations in colorectal cancer. With the increasing use of multigene next-generation sequencing panels in hereditary cancer risk assessment, clinicians will be faced with the challenge of interpreting the biologic and clinical significance of germline TP53 mutations in families whose phenotypes are atypical for Li-Fraumeni syndrome.
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Alshatwi AA, Shafi G, Hasan TN, Syed NA, Al-Hazzani AA, Alsaif MA, Alsaif AA. Differential expression profile and genetic variants of microRNAs sequences in breast cancer patients. PLoS One 2012; 7:e30049. [PMID: 22363415 PMCID: PMC3282723 DOI: 10.1371/journal.pone.0030049] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 12/08/2011] [Indexed: 11/25/2022] Open
Abstract
The technology available for cancer diagnosis and prognosis is not yet satisfactory at the molecular level, and requires further improvements. Micro RNAs (miRNAs) have been recently reported as useful biomarkers in diseases including cancer. We performed a miRNA expression profiling study using peripheral blood from breast cancer patients to detect and identify characteristic patterns. A total of 100 breast cancer patients and 89 healthy patients were recruited for miRNA genotyping and expression profiling. We found that hs-miR-196a2 in premenopausal patients, and hs-miR-499, hs-miR-146a and hs-miR-196a2 in postmenopausal patients, may discriminate breast cancer patients from healthy individuals. In addition, we found a significant association between two microRNA polymorphisms (hs-miR-196a2 and hs-miR-499) and breast cancer risk. However, no significant association between the hs-miR-146a gene and breast cancer risk was found. In summary, the study demonstrates that peripheral blood miRNAs and their expression and genotypic profiles can be developed as biomarkers for early diagnosis and prognosis of breast cancer.
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Affiliation(s)
- Ali A Alshatwi
- Molecular Cancer Biology Research Lab (MCBRL), Department of Food Sciences and Nutrition, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia.
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Pelletier C, Weidhaas JB. MicroRNA binding site polymorphisms as biomarkers of cancer risk. Expert Rev Mol Diagn 2010; 10:817-29. [PMID: 20843204 DOI: 10.1586/erm.10.59] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are well established as global gene regulators and thus, slight alterations in miRNA levels as well as their ability to regulate their targets may cause important cellular changes leading to cancer risk. 3´ untranslated region (UTR) miRNA binding site single nucleotide polymorphisms (SNPs) have added another layer of possible genetic variation involved in the complex process of oncogenesis. Identifying these key genetically inherited effectors of miRNA functioning has improved our understanding of the complexity of disease. Interest in the field has grown rapidly in only the last 5 years, with several studies reporting on the role of 3´UTR binding site SNPs as genetic markers of increased cancer susceptibility, as well as biomarkers of cancer type, outcome and response to therapy. Currently, there are numerous known miRNA binding site SNPs associated with multiple cancer subtypes.
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Affiliation(s)
- Cory Pelletier
- Yale University School of Medicine, 15 York Street, New Haven, CT 06510 USA
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Song F, Zheng H, Liu B, Wei S, Dai H, Zhang L, Calin GA, Hao X, Wei Q, Zhang W, Chen K. An miR-502-binding site single-nucleotide polymorphism in the 3'-untranslated region of the SET8 gene is associated with early age of breast cancer onset. Clin Cancer Res 2009; 15:6292-300. [PMID: 19789321 DOI: 10.1158/1078-0432.ccr-09-0826] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE MicroRNAs regulate gene expression by binding to the 3'-untranslated region (UTR) of target genes. Single-nucleotide polymorphisms of critical genes may affect their regulation by microRNAs. We have identified a single-nucleotide polymorphism within the miR-502 seed binding region in the 3'-UTR of the SET8 gene. SET8 methylates TP53 and regulates genome stability. We investigated the role of this SET8 single-nucleotide polymorphism and in concert with the TP53 codon 72 single-nucleotide polymorphism in the propensity for onset of breast cancer. EXPERIMENTAL DESIGN We measured the SET8 single-nucleotide polymorphisms in a case-control study on 1,110 breast cancer cases and 1,097 controls. RESULTS The SET8 CC and TP53 GG genotypes were independently associated with an earlier age of breast cancer onset in an allele-dose-dependent manner (for SET8, 52.2 years for TT, 51.4 for TC, and 49.5 for CC; and for TP53, 53.1 years for CC, 51.5 for GC, 50.7 for GG). Individuals with combined SET8 CC and TP53 GG genotypes developed cancer at a median age of 47.7 years as compared with 54.6 years for individuals with combined SET8 TT and TP53 CC genotypes. In the 51 breast cancer tissue samples tested, the SET8 CC genotype was associated with reduced SET8, but not miR-502, transcript levels. CONCLUSIONS These data suggest that the miR-502-binding site single-nucleotide polymorphism in the 3'-UTR of SET8 modulates SET8 expression and contributes to the early development of breast cancer, either independently or together with the TP53 codon 72 single-nucleotide polymorphism. Larger studies with multiethnic groups are warranted to validate our findings.
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Affiliation(s)
- Fengju Song
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Hospital and Institute, Tianjin, People's Republic of China
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Cheng FWT, To KF, Lee V, Shing MMK, Leung WK, Li CK. One man, one disease? BMJ Case Rep 2009; 2009:bcr07.2008.0516. [PMID: 21686767 DOI: 10.1136/bcr.07.2008.0516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
We report the case of a 12-year-old girl with a strong family history of malignancy who presented with immature teratoma and gliomatosis peritonei. Despite first and second line chemotherapy, the disease ran an unusually refractory course. Although the presentation was not the typical tumour presentation of Li-Fraumeni syndrome (LFS), we proceeded to undertake tumour genetic testing of the patient and her parents. LFS was diagnosed in this patient and her father with a sequence variation of CGG>TGG, R248W, which is one of the most common transcriptionally inactive mutations detected in LFS. Genetic counselling was offered to the father. A tumour screening programme and genetic screening for the p53 gene mutation for the surviving family members can be offered once consent is obtained from the father. This case illustrates the importance of cancer genetic study, even if the tumour presentation is not typical for any familial cancer syndrome.
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Affiliation(s)
- Frankie Wai Tsoi Cheng
- Prince of Wales Hospital, The Chinese University of Hong Kong, Department of Paediatrics, Shatin, New Territories, Hong Kong
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