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McCarthy-Leo CE, Brush GS, Pique-Regi R, Luca F, Tainsky MA, Finley RL. Comprehensive analysis of the functional impact of single nucleotide variants of human CHEK2. PLoS Genet 2024; 20:e1011375. [PMID: 39146382 PMCID: PMC11349238 DOI: 10.1371/journal.pgen.1011375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 08/27/2024] [Accepted: 07/25/2024] [Indexed: 08/17/2024] Open
Abstract
Loss of function mutations in the checkpoint kinase gene CHEK2 are associated with increased risk of breast and other cancers. Most of the 3,188 unique amino acid changes that can result from non-synonymous single nucleotide variants (SNVs) of CHEK2, however, have not been tested for their impact on the function of the CHEK2-enocded protein (CHK2). One successful approach to testing the function of variants has been to test for their ability to complement mutations in the yeast ortholog of CHEK2, RAD53. This approach has been used to provide functional information on over 100 CHEK2 SNVs and the results align with functional assays in human cells and known pathogenicity. Here we tested all but two of the 4,887 possible SNVs in the CHEK2 open reading frame for their ability to complement RAD53 mutants using a high throughput technique of deep mutational scanning (DMS). Among the non-synonymous changes, 770 were damaging to protein function while 2,417 were tolerated. The results correlate well with previous structure and function data and provide a first or additional functional assay for all the variants of uncertain significance identified in clinical databases. Combined, this approach can be used to help predict the pathogenicity of CHEK2 variants of uncertain significance that are found in susceptibility screening and could be applied to other cancer risk genes.
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Affiliation(s)
- Claire E. McCarthy-Leo
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - George S. Brush
- Department of Oncology, Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Michael A. Tainsky
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Oncology, Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Russell L. Finley
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
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Zhu JW, Charkhchi P, Adekunte S, Akbari MR. What Is Known about Breast Cancer in Young Women? Cancers (Basel) 2023; 15:cancers15061917. [PMID: 36980802 PMCID: PMC10047861 DOI: 10.3390/cancers15061917] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Breast cancer (BC) is the second leading cause of cancer-related death in women under the age of 40 years worldwide. In addition, the incidence of breast cancer in young women (BCYW) has been rising. Young women are not the focus of screening programs and BC in younger women tends to be diagnosed in more advanced stages. Such patients have worse clinical outcomes and treatment complications compared to older patients. BCYW has been associated with distinct tumour biology that confers a worse prognosis, including poor tumour differentiation, increased Ki-67 expression, and more hormone-receptor negative tumours compared to women >50 years of age. Pathogenic variants in cancer predisposition genes such as BRCA1/2 are more common in early-onset BC compared to late-onset BC. Despite all these differences, BCYW remains poorly understood with a gap in research regarding the risk factors, diagnosis, prognosis, and treatment. Age-specific clinical characteristics or outcomes data for young women are lacking, and most of the standard treatments used in this subpopulation currently are derived from older patients. More age-specific clinical data and treatment options are required. In this review, we discuss the epidemiology, clinicopathologic characteristics, outcomes, treatments, and special considerations of breast cancer in young women. We also underline future directions and highlight areas that require more attention in future studies.
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Affiliation(s)
- Jie Wei Zhu
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON M5G 2C4, Canada
- Department of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Parsa Charkhchi
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Shadia Adekunte
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Mohammad R Akbari
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON M5G 2C4, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
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3
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Boonen RA, Vreeswijk MP, van Attikum H. CHEK2 variants: linking functional impact to cancer risk. Trends Cancer 2022; 8:759-770. [DOI: 10.1016/j.trecan.2022.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/23/2022]
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Boonen RA, Wiegant WW, Celosse N, Vroling B, Heijl S, Kote-Jarai Z, Mijuskovic M, Cristea S, Solleveld-Westerink N, van Wezel T, Beerenwinkel N, Eeles R, Devilee P, Vreeswijk MP, Marra G, van Attikum H. Functional Analysis Identifies Damaging CHEK2 Missense Variants Associated with Increased Cancer Risk. Cancer Res 2022; 82:615-631. [PMID: 34903604 PMCID: PMC9359737 DOI: 10.1158/0008-5472.can-21-1845] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/14/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023]
Abstract
Heterozygous carriers of germline loss-of-function variants in the tumor suppressor gene checkpoint kinase 2 (CHEK2) are at an increased risk for developing breast and other cancers. While truncating variants in CHEK2 are known to be pathogenic, the interpretation of missense variants of uncertain significance (VUS) is challenging. Consequently, many VUS remain unclassified both functionally and clinically. Here we describe a mouse embryonic stem (mES) cell-based system to quantitatively determine the functional impact of 50 missense VUS in human CHEK2. By assessing the activity of human CHK2 to phosphorylate one of its main targets, Kap1, in Chek2 knockout mES cells, 31 missense VUS in CHEK2 were found to impair protein function to a similar extent as truncating variants, while 9 CHEK2 missense VUS resulted in intermediate functional defects. Mechanistically, most VUS impaired CHK2 kinase function by causing protein instability or by impairing activation through (auto)phosphorylation. Quantitative results showed that the degree of CHK2 kinase dysfunction correlates with an increased risk for breast cancer. Both damaging CHEK2 variants as a group [OR 2.23; 95% confidence interval (CI), 1.62-3.07; P < 0.0001] and intermediate variants (OR 1.63; 95% CI, 1.21-2.20; P = 0.0014) were associated with an increased breast cancer risk, while functional variants did not show this association (OR 1.13; 95% CI, 0.87-1.46; P = 0.378). Finally, a damaging VUS in CHEK2, c.486A>G/p.D162G, was also identified, which cosegregated with familial prostate cancer. Altogether, these functional assays efficiently and reliably identified VUS in CHEK2 that associate with cancer. SIGNIFICANCE Quantitative assessment of the functional consequences of CHEK2 variants of uncertain significance identifies damaging variants associated with increased cancer risk, which may aid in the clinical management of patients and carriers.
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Affiliation(s)
- Rick A.C.M. Boonen
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Wouter W. Wiegant
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Nandi Celosse
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Bas Vroling
- Bio-Prodict, Nijmegen, the Netherlands
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Center, Nijmegen, the Netherlands
| | | | | | - Martina Mijuskovic
- The Institute of Cancer Research, London, United Kingdom
- Illumina Cambridge Ltd., Cambridge, United Kingdom
| | - Simona Cristea
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Niko Beerenwinkel
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Rosalind Eeles
- The Institute of Cancer Research, London, United Kingdom
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Maaike P.G. Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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Ibragimova MK, Tsyganov MM, Litviakov NV. Molecular-Genetic Portrait of Breast Cancer with Triple Negative Phenotype. Cancers (Basel) 2021; 13:cancers13215348. [PMID: 34771512 PMCID: PMC8582512 DOI: 10.3390/cancers13215348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/21/2021] [Indexed: 12/31/2022] Open
Abstract
Simple Summary Breast cancer is a genetically heterogeneous disease with different molecular biological and clinical characteristics. The available knowledge about the genetic heterogeneity of the most aggressive molecular subtype of breast cancer—triple-negative—has led to discoveries in drug treatment. Identification of the molecular-genetic phenotype of breast cancer is an important prognostic factor of the disease and allows personalization of the patient’s treatment. Abstract Understanding of the genetic mechanisms and identification of the biological markers of tumor progression that form the individual molecular phenotype of transformed cells can characterize the degree of tumor malignancy, the ability to metastasize, the hormonal sensitivity, and the effectiveness of chemotherapy, etc. Breast cancer (BC) is a genetically heterogeneous disease with different molecular biological and clinical characteristics. The available knowledge about the genetic heterogeneity of the most aggressive molecular subtype of breast cancer—triple-negative (TN)—has led to discoveries in drug treatment, including the use of DNA damaging agents (platinum and PARP inhibitors) for these tumors, as well as the use of immunotherapy. Most importantly, the ability to prescribe optimal drug treatment regimens for patients with TNBC based on knowledge of the molecular-genetic characteristics of this subtype of BC will allow the achievement of high rates of overall and disease-free survival. Thus, identification of the molecular-genetic phenotype of breast cancer is an important prognostic factor of the disease and allows personalization of the patient’s treatment.
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Affiliation(s)
- Marina K. Ibragimova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia; (M.M.T.); (N.V.L.)
- National Research Tomsk State University, 634050 Tomsk, Russia
- Correspondence:
| | - Matvey M. Tsyganov
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia; (M.M.T.); (N.V.L.)
| | - Nikolai V. Litviakov
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia; (M.M.T.); (N.V.L.)
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Machlowska J, Kapusta P, Szlendak M, Bogdali A, Morsink F, Wołkow P, Maciejewski R, Offerhaus GJA, Sitarz R. Status of CHEK2 and p53 in patients with early-onset and conventional gastric cancer. Oncol Lett 2021; 21:348. [PMID: 33747205 PMCID: PMC7967923 DOI: 10.3892/ol.2021.12609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/08/2021] [Indexed: 02/05/2023] Open
Abstract
Gastric cancer (GC) is the fourth most common cause of cancer-associated death. Based on the age at diagnosis, GC is divided into early-onset GC (EOGC; ≤45 years) and conventional GC (CGC; >45 years). Mutations in the cell cycle checkpoint kinase 2 (CHEK2) and TP53 genes are associated with several types of cancer; however, their genetic defects in GC remain poorly understood. The aim of the present study was to determine the subcellular distribution of the CHEK2 protein and its redistribution following DNA damage, to improve the understanding of the DNA damage response. Genetic alterations and patterns of expression of CHEK2 and p53 proteins were investigated to identify potential biological markers and indicators of GC development. Additionally, the affected signaling pathways and their clinical importance in GC development and associated syndromes were investigated. A total of 196 GC samples (89 CGC and 107 EOGC samples) were used in the present study. DNA from 53 samples (18 CGC and 35 EOGC samples) was sequenced using targeted next-generation sequencing technology to identify and compare common and rare mutations associated with GC. Subsequently, the cytoplasmic and nuclear expression levels of CHEK2, phosphorylated (p)-CHEK2 at threonine 68 and p53 in GC tissues were determined via immunohistochemistry. Sequencing resulted in the identification of 63 single nucleotide polymorphisms (SNPs) in the CHEK2 gene amongst 5 different variants, and the intron variant c.319+379A>G was the most common SNP. In the TP53 gene, 57 different alterations were detected amongst 9 variant types, and the missense variant c.215C>G was the most common. Nuclear CHEK2 expression was high in both the EOGC and CGC subtypes. However, the prevalence of cytoplasmic CHEK2 expression (P<0.001) and nuclear p-CHEK2 expression (P=0.011) was significantly higher in CGC compared with in EOGC tissues. There was a statistically significant difference between high and low cytoplasmic CHEK2 expression in patients with p53-positive EOGC compared with in patients with p53-positive CGC (P=0.002). The present study was designed to determine the association between CHEK2 and p53 expression patterns in patients with EOGC and CGC, as well as genetic alterations in the CHEK2 and TP53 genes.
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Affiliation(s)
- Julita Machlowska
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, 31-034 Kraków, Poland.,Department of Human Anatomy, Medical University of Lublin, 20-090 Lublin, Poland
| | - Przemysław Kapusta
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, 31-034 Kraków, Poland
| | - Małgorzata Szlendak
- Department of Human Anatomy, Medical University of Lublin, 20-090 Lublin, Poland.,Department of Surgical Oncology, Medical University of Lublin, 20-090 Lublin, Poland
| | - Anna Bogdali
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, 31-034 Kraków, Poland
| | - Folkert Morsink
- Department of Pathology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Paweł Wołkow
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, 31-034 Kraków, Poland
| | - Ryszard Maciejewski
- Department of Human Anatomy, Medical University of Lublin, 20-090 Lublin, Poland
| | - G Johan A Offerhaus
- Department of Human Anatomy, Medical University of Lublin, 20-090 Lublin, Poland.,Department of Pathology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Robert Sitarz
- Department of Human Anatomy, Medical University of Lublin, 20-090 Lublin, Poland.,Department of Pathology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands.,Department of Surgery, Center of Oncology of The Lublin Region St. Jana z Dukli, 20-090 Lublin, Poland
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Cuella-Martin R, Hayward SB, Fan X, Chen X, Huang JW, Taglialatela A, Leuzzi G, Zhao J, Rabadan R, Lu C, Shen Y, Ciccia A. Functional interrogation of DNA damage response variants with base editing screens. Cell 2021; 184:1081-1097.e19. [PMID: 33606978 PMCID: PMC8018281 DOI: 10.1016/j.cell.2021.01.041] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 11/16/2020] [Accepted: 01/22/2021] [Indexed: 12/13/2022]
Abstract
Mutations in DNA damage response (DDR) genes endanger genome integrity and predispose to cancer and genetic disorders. Here, using CRISPR-dependent cytosine base editing screens, we identify > 2,000 sgRNAs that generate nucleotide variants in 86 DDR genes, resulting in altered cellular fitness upon DNA damage. Among those variants, we discover loss- and gain-of-function mutants in the Tudor domain of the DDR regulator 53BP1 that define a non-canonical surface required for binding the deubiquitinase USP28. Moreover, we characterize variants of the TRAIP ubiquitin ligase that define a domain, whose loss renders cells resistant to topoisomerase I inhibition. Finally, we identify mutations in the ATM kinase with opposing genome stability phenotypes and loss-of-function mutations in the CHK2 kinase previously categorized as variants of uncertain significance for breast cancer. We anticipate that this resource will enable the discovery of additional DDR gene functions and expedite studies of DDR variants in human disease.
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Affiliation(s)
- Raquel Cuella-Martin
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samuel B Hayward
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiao Fan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiao Chen
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jen-Wei Huang
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Junfei Zhao
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Raul Rabadan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Chao Lu
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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Gao Y, Ling C, Ma X, Wang H, Cui Y, Nie M, Tong A. Recurrent Germline Mutations of CHEK2 as a New Susceptibility Gene in Patients with Pheochromocytomas and Paragangliomas. Int J Endocrinol 2021; 2021:1392386. [PMID: 34630562 PMCID: PMC8497153 DOI: 10.1155/2021/1392386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/22/2021] [Indexed: 01/17/2023] Open
Abstract
PURPOSE Recently, pheochromocytomas and paragangliomas (PPGLs) have been strongly suspected as hereditary tumors, as approximately 40% of patients carry germline mutations. In the cancers where defects occur to corrupt DNA repair and facilitate tumorigenesis, a CHEK2 strong association has been observed. Therefore, the purpose of this study was to investigate the effect of CHEK2 mutations for its possible pathogenicity in PPGLs. METHODS Four patients with CHEK2 mutations were recruited, as previously detected by the whole exome sequencing. Sanger sequencing was used to verify the germline mutations as well as the loss of heterozygosities (LOHs) in their somatic DNAs. Immunohistochemistry was used to analyze the expression of CHEK2 and its downstream target p53 Ser20 (phosphorylated p53). RESULTS The average age of studied patients was 44.25 ± 11.18 years, at the time diagnosis. One patient had multiple tumors which recurred quickly, while two patients had distant metastasis. None of the patient had any relevant family history. Four germline CHEK2 mutations were identified (c.246_260del; c.715G > A; c.1008+3A > T; and c.1111C > T). All the patients were predicted to have either pathogenic or suspected pathogenic mutations. There was no LOH of CHEK2 gene in somatic DNAs found. Additionally, neither CHEK2 proteins nor its downstream target p53 Ser20 were expressed in the tumor tissues. The inactivation of CHEK2 leads to the decrease in the p53 phosphorylation, which might promote tumorigenesis. CONCLUSIONS For the first time, CHEK2 was identified as a susceptibility gene for PPGLs. However, the penetrance of CHEK2 gene with genotype-phenotype correlation needs to be investigated.
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Affiliation(s)
- Yinjie Gao
- NHC Key Laboratory of Endocrinology (Peking Union Medical College Hospital), Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Chao Ling
- Laboratory of Clinical Genetics (Peking Union Medical College Hospital), Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiaosen Ma
- NHC Key Laboratory of Endocrinology (Peking Union Medical College Hospital), Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Huiping Wang
- NHC Key Laboratory of Endocrinology (Peking Union Medical College Hospital), Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yunying Cui
- NHC Key Laboratory of Endocrinology (Peking Union Medical College Hospital), Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Min Nie
- NHC Key Laboratory of Endocrinology (Peking Union Medical College Hospital), Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Anli Tong
- NHC Key Laboratory of Endocrinology (Peking Union Medical College Hospital), Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
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Ansari N, Shahrabi S, Khosravi A, Shirzad R, Rezaeean H. Prognostic Significance of CHEK2 Mutation in Progression of Breast Cancer. Lab Med 2019; 50:e36-e41. [PMID: 31220302 DOI: 10.1093/labmed/lmz009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Breast cancer (BC) is one of the most common cancers among women; genetic mutations reflect the development of this disease. Mutations in cell signaling factors can be the main cause of BC development. In this study, we focused on mutations in checkpoint kinase 2 (CHEK2) and their impact as a prognostic factor in the pathogenesis of BC. CHEK2 is controlled in cell signaling pathways through the influence of upstream genes. Also, several downstream genes are regulated by CHEK2. In addition, mutations in CHEK2 lead to resistance of BC cells to chemotherapy and metastasis of cancer cells to other parts of the body. Finally, detection of mutations in CHEK2 can be used as a prognostic factor for patient response to treatment and for targeting downstream molecules of CHEK2 that are involved in the proliferation of breast tumor cells. Mutations such as c.1100delC and I157T can distinguish which patients are susceptible to metastasis.
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Affiliation(s)
- Narges Ansari
- Isfahan Bone Metabolic Disorders Research Center, Department of Internal Medicine, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Saeid Shahrabi
- Department of Hematology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Abbas Khosravi
- Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Reza Shirzad
- Research Center of Thalassemia & Hemoglobinopathy, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hadi Rezaeean
- Research Center of Thalassemia & Hemoglobinopathy, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Bhai P, Saxena R, Kulshrestha S, Verma IC. A novel CHEK2 variant identified by next generation sequencing in an Indian family with hereditary breast cancer syndrome. Cancer Genet 2019; 235-236:13-17. [PMID: 31296309 DOI: 10.1016/j.cancergen.2019.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 04/01/2019] [Accepted: 05/29/2019] [Indexed: 11/25/2022]
Abstract
Genetic variations in CHEK2 (checkpoint kinase 2) gene have been associated with hereditary predisposition to various cancers including breast and ovarian cancer. CHEK2 tumor suppressor gene encodes for a checkpoint kinase that responds to breaks in DNA, regulates DNA repair and cellular proliferation. We report a BRCA negative family with multiple affected women having breast cancer, with a novel, missense, likely pathogenic variant in the CHEK2 gene (c.1376T>G; p.Ile459Ser) that segregated with subjects with breast cancer. This case provides insight into the role of the CHEK2 gene in causing breast cancer susceptibility in families and supports the use of multigene panel testing in cases with hereditary predisposition to breast cancer.
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Affiliation(s)
- Pratibha Bhai
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, Rajinder Nagar, New Delhi 110060, India.
| | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, Rajinder Nagar, New Delhi 110060, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, Rajinder Nagar, New Delhi 110060, India.
| | - Ishwar Chander Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, Rajinder Nagar, New Delhi 110060, India
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Finnerty BM, Moore MD, Verma A, Aronova A, Huang S, Edwards DP, Chen Z, Seandel M, Scognamiglio T, Du YCN, Elemento O, Zarnegar R, Min IM, Fahey TJ. UCHL1 loss alters the cell-cycle in metastatic pancreatic neuroendocrine tumors. Endocr Relat Cancer 2019; 26:411-423. [PMID: 30689542 DOI: 10.1530/erc-18-0507] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/28/2019] [Indexed: 01/04/2023]
Abstract
Loss of ubiquitin carboxyl-terminal hydrolase L1 (UCHL1) expression by CpG promoter hypermethylation is associated with metastasis in gastroenteropancreatic neuroendocrine tumors; however, the mechanism of how UCHL1 loss contributes to metastatic potential remains unclear. In this study, we first confirmed that loss of UCHL1 expression on immunohistochemistry was significantly associated with metastatic tumors in a translational pancreatic neuroendocrine tumor (PNET) cohort, with a sensitivity and specificity of 78% and 89%, respectively. To study the mechanism driving this aggressive phenotype, BON and QGP-1 metastatic PNET cell lines, which do not produce UCHL1, were stably transfected to re-express UCHL1. In vitro assays, RNA-sequencing, and reverse-phase protein array (RPPA) analyses were performed comparing empty-vector negative controls and UCHL1-expressing cell lines. UCHL1 re-expression is associated with lower anchorage-independent colony growth in BON cells, lower colony formation in QGP cells, and a higher percentage of cells in the G0/G1 cell-cycle phase in BON and QGP cells. On RPPA proteomic analysis, there was an upregulation of cell-cycle regulatory proteins CHK2 (1.2 fold change, p=0.004) and P21 (1.2 fold change, p=0.023) in BON cells expressing UCHL1; western blot confirmed upregulation of phosphorylated CHK2 and P21. There were no transcriptomic differences detected on RNA-Sequencing between empty-vector negative controls and UCHL1-expressing cell lines. In conclusion, UCHL1 loss correlates with metastatic potential in PNETs and its re-expression induces a less aggressive phenotype in vitro, in part by inducing cell-cycle arrest through post-translational regulation of phosphorylated CHK2. UCHL1 re-expression should be considered as a functional biomarker in detecting PNETs capable of metastasis.
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Affiliation(s)
| | - Maureen D Moore
- Department of Surgery, Weill Cornell Medicine, New York, New York, USA
| | - Akanksha Verma
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Anna Aronova
- Department of Surgery, Weill Cornell Medicine, New York, New York, USA
| | - Shixia Huang
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA
| | - Dean P Edwards
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA
| | - Zhengming Chen
- Department of Healthcare Policy & Research, Weill Cornell Medicine, New York, New York, USA
| | - Marco Seandel
- Department of Surgery, Weill Cornell Medicine, New York, New York, USA
| | - Theresa Scognamiglio
- Department of Pathology & Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Yi-Chieh Nancy Du
- Department of Pathology & Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Rasa Zarnegar
- Department of Surgery, Weill Cornell Medicine, New York, New York, USA
| | - Irene M Min
- Department of Surgery, Weill Cornell Medicine, New York, New York, USA
| | - Thomas J Fahey
- Department of Surgery, Weill Cornell Medicine, New York, New York, USA
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12
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Cohen-Haguenauer O. [Hereditary predisposition to breast cancer (1): genetics]. Med Sci (Paris) 2019; 35:138-151. [PMID: 30774081 DOI: 10.1051/medsci/2019003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The main objective of oncogenetics is to characterize a subpopulation of patients at high risk of cancer development at an early age in order to provide specific recommendations for an optimized follow-up and care path. Oncogenetic counselling helps to assess individual risk from a family history. By a family approach of formal genetics, the key issue is to identify families with a strong aggregation of cancers, and, in particular, suggesting a specific syndrome of inherited predisposition to cancer. This approach can lead to the proposal of germline genetic testing in search of causal mutations. As up to know, the search for a constitutional mutation in the BRCA genes has led to the identification of a causal deleterious mutation in less than 10% of index-cases analyzed. It is therefore important to evaluate the impact of new genes in the current panorama of inherited predisposition to breast and ovarian cancer.
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Affiliation(s)
- Odile Cohen-Haguenauer
- Unité d'Oncogénétique, Service d'oncologie médicale, pôle HI-3RO et faculté de Médecine, université Paris 7 Denis Diderot, USPC - Hôpital Saint-Louis, 1, avenue Claude Vellefaux, 75475 Paris Cedex 10, France
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13
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Luo L, Gao W, Wang J, Wang D, Peng X, Jia Z, Jiang Y, Li G, Tang D, Wang Y. Study on the Mechanism of Cell Cycle Checkpoint Kinase 2 (CHEK2) Gene Dysfunction in Chemotherapeutic Drug Resistance of Triple Negative Breast Cancer Cells. Med Sci Monit 2018; 24:3176-3183. [PMID: 29761796 PMCID: PMC5978023 DOI: 10.12659/msm.907256] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background This study aimed to investigate the mechanism of CHEK2 gene dysfunction in drug resistance of triple negative breast cancer (TNBC) cells. Material/Methods To perform our study, a stable CHEK2 wild type (CHEK2 WT) or CHEK2 Y390C mutation (CHEK2 Y390C) expressed MDA-MB-231 cell line was established. MTT assay, cell apoptosis assay and cell cycle assay were carried out to analyze the cell viability, apoptosis, and cell cycle respectively. Western blotting and qRT-PCR were applied for related protein and gene expression detection. Results We found that the IC50 value of DDP (Cisplatin) to CHEK2 Y390C expressed MDA-MB-231 cells was significantly higher than that of the CHEK2 WT expressed cells and the control cells. After treatment with DDP for 48 h, cells expressing CHEK2 WT showed lower cell viability than that of the CHEK2 Y390C expressed cells and the control cells; compared with the CHEK2 Y390C expressed cells and the control cells, cells expressing CHEK2 WT showed significant G1/S arrest. Meanwhile, we found that compared with the CHEK2 Y390C expressed cells and the control cells, cell apoptosis was significantly increased in CHEK2 WT expressed cells. Moreover, our results suggested that cells expressing CHEK2 WT showed higher level of p-CDC25A, p-p53, p21, Bax, PUMA, and Noxa than that of the CHEK2 Y390C expressed cells and the control cells. Conclusions Our findings indicated that CHEK2 Y390C mutation induced the drug resistance of TNBC cells to chemotherapeutic drugs through administrating cell apoptosis and cell cycle arrest via regulating p53 activation and CHEK2-p53 apoptosis pathway.
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Affiliation(s)
- Li Luo
- Department of Oncological Hematology, First Affiliated Hospital of Guiyang College of Traditional Chinese Medicine (TCM), Guiyang, Guizhou, China (mainland).,Department of Oncology, Guihang Guiyang Hospital, Guiyang, Guizhou, China (mainland)
| | - Wei Gao
- Department of Radiation Oncology, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Jinghui Wang
- Department of Oncological Hematology, First Affiliated Hospital of Guiyang College of Traditional Chinese Medicine (TCM), Guiyang, Guizhou, China (mainland)
| | - Dingxue Wang
- Department of Oncological Hematology, First Affiliated Hospital of Guiyang College of Traditional Chinese Medicine (TCM), Guiyang, Guizhou, China (mainland)
| | - Xiaobo Peng
- Department of Oncology, Changhai Hospital, Second Military Medical University, Shanghai, China (mainland)
| | - Zhaoyang Jia
- Department of Radiotherapy, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China (mainland)
| | - Ye Jiang
- Department of Oncology, GuiHang Guiyang Hospital, Guiyang, Guizhou, China (mainland)
| | - Gongzhuo Li
- Department of Oncology, GuiHang Guiyang Hospital, Guiyang, Guizhou, China (mainland)
| | - Dongxin Tang
- Department of Science and Education, First Affiliated Hospital of Guiyang College of Traditional Chinese Medicine (TCM), Guiyang, Guizhou, China (mainland)
| | - Yajie Wang
- Department of Oncology, Changhai Hospital, Second Military Medical University, Shanghai, China (mainland)
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14
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Fan Z, Ouyang T, Li J, Wang T, Fan Z, Fan T, Lin B, Xu Y, Xie Y. Identification and analysis of CHEK2 germline mutations in Chinese BRCA1/2-negative breast cancer patients. Breast Cancer Res Treat 2018; 169:59-67. [PMID: 29356917 DOI: 10.1007/s10549-018-4673-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 01/13/2018] [Indexed: 11/25/2022]
Abstract
PURPOSE Cell-cycle-checkpoint kinase 2 (CHEK2) is an important moderate-penetrance breast cancer predisposition gene; however, recurrent CHEK2 mutations found in Caucasian women are very rare in Chinese population. We investigated the mutation spectrum and clinical relevance of CHEK2 germline mutations in Chinese breast cancer patients. METHODS The entire coding regions and splicing sites of CHEK2 were screened in 7657 Chinese BRCA1/2-negative breast cancer patients, using 62-gene panel-based sequencing. RESULTS Out of 7657 BRCA1/2-negative breast cancer patients, 26 (0.34%) carried CHEK2 pathogenic germline mutations. Most of these mutations (92.3%, 24/26) were nonsense or frameshift mutations; 84.6% (22/26) of them were in forkhead-associated (FHA) or kinase domains. Of the 18 types of CHEK2 mutations we found, 61.1% (11/18) of were novel mutations and two recurrent mutations (Y139X and R137X) were found in this cohort. Patients with CHEK2 mutations were significantly more likely to have family histories of breast and/or ovarian cancer (23.1% vs. 8.6%, p = 0.022) and family histories of any cancer (50.0% vs. 31.6%, p = 0.044); and were significantly more likely to have lymph node-positive (53.8% vs. 27.3%, p = 0.002) and progesterone receptor (PR)-positive (88.5% vs. 64.5%, p = 0.011) breast cancers. CONCLUSIONS Among Chinese breast cancer patients, the CHEK2 germline mutation rate is approximately 0.34% and two specific mutations (Y139X and R137X) are recurrent. Patients with CHEK2 mutations are significantly more likely to have family histories of cancer, and to develop lymph node-positive and/or PR-positive breast cancers.
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Affiliation(s)
- Zhenhua Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Tao Ouyang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Jinfeng Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Tianfeng Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Zhaoqing Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Tie Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Benyao Lin
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Ye Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China.
| | - Yuntao Xie
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Breast Center, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China.
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15
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Gómez-Flores-Ramos L, Álvarez-Gómez RM, Villarreal-Garza C, Wegman-Ostrosky T, Mohar A. Breast cancer genetics in young women: What do we know? MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 774:33-45. [PMID: 29173497 DOI: 10.1016/j.mrrev.2017.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 04/21/2017] [Accepted: 08/17/2017] [Indexed: 12/12/2022]
Abstract
Breast cancer (BC) in young women, generally defined in oncology as women who are 40 years of age or younger, represents 2 out of 10 BC cases in developing countries. Several research studies, including genetic cancer panel tests, genome-wide association studies, expression analyses and polymorphisms reports, have found that young women with BC exhibit a higher genetic susceptibility and specific genomic signature compared to postmenopausal women with BC. Thus, international guidelines recommend genetic counseling for this age population. This review presents the current state of the art of genetics and genomics with regards to young women with BC.
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Affiliation(s)
- Liliana Gómez-Flores-Ramos
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva, Coyoacán, Ciudad Universitaria, C.P. 04510, Mexico City, Mexico; Unidad de Investigación en Epidemiología, Subdivisión de Investigación Básica, Instituto Nacional de Cancerología, Av. San Fernando # 22, Col. Sección XVI, Delegación Tlalpan, C.P. 14080, Mexico City, Mexico
| | - Rosa María Álvarez-Gómez
- Clínica de Cáncer Hereditario, Subdivisión de Investigación Básica, Instituto Nacional de Cancerlogía, Av. San Fernando # 22, Col. Sección XVI, Delegación Tlalpan, C.P. 14080, Mexico City, Mexico
| | - Cynthia Villarreal-Garza
- Clínica de Cáncer Hereditario, Subdivisión de Investigación Básica, Instituto Nacional de Cancerlogía, Av. San Fernando # 22, Col. Sección XVI, Delegación Tlalpan, C.P. 14080, Mexico City, Mexico; Centro de Cáncer de Mama, Tecnológico de Monterrey, Centro Médico Zambrano Hellion, 6° Piso Av. Batallón de San Patricio #112 Col. Real San Agustín, San Pedro Garza García C.P. 66278, Nuevo León, Mexico
| | - Talia Wegman-Ostrosky
- Clínica de Cáncer Hereditario, Subdivisión de Investigación Básica, Instituto Nacional de Cancerlogía, Av. San Fernando # 22, Col. Sección XVI, Delegación Tlalpan, C.P. 14080, Mexico City, Mexico
| | - Alejandro Mohar
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva, Coyoacán, Ciudad Universitaria, C.P. 04510, Mexico City, Mexico; Unidad de Investigación en Epidemiología, Subdivisión de Investigación Básica, Instituto Nacional de Cancerología, Av. San Fernando # 22, Col. Sección XVI, Delegación Tlalpan, C.P. 14080, Mexico City, Mexico.
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16
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Klein CJ, Wu Y, Jentoft ME, Mer G, Spinner RJ, Dyck PJB, Dyck PJ, Mauermann ML. Genomic analysis reveals frequent TRAF7 mutations in intraneural perineuriomas. Ann Neurol 2017; 81:316-321. [PMID: 28019650 DOI: 10.1002/ana.24854] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/22/2016] [Accepted: 12/22/2016] [Indexed: 12/20/2022]
Abstract
Intraneural perineuriomas are benign peripheral nerve sheath tumors that cause progressive debilitating focal extremity weakness. The etiology of perineuriomas is largely unknown. We utilized whole exome sequencing, copy number algorithm evaluation, and high-resolution whole genome microarray to investigate for a genetic causal link to intraneural perineuriomas. Ten of 16 (60%) tumor cases had mutations in the WD40 domain of TRAF7, the same location for causal mutations of meningiomas. Two additional perineurioma cases had large chromosomal abnormalities in multiple chromosomes, including chromosome 22q. This study identifies a common cause for intraneural perineuriomas and an unexpected shared pathogenesis with intracranial meningiomas. Ann Neurol 2017;81:316-321.
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Affiliation(s)
- Christopher J Klein
- Department of Neurology, Mayo Clinic, Rochester, MN.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN.,Department of Medical Genetics, Mayo Clinic, Rochester, MN
| | - Yanhong Wu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Mark E Jentoft
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN
| | | | | | - Peter J Dyck
- Department of Neurology, Mayo Clinic, Rochester, MN
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17
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McSkimming DI, Dastgheib S, Baffi TR, Byrne DP, Ferries S, Scott ST, Newton AC, Eyers CE, Kochut KJ, Eyers PA, Kannan N. KinView: a visual comparative sequence analysis tool for integrated kinome research. MOLECULAR BIOSYSTEMS 2016; 12:3651-3665. [PMID: 27731453 PMCID: PMC5508867 DOI: 10.1039/c6mb00466k] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Multiple sequence alignments (MSAs) are a fundamental analysis tool used throughout biology to investigate relationships between protein sequence, structure, function, evolutionary history, and patterns of disease-associated variants. However, their widespread application in systems biology research is currently hindered by the lack of user-friendly tools to simultaneously visualize, manipulate and query the information conceptualized in large sequence alignments, and the challenges in integrating MSAs with multiple orthogonal data such as cancer variants and post-translational modifications, which are often stored in heterogeneous data sources and formats. Here, we present the Multiple Sequence Alignment Ontology (MSAOnt), which represents a profile or consensus alignment in an ontological format. Subsets of the alignment are easily selected through the SPARQL Protocol and RDF Query Language for downstream statistical analysis or visualization. We have also created the Kinome Viewer (KinView), an interactive integrative visualization that places eukaryotic protein kinase cancer variants in the context of natural sequence variation and experimentally determined post-translational modifications, which play central roles in the regulation of cellular signaling pathways. Using KinView, we identified differential phosphorylation patterns between tyrosine and serine/threonine kinases in the activation segment, a major kinase regulatory region that is often mutated in proliferative diseases. We discuss cancer variants that disrupt phosphorylation sites in the activation segment, and show how KinView can be used as a comparative tool to identify differences and similarities in natural variation, cancer variants and post-translational modifications between kinase groups, families and subfamilies. Based on KinView comparisons, we identify and experimentally characterize a regulatory tyrosine (Y177PLK4) in the PLK4 C-terminal activation segment region termed the P+1 loop. To further demonstrate the application of KinView in hypothesis generation and testing, we formulate and validate a hypothesis explaining a novel predicted loss-of-function variant (D523NPKCβ) in the regulatory spine of PKCβ, a recently identified tumor suppressor kinase. KinView provides a novel, extensible interface for performing comparative analyses between subsets of kinases and for integrating multiple types of residue specific annotations in user friendly formats.
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Affiliation(s)
| | - Shima Dastgheib
- Department of Computer Science, University of Georgia, Athens, GA 30602, USA
| | - Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Dominic P Byrne
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Samantha Ferries
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Steven Thomas Scott
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Claire E Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Krzysztof J Kochut
- Department of Computer Science, University of Georgia, Athens, GA 30602, USA
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA. and Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
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18
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Knappskog S, Leirvaag B, Gansmo LB, Romundstad P, Hveem K, Vatten L, Lønning PE. Prevalence of the CHEK2 R95* germline mutation. Hered Cancer Clin Pract 2016; 14:19. [PMID: 27708748 PMCID: PMC5039915 DOI: 10.1186/s13053-016-0059-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 09/21/2016] [Indexed: 12/16/2022] Open
Abstract
Background While germline CHEK2 mutations have been linked to a moderately elevated cancer risk, to date, a limited number of such mutations have been identified. Recently, we reported a germline nonsense mutation (C283T; R95*), introducing an early stop-codon, in two Norwegian patients diagnosed with locally advanced breast cancer. Both patients were resistant to anthracycline therapy, resembling what has been observed for TP53 mutations. Methods In the present study, we screened a large population based sample, including 3748 non-cancer individuals and 7081 incident cancer cases (breast cancer, n = 1717; prostate cancer n = 2501, lung cancer n = 1331 and colorectal cancer n = 1532), for the distribution of CHEK2 R95*. Results We found that 12 individuals (0.11 %) carried the R95* variant: 4 non-cancer individuals (0.11 %), 4 breast cancer cases (0.23 %), and 4 prostate cancer cases (0.16 %). Although the low number of observations precluded formal statistical assessment, our data may indicate an elevated risk for breast (OR: 2.19, 95 % CI: 0.55–8.75) and prostate cancer (OR: 1.5, 95 % CI: 0.36–6.00) associated with CHEK2 R95*. By mining international databanks, we found no individuals carrying the R95* mutation, indicating it to be restricted to the Norwegian population. Conclusion We provide proof-of-concept that previously unknown CHEK2 germline mutations may be present in certain populations. Notably, germline mutations in tumours are in general missed by contemporary massive parallel sequencing strategies, since tumour mutations are usually filtered against the germline. The fact that the CHEK2 R95* mutation may be associated with resistance to anthracyclines in cancer patients emphasizes its possible clinical importance.
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Affiliation(s)
- Stian Knappskog
- Section of Oncology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway ; Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Beryl Leirvaag
- Section of Oncology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway ; Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Liv B Gansmo
- Section of Oncology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway ; Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Pål Romundstad
- Department of Public Health, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kristian Hveem
- Department of Public Health, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lars Vatten
- Department of Public Health, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Per E Lønning
- Section of Oncology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway ; Department of Oncology, Haukeland University Hospital, Bergen, Norway
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19
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Al-Rakan MA, Hendrayani SF, Aboussekhra A. CHEK2 represses breast stromal fibroblasts and their paracrine tumor-promoting effects through suppressing SDF-1 and IL-6. BMC Cancer 2016; 16:575. [PMID: 27484185 PMCID: PMC4970236 DOI: 10.1186/s12885-016-2614-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 07/25/2016] [Indexed: 11/21/2022] Open
Abstract
Background Active fibroblasts, the predominant and the most active cells of breast cancer stroma, are responsible for tumor growth and spread. However, the molecular mediators and pathways responsible for stromal fibroblast activation, and their paracrine pro-carcinogenic effects are still not well defined. The CHEK2 tumor suppressor gene codes for a protein kinase, which plays important roles in the cellular response to various genotoxic stresses. Methods Immunoblotting, quantitative RT-PCR and Immunofluorescence were used to assess the expression of CHEK2 in different primary breast fibroblasts and in tissues. The effect of CHEK2 on the expression and secretion of SDF-1 and IL-6 was evaluated by immunoblotting and ELISA. The WST-1 colorimetric assay was used to assess cell proliferation, while the BD BioCoat Matrigel invasion chambers were utilized to determine the effects of CHEK2 on the migratory and the invasiveness capacities of breast stromal fibroblasts as well as breast cancer cells. Results We have shown that CHEK2 is down-regulated in most cancer-associated fibroblasts (CAFs) as compared to their corresponding tumor counterpart fibroblasts (TCFs) at both the mRNA and protein levels. Interestingly, CHEK2 down-regulation using specific siRNA increased the expression/secretion of both cancer-promoting cytokines SDF-1 and IL-6, and transdifferentiated stromal fibroblasts to myofibroblasts. These cells were able to enhance the proliferation of non-cancerous epithelial cells, and also boosted the migration/invasion abilities of breast cancer cells in a paracrine manner. The later effect was SDF-1/IL-6-dependent. Importantly, ectopic expression of CHEK2 in active CAFs converted these cells to a normal state, with lower migration/invasion capacities and reduced paracrine pro-carcinogenic effects. Conclusion These results indicate that CHEK2 possesses non-cell-autonomous tumor suppressor functions, and present the Chk2 protein as an important mediator in the functional interplay between breast carcinomas and their stromal fibroblasts.
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Affiliation(s)
- Maha A Al-Rakan
- Present address: Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, 11211, Kingdom of Saudi Arabia.,Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, MBC# 03, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Siti-Faujiah Hendrayani
- Present address: Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, 11211, Kingdom of Saudi Arabia.,Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, MBC# 03, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Abdelilah Aboussekhra
- Present address: Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, 11211, Kingdom of Saudi Arabia. .,Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, MBC# 03, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia.
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