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Viotto D, Russo F, Anania I, Segatto I, Rampioni Vinciguerra GL, Dall'Acqua A, Bomben R, Perin T, Cusan M, Schiappacassi M, Gerratana L, D'Andrea S, Citron F, Vit F, Musco L, Mattevi MC, Mungo G, Nicoloso MS, Sonego M, Massarut S, Sorio R, Barzan L, Franchin G, Giorda G, Lucia E, Sulfaro S, Giacomarra V, Polesel J, Toffolutti F, Canzonieri V, Puglisi F, Gattei V, Vecchione A, Belletti B, Baldassarre G. CDKN1B mutation and copy number variation are associated with tumor aggressiveness in luminal breast cancer. J Pathol 2020; 253:234-245. [PMID: 33140857 PMCID: PMC7839435 DOI: 10.1002/path.5584] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/12/2020] [Accepted: 10/29/2020] [Indexed: 12/28/2022]
Abstract
The CDKN1B gene, encoding for the CDK inhibitor p27kip1, is mutated in defined human cancer subtypes, including breast, prostate carcinomas and small intestine neuroendocrine tumors. Lessons learned from small intestine neuroendocrine tumors suggest that CDKN1B mutations could be subclonal, raising the question of whether a deeper sequencing approach could lead to the identification of higher numbers of patients with mutations. Here, we addressed this question and analyzed human cancer biopsies from breast (n = 396), ovarian (n = 110) and head and neck squamous carcinoma (n = 202) patients, using an ultra‐deep sequencing approach. Notwithstanding this effort, the mutation rate of CDKN1B remained substantially aligned with values from the literature, showing that essentially only hormone receptor‐positive breast cancer displayed CDKN1B mutations in a relevant number of cases (3%). However, the analysis of copy number variation showed that another fraction of luminal breast cancer displayed loss (8%) or gain (6%) of the CDKN1B gene, further reinforcing the idea that the function of p27kip1 is important in this type of tumor. Intriguingly, an enrichment for CDKN1B alterations was found in samples from premenopausal luminal breast cancer patients (n = 227, 4%) and in circulating cell‐free DNA from metastatic luminal breast cancer patients (n = 59, 8.5%), suggesting that CDKN1B alterations could correlate with tumor aggressiveness and/or occur later during disease progression. Notably, many of the identified somatic mutations resulted in p27kip1 protein truncation, leading to loss of most of the protein or of its C‐terminal domain. Using a gene‐editing approach in a luminal breast cancer cell line, MCF‐7, we observed that the expression of p27kip1 truncating mutants that lose the C‐terminal domains failed to rescue most of the phenotypes induced by CDKN1B gene knockout, indicating that the functions retained by the C‐terminal portion are critical for its role as an oncosuppressor, at least in luminal breast cancer. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Davide Viotto
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Francesca Russo
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy.,University of Trieste, Trieste, Italy
| | - Ilaria Anania
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Ilenia Segatto
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Gian Luca Rampioni Vinciguerra
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy.,Department of Clinical and Molecular Medicine, University of Rome 'Sapienza', Sant'Andrea Hospital, Rome, Italy
| | - Alessandra Dall'Acqua
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Riccardo Bomben
- Onco-Hematology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Tiziana Perin
- Pathology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Martina Cusan
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Monica Schiappacassi
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Lorenzo Gerratana
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy.,Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Sara D'Andrea
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Francesca Citron
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Filippo Vit
- University of Trieste, Trieste, Italy.,Onco-Hematology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Lorena Musco
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy.,University of Trieste, Trieste, Italy
| | - Maria Chiara Mattevi
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Giorgia Mungo
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Milena S Nicoloso
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy.,Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Maura Sonego
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Samuele Massarut
- Breast Surgery Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Roberto Sorio
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Luigi Barzan
- Division of Otorhinolaryngology, General Hospital of Pordenone Santa Maria degli Angeli, Pordenone, Italy
| | - Giovanni Franchin
- Radiotherapy Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Giorgio Giorda
- Gynecological Surgery Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Emilio Lucia
- Gynecological Surgery Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Sandro Sulfaro
- Unit of Pathology, General Hospital of Pordenone Santa Maria degli Angeli, Pordenone, Italy
| | - Vittorio Giacomarra
- Division of Otorhinolaryngology, General Hospital of Pordenone Santa Maria degli Angeli, Pordenone, Italy
| | - Jerry Polesel
- Cancer Epidemiology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Federica Toffolutti
- Cancer Epidemiology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Vincenzo Canzonieri
- Pathology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy.,Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Fabio Puglisi
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy.,Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Valter Gattei
- Onco-Hematology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Andrea Vecchione
- Department of Clinical and Molecular Medicine, University of Rome 'Sapienza', Sant'Andrea Hospital, Rome, Italy
| | - Barbara Belletti
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
| | - Gustavo Baldassarre
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO Aviano), IRCCS, National Cancer Institute, Aviano, Italy
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Capasso M, McDaniel LD, Cimmino F, Cirino A, Formicola D, Russell MR, Raman P, Cole KA, Diskin SJ. The functional variant rs34330 of CDKN1B is associated with risk of neuroblastoma. J Cell Mol Med 2017; 21:3224-3230. [PMID: 28667701 PMCID: PMC5706517 DOI: 10.1111/jcmm.13226] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 04/07/2017] [Indexed: 11/30/2022] Open
Abstract
The genetic aetiology of sporadic neuroblastoma is still largely unknown. We have identified diverse neuroblastoma susceptibility loci by genomewide association studies (GWASs); however, additional SNPs that likely contribute to neuroblastoma susceptibility prompted this investigation for identification of additional variants that are likely hidden among signals discarded by the multiple testing corrections used in the analysis of genomewide data. There is evidence suggesting the CDKN1B, coding for the cycle inhibitor p27Kip1, is involved in neuroblastoma. We thus assess whether genetic variants of CDKN1B are associated with neuroblastoma. We imputed all possible genotypes across CDKN1B locus on a discovery case series of 2101 neuroblastoma patients and 4202 genetically matched controls of European ancestry. The most significantly associated rs34330 was analysed in an independent Italian cohort of 311 cases and 709 controls. In vitro functional analysis was carried out in HEK293T and in neuroblastoma cell line SHEP‐2, both transfected with pGL3‐CDKN1B‐CC or pGL3‐CDKN1B‐TT constructs. We identified an association of the rs34330 T allele (‐79C/T) with the neuroblastoma risk (Pcombined = 0.002; OR = 1.17). The risk allele (T) of this single nucleotide polymorphism led to a lower transcription rate in cells transfected with a luciferase reporter driven by the polymorphic p27Kip1 promoter (P < 0.05). Three independent sets of neuroblastoma tumours carrying ‐79TT genotype showed a tendency towards lower CDKN1B mRNA levels. Our study shows that a functional variant, associated with a reduced CDKN1B gene transcription, influences neuroblastoma susceptibility.
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Affiliation(s)
- Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,Istituto di Ricerca Diagnostica e Nucleare, IRCCS SDN, Naples, Italy
| | - Lee D McDaniel
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Flora Cimmino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Andrea Cirino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Daniela Formicola
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Mike R Russell
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Pichai Raman
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kristina A Cole
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sharon J Diskin
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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Ding XF, Yin DQ, Chen Q, Zhang HY, Zhou J, Chen G. Validation of p27KIP1 expression levels as a candidate predictive biomarker of response to rapalogs in patient-derived breast tumor xenografts. Tumour Biol 2015; 36:1463-9. [PMID: 25744729 DOI: 10.1007/s13277-014-2580-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/29/2014] [Indexed: 11/28/2022] Open
Abstract
Blockade of mammalian target of rapamycin (mTOR) is a promising area in breast cancer therapy. However, in clinical trials, objective response rate with mTOR inhibitor monotherapy in breast cancer was modest. Biomarker studies designed to identify the responders of rapalogs are of increasing interest. We validated p27KIP1 expression levels as a candidate predictive biomarker of response to rapalogs. We also analyzed the correlation between rapamycin activity and p27KIP1 expression in the primary breast cancer cells and the patient-derived breast tumor xenograft models. The cells isolated from the breast tumor tissues expressing high levels of p27KIP1 were sensitive to rapamycin, whereas the cells from the tissues expressing low levels of p27KIP1 exhibited resistance to rapamycin. The correlation between p27KIP1 expression and rapamycin antitumor activity was also observed in the patient-derived breast tumor xenograft models. Moreover, we also found rapamycin significantly decreased phosphorylated p70S6K1 and phosphorylated 4EBP1 in both samples. It seemed that the different sensitivity of tumor cells to rapamycin did not owe to its different potency against mTOR activity. We further propose p27KIP1 expression level may be also a candidate predictive biomarker of rapalogs for breast cancer therapy, which requires additional clinical validation.
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Affiliation(s)
- Xiao-Fei Ding
- School of Medicine, Taizhou University, Taizhou, Zhejiang, 318000, China
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Xiang H, Li H, Ge W, Wu W, Gao M, Wang W, Hong L, Jiang D, Zhang C. Association of CDKN1B gene polymorphisms with susceptibility to breast cancer: a meta-analysis. Mol Biol Rep 2014; 40:6371-7. [PMID: 24078094 DOI: 10.1007/s11033-013-2751-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 09/14/2013] [Indexed: 01/15/2023]
Abstract
A number of case–control studies have been conducted to investigate the association of CDKN1B gene polymorphisms with breast cancer. However, these studies reported conflicting results. The aim of our study was to quantitatively summarize the association of CDKN1B gene polymorphisms with breast cancer. Systemic searches of the PubMed, Excerpta Medica Database, and Chinese Biomedical Literature Database databases were performed, with the last report up to Oct 2012. Odds ratios (ORs) with 95 % confidence intervals (CIs) were used to assess the strength of the association. Seven studies including 6,822 cases and 7,186 controls were involved in this meta-analysis, which was performed for two CDKN1B gene polymorphisms (rs2066827 and rs34330). Significant association was found for rs34330 polymorphism (T versus C: OR = 1.10, 95 % CI = 1.03–1.18, P = 0.003; CT + TT versus CC: OR = 1.38, 95 % CI = 0.98–1.93, P = 0.07; TT versus CC + CT: OR = 1.06, 95 % CI = 0.93–1.21, P = 0.38; TT versus CC: OR = 1.23, 95 % CI = 1.04–1.45, P = 0.02; CT versus CC: OR = 1.42, 95 % CI = 0.97–2.09, P = 0.07), but not for rs2066827 polymorphism (G versus T: OR = 0.99, 95 % CI = 0.91–1.08, P = 0.84; TG + GG versus TT: OR = 0.98, 95 % CI = 0.89–1.08, P = 0.69; GG versus TT + TG: OR = 1.04, 95 % CI = 0.83–1.30, P = 0.75; GG versus TT: OR = 1.03, 95 % CI = 0.82–1.30, P = 0.77; TG versus TT: OR = 0.97, 95 % CI = 0.88–1.08, P = 0.58). This meta-analysis suggests that breast cancer may be associated with CDKN1B gene rs34330 polymorphism, but not rs2066827 polymorphism.
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Sekiya T, Bronstein MD, Benfini K, Longuini VC, Jallad RS, Machado MC, Goncalves TD, Osaki LH, Higashi L, Viana J, Kater C, Lee M, Molatore S, Francisco G, Chammas R, Naslavsky MS, Schlesinger D, Gama P, Duarte YAO, Lebrão ML, Zatz M, Meirelles O, Liberman B, Fragoso MCBV, Toledo SPA, Pellegata NS, Toledo RA. p27 variant and corticotropinoma susceptibility: a genetic and in vitro study. Endocr Relat Cancer 2014; 21:395-404. [PMID: 24532476 DOI: 10.1530/erc-13-0486] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Germline mutations in p27(kip1) are associated with increased susceptibility to multiple endocrine neoplasias (MEN) both in rats and humans; however, the potential role of common polymorphisms of this gene in endocrine tumor susceptibility and tumorigenesis remains mostly unrecognized. To assess the risk associated with polymorphism rs2066827 (p27-V109G), we genotyped a large cohort of Brazilian patients with sporadic endocrine tumors (pituitary adenomas, n=252; pheochromocytomas, n=125; medullary thyroid carcinoma, n=51; and parathyroid adenomas, n=19) and 885 population-matched healthy controls and determined the odds ratios and 95% CIs. Significant associations were found for the group of patients with pituitary adenomas (P=0.01), particularly for those with ACTH-secreting pituitary adenomas (P=0.005). In contrast, no association was found with GH-secreting pituitary tumors alone or with the sporadic counterpart of MEN2-component neoplasias. Our in vitro analyses revealed increased colony formation and cell growth rate for an AtT20 corticotropin mouse cell line overexpressing the p27-V109G variant compared with cells transfected with the WT p27. However, the genotypic effects in genetic and in vitro approaches were divergent. In accordance with our genetic data showing specificity for ACTH-secreting pituitary tissues, the overexpression of p27-V109G in a GH3 somatotropin rat cell line resulted in no difference compared with the WT. Pituitary tumors are one of the major clinical components of syndromes associated with the p27 pathogenic mutations MENX and MEN4. Our genetic and in vitro data indicate that the common polymorphism rs2066827 may play a role in corticotropinoma susceptibility and tumorigenesis through a molecular mechanism not fully understood thus far.
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Affiliation(s)
- Tomoko Sekiya
- Endocrine Genetics Unit LIM-25 Neuroendocrinology Unit Adrenal Unit (LIM-42) Experimental Oncology Laboratory (LIM-24), School of Medicine, Hospital das Clinicas, University of Sao Paulo, Sao Paulo, Brazil Nursing School School of Public Health, University of Sao Paulo, Sao Paulo, Brazil Endocrinology Division, Santa Casa Hospital, Sao Paulo, Brazil Brigadeiro Hospital, Sao Paulo, Brazil Federal University of Sao Paulo, Sao Paulo, Brazil Human Genome Research Center Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil Instituto do Cérebro, Instituto Israelita de Ensino e Pesquisa Albert Einstein, Sao Paulo, Brazil National Institute of Aging, National Institutes of Health (NIH), Bethesda, Maryland, USA Institute of Pathology, Helmholtz Zentrum München, Neuherberg, Germany
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Jia ZM, Liu Y, Cui SY. Lack of association between cyclin-dependent kinase inhibitor 1B rs2066827 polymorphism and breast cancer susceptibility. Tumour Biol 2014; 35:5527-31. [PMID: 24523023 DOI: 10.1007/s13277-014-1727-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 02/04/2014] [Indexed: 01/15/2023] Open
Abstract
In order to make a comprehensive assessment of the potential association between one genetic variant in the cyclin-dependent kinase inhibitor 1B gene, rs2066827, and breast cancer risk, we conducted a meta-analysis of six epidemiological studies, which included 3,139 breast cancer cases and 2,936 controls. The data showed that rs2066827 polymorphism was not associated with increased breast cancer risk in overall population. When stratifying by the race, no noteworthy associations were observed in Asians or Caucasians. Based on this meta-analysis, we conclude that the cyclin-dependent kinase inhibitor 1B rs2066827 polymorphism might not be a risk factor for breast cancer development. Further studies, either with larger sample size or involving other SNPs and haplotypes of the cyclin-dependent kinase inhibitor 1B gene, are necessary to clarify the contribution of cyclin-dependent kinase inhibitor 1B rs2066827 in breast carcinogenesis.
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Affiliation(s)
- Zhong-Ming Jia
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital, Huangheer Road, Binzhou, 256603, Shandong, China,
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Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, Nik-Zainal S, Martin S, Varela I, Bignell GR, Yates LR, Papaemmanuil E, Beare D, Butler A, Cheverton A, Gamble J, Hinton J, Jia M, Jayakumar A, Jones D, Latimer C, Lau KW, McLaren S, McBride DJ, Menzies A, Mudie L, Raine K, Rad R, Chapman MS, Teague J, Easton D, Langerød A, Lee MTM, Shen CY, Tee BTK, Huimin BW, Broeks A, Vargas AC, Turashvili G, Martens J, Fatima A, Miron P, Chin SF, Thomas G, Boyault S, Mariani O, Lakhani SR, van de Vijver M, van 't Veer L, Foekens J, Desmedt C, Sotiriou C, Tutt A, Caldas C, Reis-Filho JS, Aparicio SAJR, Salomon AV, Børresen-Dale AL, Richardson AL, Campbell PJ, Futreal PA, Stratton MR. The landscape of cancer genes and mutational processes in breast cancer. Nature 2012; 486:400-4. [PMID: 22722201 PMCID: PMC3428862 DOI: 10.1038/nature11017] [Citation(s) in RCA: 1283] [Impact Index Per Article: 106.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 03/06/2012] [Indexed: 12/17/2022]
Abstract
All cancers carry somatic mutations in their genomes. A subset, known as driver mutations, confer clonal selective advantage on cancer cells and are causally implicated in oncogenesis, and the remainder are passenger mutations. The driver mutations and mutational processes operative in breast cancer have not yet been comprehensively explored. Here we examine the genomes of 100 tumours for somatic copy number changes and mutations in the coding exons of protein-coding genes. The number of somatic mutations varied markedly between individual tumours. We found strong correlations between mutation number, age at which cancer was diagnosed and cancer histological grade, and observed multiple mutational signatures, including one present in about ten per cent of tumours characterized by numerous mutations of cytosine at TpC dinucleotides. Driver mutations were identified in several new cancer genes including AKT2, ARID1B, CASP8, CDKN1B, MAP3K1, MAP3K13, NCOR1, SMARCD1 and TBX3. Among the 100 tumours, we found driver mutations in at least 40 cancer genes and 73 different combinations of mutated cancer genes. The results highlight the substantial genetic diversity underlying this common disease.
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Affiliation(s)
- Philip J Stephens
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
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Pillay K, McCleod H, Chetty R, Hall P. A study to investigate the role of p27 and cyclin E immunoexpression as a prognostic factor in early breast carcinoma. World J Surg Oncol 2011; 9:31. [PMID: 21410943 PMCID: PMC3069943 DOI: 10.1186/1477-7819-9-31] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 03/16/2011] [Indexed: 11/10/2022] Open
Abstract
Background Cyclin E and p27 expression is easy to assess in human tissues by standard immunohistochemical techniques. Immunohistochemistry is cost effective, relatively easy to perform and will play more of a role in the future management of cancer. The aim of this study was to investigate the role of p27 and cyclin E immunoexpression as a prognostic factor in early breast carcinoma. Methods Cyclin E and p27 immunohistochemistry was performed on sixty six cases of breast carcinoma submitted over a five year period to the Division of Anatomical Pathology, Groote Schuur hospital; Whittaker and Associates; and PathCare. All tumours included in this study were less than 5 cm in diameter (pT1 and pT2 stage) and all the patients had wide local excisions performed. Follow up information was obtained from patient folders in the Department of Radiation Oncology. Results There was no significant association of cyclin E and p27 expression with distant metastasis free survival (MFS) for all invasive carcinomas in contrast to grade, lymph node spread and vascular invasion. However, there was a statistically significant direct association of cyclin E with distant metastases in all invasive carcinomas, in the subgroup of infiltrating duct carcinomas (IDC) and in the node negative group when cyclin E was stratified as negative and positive (low/high). In this study of early breast carcinoma, only 9/66 cases showed cyclin E expression. Of these, four patients had distant metastases, one patient had a local recurrence and four patients were alive at last follow-up. Furthermore, cyclin E expression was significantly associated with grade, lymph node spread, oestrogen receptor status and histological type. None of the lobular carcinomas showed cyclin E positivity and only one case of lobular carcinoma presented with distant metastases. 59/66 cases were positive (low/high) for p27 while seven cases were negative, 22 cases showed low expression and 37 cases demonstrated high p27 expression. p27 was significantly associated with oestrogen receptor status only for all invasive carcinomas and in the IDC group. There was no statistical relationship between p27 and cyclin E, but 50 (76%) tumours with positive p27 expression were negative for cyclin E. There were similar results for the invasive ductal carcinoma subgroup. Conclusion This study shows that p27 and cyclin E are not good independent prognostic markers for early breast carcinoma in contrast to grade, lymph node spread and vascular invasion for all invasive carcinomas. However, cyclin E provides some prognostic value as there is a direct statistical association with the development of distant metastases. Many previous studies have correlated overexpression of cyclin E with an aggressive course. The inverse relationship between p27 and cyclin E expression which has been reported in the literature has been highlighted, but this was not statistically significant. Most cases showed positive p27 expression and negative Cyclin E expression. This may be due to the early stage of the disease.
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Affiliation(s)
- Komala Pillay
- Department of Anatomical Pathology,NHLS, Red Cross Chidren's Hospital/Groote Schuur Hospital, University of Cape Town, South Africa.
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Chen G, Yang N, Wang X, Zheng SY, Chen Y, Tong LJ, Li YX, Meng LH, Ding J. Identification of p27/KIP1 expression level as a candidate biomarker of response to rapalogs therapy in human cancer. J Mol Med (Berl) 2010; 88:941-52. [DOI: 10.1007/s00109-010-0635-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 04/26/2010] [Accepted: 05/05/2010] [Indexed: 01/05/2023]
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Spurdle AB, Deans AJ, Duffy D, Goldgar DE, Chen X, Beesley J, Easton DF, Antoniou AC, Peock S, Cook M, Nathanson KL, Domchek SM, MacArthur GA, Chenevix-Trench G. No evidence that CDKN1B (p27) polymorphisms modify breast cancer risk in BRCA1 and BRCA2 mutation carriers. Breast Cancer Res Treat 2008; 115:307-13. [DOI: 10.1007/s10549-008-0083-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Accepted: 05/27/2008] [Indexed: 11/25/2022]
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11
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Price GR, Armes JE, Ramus SJ, Provenzano E, Kumar B, Cowie TF, Ciciulla J, Hutchins AM, Thomas M, Venter DJ. Phenotype-directed analysis of genotype in early-onset, familial breast cancers. Pathology 2006; 38:520-7. [PMID: 17393978 DOI: 10.1080/00313020601024052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
UNLABELLED Considerable heterogeneity of morphology and disease outcome exists within breast cancers (BC), which likely reflects variable molecular pathogeneses within this broad clinical group. AIM To evaluate the underlying genomic alterations associated with familial, early-onset BC (EOBC) phenotypes, in order to improve the management of this disease. METHODS Using hierarchical clustering of morphological and immunophenotypical parameters, 116 EOBC were stratified into six groups. Conventional and array-based comparative genomic hybridisation was used to analyse the genomic alterations. RESULTS Specific areas of genomic imbalance were associated with individual phenotypes. The largest phenotypical group was high grade, oestrogen receptor and HER-2 negative. This group contained the majority of BRCA1 germline mutation-associated tumours and commonly showed loss of chromosomal regions 5cent-5q13, 5q14-22 and 4q28-32. High mitotic rate, an important indicator of tumour cell proliferation and poor prognosis, was associated with gain of 19p, mapped within 7 Mb of the telomere. This region contains the candidate oncogene CDC34, the protein product of which is involved in ubiquitin-mediated degradation of the cyclin-dependent kinase inhibitor, p27Kip1. CONCLUSION Phenotype-based analysis can be used to determine the genetic changes important in subtypes of BC. Further, the different morphological phenotypes could act as a cost-effective surrogate for genotypical stratification to facilitate optimal management of this disease.
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Affiliation(s)
- Gareth R Price
- Cancer Genomics Laboratory, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne
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Ma H, Jin G, Hu Z, Zhai X, Chen W, Wang S, Wang X, Qin J, Gao J, Liu J, Wang X, Wei Q, Shen H. Variant genotypes of CDKN1A and CDKN1B are associated with an increased risk of breast cancer in Chinese women. Int J Cancer 2006; 119:2173-8. [PMID: 16804901 DOI: 10.1002/ijc.22094] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
p21(Cip1) and p27(Kip1) are cyclin-dependent kinase inhibitors, which can arrest cell proliferation and serve as tumor suppressors. Reduced protein expression of p21(Cip1) and p27(Kip1) was frequently observed in a subset of cancers, including breast cancer. In this study, we hypothesized that genetic variants in CDKN1A (encode for p21(Cip1)) and CDKN1B (encode for p27(Kip1)) may modulate the risk of breast cancer. To test this hypothesis, we evaluated the associations of the polymorphisms of Ser31Arg and C+20T in CDKN1A and C-79T and Gly109Val in CDKN1B, as well as their combinations, with breast cancer risk in a case-control study of 368 breast cancer cases and 467 cancer-free controls in a Chinese population. We found that a significantly increased risk of breast cancer was associated with the variant genotypes of CDKN1B C-79T [adjusted OR = 1.43 (95% CI = 1.03-1.98) for -79TC/TT], compared with the -79CC genotype, but no associations were observed for other variant genotypes. However, the combined variant genotypes of the 4 loci were associated with a significantly increased breast cancer risk (adjusted OR = 1.49, 95% CI = 1.11-2.01 among subjects carrying 3 or more variant alleles), especially among premenopausal women (adjusted OR= 2.30, 95% CI = 1.45-3.66). Furthermore, in premenopausal women, this significant association remained unchanged, after including other individual risk factors in the multivariate logistic regression model, suggesting an independent role of CDKN1A and CDKN1B variants in breast cancer risk. Although the exact biological mechanism remains to be explored, our findings suggest possible involvement of CDKN1A and CDKN1B variants in the etiology of breast cancer. Further large and functional studies are needed to confirm our findings.
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Affiliation(s)
- Hongxia Ma
- Laboratory of Reproductive Medicine and Applied Toxicology, Nanjing Medical University, Nanjing, China
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Yang ZL, Huang SF, Wang QW, Miao XY, Liang S. Expression and correlations of S-phase kinase associated protein 2 and P27 protein in pancreatic cancer tissues: an analyses of 51 cases. Shijie Huaren Xiaohua Zazhi 2005; 13:2717-2719. [DOI: 10.11569/wcjd.v13.i22.2717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To detect the expression of S-phase kinase associated protein 2 (SKP2) and P27 protein in human pancreatic ductal carcinoma and chronic pancreatitis, and to investigate the clinical significance and their correlations in the pancreatic ductal carcinoma.
METHODS: SP immunohistochemical method was used to detect the expression of SKP2 and P27 in the routinely paraffin-embedded sections of specimens from patients with pancreatic ductal carcinoma (n = 51) and chronic pancreatitis (n = 10)..
RESULTS: The positive rate of SKP2 expression in the pancreatic ductal carcinoma (28/51, 54.9%) was significantly higher than that in the chronic pancreatitis (2/10, 20.0%, P < 0.05), while the rate of P27 was significantly lower [25/51(49.0%) vs 9/10(90.0%), P < 0.05]. The positive rates of SKP2 expression was significantly lower in the well-differentiated (7/20, 35.0%) and non-metastasis cases (5/16, 31.2%) than those in the poorly-differentiated (14/19, 73.7%) and metastasis ones (23/35, 65.7%) (P < 0.05), while the rate of P27 expression was significantly higher in the well-differentiated (13/20, 65.0%) and non-metastasis cases (12/16, 75.0%) than those in the poorly-differentiated (6/19, 31.5%) and metastasis ones (13/35, 37.1%) (P < 0.05 or P < 0.01). The expression of SKP2 and P27 were closely correlated in the pancreatic ductal carcinoma tissue (χ2 = 14.33, P < 0.01)..
CONCLUSION: SKP2 and P27 are important biological markers for reflecting the carcinogenesis, progression, and prognosis of pancreatic ductal carcinoma. The positive expression of SKP2 or the negative expression of P27 reveals more serious status of the illness, the tendency of metastasis and unfavorable prognosis. There may be a co-regulatory relationship between SKP2 and P27 expression.
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