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Hussain MS, Majami AA, Ali H, Gupta G, Almalki WH, Alzarea SI, Kazmi I, Syed RU, Khalifa NE, Bin Break MK, Khan R, Altwaijry N, Sharma R. The complex role of MEG3: An emerging long non-coding RNA in breast cancer. Pathol Res Pract 2023; 251:154850. [PMID: 37839358 DOI: 10.1016/j.prp.2023.154850] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/24/2023] [Accepted: 10/02/2023] [Indexed: 10/17/2023]
Abstract
MEG3, a significant long non-coding RNA (lncRNA), substantially functions in diverse biological processes, particularly breast cancer (BC) development. Within the imprinting DLK-MEG3 region on human chromosomal region 14q32.3, MEG3 spans 35 kb and encompasses ten exons. It exerts regulatory effects through intricate interactions with miRNAs, proteins, and epigenetic modifications. MEG3's multifaceted function in BC is evident in gene expression modulation, osteogenic tissue differentiation, and involvement in bone-related conditions. Its role as a tumor suppressor is highlighted by its influence on miR-182 and miRNA-29 expression in BC. Additionally, MEG3 is implicated in acute myocardial infarction and endothelial cell function, emphasising cell-specific regulatory mechanisms. MEG3's impact on gene activity encompasses transcriptional and post-translational adjustments, including DNA methylation, histone modifications, and interactions with transcription factors. MEG3 dysregulation is linked to unfavourable outcomes and drug resistance. Notably, higher MEG3 expression is associated with enhanced survival in BC patients. Overcoming challenges such as unravelling context-specific interactions, understanding epigenetic control, and translating findings into clinical applications is imperative. Prospective endeavours involve elucidating underlying mechanisms, exploring epigenetic alterations, and advancing MEG3-based diagnostic and therapeutic approaches. A comprehensive investigation into broader signaling networks and rigorous clinical trials are pivotal. Rigorous validation through functional and molecular analyses will shed light on MEG3's intricate contribution to BC progression.
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Affiliation(s)
- Md Sadique Hussain
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, 302017, Jaipur, Rajasthan, India
| | - Abdullah A Majami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Haider Ali
- Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan.
| | - Gaurav Gupta
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India; School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, 302017, Jaipur, India
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rahamat Unissa Syed
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia; Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia
| | - Nasrin E Khalifa
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia; Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia; Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum, 11115, Sudan
| | - Mohammed Khaled Bin Break
- Medical and Diagnostic Research Centre, University of Hail, Hail 55473, Saudi Arabia; Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
| | - Ruqaiyah Khan
- Department of Basic Health Sciences, Deanship of Preparatory Year for the Health Colleges, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Najla Altwaijry
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint, Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Rahul Sharma
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, 302017, Jaipur, Rajasthan, India
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Kang J, Lee JY, Lee S, Kim D, Lim J, Jun HR, Jeon S, Kim YA, Park HS, Kim KP, Chun SM, Lee HJ, Yoo C. Establishing Patient-Derived Cancer Cell Cultures and Xenografts in Biliary Tract Cancer. Cancer Res Treat 2023; 55:219-230. [PMID: 35410113 PMCID: PMC9873337 DOI: 10.4143/crt.2021.1166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/01/2022] [Indexed: 02/04/2023] Open
Abstract
PURPOSE Biliary tract cancers (BTCs) are rare and show a dismal prognosis with limited treatment options. To improve our understanding of these heterogeneous tumors and develop effective therapeutic agents, suitable preclinical models reflecting diverse tumor characteristics are needed. We established and characterized new patient-derived cancer cell cultures and patient-derived xenograft (PDX) models using malignant ascites from five patients with BTC. MATERIALS AND METHODS Five patient-derived cancer cell cultures and three PDX models derived from malignant ascites of five patients with BTC, AMCBTC-01, -02, -03, -04, and -05, were established. To characterize the models histogenetically and confirm whether characteristics of the primary tumor were maintained, targeted sequencing and histopathological comparison between primary tissue and xenograft tumors were performed. RESULTS From malignant ascites of five BTC patients, five patient-derived cancer cell cultures (100% success rate), and three PDXs (60% success rate) were established. The morphological characteristics of three primary xenograft tumors were compared with those of matched primary tumors, and they displayed a similar morphology. The mutated genes in samples (models, primary tumor tissue, or both) from more than one patient were TP53 (n=2), KRAS (n=2), and STK11 (n=2). Overall, the pattern of commonly mutated genes in BTC cell cultures was different from that in commercially available BTC cell lines. CONCLUSION We successfully established the patient-derived cancer cell cultures and xenograft models derived from malignant ascites in BTC patients. These models accompanied by different genetic characteristics from commercially available models will help better understand BTC biology.
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Affiliation(s)
- Jihoon Kang
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea,Center for Research and Development, Oncocross Ltd., Seoul,
Korea
| | - Ji-Young Lee
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Seoul,
Korea,Center for Cancer Genome Discovery, Asan Institute for Life Science, Asan Medical Center, Seoul,
Korea
| | - Sunmin Lee
- University of Ulsan Digestive Diseases Research Center, Seoul,
Korea
| | - Danbee Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
| | - Jinyeong Lim
- Center for Cancer Genome Discovery, Asan Institute for Life Science, Asan Medical Center, Seoul,
Korea
| | - Ha Ra Jun
- Center for Cancer Genome Discovery, Asan Institute for Life Science, Asan Medical Center, Seoul,
Korea
| | - Seyeon Jeon
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Seoul,
Korea
| | - Young-Ae Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
| | - Hye Seon Park
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
| | - Kyu-pyo Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
| | - Sung-Min Chun
- Center for Cancer Genome Discovery, Asan Institute for Life Science, Asan Medical Center, Seoul,
Korea,Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
| | - Hee Jin Lee
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
| | - Changhoon Yoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
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Zidane M, Truong T, Lesueur F, Xhaard C, Cordina-Duverger E, Boland A, Blanché H, Ory C, Chevillard S, Deleuze JF, Souchard V, Ren Y, Zemmache MZ, Canale S, Borson-Chazot F, Schvartz C, Mariné Barjoan E, Guizard AV, Laurent-Puig P, Mulot C, Guibon J, Karimi M, Schlumberger M, Adjadj E, Rubino C, Guenel P, Cazier JB, de Vathaire F. Role of DNA Repair Variants and Diagnostic Radiology Exams in Differentiated Thyroid Cancer Risk: A Pooled Analysis of Two Case-Control Studies. Cancer Epidemiol Biomarkers Prev 2021; 30:1208-1217. [PMID: 33827984 DOI: 10.1158/1055-9965.epi-20-1142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/12/2020] [Accepted: 03/29/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Given the increased use and diversity of diagnostic procedures, it is important to understand genetic susceptibility to radiation-induced thyroid cancer. METHODS On the basis of self-declared diagnostic radiology examination records in addition to existing literature, we estimated the radiation dose delivered to the thyroid gland from diagnostic procedures during childhood and adulthood in two case-control studies conducted in France. A total of 1,071 differentiated thyroid cancer (DTC) cases and 1,188 controls from the combined studies were genotyped using a custom-made Illumina OncoArray DNA chip. We focused our analysis on variants in genes involved in DNA damage response and repair pathways, representing a total of 5,817 SNPs in 571 genes. We estimated the OR per milli-Gray (OR/mGy) of the radiation dose delivered to the thyroid gland using conditional logistic regression. We then used an unconditional logistic regression model to assess the association between DNA repair gene variants and DTC risk. We performed a meta-analysis of the two studies. RESULTS The OR/mGy was 1.02 (95% confidence interval, 1.00-1.03). We found significant associations between DTC and rs7164173 in CHD2 (P = 5.79 × 10-5), rs6067822 in NFATc2 (P = 9.26 × 10-5), rs1059394 and rs699517 both in ENOSF1/THYS, rs12702628 in RPA3, and an interaction between rs7068306 in MGMT and thyroid radiation doses (P = 3.40 × 10-4). CONCLUSIONS Our results suggest a role for variants in CDH2, NFATc2, ENOSF1/THYS, RPA3, and MGMT in DTC risk. IMPACT CDH2, NFATc2, ENOSF1/THYS, and RPA3 have not previously been shown to be associated with DTC risk.
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Affiliation(s)
- Monia Zidane
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Thérèse Truong
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Fabienne Lesueur
- Inserm, U900, Institut Curie, Université PSL, Mines ParisTech, Paris, France
| | - Constance Xhaard
- INSERM Centre d'Investigation Clinique CIC-P 1433, CHRU Nancy, France
- INSERM U1116, FCRIN INI-CRCT, Lorraine Université, Nancy, France
| | - Emilie Cordina-Duverger
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Hélène Blanché
- Fondation Jean Dausset-CEPH (Centre Etude du Polymorphisme Humain), Paris, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Catherine Ory
- CEA, Direction de la Recherche Fondamentale, Institut de Biologie François Jacob, iRCM, SREIT, Laboratoire de Cancérologie Expérimentale (LCE), Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Sylvie Chevillard
- CEA, Direction de la Recherche Fondamentale, Institut de Biologie François Jacob, iRCM, SREIT, Laboratoire de Cancérologie Expérimentale (LCE), Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
- Fondation Jean Dausset-CEPH (Centre Etude du Polymorphisme Humain), Paris, France
- Laboratory of Excellence GENMED (Medical Genomics)
| | - Vincent Souchard
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Yan Ren
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Mohammed Zakarya Zemmache
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | | | - Françoise Borson-Chazot
- Rhône-Alpes Thyroid Cancer Registry, Cancer Research Center of Lyon (UMR INSERM 1052, CNRS 5286), RTH Laennec Faculty of Medicine, University of Lyon, Lyon
| | - Claire Schvartz
- Thyroid Cancer Registry of Champagne-Ardennes, Institut Jean Godinot, Reims, Cancer Registry of Isère, Meylan
| | | | - Anne-Valérie Guizard
- Registre Général des Tumeurs du Calvados, Centre François Baclesse, Caen, France
- U1086 INSERM-UCN "ANTICIPE," Caen, France
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, EPIGENETEC, Paris, France
| | - Claire Mulot
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, EPIGENETEC, Paris, France
| | - Julie Guibon
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
- Inserm, U900, Institut Curie, Université PSL, Mines ParisTech, Paris, France
| | - Mojgan Karimi
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Martin Schlumberger
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Elizabeth Adjadj
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
| | - Carole Rubino
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Pascal Guenel
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Jean-Baptiste Cazier
- Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | - Florent de Vathaire
- INSERM, Centre for Research in Epidemiology and Population Health (CESP), 94800 Villejuif, France.
- Université Paris-Sud Orsay, Villejuif, France
- Gustave Roussy, Villejuif, France
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Branca JA, Low BE, Saxl RL, Sargent JK, Doty RA, Wiles MV, Dumont BL, Hasham MG. Loss of TRP53 (p53) accelerates tumorigenesis and changes the tumor spectrum of SJL/J mice. Genes Cancer 2020; 11:83-94. [PMID: 32577159 PMCID: PMC7289902 DOI: 10.18632/genesandcancer.198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Known as the guardian of the genome, transformation-related protein 53 (TRP53) is a well -known tumor suppressor. Here, we describe a novel TRP53 deficient mouse model on a tumor prone background—SJL/J mice. The absence of TRP53 (TRP53 nullizygosity) leads to a shift in the tumor spectrum from a non-Hodgkin’s-like disease to thymic lymphomas and testicular teratomas at a very rapid tumor onset averaging ~12 weeks of age. In haplotype studies, comparing tumor prone versus tumor resistant Trp53 null mouse strains, we found that other tumor suppressor, DNA repair and/or immune system genes modulate tumor incidence in TRP53 null strains, suggesting that even a strong tumor suppressor such as TRP53 is modulated by genetic background. Due to their rapid development of tumors, the SJL/J TRP53 null mice generated here can be used as an efficient chemotherapy or immunotherapy screening mouse model.
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Affiliation(s)
| | | | - Ruth L Saxl
- The Jackson Laboratory, Bar Harbor, Maine, USA
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Qiu B, Jiang W, Qiu W, Mu W, Qin Y, Zhu Y, Zhang J, Wang Q, Liu D, Qu Z. Pine needle oil induces G2/M arrest of HepG2 cells by activating the ATM pathway. Exp Ther Med 2018; 15:1975-1981. [PMID: 29434792 PMCID: PMC5776635 DOI: 10.3892/etm.2017.5648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 08/23/2017] [Indexed: 11/06/2022] Open
Abstract
Over the last two decades, inducing DNA damage of cancer cells by natural medicines has become a research hotspot in the field of cancer treatment. Although various natural medicines have anticancer effects, very few studies have been conducted to explore the anti-cancer effect of pine needle oil. In the present study, the role of pine needle oil in inducing G2/M arrest in HepG2 cells was investigated. The data revealed that pine needle oil could induce DNA damage in a dose-dependent manner. In the pine needle oil-treated HepG2 cells, the protein levels of phosphorylated (p)-ataxia-telangiectasia mutated (ATM), γ-H2A histone family, member X, p-p53, p-checkpoint kinase 2 and p-cell division cycle 25C were evidently increased, indicating that pine needle oil facilitated G2/M arrest in HepG2 cells through the ATM pathway. In response to the treatment with pine needle oil, ATM was activated in HepG2 cells, which subsequently phosphorylated downstream targets and induced G2/M arrest. In summary, the data of the present study indicated that pine needle oil induces G2/M arrest in HepG2 cells by facilitating ATM activation.
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Affiliation(s)
- Bing Qiu
- Department of Gastroenterology, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
| | - Wei Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang 154002, P.R. China
| | - Wenliang Qiu
- Department of Gastroenterology, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
| | - Wenling Mu
- Department of Gastroenterology, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
| | - Yujing Qin
- Department of Gastroenterology, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
| | - Yongcui Zhu
- Department of Gastroenterology, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
| | - Jianying Zhang
- Department of Gastroenterology, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
| | - Qingyi Wang
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Dongjie Liu
- Department of Gastroenterology, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
| | - Zhangyi Qu
- Department of Hygienic Microbiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
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Wu M, Sheng Z, Jiang L, Liu Z, Bi Y, Shen Y. Overexpression of RAD51B predicts a preferable prognosis for non-small cell lung cancer patients. Oncotarget 2017; 8:91471-91480. [PMID: 29207658 PMCID: PMC5710938 DOI: 10.18632/oncotarget.20676] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/18/2017] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related death. The majority of patients are diagnosed at an incurable advanced stage with poor prognosis. A recent study associated the methylation of homologous recombination genes with expression of immune checkpoints in lung squamous cell carcinoma. However, the correlation between them remains unclear. In our study, we propose that RAD51B, a repair gene in the homologous recombination process, which is noticed to be a key player in the maintenance of chromosome integrity and in sensing DNA damage, can act as an independent factor affecting the prognosis of non-small-cell lung cancer (NSCLC). Univariate analysis showed that overexpression of RAD51B is statistically significant correlated with better prognosis (P=0.013). Further, the multivariate Cox regression analysis showed that the morbidity of patients with high expression of RAD51B was decreased by 26% compared to those with low expression (HR=0.74, 95%CI: 0.59-0.93), especially for the patients with squamous cell carcinoma (HR=0.68, 95%CI: 0.51-0.90). In conclusion, RAD51B in mRNA level can be an important indicator to decide the prognosis of NSCLC and its overexpression predicts a preferable prognosis for NSCLC. Our results serve as a foundation for the investigation of the role of RAD51B in NSCLC, which may lead to potential therapeutic innovations.
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Affiliation(s)
- Mengyin Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College, Soochow University, Suzhou, China
| | - Zufeng Sheng
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College, Soochow University, Suzhou, China
| | - Lingyan Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College, Soochow University, Suzhou, China
| | - Zhengyuan Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College, Soochow University, Suzhou, China
| | - Yuhua Bi
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College, Soochow University, Suzhou, China
| | - Yueping Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College, Soochow University, Suzhou, China
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7
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Häberle L, Hein A, Rübner M, Schneider M, Ekici AB, Gass P, Hartmann A, Schulz-Wendtland R, Beckmann MW, Lo WY, Schroth W, Brauch H, Fasching PA, Wunderle M. Predicting Triple-Negative Breast Cancer Subtype Using Multiple Single Nucleotide Polymorphisms for Breast Cancer Risk and Several Variable Selection Methods. Geburtshilfe Frauenheilkd 2017; 77:667-678. [PMID: 28757654 DOI: 10.1055/s-0043-111602] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Studies of triple-negative breast cancer have recently been extending the inclusion criteria and incorporating additional molecular markers into the selection criteria, opening up scope for targeted therapies. The screening phases required for studies of this type are often prolonged, since the process of determining the molecular subtype and carrying out additional biomarker assessment is time-consuming. Parameters such as germline genotypes capable of predicting the molecular subtype before it becomes available from pathology might be helpful for treatment planning and optimizing the timing and cost of screening phases. This appears to be feasible, as rapid and low-cost genotyping methods are becoming increasingly available. The aim of this study was to identify single nucleotide polymorphisms (SNPs) for breast cancer risk capable of predicting triple negativity, in addition to clinical predictors, in breast cancer patients. METHODS This cross-sectional observational study included 1271 women with invasive breast cancer who were treated at a university hospital. A total of 76 validated breast cancer risk SNPs were successfully genotyped. Univariate associations between each SNP and triple negativity were explored using logistic regression analyses. Several variable selection and regression techniques were applied to identify a set of SNPs that together improve the prediction of triple negativity in addition to the clinical predictors of age at diagnosis and body mass index (BMI). The most accurate prediction method was determined by cross-validation. RESULTS The SNP rs10069690 (TERT, CLPTM1L) was the only significant SNP (corrected p = 0.02) after correction of p values for multiple testing in the univariate analyses. This SNP and three additional SNPs from the genes RAD51B, CCND1, and FGFR2 were selected for prediction of triple negativity. The addition of these SNPs to clinical predictors increased the cross-validated area under the curve (AUC) from 0.618 to 0.625. Age at diagnosis was the strongest predictor, stronger than any genetic characteristics. CONCLUSION Prediction of triple-negative breast cancer can be improved if SNPs associated with breast cancer risk are added to a prediction rule based on age at diagnosis and BMI. This finding could be used for prescreening purposes in complex molecular therapy studies for triple-negative breast cancer.
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Affiliation(s)
- Lothar Häberle
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Breast Center for Franconia, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.,Biostatistics Unit, Department of Gynecology and Obstetrics, Erlangen University Hospital, Erlangen, Germany
| | - Alexander Hein
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Breast Center for Franconia, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Matthias Rübner
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Breast Center for Franconia, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Michael Schneider
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Breast Center for Franconia, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Paul Gass
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Breast Center for Franconia, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, Erlangen University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Rüdiger Schulz-Wendtland
- Institute of Diagnostic Radiology, Erlangen University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Breast Center for Franconia, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Wing-Yee Lo
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tübingen, Tübingen, Germany
| | - Werner Schroth
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tübingen, Tübingen, Germany
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Breast Center for Franconia, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Marius Wunderle
- Department of Gynecology and Obstetrics, Erlangen University Hospital, University Breast Center for Franconia, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
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Whole-Genome Sequencing Reveals Diverse Models of Structural Variations in Esophageal Squamous Cell Carcinoma. Am J Hum Genet 2016; 98:256-74. [PMID: 26833333 PMCID: PMC4746371 DOI: 10.1016/j.ajhg.2015.12.013] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 12/15/2015] [Indexed: 01/02/2023] Open
Abstract
Comprehensive identification of somatic structural variations (SVs) and understanding their mutational mechanisms in cancer might contribute to understanding biological differences and help to identify new therapeutic targets. Unfortunately, characterization of complex SVs across the whole genome and the mutational mechanisms underlying esophageal squamous cell carcinoma (ESCC) is largely unclear. To define a comprehensive catalog of somatic SVs, affected target genes, and their underlying mechanisms in ESCC, we re-analyzed whole-genome sequencing (WGS) data from 31 ESCCs using Meerkat algorithm to predict somatic SVs and Patchwork to determine copy-number changes. We found deletions and translocations with NHEJ and alt-EJ signature as the dominant SV types, and 16% of deletions were complex deletions. SVs frequently led to disruption of cancer-associated genes (e.g., CDKN2A and NOTCH1) with different mutational mechanisms. Moreover, chromothripsis, kataegis, and breakage-fusion-bridge (BFB) were identified as contributing to locally mis-arranged chromosomes that occurred in 55% of ESCCs. These genomic catastrophes led to amplification of oncogene through chromothripsis-derived double-minute chromosome formation (e.g., FGFR1 and LETM2) or BFB-affected chromosomes (e.g., CCND1, EGFR, ERBB2, MMPs, and MYC), with approximately 30% of ESCCs harboring BFB-derived CCND1 amplification. Furthermore, analyses of copy-number alterations reveal high frequency of whole-genome duplication (WGD) and recurrent focal amplification of CDCA7 that might act as a potential oncogene in ESCC. Our findings reveal molecular defects such as chromothripsis and BFB in malignant transformation of ESCCs and demonstrate diverse models of SVs-derived target genes in ESCCs. These genome-wide SV profiles and their underlying mechanisms provide preventive, diagnostic, and therapeutic implications for ESCCs.
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