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Breast cancer genomic testing

Haiyan Gao, Mei Yang, Xiaolan Zhang
The present study aimed to investigate potential recurrence-risk biomarkers based on significant pathways for Luminal A breast cancer through gene expression profile analysis. Initially, the gene expression profiles of Luminal A breast cancer patients were downloaded from The Cancer Genome Atlas database. The differentially expressed genes (DEGs) were identified using a Limma package and the hierarchical clustering analysis was conducted for the DEGs. In addition, the functional pathways were screened using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses and rank ratio calculation...
April 2018: Oncology Letters
Jingxiao Wang, Xinjie Yang, Haibo Han, Limin Wang, Weiqian Bao, Shanshan Wang, Robert M Hoffman, Meng Yang, Hui Qi, Chao An, Kaiwen Hu
Objective: Triple-negative breast cancer (TNBC) is highly invasive and metastatic, which is in urgent need of transformative therapeutics. Tubeimu (TBM), the rhizome of Bolbostemma paniculatum (Maxim.) Franquet, is one of the Chinese medicinal herbs used for breast diseases since the ancient times. The present study evaluated the efficacy, especially the anti-metastatic effects of the dichloromethane extract of Tubeimu (ETBM) on TNBC orthotopic mouse models and cell lines. Methods: We applied real-time imaging on florescent orthotopic TNBC mice model and tested cell migration and invasion abilities with MDA-MB-231 cell line...
February 2018: Chinese Journal of Cancer Research, Chung-kuo Yen Cheng Yen Chiu
Lauren E Wilson, Craig Evan Pollack, Melissa A Greiner, Michaela A Dinan
PURPOSE: We sought to determine whether physician-level characteristics were associated with 21-gene recurrence score (RS) genomic testing to evaluate recurrence risk and benefit of adjuvant chemotherapy in patients with estrogen receptor-positive, node-negative breast cancer. METHODS: Retrospective cohort study of a nationally representative sample of Medicare beneficiaries using Surveillance, Epidemiology, and End Results program-Medicare data linked with the American Medical Association physician master file...
March 13, 2018: Breast Cancer Research and Treatment
Nirmesh Patel, Daniel Weekes, Konstantinos Drosopoulos, Patrycja Gazinska, Elodie Noel, Mamun Rashid, Hasan Mirza, Jelmar Quist, Fara Brasó-Maristany, Sumi Mathew, Riccardo Ferro, Ana Mendes Pereira, Cynthia Prince, Farzana Noor, Erika Francesch-Domenech, Rebecca Marlow, Emanuele de Rinaldis, Anita Grigoriadis, Spiros Linardopoulos, Pierfrancesco Marra, Andrew N J Tutt
Triple negative breast cancers (TNBCs) lack recurrent targetable driver mutations but demonstrate frequent copy number aberrations (CNAs). Here, we describe an integrative genomic and RNAi-based approach that identifies and validates gene addictions in TNBCs. CNAs and gene expression alterations are integrated and genes scored for pre-specified target features revealing 130 candidate genes. We test functional dependence on each of these genes using RNAi in breast cancer and non-malignant cells, validating malignant cell selective dependence upon 37 of 130 genes...
March 13, 2018: Nature Communications
Qiong Song, Qiu Chen, Qimin Wang, Longqiu Yang, Dongdong Lv, Guangli Jin, Jiaying Liu, Baolin Li, Xuejie Fei
BACKGROUND: Breast cancer is one of the leading causes of death in women worldwide. Fast growth is the important character of breast cancer, which makes sure the subsequent metastasize and invasion breast cancer. Golgi related genes GOLPH3 has been reported to regulate many kinds of cancers proliferation. However, its upregulator remains largely unknown. miRNA modulate gene expression by post-transcriptional repression to participate in many signaling pathway of breast cancer cell proliferation...
March 9, 2018: BMC Cancer
Joseph S Baxter, Olivia C Leavy, Nicola H Dryden, Sarah Maguire, Nichola Johnson, Vita Fedele, Nikiana Simigdala, Lesley-Ann Martin, Simon Andrews, Steven W Wingett, Ioannis Assiotis, Kerry Fenwick, Ritika Chauhan, Alistair G Rust, Nick Orr, Frank Dudbridge, Syed Haider, Olivia Fletcher
Genome-wide association studies (GWAS) have identified approximately 100 breast cancer risk loci. Translating these findings into a greater understanding of the mechanisms that influence disease risk requires identification of the genes or non-coding RNAs that mediate these associations. Here, we use Capture Hi-C (CHi-C) to annotate 63 loci; we identify 110 putative target genes at 33 loci. To assess the support for these target genes in other data sources we test for associations between levels of expression and SNP genotype (eQTLs), disease-specific survival (DSS), and compare them with somatically mutated cancer genes...
March 12, 2018: Nature Communications
Trinidad Dierssen-Sotos, Camilo Palazuelos-Calderón, José-Juan Jiménez-Moleón, Nuria Aragonés, Jone M Altzibar, Gemma Castaño-Vinyals, Vicente Martín-Sanchez, Inés Gómez-Acebo, Marcela Guevara, Adonina Tardón, Beatriz Pérez-Gómez, Pilar Amiano, Victor Moreno, Antonio J Molina, Jéssica Alonso-Molero, Conchi Moreno-Iribas, Manolis Kogevinas, Marina Pollán, Javier Llorca
BACKGROUND: Reproductive factors are well known risk factors for breast cancer; however, little is known about how genetic variants in hormonal pathways interact with that relationship. METHODS: One thousand one hundred thirty nine cases of breast cancer in women and 1322 frequency-matched controls were compared. Genetic variants in hormonal pathways (identified in the Kyoto Encyclopedia of Genes and Genomes) were screened according to their relationship with breast cancer using the Cochran-Armitage statistic...
March 12, 2018: BMC Cancer
Maria Sol Brassesco, Julia Alejandra Pezuk, Karina Bezerra Salomao, Gabriela Molinari Roberto, Carlos Alberto Scrideli, Luiz Gonzaga Tone
Over the last decade, the inhibition of PLK1 has proven potent antiproliferative activity in vitro. However, the effectiveness of most synthetic targeted drugs has not translated into clinics. Herein, we investigated the in vitro effects of two second-generation PLK1 inhibitors BI 6727 and GSK461364 in breast cancer cell lines as monotherapy or in combination with other drugs or ionizing radiation. MATERIAL AND METHODS: Cell survival was analyzed through XTT®, clonogenicity and caspase-3 activation assays were also studied, and drug interactions analyzed through a nonlinear regression of a sigmoid dose response model...
February 28, 2018: Anti-cancer Agents in Medicinal Chemistry
I V Deryusheva, M Tsyganov, E Y Garbukov, M K Ibragimova, Ju G Kzhyshkovska, E Slonimskaya, N V Cherdyntseva, N V Litviakov
One of the factors providing the diversity and heterogeneity of malignant tumors, particularly breast cancer, are genetic variations, due to gene polymorphism, and, especially, the phenomenon of loss of heterozygosity (LOH). It has been shown that LOH in some genes could be a good prognostic marker. AIM: To perform genome-wide study on LOH in association with metastasis-free survival in breast cancer. MATERIALS AND METHODS: The study involved 68 patients with breast cancer...
July 2017: Experimental Oncology
Christine Desmedt, Roberto Salgado, Marco Fornili, Giancarlo Pruneri, Gert Van den Eynden, Gabriele Zoppoli, Françoise Rothé, Laurence Buisseret, Soizic Garaud, Karen Willard-Gallo, David Brown, Yacine Bareche, Ghizlane Rouas, Christine Galant, François Bertucci, Sherene Loi, Giuseppe Viale, Angelo Di Leo, Andrew R Green, Ian O Ellis, Emad A Rakha, Denis Larsimont, Elia Biganzoli, Christos Sotiriou
Background: Invasive lobular breast cancer (ILC) is the second most common histological subtype of breast cancer after invasive ductal cancer (IDC). Here, we aimed at evaluating the prevalence, levels, and composition of tumor-infiltrating lymphocytes (TILs) and their association with clinico-pathological and outcome variables in ILC, and to compare them with IDC. Methods: We considered two patient series with TIL data: a multicentric retrospective series (n = 614) and the BIG 02-98 study (n = 149 ILC and 807 IDC)...
February 20, 2018: Journal of the National Cancer Institute
Junnan Xu, Tao Sun, Xiangyu Guo, Yan Wang, Mingxi Jing
A number of previous studies have indicated the presence of a link between estrogen receptor-α (ERα) methylation and triple-negative breast cancer (TNBC). However, the association between ERα methylation and drug resistance during the treatment of TNBC remains unclear. Methylation-specific polymerase chain reaction was used to investigate the methylation of ERα in the genomic DNA of 35 patients with TNBC who were defined as cisplatin-based chemotherapy-resistant using chemosensitivity testing. Survival probabilities by covariates were assessed using Kaplan-Meier estimator survival analysis and Cox's proportional hazards models, adjusting for age, menopausal status, tumor size, lymph node metastasis and ERα promoter DNA methylation...
March 2018: Oncology Letters
Amanda M Willis, Sian K Smith, Bettina Meiser, Mandy L Ballinger, David M Thomas, Martin Tattersall, Mary-Anne Young
Germline genomic testing is increasingly used in research to identify genetic causes of disease, including cancer. However, there is evidence that individuals who are notified of clinically actionable research findings have difficulty making informed decisions regarding uptake of genetic counseling for these findings. This study aimed to produce and pilot test a decision aid to assist participants in genomic research studies who are notified of clinically actionable research findings to make informed choices regarding uptake of genetic counseling...
February 17, 2018: Journal of Genetic Counseling
Allison H West, Kathleen R Blazer, Jessica Stoll, Matthew Jones, Caroline M Weipert, Sarah M Nielsen, Sonia S Kupfer, Jeffrey N Weitzel, Olufunmilayo I Olopade
Comprehensive genomic cancer risk assessment (GCRA) helps patients, family members, and providers make informed choices about cancer screening, surgical and chemotherapeutic risk reduction, and genetically targeted cancer therapies. The increasing availability of multigene panel tests for clinical applications allows testing of well-defined high-risk genes, as well as moderate-risk genes, for which the penetrance and spectrum of cancer risk are less well characterized. Moderate-risk genes are defined as genes that, when altered by a pathogenic variant, confer a 2 to fivefold relative risk of cancer...
February 14, 2018: Familial Cancer
Claus H Gravholt, Simon Chang, Mikkel Wallentin, Jens Fedder, Philip Moore, Anne Skakkebæk
Although first identified over 70 years ago, Klinefelter syndrome (KS) continue to pose significant diagnostic challenges, as many patients are still misdiagnosed, or remain undiagnosed. In fact, as few as 25% of KS patients are accurately diagnosed, and most of these diagnoses are not made until adulthood. Classic characteristics of KS include small testes, infertility, hypergonadothropic hypogonadism, and cognitive impairment. However, the pathophysiology behind KS is not well understood, although genetic effects are also thought to play a role...
February 9, 2018: Endocrine Reviews
Kevin Litchfield, Chey Loveday, Max Levy, Darshna Dudakia, Elizabeth Rapley, Jeremie Nsengimana, D Tim Bishop, Alison Reid, Robert Huddart, Peter Broderick, Richard S Houlston, Clare Turnbull
Testicular germ cell tumour (TGCT), the most common cancer in young men, has a significant heritable basis that has long raised questions as to the existence of underlying major high-penetrance susceptibility gene(s). To determine the contribution of rare gene mutations to the inherited risk of TGCT, we analysed germline whole-exome data for 919 TGCT cases and 1609 cancer-free controls. We compared frequencies between TGCT cases and controls of rare (<1%) and low-frequency (1-5%) coding variants (1) individually and (2) collapsed at the gene level via burden testing (T1, disruptive; T2, all deleterious; and T3, all nonsynonymous) using Fisher's exact test with Bonferroni correction of significance thresholds...
February 9, 2018: European Urology
Jiebiao Wang, Qianying Liu, Brandon L Pierce, Dezheng Huo, Olufunmilayo I Olopade, Habibul Ahsan, Lin S Chen
There is a growing recognition that gene-environment interaction (G × E) plays a pivotal role in the development and progression of complex diseases. Despite a wealth of genetic data on various complex diseases/traits generated from association and sequencing studies, detecting G × E via genome-wide analysis remains challenging due to power issues. In genome-wide G × E studies, a common strategy to improve power is to first conduct a filtering test and retain only the genetic variants that pass the filtering step for subsequent G × E analyses...
February 11, 2018: Genetic Epidemiology
Xuelu Li, Yuan Zhang, Jinlei Ding, Min Wang, Na Li, Hui Yang, Kainan Wang, Dandan Wang, Peter Ping Lin, Man Li, Zuowei Zhao, Pixu Liu
Despite marked advances in breast cancer therapy, breast cancer-associated leptomeningeal metastasis (LM), a particularly aggressive syndrome with multifocal seeding of the leptomeninges by tumor cells, still carries an abysmal prognosis. A major problem with breast cancer LM surveillance is the lack of an effective and sensitive means to track dynamic changes of the disease. Cytology detection of cerebrospinal fluid (CSF) is considered the gold standard for LM diagnosis but has a high false-negative rate with a limited sensitivity...
January 5, 2018: Oncotarget
Ana Isabel Sánchez-Bermúdez, Ma Desamparados Sarabia-Meseguer, Ángeles García-Aliaga, Miguel Marín-Vera, José Antonio Macías-Cerrolaza, Pilar Sánchez Henaréjos, Verónica Guardiola-Castillo, Francisco Ayala-de la Peña, José Luis Alonso-Romero, José Antonio Noguera-Velasco, Francisco Ruiz-Espejo
RAD51C and RAD51D have been defined as susceptibility genes for hereditary breast and ovarian cancer syndrome in several studies. In the present study, a mutation analysis of these genes was performed on non BRCA1/2 families. RAD51C and RAD51D genes were analyzed in 141 and 77 families, respectively. The analysis included direct sequencing and multiple ligation probe analysis. The RAD51C pathogenic variant c.404G > A was identified in a breast and ovarian cancer family (0.7%), while the RAD51D pathogenic variant c...
January 31, 2018: European Journal of Medical Genetics
Suhas Vasaikar, Giorgos Tsipras, Natalia Landázuri, Helena Costa, Vanessa Wilhelmi, Patrick Scicluna, Huanhuan L Cui, Abdul-Aleem Mohammad, Belghis Davoudi, Mingmei Shang, Sharan Ananthaseshan, Klas Strååt, Giuseppe Stragliotto, Afsar Rahbar, Kum Thong Wong, Jesper Tegner, Koon-Chu Yaiw, Cecilia Söderberg-Naucler
BACKGROUND: Glioblastoma (GBM) is the most common malignant brain tumor with median survival of 12-15 months. Owing to uncertainty in clinical outcome, additional prognostic marker(s) apart from existing markers are needed. Since overexpression of endothelin B receptor (ETBR) has been demonstrated in gliomas, we aimed to test whether ETBR is a useful prognostic marker in GBM and examine if the clinically available endothelin receptor antagonists (ERA) could be useful in the disease treatment...
February 6, 2018: BMC Cancer
Özge Saatci, Simone Borgoni, Özge Akbulut, Selvi Durmuş, Umar Raza, Erol Eyüpoğlu, Can Alkan, Aytekin Akyol, Özgür Kütük, Stefan Wiemann, Özgür Şahin
Trastuzumab-refractory, HER2 (human epidermal growth factor receptor 2)-positive breast cancer is commonly treated with trastuzumab emtansine (T-DM1), an antibody-drug conjugate of trastuzumab and the microtubule-targeting agent, DM1. However, drug response reduces greatly over time due to acquisition of resistance whose molecular mechanisms are mostly unknown. Here, we uncovered a novel mechanism of resistance against T-DM1 by combining whole transcriptome sequencing (RNA-Seq), proteomics and a targeted small interfering RNA (siRNA) sensitization screen for molecular level analysis of acquired and de novo T-DM1-resistant models of HER2-overexpressing breast cancer...
February 2, 2018: Oncogene
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