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JOURNAL ARTICLE
Yiyuan Liu, Jinyao Wu, Lingzhi Chen, Juan Zou, Qiuping Yang, Huiting Tian, Daitian Zheng, Zeqi Ji, Jiehui Cai, Zhiyang Li, Yexi Chen
Breast cancer is the most frequent form of cancer in women and the primary cause of cancer-related deaths globally. DNA methylation and demethylation are important processes in human tumorigenesis. Ten-eleven translocation 3 ( TET3 ) is a DNA demethylase. Prior research has demonstrated that TET3 is highly expressed in various human malignant tumors. However, the exact function and mechanism of TET3 in breast cancer remain unclear. In this study, we investigated TET3 expression in breast cancer and its correlation with clinicopathological characteristics of breast cancer patients...
February 15, 2024: Heliyon
#22
JOURNAL ARTICLE
Talip Zengin, Başak Abak Masud, Tuğba Önal-Süzek
For humans, the parallel processing capability of visual recognition allows for faster comprehension of complex scenes and patterns. This is essential, especially for clinicians interpreting big data for whom the visualization tools play an even more vital role in transforming raw big data into clinical decision making by managing the inherent complexity and monitoring patterns interactively in real time. The Cancer Genome Atlas (TCGA) database's size and data variety challenge the effective utilization of this valuable resource by clinicians and biologists...
January 13, 2024: Cancers
#23
JOURNAL ARTICLE
Cynthia X Ma, Vera J Suman, Souzan Sanati, Kiran Vij, Meenakshi Anurag, A Marilyn Leitch, Gary W Unzeitig, Jeremy Hoog, Aranzazu Fernandez-Martinez, Cheng Fan, Richard A Gibbs, Mark A Watson, Travis J Dockter, Olwen Hahn, Joseph M Guenther, Abigail Caudle, Erika Crouch, Amy Tiersten, Monica Mita, Wajeeha Razaq, Tina J Hieken, Yang Wang, Mothaffar F Rimawi, Anna Weiss, Eric P Winer, Kelly K Hunt, Charles M Perou, Matthew J Ellis, Ann H Partridge, Lisa A Carey
IMPORTANCE: Adding fulvestrant to anastrozole (A+F) improved survival in postmenopausal women with advanced estrogen receptor (ER)-positive/ERBB2 (formerly HER2)-negative breast cancer. However, the combination has not been tested in early-stage disease. OBJECTIVE: To determine whether neoadjuvant fulvestrant or A+F increases the rate of pathologic complete response or ypT1-2N0/N1mic/Ki67 2.7% or less residual disease (referred to as endocrine-sensitive disease) over anastrozole alone...
January 18, 2024: JAMA Oncology
#24
JOURNAL ARTICLE
Mireya Cisneros-Villanueva, Marco Antonio Fonseca-Montaño, Magdalena Ríos-Romero, César López-Camarillo, Silvia Jiménez-Morales, Elizabeth Langley, Alan Sajid Rosette-Rueda, Alberto Cedro-Tanda, Daniel Hernández-Sotelo, Alfredo Hidalgo-Miranda
At the molecular level, triple-negative breast cancer (TNBC) is frequently categorized as PAM50 basal-like subtype, but despite the advances in molecular analyses, the clinical outcome for these subtypes is uncertain. Long non-coding RNAs (lncRNAs) are master regulators of genes involved in hallmarks of cancer, which makes them suitable biomarkers for breast cancer (BRCA) diagnosis and prognosis. Here, we evaluated the regulatory role of lncRNA SOX9-AS1 in these subtypes. Using the BRCA-TCGA cohort, we observed that SOX9-AS1 was significantly overexpressed in basal-like and TNBC in comparison with other BRCA subtypes...
January 17, 2024: Scientific Reports
#25
JOURNAL ARTICLE
Dawei Zhao, Wanfeng Li, Yan Wang, Gengyue Zhang, Xinhua Bai, Hong Yu
BACKGROUND: High temperature requirement A1 (HTRA1), a member of the HTRA family, is a serine peptidase involved in many crucial bioprocesses such as proliferation, mitochondrial homeostasis, apoptosis, and protein quality control. It also plays an important role in the development of various tumors. However, the potential role and mechanisms of action of HTRA1 in breast cancer (BRCA) remain unclear. We conducted a bioinformatics-based study to investigate HTRA1 expression in BRCA alongside its associations with immune-cell infiltrates and survival outcomes...
December 31, 2023: Translational Cancer Research
#26
JOURNAL ARTICLE
Francesco Schettini, Michela Palleschi, Francesca Mannozzi, Fara Brasó-Maristany, Lorenzo Cecconetto, Patricia Galván, Marita Mariotti, Alessia Ferrari, Emanuela Scarpi, Anna Miserocchi, Oriana Nanni, Esther Sanfeliu, Aleix Prat, Andrea Rocca, Ugo De Giorgi
BACKGROUND: The optimal treatment approach for hormone receptor-positive/HER2-negative metastatic breast cancer (HR+/HER2-negative MBC) with aggressive characteristics remains controversial, with lack of randomized trials comparing cyclin-dependent kinase (CDK)4/6-inhibitors (CDK4/6i) + endocrine therapy (ET) with chemotherapy + ET. MATERIALS AND METHODS: We conducted an open-label randomized phase II trial (NCT03227328) to investigate whether chemotherapy + ET is superior to CDK4/6i + ET for HR+/HER2-negative MBC with aggressive features...
January 4, 2024: Oncologist
#27
JOURNAL ARTICLE
Naer A, Pengfei Lyu, Yue Yu, Meiling Liu, Shaohua Cheng, Meiyan Chen, Yunhong Liu, Xuchen Cao
PICALM (phosphatidylinositol-binding clathrin assembly protein) mutations have been linked to a number of human disorders, including leukemia, Alzheimer's disease, and Parkinson's disease. Nevertheless, the effect of PICALM on cancer, particularly on prognosis and immune infiltration in individuals with BRCA, is unknown. We obtained the data of breast cancer patients from The Cancer Genome Atlas (TCGA) database, and analyzed the expression of PICALM in breast cancer, its impact on survival' and its role in tumor immune invasion...
January 4, 2024: Applied Biochemistry and Biotechnology
#28
JOURNAL ARTICLE
Tessa Higgins, Olga Kantor, Beth Harrison, Julia Giordano, Monica McGrath, Harold J Burstein, Stuart J Schnitt, Tasnim Rahman, Halley Vora, Ana Garrido-Castro, Sara M Tolaney, Funda Meric-Bernstam, Tari A King, Elizabeth A Mittendorf
BACKGROUND: We sought to better define estrogen receptor-low-positive (ER-low+) breast cancer biology and determine the utility of the Oncotype DX Breast Recurrence Score® (RS) assay in this population. METHODS: Patients with information regarding percentage ER positivity and PAM50 subtype were identified in The Cancer Genome Atlas (TCGA) and subtype distribution was determined. Next, patients with ER-low+ (ER 1-10%), HER2- breast cancer undergoing upfront surgery with known RS result were identified in the National Cancer Database (NCDB) and our institutional Dana-Farber Brigham Cancer Center (DF/BCC) database; RS distribution was examined...
December 31, 2023: Annals of Surgical Oncology
#29
JOURNAL ARTICLE
Yaqing Zhou, Xing Wei, Weimiao Li, Shuqun Zhang, Yonglin Zhao
Breast cancer (BRCA) is a common neoplasm characterized by high levels of molecular heterogeneity. Previous studies have noted the importance of mitophagy for the progression and prognosis of BRCA. However, little was found in the similarity and difference of mitophagy-related gene expression patterns of BRCA. This study intended to investigate the differences in functional activation, somatic mutation, and immune-related characteristics among different subtypes of BRCA associated with mitophagy. Based on bioinformatics analysis, we systematically examined the heterogeneity of breast cancer concerning mitophagy and observed two distinct subtypes with different tumor microenvironments and prognoses...
December 2023: Heliyon
#30
Evan D Paul, Barbora Huraiová, Natália Valková, Natalia Birknerova, Daniela Gábrišová, Sona Gubova, Helena Ignačáková, Tomáš Ondris, Silvia Bendíková, Jarmila Bíla, Katarína Buranovská, Diana Drobná, Zuzana Krchnakova, Maryna Kryvokhyzha, Daniel Lovíšek, Viktoriia Mamoilyk, Veronika Mančíková, Nina Vojtaššáková, Michaela Ristová, Iñaki Comino-Méndez, Igor Andrašina, Pavel Morozov, Thomas Tuschl, Fresia Pareja, Pavol Čekan
On a retrospective cohort of 1,082 FFPE breast tumors, we demonstrated the analytical validity of a test using multiplexed RNA-FISH-guided laser capture microdissection (LCM) coupled with RNA-sequencing (mFISHseq), which showed 93% accuracy compared to immunohistochemistry. The combination of these technologies makes strides in i) precisely assessing tumor heterogeneity, ii) obtaining pure tumor samples using LCM to ensure accurate biomarker expression and multigene testing, and iii) providing thorough and granular data from whole transcriptome profiling...
December 6, 2023: medRxiv
#31
JOURNAL ARTICLE
Aristeidis G Telonis, Daniel A Rodriguez, Philip M Spanheimer, Maria E Figueroa, Neha Goel
OBJECTIVE: We aim to determine whether incremental changes in genetic ancestry percentages influence molecular and clinical outcome characteristics of breast cancer in an admixed population. SUMMARY BACKGROUND DATA: Breast cancer patients are predominantly characterized as "Black" or "White" based on self-identified race/ethnicity or arbitrary genetic ancestry cutoffs. This limits scientific discovery in populations that are admixed or of mixed race/ethnicity as they cannot be classified based on historical race/ethnicity boxes or genetic ancestry cutoffs...
December 11, 2023: Annals of Surgery
#32
JOURNAL ARTICLE
Juana Moro, Agustina Grinpelc, Paula Lucía Farré, Rocío Belén Duca, Ezequiel Lacunza, Karen Daniela Graña, Georgina Daniela Scalise, Guillermo Nicolás Dalton, Cintia Massillo, Flavia Piccioni, Federico Dimase, Emilio Batagelj, Adriana De Siervi, Paola De Luca
Metabolic syndrome (MS) is a risk factor for breast cancer (BC) that increases its aggressiveness and metastasis. The prevalence of MS is higher in triple-negative breast cancer (TNBC), which is the molecular subtype with the worst prognosis. The molecular mechanisms underlying this association have not been fully elucidated. MiRNAs are small, non-coding RNAs that regulate gene expression. Aberrant expression of miRNAs in both tissues and fluids are linked to several pathologies. The aim of this work was to identify circulating miRNAs in patients with alterations associated with MS (AAMS) that also impact on BC...
November 25, 2023: International Journal of Molecular Sciences
#33
JOURNAL ARTICLE
Yu-Tien Chang, Zhi-Jie Hong, Jyh-Cherng Yu, Wei-Zhi Lin, Tzu-Ya Huang, Hsueh-Han Tsai, An-Chieh Feng, Kuo-Feng Hsu, Chi-Cheng Huang, Chi-Ming Chu, Chia-Ming Liang, Guo-Shiou Liao
Gene expression signatures provide valuable information to guide postoperative treatment in breast cancer (BC) patients. However, genetic tests are prohibitively expensive for the majority of BC patients. Immunohistochemical staining (IHC) subtype classification system has been widely used for treatment guideline and is affordable to most BC patients. We aimed to revise immunohistochemical staining (IHC) subtyping to better match gene expression-based Prediction Analysis of Microarray 50 (PAM50) subtyping. Real world data of 372 BC patients were recruited in the Tri-Service General Hospital between Jan 2019 and Dec 2021...
2023: American Journal of Cancer Research
#34
JOURNAL ARTICLE
Synnøve Yndestad, Christina Engebrethsen, Andrea Herencia-Ropero, Oleksii Nikolaienko, Olav K Vintermyr, Reidun K Lillestøl, Laura Minsaas, Beryl Leirvaag, Gjertrud T Iversen, Bjørnar Gilje, Egil S Blix, Helge Espelid, Steinar Lundgren, Jürgen Geisler, Hildegunn S Aase, Turid Aas, Einar G Gudlaugsson, Alba Llop-Guevara, Violeta Serra, Emiel A M Janssen, Per E Lønning, Stian Knappskog, Hans P Eikesdal
PURPOSE: Homologous recombination deficiency (HRD) is highly prevalent in triple-negative breast cancer (TNBC) and associated with response to PARP inhibition (PARPi). Here, we studied the prevalence of HRD in non-TNBC to assess the potential for PARPi in a wider group of patients with breast cancer. METHODS: HRD status was established using targeted gene panel sequencing (360 genes) and BRCA1 methylation analysis of pretreatment biopsies from 201 patients with primary breast cancer in the phase II PETREMAC trial (ClinicalTrials...
September 2023: JCO Precision Oncology
#35
JOURNAL ARTICLE
Anupama Praveen Kumar, Diego Vicente, Jianfang Liu, Praveen-Kumar Raj-Kumar, Brenda Deyarmin, Xiaoying Lin, Craig D Shriver, Hai Hu
PURPOSE: To explore the association of clinicopathologic and molecular factors with the occurrence of positive margins after first surgery in breast cancer. METHODS: The clinical and RNA-Seq data for 951 (75 positive and 876 negative margins) primary breast cancer patients from The Cancer Genome Atlas (TCGA) were used. The role of each clinicopathologic factor for margin prediction and also their impact on survival were evaluated using logistic regression, Fisher's exact test, and Cox proportional hazards regression models...
December 1, 2023: Breast Cancer Research and Treatment
#36
JOURNAL ARTICLE
Lanying Wei, Yucui Xin, Mengchen Pu, Yingsheng Zhang
To effectively understand the underlying mechanisms of disease and inform the development of personalized therapies, it is critical to harness the power of differential co-expression (DCE) network analysis. Despite the promise of DCE network analysis in precision medicine, current approaches have a major limitation: they measure an average differential network across multiple samples, which means the specific etiology of individual patients is often overlooked. To address this, we present Cosinet, a DCE-based single-sample network rewiring degree quantification tool...
February 2024: Life Science Alliance
#37
JOURNAL ARTICLE
William Lautert-Dutra, Camila M Melo, Luiz P Chaves, Francisco C Souza, Cheryl Crozier, Adam E Sundby, Elizabeth Woroszchuk, Fabiano P Saggioro, Filipe S Avante, Rodolfo B Dos Reis, Jeremy A Squire, Jane Bayani
The diverse clinical outcomes of prostate cancer have led to the development of gene signature assays predicting disease progression. Improved prostate cancer progression biomarkers are needed as current RNA biomarker tests have varying success for intermediate prostate cancer. Interest grows in universal gene signatures for invasive carcinoma progression. Early breast and prostate cancers share characteristics, including hormone dependence and BRCA1/2 mutations. Given the similarities in the pathobiology of breast and prostate cancer, we utilized the NanoString BC360 panel, comprising the validated PAM50 classifier and pathway-specific signatures associated with general tumor progression as well as breast cancer-specific classifiers...
2023: Frontiers in Oncology
#38
Michael D Iglesia, Reyka G Jayasinghe, Siqi Chen, Nadezhda V Terekhanova, John M Herndon, Erik Storrs, Alla Karpova, Daniel Cui Zhou, Nataly Naser Al Deen, Andrew T Shinkle, Rita Jui-Hsien Lu, Wagma Caravan, Andrew Houston, Yanyan Zhao, Kazuhito Sato, Preet Lal, Cherease Street, Fernanda Martins Rodrigues, Austin N Southard-Smith, André Luiz N Targino da Costa, Houxiang Zhu, Chia-Kuei Mo, Lisa Crowson, Robert S Fulton, Matthew A Wyczalkowski, Catrina C Fronick, Lucinda A Fulton, Hua Sun, Sherri R Davies, Elizabeth L Appelbaum, Sara E Chasnoff, Madelyn Carmody, Candace Brooks, Ruiyang Liu, Michael C Wendl, Clara Oh, Diane Bender, Carlos Cruchaga, Oscar Harari, Andrea Bredemeyer, Kory Lavine, Ron Bose, Julie Margenthaler, Jason M Held, Samuel Achilefu, Foluso Ademuyiwa, Rebecca Aft, Cynthia Ma, Graham A Colditz, Tao Ju, Stephen T Oh, James Fitzpatrick, E Shelley Hwang, Kooresh I Shoghi, Milan G Chheda, Deborah J Veis, Feng Chen, Ryan C Fields, William E Gillanders, Li Ding
Breast cancer is a heterogeneous disease, and treatment is guided by biomarker profiles representing distinct molecular subtypes. Breast cancer arises from the breast ductal epithelium, and experimental data suggests breast cancer subtypes have different cells of origin within that lineage. The precise cells of origin for each subtype and the transcriptional networks that characterize these tumor-normal lineages are not established. In this work, we applied bulk, single-cell (sc), and single-nucleus (sn) multi-omic techniques as well as spatial transcriptomics and multiplex imaging on 61 samples from 37 breast cancer patients to show characteristic links in gene expression and chromatin accessibility between breast cancer subtypes and their putative cells of origin...
November 2, 2023: bioRxiv
#39
REVIEW
Qintao Ge, Jiawei Li, Feixiang Yang, Xuefeng Tian, Meng Zhang, Zongyao Hao, Chaozhao Liang, Jialin Meng
Tumour classifications play a pivotal role in prostate cancer (PCa) management. It can predict the clinical outcomes of PCa as early as the disease is diagnosed and then guide therapeutic schemes, such as active monitoring, standalone surgical intervention, or surgery supplemented with postoperative adjunctive therapy, thereby circumventing disease exacerbation and excessive treatment. Classifications based on clinicopathological features, such as prostate cancer-specific antigen, Gleason score, and TNM stage, are still the main risk stratification strategies and have played an essential role in standardized clinical decision-making...
2023: Annals of Medicine
#40
JOURNAL ARTICLE
Aleix Prat, Nadia Solovieff, Fabrice Andre, Joyce O'Shaughnessy, David A Cameron, Wolfgang Janni, Gabe S Sonke, Yoon-Sim Yap, Denise A Yardley, Ann H Partridge, Astrid Thuerigen, Juan Pablo Zarate, Agnes Lteif, Fei Su, Lisa A Carey
BACKGROUND: The MONALEESA-2, -3, -7 trials demonstrated statistically significant and clinically meaningful progression-free survival (PFS) and overall survival (OS) benefits with ribociclib + endocrine therapy (ET) vs ET alone in hormone receptor-positive, human epidermal growth factor receptor 2-negative (HR+/HER2-) advanced breast cancer (ABC). Understanding the association of intrinsic subtypes with survival outcomes could potentially guide treatment decisions. Here, we evaluated the association of intrinsic subtypes with OS in MONALEESA-2, -3, -7...
November 8, 2023: Clinical Cancer Research
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