scholarly journals Cis-acting Super-Enhancer lncRNAs as Biomarkers of Early-Stage Breast Cancer

2021 ◽  
Author(s):  
Ali Salman Ropri ◽  
Rebecca DeVaux ◽  
Jonah Eng ◽  
Sridar V. Chittur ◽  
Jason Herschkowitz
Keyword(s):  
Breast Cancer ◽  
Ductal Carcinoma ◽  
Early Stage ◽  
Global Analysis ◽  
Standard Of Care ◽  
Differentially Expressed ◽  
Current Standard ◽  
Cis Acting ◽  
Super Enhancer ◽  
Estrogen Production

Abstract Background Increased breast cancer screening over the past four decades has led to a substantial rise in the diagnosis of ductal carcinoma in situ (DCIS). Although DCIS lesions precede invasive ductal carcinoma (IDC), they do not always transform into cancer. The current standard-of-care for DCIS is an aggressive course of therapy to prevent invasive and metastatic disease resulting in over-diagnosis and over-treatment. Thus, there is a critical need to identify functional determinants of progression of DCIS to IDC to allow discrimination between indolent and aggressive disease. Recent studies show that super-enhancers, in addition to promoting other gene transcription, are themselves transcribed producing super-enhancer associated long noncoding RNAs (SE-lncRNAs). These SE-lncRNAs can interact with their associated enhancer regions in cis and influence activities and expression of neighboring genes. Furthermore, they represent a novel, untapped group of therapeutic targets.MethodsWith an integrative analysis of enhancer loci with global expression of SE-lncRNAs in the MCF10A progression series, we have identified differentially expressed SE-lncRNAs which can identify mechanisms for DCIS to IDC progression. Furthermore, cross-referencing these SE-lncRNAs with patient samples in the TCGA database, we have unveiled 31 clinically relevant SE-lncRNAs that potentially interact with their enhancer to regulate nearby gene expression. To complement SE-lncRNA expression studies, we conducted an unbiased global analysis of super-enhancers that are acquired or lost in progression. ResultsHere we designate SE-lncRNAs RP11-379F4.4 and RP11-465B22.8 as potential markers of progression of DCIS to IDC through regulation of the expression of their neighboring genes (RARRES1 and miR200b respectively). Moreover, we classified 403 super-enhancer regions in MCF10A normal cells, 627 in AT1, 1053 in DCIS, and 320 in CA1 cells. Comparison analysis of acquired/lost super-enhancer regions with super-enhancer regions classified in 47 ER positive patients, 10 Triple Negative Breast Cancer (TNBC) patients, and 11 TNBC cell lines reveal critically acquired pathways including STAT signaling and NF-kB signaling. In contrast, protein folding and local estrogen production are identified as major pathways lost in progression.ConclusionCollectively, these analyses identify differentially expressed SE-lncRNAs and acquired/lost super-enhancers in progression of breast cancer important for promoting DCIS lesions to IDC.

scholarly journals Cis-acting super-enhancer lncRNAs as biomarkers to early-stage breast cancer

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Ali S. Ropri ◽  
Rebecca S. DeVaux ◽  
Jonah Eng ◽  
Sridar V. Chittur ◽  
Jason I. Herschkowitz
Keyword(s):  
Breast Cancer ◽  
Ductal Carcinoma ◽  
Early Stage ◽  
Global Analysis ◽  
Standard Of Care ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Current Standard ◽  
Super Enhancer ◽  
Estrogen Production

Abstract Background Increased breast cancer screening over the past four decades has led to a substantial rise in the diagnosis of ductal carcinoma in situ (DCIS). Although DCIS lesions precede invasive ductal carcinoma (IDC), they do not always transform into cancer. The current standard-of-care for DCIS is an aggressive course of therapy to prevent invasive and metastatic disease resulting in over-diagnosis and over-treatment. Thus, there is a critical need to identify functional determinants of progression of DCIS to IDC to allow discrimination between indolent and aggressive disease. Recent studies show that super-enhancers, in addition to promoting other gene transcription, are themselves transcribed producing super-enhancer associated long noncoding RNAs (SE-lncRNAs). These SE-lncRNAs can interact with their associated enhancer regions in cis and influence activities and expression of neighboring genes. Furthermore, they represent a novel, untapped group of therapeutic targets. Methods With an integrative analysis of enhancer loci with global expression of SE-lncRNAs in the MCF10A progression series, we have identified differentially expressed SE-lncRNAs which can identify mechanisms for DCIS to IDC progression. Furthermore, cross-referencing these SE-lncRNAs with patient samples in the The Cancer Genome Atlas (TCGA) database, we have unveiled 27 clinically relevant SE-lncRNAs that potentially interact with their enhancer to regulate nearby gene expression. To complement SE-lncRNA expression studies, we conducted an unbiased global analysis of super-enhancers that are acquired or lost in progression. Results Here we designate SE-lncRNAs RP11-379F4.4 and RP11-465B22.8 as potential markers of progression of DCIS to IDC through regulation of the expression of their neighboring genes (RARRES1 and miR-200b, respectively). Moreover, we classified 403 super-enhancer regions in MCF10A normal cells, 627 in AT1, 1053 in DCIS, and 320 in CA1 cells. Comparison analysis of acquired/lost super-enhancer regions with super-enhancer regions classified in 47 ER positive patients, 10 triple negative breast cancer (TNBC) patients, and 11 TNBC cell lines reveal critically acquired pathways including STAT signaling and NF-kB signaling. In contrast, protein folding, and local estrogen production are identified as major pathways lost in progression. Conclusion Collectively, these analyses identify differentially expressed SE-lncRNAs and acquired/lost super-enhancers in progression of breast cancer important for promoting DCIS lesions to IDC.

scholarly journals De-Escalation of Therapy for Patients with Early-Stage Squamous Cell Carcinoma of the Anus

Cancers ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 2099
Author(s):  
Eric Miller ◽  
Jose Bazan
Keyword(s):  
Squamous Cell Carcinoma ◽  
Radiation Therapy ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Early Stage ◽  
Intensity Modulated Radiation Therapy ◽  
Late Toxicity ◽  
Standard Of Care ◽  
The Elderly ◽  
Current Standard

The incidence of squamous cell carcinoma of the anus (SCCA) is increasing, particularly in the elderly, with increased mortality in this age group. While the current standard of care for localized SCCA remains chemoradiation (CRT), completion of this treatment can be challenging with risks for severe acute and late toxicity. It remains unclear if full course CRT is required for the management of early-stage SCCA or if de-escalation of treatment is possible without compromising patient outcomes. Alternative therapies include radiation therapy alone or local excision for appropriate patients. Modifying standard CRT may also reduce toxicity including the routine use of intensity-modulated radiation therapy for treatment delivery, modification of treatment volumes, and selection and dosing of concurrent systemic therapy agents. Finally, we provide an overview of currently accruing prospective trials focused on defining the role of de-escalation of therapy in patients with early-stage SCCA.

Uncommon Breast Malignancies: Presentation Pattern, Prognostic Issue and Treatment Outcome in an Italian Single Institution Experience

2013 ◽  
Vol 99 (1) ◽  
pp. 39-44
Author(s):  
Claudia Maria Regina Bareggi ◽  
Dario Consonni ◽  
Barbara Galassi ◽  
Donatella Gambini ◽  
Elisa Locatelli ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Treatment Outcome ◽  
Invasive Ductal Carcinoma ◽  
Ductal Carcinoma ◽  
Early Stage ◽  
Medullary Carcinoma ◽  
Mucinous Carcinoma ◽  
Lymph Node Involvement ◽  
Tubular Carcinoma ◽  
Breast Malignancies

Aims and background Often neglected by large clinical trials, patients with uncommon breast malignancies have been rarely analyzed in large series. Patients and methods Of 2,052 patients diagnosed with breast cancer and followed in our Institution from January 1985 to December 2009, we retrospectively collected data on those with uncommon histotypes, with the aim of investigating their presentation characteristics and treatment outcome. Results Rare histotypes were identified in 146 patients (7.1% of our total breast cancer population), being classified as follows: tubular carcinoma in 75 (51.4%), mucinous carcinoma in 36 (24.7%), medullary carcinoma in 25 (17.1%) and papillary carcinoma in 10 patients (6.8%). Whereas age at diagnosis was not significantly different among the diverse diagnostic groups, patients with medullary and papillary subtypes had a higher rate of lymph node involvement, similar to that of invasive ductal carcinoma. Early stage diagnosis was frequent, except for medullary carcinoma. Overall, in comparison with our invasive ductal carcinoma patients, those with rare histotypes showed a significantly lower risk of recurrence, with a hazard ratio of 0.28 (95% CI, 0.12–0.62; P = 0.002). Conclusions According to our analysis, patients with uncommon breast malignancies are often diagnosed at an early stage, resulting in a good prognosis with standard treatment.

scholarly journals Comparison of Estrogen and Progesterone Receptor Antibody Reagents Using Proficiency Testing Data

2017 ◽  
Vol 141 (10) ◽  
pp. 1402-1412 ◽  
Author(s):  
Megan L. Troxell ◽  
Thomas Long ◽  
Jason L. Hornick ◽  
Abiy B. Ambaye ◽  
Kristin C. Jensen
Keyword(s):  
Breast Cancer ◽  
Progesterone Receptor ◽  
Proficiency Testing ◽  
Immunohistochemical Analysis ◽  
Predictive Testing ◽  
Standard Of Care ◽  
Tissue Microarrays ◽  
Current Standard ◽  
Testing Data ◽  
Positive Results

Context.— Immunohistochemical analysis of estrogen receptor (ER) and progesterone receptor (PgR) expression in breast cancer is the current standard of care and directly determines therapy. In 2010 the American Society of Clinical Oncology and the College of American Pathologists (ASCO/CAP) published guidelines for ER and PgR predictive testing, encompassing preanalytic, analytic, postanalytic factors; antibody validation; and proficiency testing. Objective.— To compare the performance of different antibody reagents for ER and PgR immunohistochemical analysis by using CAP proficiency testing data. Design.— The CAP PM2 survey uses tissue microarrays of ten 2-mm cores per slide. We analyzed survey data from 80 ER and 80 PgR cores by antibody clone from more than 1200 laboratories. Results.— Laboratories used the ER antibodies SP1 (72%), 6F11 (17%), 1D5 (3%), and the PgR antibodies 1E2 (61%), 16 (12%), PgR-636 (13%), PgR-1294 (8%) in 2015. While 63 of 80 ER cores (79%) were scored similarly using each of the 3 antibodies, there were significant differences for others, with SP1 yielding more positive interpretations. Four cores were scored as ER negative by more than half of the laboratories using 1D5 or 6F11, while SP1 produced positive results in more than 70% of laboratories using that antibody. Despite the greater variety of PgR antibody reagents and greater PgR tumor heterogeneity, 61 of 80 cores (76%) were scored similarly across the 4 PgR antibodies. Conclusions.— Accurate ER and PgR testing in breast cancer is crucial for appropriate treatment. The CAP proficiency testing data demonstrate differences in staining results by ER clone, with SP1 yielding more positive results.

scholarly journals Descriptive analysis of 192 cases of breast cancer occurring before age 40 in Yaounde, Cameroon

2017 ◽  
Vol 6 (7) ◽  
pp. 2704 ◽  
Author(s):  
Félix Essiben ◽  
Pascal Foumane ◽  
Esther JNU Meka ◽  
Michèle Tchakounté ◽  
Julius Sama Dohbit ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Ductal Carcinoma ◽  
Early Stage ◽  
Descriptive Analysis ◽  
Survival Rates ◽  
The United States ◽  
Therapeutic Modalities ◽  
History Of ◽  
Case Files ◽  
Common Histological Type

Background: Breast cancer is today a global health problem. With 1,671,149 new cases diagnosed in 2012, it is the most common female cancer in the world and accounts for 11.9% of all cancers and it affects more people than prostate cancer. In 2008, The United States statistics showed that, for all cancer that affect women before 40 years, more than 40% of them concerned the breast. The aim of this study was to describe the clinical, histopathological and therapeutic aspects of breast cancer in women under 40 years of age in Yaoundé.Methods: This was a retrospective study with data collected from 192 medical case files of women treated over a period of 12 years, from January 2004 to December 2015 at the Yaounde General Hospital and the Yaounde Gyneco-Obstetric and Pediatric Hospital. Microsoft Epi Info version 3.4.5 and SPSS version 20.0 softwares were used for data analysis.Results: From 2004 to 2015, 1489 cases of breast cancer were treated in both hospitals. Of these, 462 women were less than 40 years old, representing a proportion of 31.0%. The mean age at diagnosis was 33.5±5.0 years and 17.7% of women had a family history of breast cancer. The average time before an initial consultation was 6.7±6.6 months.  Most cases were classified as T4 (46.1%). The most common histological type was ductal carcinoma (87.4%). Grades SBR II and SBR III were predominant (76.4%). Axillary dissection (64.4%) and neoadjuvant chemotherapy (43.9%) were the main therapeutic modalities. The overall survival rate at 5 years was 51.2%. Five-year survival rates with no local recurrence and no metastatic occurrence were 35.8% and 43.2% respectively.Conclusions: Breast cancer largely affects women under the age of 40 and is often discovered late, at an advanced stage. The prognosis appears poor. Only screening could facilitate diagnosis at an early stage of the disease for better outcomes.

scholarly journals Use of cyclin-dependent kinase 4/6 (CDK4/6) inhibitors in older patients with ER-positive HER2-negative breast cancer: Young International Society of Geriatric Oncology review paper

2018 ◽  
Vol 10 ◽  
pp. 175883591880961 ◽  
Author(s):  
Nicolò Matteo Luca Battisti ◽  
Nienke De Glas ◽  
Mina S. Sedrak ◽  
Kah Poh Loh ◽  
Gabor Liposits ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Older Adults ◽  
Older Patients ◽  
Geriatric Oncology ◽  
Growth Factor Receptor ◽  
Standard Of Care ◽  
Cyclin Dependent Kinase ◽  
Current Standard ◽  
Oncology Review ◽  
Er Positive

The current standard of care for the management of estrogen receptor (ER)-positive and human epidermal growth factor receptor 2 (HER2)-negative breast cancer has been redefined by the introduction of cyclin-dependent kinase 4/6 (CDK4/6) inhibitors. Although adults aged 65 years and older account for the majority of patients with breast cancer, limited data are available about the age-specific dosing, tolerability, and benefit of CDK4/6 inhibitors in this growing population. Older adults are under-represented in clinical trials and as a result, clinicians are forced to extrapolate from findings in younger and healthier patients when making treatment decisions for older patients. In this article, we review the limited age-specific evidence on the efficacy, toxicity, and quality of life (QoL) outcomes associated with the use of CDK4/6 inhibitors in older adults. We also describe ongoing trials evaluating CDK4/6 inhibitors in the older population and highlight that only a minority of adjuvant and metastatic trials of CDK4/6 inhibitors in the general breast cancer population includes geriatric assessments. Finally, we propose potential strategies to help guide decision making for fit and unfit older patients based on disease endocrine sensitivity, the need for rapid response and geriatric assessment.

scholarly journals Intraoperative radiation therapy for early stage breast cancer: experiences from Iran

2020 ◽  
Author(s):  
Vahid Zangouri ◽  
Hamid Nasrollahi ◽  
Ali Taheri ◽  
Majid Akrami ◽  
Peyman Arasteh ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Radiation Therapy ◽  
Patient Selection ◽  
Tumor Size ◽  
Ductal Carcinoma ◽  
Early Stage ◽  
Intraoperative Radiation Therapy ◽  
Study Patient ◽  
Intraoperative Radiation

Abstract Background and objective Currently no definite guideline exists on the use of intraoperative radiation therapy (IORT) among patients with early stage BC. We report our experiences with IORT among breast cancer (BC) patients in our region.Methods All patient who received radical IORT from April 2014 on to March 2020 were included in the study. Patient selection criteria were as followed: age equal or older than 45 years old; all cases of invasive carcinomas, moreover in lobular carcinomas only after MRI and confirmation, and in cases with ductal carcinoma in-situ (DCIS) only those with low, intermediate grade, tumor size of equal or less than 2.5cm and a margin of 2-3mm; those between 45 and 50 years old with a tumor size of 0-2cm, those between 50 and 55 years old with a tumor size of 2-2.5cm, and those ≥55 years old with a tumor size of 2.5-3cm; those with invasive tumors a negative margin and in cases of DCIS a margin of 3mm; a negative nodal status (exception in patients with micrometastasis); and a positive estrogen receptor status. Results Overall, 252 patients entered the study. Mean (SD) age of patients was 56.43±7.79 years. In total, 32.9% of patients had a family history of BC. Mean tumor size was 1.56±0.55 cm. Median (IQR) follow-up of patients was 24 (13, 36) months. Overall, 6 patients (2.4%) experienced recurrence in follow-up visits, among which three (1.2%) were local recurrence, two (0.8%) were regional recurrence and one patients (0.4%) had metastasis.Median (IQR) time to recurrence was 23 (13, 36) among the six patient who had recurrence. Overall, 11 patients (4.3%) with DCIS in our study received IORT. All these patients had free margins in histopathology examination. None of these patients experience recurrence.Conclusion For the first time, we categorized patients according to age and tumor size and older patients with larger tumor sizes were considered appropriate candidates for IORT. Our series showed a successful experience with the use of IORT in a region where facilities for IORT are limited using our modified criteria for patient selection.

scholarly journals Integrative transcriptome data mining for identification of core lncRNAs in breast cancer

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7821 ◽  
Author(s):  
Xiaoming Zhang ◽  
Jing Zhuang ◽  
Lijuan Liu ◽  
Zhengguo He ◽  
Cun Liu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Prognostic Value ◽  
Early Stage ◽  
Expression Profiles ◽  
Diagnostic Value ◽  
The Cancer Genome Atlas ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Data Set

Background Cumulative evidence suggests that long non-coding RNAs (lncRNAs) play an important role in tumorigenesis. This study aims to identify lncRNAs that can serve as new biomarkers for breast cancer diagnosis or screening. Methods First, the linear fitting method was used to identify differentially expressed genes from the breast cancer RNA expression profiles in The Cancer Genome Atlas (TCGA). Next, the diagnostic value of all differentially expressed lncRNAs was evaluated using a receiver operating characteristic (ROC) curve. Then, the top ten lncRNAs with the highest diagnostic value were selected as core genes for clinical characteristics and prognosis analysis. Furthermore, core lncRNA-mRNA co-expression networks based on weighted gene co-expression network analysis (WGCNA) were constructed, and functional enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID). The differential expression level and diagnostic value of core lncRNAs were further evaluated by using independent data set from Gene Expression Omnibus (GEO). Finally, the expression status and prognostic value of core lncRNAs in various tumors were analyzed based on Gene Expression Profiling Interactive Analysis (GEPIA). Results Seven core lncRNAs (LINC00478, PGM5-AS1, AL035610.1, MIR143HG, RP11-175K6.1, AC005550.4, and MIR497HG) have good single-factor diagnostic value for breast cancer. AC093850.2 has a prognostic value for breast cancer. AC005550.4 and MIR497HG can better distinguish breast cancer patients in early-stage from the advanced-stage. Low expression of MAGI2-AS3, LINC00478, AL035610.1, MIR143HG, and MIR145 may be associated with lymph node metastasis in breast cancer. Conclusion Our study provides candidate biomarkers for the diagnosis and prognosis of breast cancer, as well as a bioinformatics basis for the further elucidation of the molecular pathological mechanism of breast cancer.

scholarly journals Metabolic Reprogramming in Breast Cancer and Its Therapeutic Implications

Cells ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 89 ◽  
Author(s):  
Nishant Gandhi ◽  
Gokul Das
Keyword(s):  
Breast Cancer ◽  
Estrogen Receptor Alpha ◽  
Cancer Metabolism ◽  
Growth Factor Receptor ◽  
Standard Of Care ◽  
Metabolic Reprogramming ◽  
Metabolic Phenotype ◽  
Current Standard ◽  
Therapeutic Implications ◽  
Altered Metabolism

Current standard-of-care (SOC) therapy for breast cancer includes targeted therapies such as endocrine therapy for estrogen receptor-alpha (ERα) positive; anti-HER2 monoclonal antibodies for human epidermal growth factor receptor-2 (HER2)-enriched; and general chemotherapy for triple negative breast cancer (TNBC) subtypes. These therapies frequently fail due to acquired or inherent resistance. Altered metabolism has been recognized as one of the major mechanisms underlying therapeutic resistance. There are several cues that dictate metabolic reprogramming that also account for the tumors’ metabolic plasticity. For metabolic therapy to be efficacious there is a need to understand the metabolic underpinnings of the different subtypes of breast cancer as well as the role the SOC treatments play in targeting the metabolic phenotype. Understanding the mechanism will allow us to identify potential therapeutic vulnerabilities. There are some very interesting questions being tackled by researchers today as they pertain to altered metabolism in breast cancer. What are the metabolic differences between the different subtypes of breast cancer? Do cancer cells have a metabolic pathway preference based on the site and stage of metastasis? How do the cell-intrinsic and -extrinsic cues dictate the metabolic phenotype? How do the nucleus and mitochondria coordinately regulate metabolism? How does sensitivity or resistance to SOC affect metabolic reprogramming and vice-versa? This review addresses these issues along with the latest updates in the field of breast cancer metabolism.

Sign in / Sign up

Export Citation Format

Share Document