Molecular Classification Of Breast Cancer Research Articles

Receptor-based Surrogate Subtypes and Discrepancies with Breast Cancer Intrinsic Subtypes: Implications for Image Biomarker Development.

Purpose To determine the concordance and accuracy of imaging surrogates of immunohistochemical (IHC) markers and the molecular classification of breast cancer. Materials and Methods A total of 3050 patients from 17 public breast cancer data sets containing IHC marker receptor status (estrogen receptor/progesterone receptor/human epidermal growth factor receptor 2 [HER2]) and their molecular classification (basal-like, HER2-enriched, luminal A or B) were analyzed. Diagnostic accuracy and concordance as measured with the κ statistic were calculated between the IHC and molecular classifications. Simulations were performed to assess the relationship between accuracy of imaging-based IHC markers to predict molecular classification. A simulation was performed to examine effects of misclassification of molecular type on patient survival. Results Accuracies of intrinsic subtypes based on IHC subtype were 71.7% (luminal A), 53.7% (luminal B), 64.8% (HER2-enriched), and 81.7% (basal-like). The κ agreement was fair (κ = 0.36) for luminal A and HER2-enriched subtypes, good (κ = 0.65) for the basal-like subtype, and poor (κ = 0.09) for the luminal B subtypes. Introduction of image misclassification by simulation lowered image-true subtype accuracies and κ values. Simulation analysis showed that misclassification caused survival differences between luminal A and basal-like subtypes to decrease. Conclusion There is poor concordance between triple-receptor status and intrinsic molecular subtype in breast cancer, arguing against their use in the design of prognostic genomic-based image biomarkers. © RSNA, 2018 Online supplemental material is available for this article.

Role of P-53 Gene in Preventing Breast Cancer

Breast cancer affects more than one million patients annually in the world and is a leading cause of mortality. Histological type, grade, tumor size, lymph node involvement, and estrogen receptor and HER-2 receptor status, all influence prognosis and the probability of response to systemic therapies. P53 gene is mutated in about 30% of breast cancers/.The possible links between alterations of p53 and clinical or pathological features of breast tumors have been widely investigated. The first study to examine gene-expression patterns of breast cancer suggested that at least four major molecular classes of breast cancer exist: luminal-like, basal-like, normal like, and HER-2 positive. Basal-like breast cancer account for 15% of breast cancers and are often described as triple negative breast cancers (TNBCs). In fact, TNBCs, defined by lack of expression of estrogen receptor, progesterone receptor, and HER2, probably include both basal-like breast cancers and some poorly differentiated luminal breast cancers. They are also associated with a younger age and a poor prognosis. TNBCs also have an increased frequency of TP53 mutations. Recently, it was shown that mutant p53 status was a strongly unfavorable prognostic factor for relapse-free survival and overall survival only in a triple negative group in patients treated with adjuvant anthracycline-containing chemotherapy. Inflammatory breast cancer (IBC) is a clinical diagnosis known as the T4d category in the TNM classification. It is a distinct clinical subtype of locally advanced breast cancer (LABC), with a particularly aggressive behavior and poor prognosis. TP53 mutations are more frequent in inflammatory breast cancer (50%) than in non-inflammatory breast cancer (20–30%). The results from these studies served as the justification for attempts to vaccinate patients using p53-derived peptides, and a number of clinical trials are in progress. The most advanced work used a long synthetic peptide mixture derived from p53 (p53-SLP; Netherlands).The vaccine is delivered in the adjuvant setting and induces T helper type I response in the majority of patients. However, the response may not be potent enough to result in clinical benefit as a mono-therapy because most patients had T-helper cells that failed to produce key cytokines, indicating that this treatment should also be associated with another type of conventional or immunotherapy therapy.

Abstract 3112: Distinct oncogenic events induce different DNA methylation and copy number changes in human mammary epithelial cells

Abstract Gene expression differences, combined with distinct patterns of genomic rearrangements and epigenetic modifications constitute the bases of molecular classification of breast cancer. Molecular subtypes may originate from different cell lineages in the mammary gland, but also from the early activation of oncogenes that may drive the establishment of these molecular subtypes. However, in the natural history of human cancer, it is difficult to discriminate between these two factors : cell lineage and initial oncogenic alterations. In this work, we designed an experimental strategy aiming at determining whether activation of distinct oncogenic pathways in human mammary epithelial cells (HMEC) could lead to different patterns of genetic and epigenetic changes. We show that initial activation of CCNE1, WNT1 and RASv12 in shp53 immortalized HMECs results in different and reproducible profiles of mRNA and miR expression, copy number alterations (CNA) and DNA methylation modifications. Interestingly, first the extend of CNA measured as fraction of the genome altered was lower in HMECs transformed by RAS than CCNE1 and WNT1 transformed HMECs revealing a lower genetic instability. This was confirmed by less numerous γH2Ax and 53BP1 nuclear foci in HMECs transformed by RAS. Second, HMECs transformed by RAS bore specific profiles of CNAs and DNA methylation, clearly distinct of those shown by CCNE1 and WNT1 transformed HMECs. Genes differentially expressed in the RAS and the CCNE1/WNT1 clusters and included in CNAs or with variable CpG methylation were mostly different, depicting the activation of distinct signaling pathways in these two clusters. These data indicate that early activation of distinct oncogenic pathways may leads to adaptive events resulting in specific pattern of CNAs and DNA methylation changes. We postulated that the early activation of oncogenes may be an important determinant of the establishment of breast cancer molecular subtypes along with cell lineage origin. Citation Format: Stan P. du manoir, Claire Fonti, Anne Saumet, Amanda Abi-Khalil, Béatrice Orsetti, Cleroux Elouan, Ambre Bender, Michael Dumas, Jacques Colinge, Michael Weber, Charles Theillet. Distinct oncogenic events induce different DNA methylation and copy number changes in human mammary epithelial cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3112.

IDENTIFICATION OF PARP1 AS A POTENTIAL THERAPEUTIC TARGET IN TRIPLE NEGATIVE AND BASAL-LIKE BREAST CANCER MOLECULAR SUBTYPES AMONG WEST ALGERIAN PATIENTS

Purpose: Breast cancer is partly responsible for the therapeutic failures of tumors with the most worsening prognoses. Increasing understanding of the cellular aberrations inherent to cancer cells was an important step towards therapy individualization. Poly (ADP-ribose) polymerase-1 (PARP1) as a promising novel target in breast cancer was an example of this strategy. However, the biological and clinical significance of PARP1 expression and its associations with outcome remain to be defined. We aimed in present study to explore PARP1 expression in breast cancers samples among west Algerian patients. Materials and Methods: We classified 78 primary breast cancers collected and diagnosed at the Regional Military Hospital of Oran (Algeria) using immunohistochemical biomarkers then; we examined immunohistochemical PARP1 expression and assessed its correlation with clinicopathological parameters and breast cancer molecular subtypes. Results: PARP1 nuclear overexpression was found in (44, 8%) of all infiltrating breast carcinomas. PARP-1 protein overexpression was associated to higher tumor grade (P=0.036), hormone-negative tumors (P=0.005) and estrogen-negative tumors (P=0.003). Moreover, PARP1 was significantly expressed in Triple-negative (P=0.015) and basal-like breast cancers, but was also present in HER2 positive breast cancers (P=0.014). Conclusions: Our data highlights the interest of immunohistochemical biomarkers in breast cancer molecular classification. We found that PARP1 overexpression is associated with triple-negative and basal-like tumors and could be a potential therapeutic in these two pejorative breast cancer subtypes. Furthermore, PARP1 overexpression could be a predictive biomarker of therapeutic resistance in HER2 positive tumors.The assessment of PARP1 protein expression may improve the selection of patients for PARP1 inhibitor therapy.

Prevalence of Breast Cancer Intrinsic Subtypes and Its Association with Clinico-Pathological Feature

Breast cancer is the commonest cancer in women worldwide and represents a highly heterogeneous group of tumours particularly in terms of molecular features, prognosis and response to therapy. Breast cancer molecular classification can predict the prognosis of breast cancer in terms of recurrence and help and guide us regarding the treatment decision about systemic therapy. Breast carcinomas may be stratified into subtypes similar to those defined by Gene expression profiling using a panel of immune-histochemical (IHC) markers. Routine IHC evaluations of breast cancers may, therefore, provide a reasonable alternative to costly genetic assays especially in under-resourced healthcare systems. The purpose of this study is to investigate the prevalence of molecular subtypes and correlate it to clinic-pathological features. Methods: From 2005 to 2017 total of 4847 Breast cancer patients, in whom complete information was available to classify them into luminal subtypes were retrieved and classified into intrinsic subtypes and patients information in each type was collected about age, tumour size, stage, grade and nodal status. Results: In luminal classification, a highly significant difference was found in mean age (p<0.001) tumour size (p<0.001), grade, metastasis and Ki67. The statistical significance of Her 2 positive and triple negative was found with stage, grade, metastasis and Ki67. Conclusions: IHC assignment into Luminal subtypes is clinically informative in our patients and routinely using this in our practice could identify patients that may need a more aggressive treatment to reduce the likelihood of recurrences.

The influence of molecular classification of breast cancer on the safety of breast-conserving surgery

Objective: To analyze the relationship between the breast cancer molecular classification and the prognosis of patients underwent breast-conserving therapy and to discuss the safety of the breast conserving surgery from the choice of operation in terms of breast cancer molecular classification. Methods: Clinical data of 618 patients with breast-conserving therapy in Tianjin Medical University Cancer Institute and Hospital from August 2005 to August 2010 were analyzed retrospectively. According to the molecular classification when breast cancer was diagnosed, patients were subdivided into five groups, including Luminal A, Luminal B1, Luminal B2, HER-2-positive and Triple-negative. Clinicopathological characteristics and prognosis were compared among five groups and the influencing factors of local recurrence, distant metastasis and overall survival were analyzed. Results: Among 618 patients, there were 148 cases Luminal A, 231 cases Luminal B1, 63 cases Luminal B2, 40 cases HER-2-positive and 136 cases Triple-negative. The age, family history, TNM stage, calcification, histological grade, pathological type and response to endocrine therapy of these 5 molecular types of breast cancer patients were significantly different (all P<0.05). The 5-year local regional recurrence-free survival rates of Luminal A, Luminal B1, Luminal B2, HER-2-positive and Triple-negative were 99.3%, 98.7%, 98.4%, 94.9% and 95.9%, respectively, without significant differences (P=0.104). The 5-year distant metastasis-free survival rates of these 5 types were 97.3%, 95.7%, 93.7%, 87.5% and 91.4%, respectively, with significant differences (P=0.013). Moreover, the 5-year overall survival rates of these 5 types were 98.6%, 97.8%, 98.4%, 92.5% and 95.6%, respectively, without significant differences (P=0.153). Multifactor analysis showed that radiotherapy (HR=0.036, P=0.049) and the number of lymph node metastases (HR=10.72, P=0.004) were independent factors of local recurrence of breast cancer patients underwent breast-conserving therapy. The age (HR=0.369, P=0.046), status of surgical margin (HR=5.486, P=0.007), number of lymph node metastases (HR=2.882, P=0.023) and molecular typing (HR=5.191, P=0.008) were independent factors of distant metastasis of above breast cancer patients. None of the factors were found to be independent factors of the overall survival of these breast cancer patients. Conclusions: Breast conserving therapy does not increase the risks of local recurrence and death of HER-2-positive and Triple-negative breast cancer patients. Therefore, breast conserving therapy can be accepted by patients with HER-2-positive and Triple-negative breast cancer.

P-53 Gene As Marker in Breast Cancer

Purpose: Aim of this current review is to emphasis a possible links between alterations of P-53 gene together with its protein in pathological features of breast cancer. Design: The study examines the gene-expression patterns of breast cancer suggested that at least four major molecular classes of breast cancer exist: luminal-like, basal-like, normal like, and HER-2 positive. Basal-like breast cancer account for 15% of breast cancers and are often described as triple negative breast cancers (TNBCs). In fact, TNBCs, defined by lack of expression of estrogen receptor, progesterone receptor, and HER2, probably include both basal-like breast cancers and some poorly differentiated luminal breast cancers. They are also associated with a younger age and a poor prognosis. TNBCs also have an increased frequency of TP53 mutations. Inflammatory breast cancer (IBC) is a clinical diagnosis known as the T4d category in the TNM classification. It is a distinct clinical subtype of locally advanced breast cancer (LABC), with a particularly aggressive behavior and poor prognosis. Results: TP53 mutations are more frequent in inflammatory breast cancer (50%) than in non-inflammatory breast cancer (20-30%). Histological type, grade, tumor size, lymph node involvement, and estrogen receptor and HER-2 receptor status, all influence prognosis and the probability of response to systemic therapies. P53 gene is mutated in about 30% of breast cancers. Conclusion: Recently studies shown that mutant P-53 gene status was a strongly unfavorable prognostic factor for relapse-free survival and overall survival only in a triple negative group in patients treated with adjuvant anthracycline-containing chemotherapy. The results from these studies served as the justification for attempts to vaccinate patients using p53-derived peptides, and a number of clinical trials are in progress.

Modulation of Molecular Biomarker Expression in Response to Chemotherapy in Invasive Ductal Carcinoma.

Breast cancer (BC) has varied morphological and biological features and is classified based on molecular and morphological examinations. Molecular classification of BC is based on biological gene-expression profiling. In this study, biomarker modulation was assessed during BC treatment in 30 previously untreated patients. Heterogeneity among patients was pathologically diagnosed and classified into luminal and basal-like immunohistochemical profiles based on estrogen, progesterone, and human epidermal growth factor receptor (ER/PR/HER2) status. Marker heterogeneity was compared with mRNA biomarker expression in patients with BC before and after therapy. Reverse transcription-polymerase chain reaction was performed for molecular characterization. Expression and modulation of biological markers, CK19, hMAM, CEA, MUC, Myc, Ki-67, HER2/neu, ErbB2, and ER, were assessed after treatment, where the expression of the biomarkers CK19, Ki-67, Myc, and CEA was noted to be significantly decreased. Marker expression modulation was determined according to different stages and pathological characteristics of patients; coexpression of three markers (CK19, Ki-67, and Myc) was specifically modulated after therapy. In the histopathologically classified basal-like group, two markers (CK19 and Ki-67) were downregulated and could be considered as diagnostic biomarkers. In conclusion, pathological characteristics and marker variation levels can be evaluated to decide a personalized treatment for patients.

Prognostic evaluation of vitamin D deficiency in breast cancer patients: a pilot study in India

Background : Vitamin D deficiency has been associated with poor prognosis in breast cancer. A new molecular classification of breast cancer is being increasingly used that is based on expression of estrogen receptors, progesterone receptors and Her2/neu amplification and is found to correlate well with prognosis and outcome of disease. The present study was designed to determine serum vitamin D deficiency in these molecular subtypes of breast cancer. Methods: Estimation of serum vitamin D levels by chemiluminiscence was done in a cohort of 99 breast cancer patients and 25 age matched healthy controls. Breast cancer patients were further grouped into luminal A, luminal B, Her2/neu enriched and triple negative subtypes based on immunohistochemistry results. Non-parametric tests were performed to compare vitamin D levels in different groups. Results: 54.6%, 60%, 66.6% and 84.2% of patients with luminal A, luminal B, Her2/neu enriched and triple negative subtypes respectively were found to be vitamin D deficient (<20ng/mL) as compared to only 20% in healthy controls. More aggressive Her2/neu enriched and triple negative subtype patients had significantly lower serum vitamin D levels than the luminal subtypes of breast cancer. Conclusion: Vitamin D deficiency is more prevalent and significantly lower levels are found in more aggressive subtypes of breast cancer. Vitamin D supplementation must be considered in these forms of breast cancer to improve outcome.

Tumor Heterogeneity in Breast Cancer.

Breast cancer is a heterogeneous disease and differs greatly among different patients (intertumor heterogeneity) and even within each individual tumor (intratumor heterogeneity). Clinical and morphologic intertumor heterogeneity is reflected by staging systems and histopathologic classification of breast cancer. Heterogeneity in the expression of established prognostic and predictive biomarkers, hormone receptors, and human epidermal growth factor receptor 2 oncoprotein is the basis for targeted treatment. Molecular classifications are indicators of genetic tumor heterogeneity, which is probed with multigene assays and can lead to improved stratification into low- and high-risk groups for personalized therapy. Intratumor heterogeneity occurs at the morphologic, genomic, transcriptomic, and proteomic levels, creating diagnostic and therapeutic challenges. Understanding the molecular and cellular mechanisms of tumor heterogeneity that are relevant to the development of treatment resistance is a major area of research. Despite the improved knowledge of the complex genetic and phenotypic features underpinning tumor heterogeneity, there has been only limited advancement in diagnostic, prognostic, or predictive strategies for breast cancer. The current guidelines for reporting of biomarkers aim to maximize patient eligibility for targeted therapy, but do not take into account intratumor heterogeneity. The molecular classification of breast cancer is not implemented in routine clinical practice. Additional studies and in-depth analysis are required to understand the clinical significance of rapidly accumulating data. This review highlights inter- and intratumor heterogeneity of breast carcinoma with special emphasis on pathologic findings, and provides insights into the clinical significance of molecular and cellular mechanisms of heterogeneity.

Breast cancer in the 21st century: From early detection to new therapies

The analysis of the causes that have given rise to a change in tendency in the incidence and mortality rates of breast cancer in the last few decades generates important revelations regarding the role of breast screening, the regular application of adjuvant therapies and the change of risk factors. The benefits of early detection have been accompanied by certain adverse effects, even in terms of an excessive number of prophylactic mastectomies. Recently, several updates have been published on the recommendations in breast cancer screening at an international level. On the other hand, the advances in genomics have made it possible to establish a new molecular classification of breast cancer. Our aim is to present an updated overview of the epidemiological situation of breast cancer, as well as some relevant issues from the point of view of diagnosis, such as molecular classification and different strategies for both population-based and opportunistic screening.

El cáncer de mama en el siglo XXI: de la detección precoz a los nuevos tratamientos

The analysis of the causes that have given rise to a change in tendency in the incidence and mortality rates of breast cancer in the last few decades generates important revelations regarding the role of breast screening, the regular application of adjuvant therapies and the change of risk factors. The benefits of early detection have been accompanied by certain adverse effects, even in terms of an excessive number of prophylactic mastectomies. Recently, several updates have been published on the recommendations in breast cancer screening at an international level. On the other hand, the advances in genomics have made it possible to establish a new molecular classification of breast cancer. Our aim is to present an updated overview of the epidemiological situation of breast cancer, as well as some relevant issues from the point of view of diagnosis, such as molecular classification and different strategies for both population-based and opportunistic screening.

Clinical application of a microfluidic chip for immunocapture and quantification of circulating exosomes to assist breast cancer diagnosis and molecular classification.

Increasing attention has been attracted by exosomes in blood-based diagnosis because cancer cells release more exosomes in serum than normal cells and these exosomes overexpress a certain number of cancer-related biomarkers. However, capture and biomarker analysis of exosomes for clinical application are technically challenging. In this study, we developed a microfluidic chip for immunocapture and quantification of circulating exosomes from small sample volume and applied this device in clinical study. Circulating EpCAM-positive exosomes were measured in 6 cases breast cancer patients and 3 healthy controls to assist diagnosis. A significant increase in the EpCAM-positive exosome level in these patients was detected, compared to healthy controls. Furthermore, we quantified circulating HER2-positive exosomes in 19 cases of breast cancer patients for molecular classification. We demonstrated that the exosomal HER2 expression levels were almost consistent with that in tumor tissues assessed by immunohistochemical staining. The microfluidic chip might provide a new platform to assist breast cancer diagnosis and molecular classification.

Phosphorylation of androgen receptors at serine 515 is a potential prognostic marker for triple negative breast cancer.

1.7 million cases of breast cancer are diagnosed every year with 522,000 deaths. Molecular classifications of breast cancer have resulted in improved treatments. However, treatments for triple negative breast cancer (TNBC) are lacking. Analysis of molecular targets for TNBC is a priority. One potential candidate is androgen receptor (AR) phosphorylation. This study assessed the role of AR phosphorylation at ser81/ser515 and their two upstream effectors, cyclin-dependent kinase 1 (pCDK1) and extracellular-regulated kinase 1/2 (pERK1/2) in 332 ductal breast cancer patients by immunohistochemistry.pERK1/2 combined with AR-515 associated with improved cancer-specific survival (CSS, p = 0.038), decreased size (p = 0.001), invasive grade (p < 0.001), necrosis (p = 0.003), b-lymphocytes (p = 0.020), molecular subtype (p < 0.001) and estrogen receptor (ER)/progesterone receptor (PR)-status (p < 0.001). The cohort was therefore stratified into ER+ve and ER-ve patients. In ER+ve tumours, pERK1/2 combined with AR-515 associated with improved CSS (p = 0.038), smaller size (p = 0.004), invasive grade (p = 0.001), decreased b-lymphocytes (p = 0.013) and increased plasma cells (p = 0.048). In contrast, in TNBC patients, phosphorylation of AR-515 associated with poorer CSS (p = 0.007). pERK1/2 combined with AR-515 associated with decreased inflammation (p = 0.003), increased tumour stroma (p = 0.003) and tumour budding (p = 0.011), with trends towards decrease CSS (p = 0.065) and macrophage levels (p = 0.093).In Conclusions, AR-515 may be an important regulator of inflammation in breast cancer potential via ERK1/2 phosphorylation. AR-515 is a potential prognostic marker and therapeutic target for TNBC.

Research progress of circulating tumor cells in breast cancer

Breast cancer is the most common malignant tumor in female, and the recurrence and metastasis is the leading cause of death. Previous image evaluation of breast cancer could not detect the tumor at its early stage timely. The circulating tumor cells in the peripheral blood are like the seeds buried in the body, which cause the later recurrence and metastasis. So we can detect circulating tumor cells in peripheral blood to evaluate breast cancer progression. In present study, circulating tumor cells can be implied more than three ways in clinical application of breast cancer. They could be used to monitor the therapeutic effect in breast cancer therapy timely, to analyze molecular classification of breast cancer and conduct clinical drug sensitivity tests. Although the value of circulating tumor cells in breast cancer has been widely recognized, many factors limited their application in clinical. Thus, we conduct this review about the current progress of circulating tumor cells in breast cancer. Key words: Neoplastic cells, circulating; Breast neoplasms; Therapeutic uses; Review

Genomic Pathology and Biomarkers in Breast Cancer.

Breast cancer is a highly heterogeneous disease. There are significant differences in morphology, immunophenotype, clinical behavior, and treatment response in breast cancer, which pose the greatest challenge for managing breast cancer patients. Great advances in breast cancer have been made at the molecular and genomic levels, which not only help us greatly in better understanding the heterogeneity and the carcinogenesis for breast cancer, but also help us in identifying new prognostic markers and therapeutic targets. In this review, we discuss these new findings in detail: (1) the two main pathways of the pathogenesis for breast cancer; (2) the traditional biomarkers including ER, PR, HER2, and some controversial biomarkers - Ki67, p53, AR, FRA for breast cancer; (3) the molecular classification of breast cancer, its IHC surrogates and its application in clinical management; (4) the multigene tests and their applications for breast cancer management; (5) next-generation sequencing and its clinical application for breast cancer; and (6) TIL and PD1/PD-L1 and their application in breast cancer.

Study of Molecular Classes of Breast Cancer using Immunohistochemical Surrogate Markers in Correlation with Other Prognostic Parameters

Study of Molecular Classes of Breast Cancer using Immunohistochemical Surrogate Markers in Correlation with Other Prognostic Parameters

Molecular classification of breast cancer: what the pathologist needs to know

Breast cancer is a heterogeneous disease featuring distinct histological, molecular and clinical phenotypes. Although traditional classification systems utilising clinicopathological and few molecular markers are well established and validated, they remain insufficient to reflect the diverse biological and clinical heterogeneity of breast cancer. Advancements in high-throughput molecular techniques and bioinformatics have contributed to the improved understanding of breast cancer biology, refinement of molecular taxonomies and the development of novel prognostic and predictive molecular assays. Application of such technologies is already underway, and is expected to change the way we manage breast cancer. Despite the enormous amount of work that has been carried out to develop and refine breast cancer molecular prognostic and predictive assays, molecular testing is still in evolution. Pathologists should be aware of the new technology and be ready for the challenge. In this review, we provide an update on the application of molecular techniques with regard to breast cancer diagnosis, prognosis and outcome prediction. The current contribution of emerging technology to our understanding of breast cancer is also highlighted.

Tumoral heterogeneity of breast cancer

The objective of this literature review is to describe the types of tumor heterogeneity in breast cancer and their clinical implication. Two kinds of tumor heterogeneity are described: intertumor heterogeneity and intra-tumor heterogeneity. In breast cancer, inter-tumor heterogeneity was best characterized in the 2000s thanks to high throughput analyses. These analyzes resulted in a molecular classification of breast cancers distinguishing four subtypes: Luminal A, Luminal B, HER 2+ and basal like. This variability may be observed between the primary tumor and metastases, namely the temporal intratumor heterogeneity. The average discrepancy for the progesterone receptor, estrogen, and between HER2 status appears to be 33%, 20% and 8%, respectively. It is then interesting to study the heterogeneity within the primary tumor: this spatial intra-tumor heterogeneity is poorly known. Physiopathology of intra-tumor heterogeneity light be deciphered by studies on cancer stem cells and clonal evolution model. In addition, the tumor microenvironment seems to actively contribute to this heterogeneity. The major interest to study this heterogeneity is the clinical implication that could result. While precision medicine is emerging, it is important to capture the heterogeneity of each specific tumor type. These new biological knowledge will allow us to anticipate such heterogeneity and individualize the management of breast cancer.

Comprehensive landscape of subtype-specific coding and non-coding RNA transcripts in breast cancer.

Molecular classification of breast cancer into clinically relevant subtypes helps improve prognosis and adjuvant-treatment decisions. The aim of this study is to provide a better characterization of the molecular subtypes by providing a comprehensive landscape of subtype-specific isoforms including coding, long non-coding RNA and microRNA transcripts. Isoform-level expression of all coding and non-coding RNAs is estimated from RNA-sequence data of 1168 breast samples obtained from The Cancer Genome Atlas (TCGA) project. We then search the whole transcriptome systematically for subtype-specific isoforms using a novel algorithm based on a robust quasi-Poisson model. We discover 5451 isoforms specific to single subtypes. A total of 27% of the subtype-specific isoforms have better accuracy in classifying the intrinsic subtypes than that of their corresponding genes. We find three subtype-specific miRNA and 707 subtype-specific long non-coding RNAs. The isoforms from long non-coding RNAs also show high performance for separation between Luminal A and Luminal B subtypes with an AUC of 0.97 in the discovery set and 0.90 in the validation set. In addition, we discover 1500 isoforms preferentially co-expressed in two subtypes, including 369 isoforms co-expressed in both Normal-like and Basal subtypes, which are commonly considered to have distinct ER-receptor status. Finally, analyses at protein level reveal four subtype-specific proteins and two subtype co-expression proteins that successfully validate results from the isoform level.