Breast cancer classification and prognosis based on gene expression profiles from a population-based study

Fourier transform infrared spectroscopy based spectral biomarkers of metastasized breast cancer progression

Breast cancer is a global health issue and the second leading cause of cancer death in women. Breast cancer tends to migrate to bone and causes bone metastases which is ultimately the cause of death. Here, we report the use of FTIR to identify spectral biomarkers of cancer progression on 3D in vitro model of breast cancer bone metastasis. Our results indicate that the following spectral biomarkers can monitor cancer progression, for example, lipids (CH2 asymmetric/CH2 symmetric stretch), Amide I/Amide II, and RNA/DNA. Principal component analysis also confirmed the involvement of protein, lipids and nucleic acids in cancer progression on sequential culture. The collective observations from this study suggest successful application of FTIR as a non-invasive and accurate method to identify biochemical changes in cancer cells during the progression of breast cancer bone metastasis.

BRCA1 and BRCA2 Germline Mutation Analysis in Hereditary Breast/Ovarian Cancer Families from the Aures Region (Eastern Algeria): First Report

Breast cancer is currently the leading cause of cancer morbidity and mortality among Algerian women. In this study, we aimed to investigate the mutation spectrum of BRCA1 and BRCA2 genes in hereditary breast/ovarian cancer (HBOC) families from the Aures region (eastern Algeria). High risk breast/ovarian cancer families were selected from overall 1162 consecutive patients collected from cancer registry of anticancer center of Batna. Breast cancers were diagnosed between 2011 and 2015. Recurrent mutations on BRCA1 and BRCA2 previously found in Algerian patients were screened using PCR-direct sequencing in 113 HBOC families. In addition, for the first time in Algeria, HBOC patients were analyzed by NGS using a cancer panel of 30 hereditary cancer genes or BRCA1/2 genetic test. Six distinct deleterious mutations in BRCA1 and BRCA2 and a new VUS in PALB2 were detected in ten patients. Two distinct BRCA2 pathogenic variants c.1813dupA and c.8485C > T detected in two young female triple negative breast cancer (TNBC) patients, respectively, with a family history of male breast cancer, are reported here for the first time in Algerian population. Interestingly, we also detected a BRCA exon 15 deletion in two unrelated young female TNBC patients with strong family history of breast/ovarian cancer. Our study showed differences in the distribution of the mutation spectrum of BRCA genes between the Aures region and the north central region of Algeria. Our results will contribute in the implementation of genetic counseling and testing for patients and families at risk of hereditary breast and ovarian cancer.

Effects of the pesticide chlorpyrifos on breast cancer disease. Implication of epigenetic mechanisms

Chlorpyrifos (CPF) is an organophosphorus pesticide used for agricultural pest control all over the world. We have previously demonstrated that environmental concentrations of this pesticide alter mammary gland histological structure and hormonal balance in rats chronically exposed. In this work, we analyzed the effects of CPF on mammary tumors development. Our results demonstrated that CPF increases tumor incidence and reduces latency of NMU-induced mammary tumors. Although no changes were observed in tumor growth rate, we found a reduced steroid hormone receptor expression in the tumors of animals exposed to the pesticide. Moreover, we analyzed the role of epigenetic mechanisms in CPF effects. Our results indicated that CPF alters HDAC1 mRNA expression in mammary gland, although no changes were observed in DNA methylation. In summary, we demonstrate that the exposure to CPF promotes mammary tumors development with a reduced steroid receptors expression. It has also been found that CPF affects HDAC1 mRNA levels in mammary tissue pointing that CPF may act as a breast cancer risk factor.

pAKT pathway activation is associated with PIK3CA mutations and good prognosis in luminal breast cancer in contrast to p-mTOR pathway activation

Numerous studies have focused on the PI3K/AKT/mTOR pathway in estrogen receptor positive (ER) breast cancer (BC), as a linear signal transduction pathway and reported its association with worse clinical outcomes. We developed gene signatures that reflect the level of expression of phosphorylated-Serine473-AKT (pAKT) and phosphorylated-Serine2448-mTOR (p-mTOR) separately, capturing their corresponding level of pathway activation. Our analysis revealed that the pAKT pathway activation was associated with luminal A BC while the p-mTOR pathway activation was more associated with luminal B BC (Kruskal-Wallis test p < 10^-10). pAKT pathway activation was significantly associated with better outcomes (multivariable HR, 0.79; 95%CI, 0.74-0.85; p = 2.5 × 10^-10) and PIK3CA mutations (p = 0.0001) whereas p-mTOR pathway activation showed worse outcomes (multivariable HR,1.1; 95%CI, 1.1-1.2; p = 9.9 × 10^-4) and associated with p53 mutations (p = 0.04). in conclusion, our data show that pAKT and p-mTOR pathway activation have differing impact on prognosis and suggest that they are not linearly connected in luminal breast cancers.

Whole genome sequencing of breast cancer

Breast cancer was the first to take advantage of targeted therapy using endocrine therapy, and for up to 20% of all breast cancer patients a further significant improvement has been obtained by HER2‐targeted therapy. Greater insight in precision medicine is to some extent driven by technical and computational progress, with the first wave of a true technical advancement being the application of transcriptomic analysis. Molecular subtyping further improved our understanding of breast cancer biology and has through a new tumor classification enabled allocation of personalized treatment regimens. The next wave in technical progression must be next‐generation‐sequencing which is currently providing new and exciting results. Large‐scale sequencing data unravel novel somatic and potential targetable mutations as well as allowing the identification of new candidate genes predisposing for familial breast cancer. So far, around 15% of all breast cancer patients are genetically predisposed with most genes being factors in pathways implicated in genome maintenance. This review focuses on whole‐genome sequencing and the new possibilities that this technique, together with other high‐throughput analytic approaches, provides for a more individualized treatment course of breast cancer patients.

Examination of the Biomark assay as an alternative to Oncotype DX for defining chemotherapy benefit

Currently the 21-gene recurrence score (RS) assay called Oncotype DX is recommended by the National Comprehensive Cancer Network guideline for defining the benefit of chemotherapy. To overcome the cost disadvantages of the Oncotype DX assay and the turnaround time, a multigene assay was examined to compare the correlation of the RS and the predicted score (PS) of the present study. Paraffin-embedded tissues of 50 cases with early-stage estrogen receptor (ER)-positive breast cancer, who underwent the Oncotype DX test were used. A total of 149 candidate genes with high correlation to the RS were identified, in another project (Lee et al, unpublished data). Reverse transcription-quantitative polymerase chain reaction biomark assays were conducted using the dynamic array integrated fluidic circuit and the correlation analysis was performed with BRB ArrayTools. A predictive model was developed by the coefficient and gene expression, and 41 genes were identified. If the cut-off was ≥18, the predicted model was 18/50 cases, and the RS was 19, indicating that the differential rate of predicted response against RS was 2%. If the cutoff was ≥11, the predicted model was 38/50 cases and the RS was 34, indicating a difference of 8%. Genes common to the Oncotype DX and the Biomark assay include marker of proliferation Ki-67, aurora kinase A, Erb-B2 receptor tyrosine kinase 2, glutathione S-transferase Mu 1, estrogen receptor 1, progesterone receptor, B-cell lymphoma 2, signal peptide CUB domain EGF-like 2 and 5 reference genes. The remaining 28 genes are involved in various pathways and functions. This result indicates that there is a significant correlation between PS and RS scores, although validation of results is required to accurately determine the risk of distant recurrence. The Biomark assay is an easy and inexpensive way to measure mRNA expression. The present study demonstrates the possibility of the Biomark assay as an alternative for defining chemotherapy benefit in individual patients with ER-positive early-stage breast cancer.

Molecular subtypes are prognostic for N3 breast cancer patients in the modern therapeutic era

Nodal (N) status and molecular subtypes are well-known prognostic factors for breast cancer patients. The aim of the present study was to evaluate whether there was a prognostic role of molecular subtypes for pN3a breast cancer patients in the modern therapeutic era. The present study retrospectively evaluated a total of 521 breast cancer patients who had 10 or more metastatic lymph nodes and received adjuvant systemic therapy at the Oncology Department of four different centers in Turkey between 2000-2015. Patients were divided into four molecular subtypes by immunohistochemical staining. There were no significant differences in relapse rates according to the molecular subtypes (P=0.07). The five year disease free survival rate was 62% for the whole study population, 67% for Luminal A tumors, 53% for Luminal B tumors, 64% for human epidermal growth factor receptor 2-positive tumors and 56% for triple negative tumors. Luminal A patients had a better progression free survival when compared with Luminal B (P=0.026) and triple negative (P=0.07) patients. pT stage (P<0.001), and breast cancer subtype (P<0.001), remained significant independent factors for disease free survival. Therefore, breast cancer subtypes are still prognostic for patients with pN3 breast cancer.

Serum amyloid A predisposes inflammatory tumor microenvironment in triple negative breast cancer

Acute-phase proteins (APPs) are associated with a variety of disorders such as infection, inflammatory diseases, and cancers. The signature profile of APPs in breast cancer (BC) is poorly understood. Here, we identified serum amyloid A (SAA) for proinflammatory predisposition in BC through the signature profiles of APPs, interleukin (IL) and tumor necrosis factor (TNF) superfamily using publicly available datasets of tumor samples and cell lines. Triple-negative breast cancer (TNBC) subtype highly expressed SAA1/2 compared to HER2, luminal A (LA) and luminal B (LB) subtypes. IL1A, IL1B, IL8/CXCL8, IL32 and IL27RA in IL superfamily and CD70, TNFSF9 and TNFRSF21 in TNF superfamily were highly expressed in TNBC compared to other subtypes. SAA is restrictedly regulated by nuclear factor (NF)-κB and IL-1β, an NF-κB activator highly expressed in TNBC, increased the promoter activity of SAA1 in human TNBC MDA-MB231 cells. Interestingly, two κB-sites contained in SAA1 promoter were involved, and the proximal region (-96/-87) was more critical than the distal site (-288/-279) in regulating IL-1β-induced SAA1. Among the SAA receptors, TLR1 and TLR2 were highly expressed in TNBC. Cu-CPT22, TLR1/2 antagonist, abrogated IL-1β-induced SAA1 promoter activity. In addition, SAA1 induced IL8/CXCL8 promoter activity, which was partially reduced by Cu-CPT22. Notably, SAA1/2, TLR2 and IL8/CXCL8 were associated with a poor overall survival in mesenchymal-like TNBC. Taken together, IL-1-induced SAA via NF-κB-mediated signaling could potentiate an inflammatory burden, leading to cancer progression and high mortality in TNBC patients.

Treatment with DHA Modifies the Response of MDA-MB-231 Breast Cancer Cells and Tumors from nu/nu Mice to Doxorubicin through Apoptosis and Cell Cycle Arrest

Background

Docosahexaenoic acid (DHA) has been shown to reduce growth of breast cancer cells in vitro and in vivo; it may also benefit the action of cytotoxic cancer drugs. The mechanisms for these observations are not completely understood.

Objectives

We sought to explore how pretreatment of MDA-MB-231 breast cancer cells with DHA alters gene expression with doxorubicin (DOX) treatment and confirm that feeding DHA to tumor-bearing nu/nu mice improves the efficacy of DOX.

Methods

MDA-MB-231 cells were subjected to 4 conditions: a control mixture of 40 μM linoleic and 40 μM oleic acid (OALA), DHA (60 μM plus OALA), OALA DOX (0.41 μM), or DHA DOX (plus OALA) and assessed for effects on viability and function. Female nu/nu mice (6 wk old) bearing MDA-MB-231 tumors were randomly assigned to a nutritionally complete diet (20 g ± 2.8 g DHA/100 g diet) containing a polyunsaturated:saturated fat ratio of 0.5, with or without injections 2 times/wk of 5 mg DOX/kg for 4 wk.

Results

Microarray and protein analysis indicated that DHA DOX cells, compared with OALA DOX, had upregulated expression of apoptosis genes, Caspase-10 (1.3-fold), Caspase-9 (1.4-fold), and Receptor (TNFRSF)-interacting serine-threonine kinase 1 (RIPK1) (1.2-fold), while downregulating cell cycle genes, Cyclin B1 (-2.1-fold), WEE1 (-1.6-fold), and cell division cycle 25 homolog C (CDC25C) (-1.8-fold) (P < 0.05). DHA DOX-treated mice had 50% smaller tumors than control mice (P < 0.05). Analysis of proapoptotic proteins from tumors of DHA DOX mice showed increased Caspase-10 (by 68%) and BH3 interacting domain death agonist (Bid) (by 50%), decreased B-cell CLL/lymphoma 2 (BCL2) (by 24%), and decreased cell cycle proteins Cyclin B1 and Cdc25c (both by 42%), compared with control mice (P < 0.05).

Conclusions

Supplementation with DHA facilitates the action of DOX in MDA-MB-231 cells and in nu/nu mice, which may occur via amplification of the effect of DOX on apoptosis and cell cycle genes.

Single Cell Omics of Breast Cancer: An Update on Characterization and Diagnosis

Breast cancer is recognized for its different clinical behaviors and patient outcomes, regardless of common histopathological features at diagnosis. The heterogeneity and dynamics of breast cancer undergoing clonal evolution produces cells with distinct degrees of drug resistance and metastatic potential. Presently, single cell analysis have made outstanding advancements, overshadowing the hurdles of heterogeneity linked with vast populations. The speedy progression in sequencing analysis now allow unbiased, high-output and high-resolution elucidation of the heterogeneity from individual cell within a population. Classical therapeutics strategies for individual patients are governed by the presence and absence of expression pattern of the estrogen and progesterone receptors and human epidermal growth factor receptor 2. However, such tactics for clinical classification have fruitfulness in selection of targeted therapies, short-term patient responses but unable to predict the long-term survival. In any phenotypic alterations, like breast cancer disease, molecular signature have proven its implication, as we aware that individual cell's state is regulated at diverse levels, such as DNA, RNA and protein, by multifaceted interplay of intrinsic biomolecules pathways existing in the organism and extrinsic stimuli such as ambient environment. Thus for complete understanding, complete profiling of single cell requires a synchronous investigations from different levels (multi-omics) to avoid incomplete information produced from single cell. In this article, initially we briefed on novel updates of various methods available to explore omics and then we finally pinpointed on various omics (i.e. genomics, transcriptomics, epigenomics, proteomics and metabolomics) data and few special aspects of circulating tumor cells, disseminated tumor cells and cancer stem cells, so far available from various studies that can be used for better management of breast cancer patients.

Network pharmacology and RNA sequencing studies on triterpenoid saponins from Bupleurum chinense for the treatment of breast cancer

Breast cancer remains the most commonly diagnosed malignancy among women, which is frequently associated with adverse side-effects and high metastasis. Bupleurum chinense DC. has been empirically and extensively used as the core prescription for more than half of Chinese formulations for the adjuvant therapy of breast cancer, and its biological activity against breast cancer has been proven by both in vitro and in vivo experiments. Saikosaponin compounds are the characteristic constituent of B. chinense, which exhibit significant cytotoxicity toward several cancer cells. However, the specific mechanisms of these compounds in the treatment of breast cancer have not been comprehensively understood. Therefore, we aimed to determine more potentially therapeutic targets and investigate the biological mechanisms of B. chinense. In the present study, we adopted network pharmacology and bioinformatics analysis to facilitate this requirement. Consequently, the network analysis revealed that saikosaponin-f (39), saikosaponin-d (14), saikosaponin-c (26), saikosaponin-h (54), saikosaponin-g (41), 3′′,6′′-O-diacetylsaikosaponin-d (20), 11α-methoxy-saikosaponin-f (40), and 6′′-O-acetylsaikosaponin-b₁ (48) might play important roles in the treatment of breast cancer. In addition, the apoptosis regulator Bcl-2 (BCL-2), C-X-C chemokine receptor type 4 (CXCR4), probable ATP-dependent RNA helicase DDX5 (DDX5), protein kinase C alpha (PRKCA), and proto-oncogene tyrosine-protein kinase Src (SRC) were the potential therapeutic targets that exhibited intense interactions. Mechanistically, a gene enrichment analysis revealed that the action of B. chinense against breast cancer was achieved by the regulation of several biological signaling pathways, such as pathways in cancer, PI3K-Akt signaling pathway, EGFR tyrosine kinase inhibitor resistance, microRNAs in cancer, etc. More importantly, we verified that the predictions involving saikosaponin-d by the cytotoxicity assay, apoptosis analysis, and RNA sequencing methods were partly consistent with those obtained from the network pharmacology prediction.

The network pharmacology and RNA sequencing studies were used to explore potential therapeutic targets and biological mechanisms of B. chinense for the treatment of breast cancer.

Increases in Tumor N-Glycan Polylactosamines Associated with Advanced HER2-Positive and Triple-Negative Breast Cancer Tissues

PURPOSE

Using a recently developed matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) method, human breast cancer formalin-fixed paraffin-embedded (FFPE) tissue sections and tissue microarrays (TMA) are evaluated for N-linked glycan distribution in the tumor microenvironment.

EXPERIMENTAL DESIGN

Tissue sections representing multiple human epidermal growth factor receptor 2 (HER2) receptor-positive and triple-negative breast cancers (TNBC) in both TMA and FFPE slide format are processed for high resolution N-glycan MALDI-IMS. An additional FFPE tissue cohort of primary and metastatic breast tumors from the same donors are also evaluated.

RESULTS

The cumulative N-glycan MALDI-IMS analysis of breast cancer FFPE tissues and TMAs indicate the distribution of specific glycan structural classes to stromal, necrotic, and tumor regions. A series of high-mannose, branched and fucosylated glycans are detected predominantly within tumor regions. Additionally, a series of polylactosamine glycans are detected in advanced HER2+, TNBC, and metastatic breast cancer tissues. Comparison of tumor N-glycan species detected in paired primary and metastatic tissues indicate minimal changes between the two conditions.

CONCLUSIONS AND CLINICAL RELEVANCE

The prevalence of tumor-associated polylactosamine glycans in primary and metastatic breast cancer tissues indicates new mechanistic insights into the development and progression of breast cancers. The presence of these glycans could be targeted for therapeutic strategies and further evaluation as potential prognostic biomarkers.

KLP-PI: a new prognostic index for luminal B HER-2-negative breast cancer

Luminal B HER-2-negative (LBHN) subtype is one of the major subtypes of breast cancer according to different features, clinical behaviors, and treatment response. The LBHN subtype shows a poor prognosis and is insensitive to endocrine therapy. Our work aim is to investigate the prognostic factor in the LBHN subgroup and, meanwhile, try to obtain an optimal prognostic index (PI) contrapose LBHN subgroup which helps to guide chemotherapy. A total of 515 female LBNH patients who underwent diagnosis and surgery at our hospitals from August 2008 to August 2018 were enrolled. Clinical-pathological information was obtained and immunohistochemistry result was available. From these cases, a 30% Ki-67 LI was employed to divide LBHN into two groups with low and high levels; high Ki-67 LI was associated with GIII tumor grade (P < 0.001), positive axillary lymph nodes (ALN) status (P = 0.018) and negative PR status (P = 0.016), and also seemed to be related to T2-T3 tumor size (P = 0.058). High Ki-67 level (HR = 3.30; P < 0.011), positive ALN (HR = 7.29; P < 0.001) and PR negative (HR = 2.63; P = 0.034) significantly associated with poor 5-year DFS in multivariate Cox's proportional hazard regression model. A novel prognosis prediction model (KLP-PI), based on Ki-67 LI, ALN and PR status, showed a better discriminatory ability compared with traditional Nottingham prognostic index targeted to LBHN breast cancer. Our study highlights that high Ki-67 LI, positive ALN and negative PR status were associated with poor outcome in LBHN patients, and composed by these prognostic factors, KLP-PI improves the prognostic assessment using the Nottingham Prognostic Index when aiming at LBHN subtype.

Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories

Identifying the earliest somatic changes in prostate cancer can give important insights into tumor evolution and aids in stratifying high- from low-risk disease. We integrated whole genome, transcriptome and methylome analysis of early-onset prostate cancers (diagnosis ≤55 years). Characterization across 292 prostate cancer genomes revealed age-related genomic alterations and a clock-like enzymatic-driven mutational process contributing to the earliest mutations in prostate cancer patients. Our integrative analysis identified four molecular subgroups, including a particularly aggressive subgroup with recurrent duplications associated with increased expression of ESRP1, which we validate in 12,000 tissue microarray tumors. Finally, we combined the patterns of molecular co-occurrence and risk-based subgroup information to deconvolve the molecular and clinical trajectories of prostate cancer from single patient samples.

Integrated landscape of copy number variation and RNA expression associated with nodal metastasis in invasive ductal breast carcinoma

Background

Lymph node metastasis (NM) in breast cancer is a clinical predictor of patient outcomes, but how its genetic underpinnings contribute to aggressive phenotypes is unclear. Our objective was to create the first landscape analysis of CNV-associated NM in ductal breast cancer. To assess the role of copy number variations (CNVs) in NM, we compared CNVs and/or associated mRNA expression in primary tumors of patients with NM to those without metastasis.

Results

We found CNV loss in chromosomes 1, 3, 9, 18, and 19 and gains in chromosomes 5, 8, 12, 14, 16-17, and 20 that were associated with NM and replicated in both databases. In primary tumors, per-gene CNVs associated with NM were ten times more frequent than mRNA expression; however, there were few CNV-driven changes in mRNA expression that differed by nodal status. Overlapping regions of CNV changes and mRNA expression were evident for the CTAGE5 gene. In 8q12, 11q13-14, 20q1, and 17q14-24 regions, there were gene-specific gains in CNV-driven mRNA expression associated with NM.

Methods

Data on CNV and mRNA expression from the TCGA and the METABRIC consortium of breast ductal carcinoma were utilized to identify CNV-based features associated with NM. Within each dataset, associations were compared across omic platforms to identify CNV-driven variations in gene expression. Only replications across both datasets were considered as determinants of NM.

Conclusions

Gains in CTAGE5, NDUFC2, EIF4EBP1, and PSCA genes and their expression may aid in early diagnosis of metastatic breast carcinoma and have potential as therapeutic targets.

Optimise not compromise: The importance of a multidisciplinary breast cancer patient pathway in the era of oncoplastic and reconstructive surgery

Modern breast cancer care is a complex multidisciplinary undertaking in which the integrated function of multiple constituent parts is critical, and where changes to one therapeutic component may profoundly influence the delivery and outcomes of another. Oncoplastic and reconstructive breast surgery has evolved in the era of longer survival rates for women with breast cancer and aims to enhance oncological and cosmetic outcomes. However, concurrently there has been an expansion in the indications for post-mastectomy radiation therapy (Abdulkarim et al., 2011; Early Breast Cancer Trialists' Collaborative Group (EBCTCG), 2014; Poortmans et al., 2015; Wang et al., 2011), the recognition of several biologically distinct breast cancer subtypes (Perou et al., 2000; Sørlie et al., 2001, 2003; Cheang et al., 2008, 2009; Sotiriou et al., 2003; Millar et al., 2011; Blows et al., 2010; Schnitt, 2010; Haque et al., 2012; Dai et al., 2015) and the development of recommendations for prophylactic surgery for high-risk women, including BRCA-mutation carriers (James et al., 2006; Domchek et al., 2010). Primary systemic therapy is increasingly utilised yet has varying efficacy depending on tumour biology (Cortazar et al., 2014). In this paper we review the evidence which informs the multidisciplinary team opinion in the era of oncoplastic and reconstructive breast surgery. We aim to describe an optimal multidisciplinary approach which balances competing risks of multimodal therapies to optimise oncological and cosmetic outcomes.

Tumor-Infiltrating Lymphocytes in Breast Cancer. Association with Clinical and Pathological Parameters

In patients with primary resectable breast cancer, a positive correlation between the age and the count of CD16⁺ lymphocytes and a negative correlation of this parameter with the number of regulatory CD4⁺CD25⁺CD127^- cells and proliferative activity of Ki-67 tumor cells were revealed. Higher level of Ki-67 was associated with reduced number of effector lymphocytes (CD8⁺ and CD16⁺) and elevated content of regulatory CD8⁺CD11b^-CD28^- T cells. The absence of expression of estrogen receptors was associated with reduced cytotoxic potential of CD8⁺ T cell in comparison with ER⁺ breast cancer. The percentage of CD8⁺ lymphocytes (CD3⁺CD8⁺ and CD8⁺CD11b⁺CD28⁺) among lymphocytes infiltrating the tumor was higher in PR⁺ breast cancer than in PR^- tumors. With increasing the tumor load, the number of lymphocytes expressing CD16 marker and their cytotoxic potential decreased.

Molecular patterns of cancer colonisation in lymph nodes of breast cancer patients

Lymph node (LN) metastasis is an important prognostic parameter in breast carcinoma, a crucial site for tumour–immune cell interaction and a gateway for further dissemination of tumour cells to other metastatic sites. To gain insight into the underlying molecular changes from the pre-metastatic, via initial colonisation to the fully involved LN, we reviewed transcriptional research along the evolving microenvironment of LNs in human breast cancers patients. Gene expression studies were compiled and subjected to pathway-based analyses, with an emphasis on immune cell-related genes. Of 366 studies, 14 performed genome-wide gene expression comparisons and were divided into six clinical-biological scenarios capturing different stages of the metastatic pathway in the LN, as follows: metastatically involved LNs are compared to their patient-matched primary breast carcinomas (scenario 1) or the normal breast tissue (scenario 2). In scenario 3, uninvolved LNs were compared between LN-positive patients and LN-negative patients. Scenario 4 homed in on the residual uninvolved portion of involved LNs and compared it to the patient-matched uninvolved LNs. Scenario 5 contrasted uninvolved and involved LNs, whilst in scenario 6 involved (sentinel) LNs were assessed between patients with other either positive or negative LNs (non-sentinel).

Gene lists from these chronological steps of LN metastasis indicated that gene patterns reflecting deficiencies in dendritic cells and hyper-proliferation of B cells parallel to tumour promoting pathways, including cell adhesion, extracellular matrix remodelling, cell motility and DNA repair, play key roles in the changing microenvironment of a pro-metastatic to a metastatically involved LN. Similarities between uninvolved LNs and the residual uninvolved portion of involved LNs hinted that LN alterations expose systemic tumour-related immune responses in breast cancer patients. Despite the diverse settings, gene expression patterns at different stages of metastatic colonisation in LNs were recognised and may provide potential avenues for clinical interventions to counteract disease progression for breast cancer patients.

Breast Cancer Research in the Caribbean: Analysis of Reports From 1975 to 2017

PURPOSE

Breast cancer is among the leading causes of death resulting from cancer in Caribbean women. Studies examining exogenous and genetically predetermined endogenous risk factors are critical to define breast cancer susceptibility in Caribbean women. The purpose of this systematic review is to assess the existing scientific literature in the last 42 years (1975 to 2017) to describe the body of research generated for the population of this region and determine future research directions.

METHODS

We selected published research articles using a combination of definite keyword searches in PubMed. Only articles presenting the Caribbean population as the focus of their research objectives were included in this analysis.

RESULTS

Studies on breast cancer in the Caribbean are limited. A majority of publications on Caribbean populations were descriptive, focusing on cancer trends and clinicopathologic factors. High incidence and mortality rates for breast cancer are reported for the region, and there seem to be some differences between countries in the frequency of cases according to age at presentation. A limited number of epidemiologic, behavioral, and genetic and molecular studies were conducted in more recent years.

CONCLUSION

A regional strategy for cancer registration is needed for the Caribbean to address possible underestimates of breast cancer incidence. Furthermore, behavioral, molecular, genetic, and epidemiologic investigations of breast cancer are critical to address the concerns related to currently described high incidence and mortality rates in the Caribbean.

Prediction of pathological complete response and prognosis in patients with neoadjuvant treatment for triple-negative breast cancer

Background

It has been reported that pathological complete response is an important surrogate marker for disease-free survival and overall survival in patients with triple-negative breast cancer. This study investigates predictors of the response to neoadjuvant platinum-based or anthracycline-based treatment, and of the prognosis, in patients with triple-negative breast cancer.

Methods

A total of 121 patients with triple-negative breast cancer received neoadjuvant treatment with either platinum or anthracycline between 2008 and 2013. Pathological complete response was assessed relative to different treatments using logistic regression models with age, clinical tumor stage, grading, and Ki-67 as predictors and interaction terms, to obtain adjusted and subgroup-specific results. The impact of the pathological complete response rate on disease-free survival and overall survival was also analyzed.

Results

The pathological complete response rate was higher after platinum/taxane treatment compared with anthracycline/taxane (50.0% vs. 41.8%), but this was not significant in the adjusted analysis (OR 1.44; 95% CI, 0.68 to 3.09). A high histological grade (G3) was a predictor for higher pathological complete response in platinum-based therapy (OR 2.27; 95% CI, 1.00 to 5.30). The effect of neoadjuvant chemotherapy on pathological complete response was significantly different for G1–2 vs. G3 (P_interaction = 0.013), and additional subgroup-specific differences were noted. Pathological complete response was a predictor for improved disease-free survival and overall survival in both treatment groups, with and without platinum chemotherapy.

Conclusions

This retrospective study of patients with triple-negative breast cancer adds to the evidence that the treatment effect of platinum may be greatest particularly in G3 tumors. In addition, the effect of pathological complete response on the prognosis does not depend on the treatment used.

Combining DNA methylation and RNA sequencing data of cancer for supervised knowledge extraction

Background

In the Next Generation Sequencing (NGS) era a large amount of biological data is being sequenced, analyzed, and stored in many public databases, whose interoperability is often required to allow an enhanced accessibility. The combination of heterogeneous NGS genomic data is an open challenge: the analysis of data from different experiments is a fundamental practice for the study of diseases. In this work, we propose to combine DNA methylation and RNA sequencing NGS experiments at gene level for supervised knowledge extraction in cancer.

Methods

We retrieve DNA methylation and RNA sequencing datasets from The Cancer Genome Atlas (TCGA), focusing on the Breast Invasive Carcinoma (BRCA), the Thyroid Carcinoma (THCA), and the Kidney Renal Papillary Cell Carcinoma (KIRP). We combine the RNA sequencing gene expression values with the gene methylation quantity, as a new measure that we define for representing the methylation quantity associated to a gene. Additionally, we propose to analyze the combined data through tree- and rule-based classification algorithms (C4.5, Random Forest, RIPPER, and CAMUR).

Results

We extract more than 15,000 classification models (composed of gene sets), which allow to distinguish the tumoral samples from the normal ones with an average accuracy of 95%. From the integrated experiments we obtain about 5000 classification models that consider both the gene measures related to the RNA sequencing and the DNA methylation experiments.

Conclusions

We compare the sets of genes obtained from the classifications on RNA sequencing and DNA methylation data with the genes obtained from the integration of the two experiments. The comparison results in several genes that are in common among the single experiments and the integrated ones (733 for BRCA, 35 for KIRP, and 861 for THCA) and 509 genes that are in common among the different experiments. Finally, we investigate the possible relationships among the different analyzed tumors by extracting a core set of 13 genes that appear in all tumors. A preliminary functional analysis confirms the relation of part of those genes (5 out of 13 and 279 out of 509) with cancer, suggesting to focus further studies on the new individuated ones.

Electronic supplementary material

The online version of this article (10.1186/s13040-018-0184-6) contains supplementary material, which is available to authorized users.

Prognostic indices predictive of short-term disease-free survival of breast carcinoma patients receiving primary surgical treatment in Sri Lanka

Background

Breast carcinoma (BCa) is the commonest malignancy among women worldwide and in Sri Lanka. Several prognostic indices are described for BCa.

Aims

To assess clinicopathological features and prognostic indices derived from routine clinical, histopathological and immunohistochemical (IHC) data, in a cohort of patients undergoing primary surgery for BCa and to determine their prognostic impact on short-term disease free survival.

Setting and Design

: This is a bidirectional cohort study of 208 women undergoing primary surgery for BCa at the National Hospital of Sri Lanka, from 2012-2014, excluding post-neoadjuvant chemotherapy cases.

Material and Methods

Clinical details, tumor size and nodal status were obtained from histopathology reports. Histopathology and estrogen/progesterone receptor and HER2 status were reviewed. Molecular subtype based on IHC was determined. Nodal ratio (number of positive nodes/total number retrieved) and Nottingham prognostic index were calculated. Follow up information was obtained by patient interviews and record review.

Statistical Analysis

Data was analyzed by univariate and multivariate Cox regression using SPSS19.0.

Results

Mean follow-up duration was 27.16 months (0.5-52 months, s = 9.35 months). 174 (82.9%) remained disease free with 19 (9%) deaths. Thirteen (6.2%) survived with metastasis and 4 (1.9%) with recurrences. On univariate Cox regression, tumor, nodal and TNM stages, nodal ratio and lymphovascular invasion (LVI) were predictive of disease free survival (DFS) (P = 0.001, P = 0.021, P = 0.022, P = 0.002, P = 0.018). On multivariate analysis TNM stage and LVI were predictive of DFS.

Conclusion

TNM stage and LVI were the most important predictors of short-term disease free survival in this study population, confirming that early detection of BCa at a lower stage has a significant impact on short-term outcomes.

Inhibition of BTF3 sensitizes luminal breast cancer cells to PI3Kα inhibition through the transcriptional regulation of ERα

Selective phosphatidylinositol 3 kinase (PI3K) inhibitors are being actively tested in clinical trials for ERα-positive (ER+) breast cancer due to the presence of activating PIK3CA mutations. However, recent studies have revealed that increased ERα transcriptional activity limits the efficacy of PI3K inhibitor monotherapy for ER + breast cancers. Herein, we report the identification of BTF3 as an oncogenic transcription factor that regulates ERα expression in luminal breast cancers. Our TCGA analysis reveals high expression levels of BTF3 in luminal/ER + breast cancer and cell line models harboring ERα overexpression. Concordantly, BTF3 expression is highly and strongly associated with ESR1 expression in multiple breast cancer cohorts. We further show that BTF3 promotes the proliferation, survival and migration of ER + breast cancer cells by modulating ESR1 expression and ERα-dependent transcription. Moreover, BTF3 knockdown sensitizes ER + breast cancer cells to the PI3Kα inhibitor BYL-719 in both in vitro and in vivo models. Together, our findings highlight a novel role of BTF3 in modulation of ERα-dependent transcriptional activity and its potential as a predictive marker for the response to PI3K-targeted therapy in ER + breast cancer.

Ancillary Prognostic and Predictive Testing in Breast Cancer: Focus on Discordant, Unusual, and Borderline Results

Ancillary testing in breast cancer has become standard of care to determine what therapies may be most effective for individual patients with breast cancer. Single-marker tests are required on all newly diagnosed and newly metastatic breast cancers. Markers of proliferation are also used, and include both single-marker tests like Ki67 as well as panel-based gene expression tests, which have made more recent contributions to prognostic and predictive testing in breast cancers. This review focuses on pathologist interpretation of these ancillary test results, with a focus on expected versus unexpected results and troubleshooting borderline, unusual, or discordant results.

The cell cycle regulatory DREAM complex is disrupted by high expression of oncogenic B-Myb

Overexpression of the oncogene MYBL2 (B-Myb) is associated with increased cell proliferation and serves as marker of poor prognosis in cancer. However, the mechanism by which B-Myb alters the cell cycle is not fully understood. In proliferating cells, B-Myb interacts with the MuvB core complex including LIN9, LIN37, LIN52, RBBP4, and LIN54, forming the MMB (Myb-MuvB) complex, and promotes transcription of genes required for mitosis. Alternatively, the MuvB core interacts with Rb-like protein p130 and E2F4-DP1 to form the DREAM complex that mediates global repression of cell cycle genes in G0/G1, including a subset of MMB target genes. Here, we show that overexpression of B-Myb disrupts the DREAM complex in human cells, and this activity depends on the intact MuvB-binding domain in B-Myb. Furthermore, we found that B-Myb regulates the protein expression levels of the MuvB core subunit LIN52, a key adaptor for assembly of both the DREAM and MMB complexes, by a mechanism that requires S28 phosphorylation site in LIN52. Given that high expression of B-Myb correlates with global loss of repression of DREAM target genes in breast and ovarian cancer, our findings offer mechanistic insights for aggressiveness of cancers with MYBL2 amplification, and establish the rationale for targeting B-Myb to restore cell cycle control.

Recurrence prediction using microRNA expression in hormone receptor positive breast cancer during tamoxifen treatment

PURPOSE

To identify miRNAs associated with distant recurrence during tamoxifen treatment and build a recurrence prediction model.

MATERIALS AND METHODS

We measured the expression of five miRNAs (miR-134, miR-125b-5P, miRNA-30a, miR-10a-5p and miR-222). A total of 176 tumour tissues from 176 patients who had hormone receptor positive breast cancer with tamoxifen treatment were used to measure miRNA expression using quantitative real-time PCR (qRT-PCR).

RESULTS

The five miRNAs were all up-regulated in distant recurrence cases within 5 years after surgery and during tamoxifen treatment. Kaplan-Meier survival analyses based on expression cut-offs determined by receiver characteristics curves (ROC) showed that high expression of miR-134, miR-125b-5P, miRNA-30a, miR-10a-5p and miR-222 were significantly (log-rank p-value =0.006, p-value <0.0001, p-value <0.0001, p-value <0.0001 and p-value <0.0001, respectively) associated with short relapse-free time. Our results were used to build a combined 3 miRNAs expression model. It could be used to categorize high-risk subset of patients with short relapse-free survival (AUC =0.891, p-value <0.0001).

CONCLUSIONS

Distant recurrence during tamoxifen treatment of hormone positive breast cancer might be affected by tamoxifen resistance related miRNAs. Such distant recurrence can be predicted using miRNA measurement.

Mechanistic evaluation of phytochemicals in breast cancer remedy: current understanding and future perspectives

Breast cancer is one of the most commonly diagnosed cancers around the globe and accounts for a large proportion of fatalities in women. Despite the advancement in therapeutic and diagnostic procedures, breast cancer still represents a major challenge. Current anti-breast cancer approaches include surgical removal, radiotherapy, hormonal therapy and the use of various chemotherapeutic drugs. However, drug resistance, associated serious adverse effects, metastasis and recurrence complications still need to be resolved which demand safe and alternative strategies. In this scenario, phytochemicals have recently gained huge attention due to their safety profile and cost-effectiveness. These phytochemicals modulate various genes, gene products and signalling pathways, thereby inhibiting breast cancer cell proliferation, invasion, angiogenesis and metastasis and inducing apoptosis. Moreover, they also target breast cancer stem cells and overcome drug resistance problems in breast carcinomas. Phytochemicals as adjuvants with chemotherapeutic drugs have greatly enhanced their therapeutic efficacy. This review focuses on the recently recognized molecular mechanisms underlying breast cancer chemoprevention with the use of phytochemicals such as curcumin, resveratrol, silibinin, genistein, epigallocatechin gallate, secoisolariciresinol, thymoquinone, kaempferol, quercetin, parthenolide, sulforaphane, ginsenosides, naringenin, isoliquiritigenin, luteolin, benzyl isothiocyanate, α-mangostin, 3,3'-diindolylmethane, pterostilbene, vinca alkaloids and apigenin.

A nomogram prediction for the survival of patients with triple negative breast cancer

Triple negative breast cancer (TNBC) is a subtype of breast cancer with poor prognosis. In this study, we aimed to conduct a nomogram to predict the survival of individual with TNBC by incorporating significant clinical and laboratory parameters. 404 TNBC patients from the Affiliated Union Hospital of Fujian Medical University between 2006 and 2012 were selected in the training cohort. Cox univariate and multivariate regression analyses were adopted to identify independent prognostic factors. The predictive accuracy and discriminative ability of this nomogram were evaluated by concordance index (C-index) and calibration curve. The accuracy of this nomogram was also compared with the 8^th AJCC TNM staging system. An external validation cohort was further performed in an independent cohort of 200 patients between 2012 and 2014. Seven independent prognostic factors, including family history of breast cancer, tumor location, number of positive lymph nodes, histological grade, serum CEA, CA125 and CA153 were identified as independent prognostic factors. A nomogram incorporating these prognostic factors was subsequently conducted and the calibration plot on the probability for 3 or 5 years overall survival (OS) showed an optimal agreement between the nomogram prediction and actual observations. In addition, the C-index of this nomogram was higher than that of TNM staging system in both training and validation cohort (training cohort, 0.76 vs. 0.66, p<0.001 and validation cohort, 0.72 vs. 0.64, p=0.002, respectively). This proposed nomogram could provide more accurate individual prediction for the prognosis of the patients with TNBC and was able to help physicians to identify subgroups of patients at different risk and to decide who need intensive follow-up or additional treatment.

Challenges and perspectives in the treatment of diabetes associated breast cancer

Type 2 diabetes mellitus is one of the most common chronic disease worldwide and affects all cross-sections of the society including children, women, youth and adults. Scientific evidence has linked diabetes to higher incidence, accelerated progression and increased aggressiveness of different cancers. Among the different forms of cancer, research has reinforced a link between diabetes and the risk of breast cancer. Some studies have specifically linked diabetes to the highly aggressive, triple negative breast cancers (TNBCs) which do not respond to conventional hormonal/HER2 targeted interventions, have chances of early recurrence, metastasize, tend to be more invasive in nature and develop drug resistance. Commonly used anti-diabetic drugs, such as metformin, have recently gained importance in the treatment of breast cancer due to their proposed anti-cancer properties. Here we discuss the link between diabetes and breast cancer, the metabolic disturbances in diabetes that support the development of breast cancer, the challenges involved and future perspective and directions. We link the three main metabolic disturbances (dyslipidemia, hyperinsulinemia and hyperglycemia) that occur in diabetes to potential aberrant molecular pathways that may lead to the development of an oncogenic phenotype of the breast tissue, thereby leading to acceleration of cell growth, proliferation, migration, inflammation, angiogenesis, EMT and metastasis and inhibition of apoptosis in breast cancer cells. Furthermore, managing diabetes and treating cancer using a combination of anti-diabetic and classical anti-cancer drugs should prove to be more efficient in the treatment diabetes associated cancers.

Genetic Markers in Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) accounts for 15% to 20% of breast cancer cases and is characterized by the absence of estrogen, progesterone, and human epidermal growth factor 2 receptors. Though TNBC is a highly heterogenic and aggressive disease, TNBC patients have better response to neoadjuvant therapy compared to other breast cancer subtypes. Nevertheless, patients with residual disease have a very poor prognosis, with higher probability of relapse and lower overall survival in the first years after diagnosis. TNBC has 6 subtypes with distinct molecular signatures with different prognoses and probably different responses to therapy. The precise stratification of TNBC is therefore crucial for the development of potent standardized and targeted therapies. In spite of intensive research into finding new molecular biomarkers and designing personalized therapeutic approaches, BRCA mutational status is the only clinically validated biomarker for personalized therapy in TNBC. Recent studies have reported several promising biomarkers that are currently being validated through clinical trials. The objective of this review was to summarize the clinically relevant genetic markers for TNBC that could serve as diagnostic, prognostic, or predictive or could improve personalized therapeutic strategies.

Identification of potential core genes in triple negative breast cancer using bioinformatics analysis

Background

Triple-negative breast cancer (TNBC) is a subtype of breast cancer with poor clinical outcome and limited treatment options. Lacking molecular targets, chemotherapy is the main adjuvant treatment for TNBC patients.

Materials and methods

To explore potential therapeutic targets for TNBC, we analyzed three microarray datasets (GSE38959, GSE45827, and GSE65194) derived from the Gene Expression Omnibus (GEO) database. The GEO2R tool was used to screen out differentially expressed genes (DEGs) between TNBC and normal tissue. Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed using the Database for Annotation, Visualization and Integrated Discovery to identify the pathways and functional annotation of DEGs. Protein–protein interaction of these DEGs was analyzed based on the Search Tool for the Retrieval of Interacting Genes database and visualized by Cytoscape software. In addition, we used the online Kaplan–Meier plotter survival analysis tool to evaluate the prognostic value of hub genes expression in breast cancer patients.

Results

A total of 278 upregulated DEGs and 173 downregulated DEGs were identified. Among them, ten hub genes with a high degree of connectivity were picked out. Overexpression of these hub genes was associated with unfavorable prognosis of breast cancer, especially, CCNB1 overexpression was observed and indicated poor outcome of TNBC.

Conclusion

Our study suggests that CCNB1 was overexpressed in TNBC compared with normal breast tissue, and overexpression of CCNB1 was an unfavorable prognostic factor of TNBC patients. Further study is needed to explore the value of CCNB1 in the treatment of TNBC.

Subtyping Of Triple Negative Breast Carcinoma On The Basis Of RTK Expression

Background: "Triple-negative breast cancers" (TNBC) comprise a heterogeneous group of about 15% of invasive BCs lacking the expression of estrogen and progesterone receptors (ER, PR) and the expression of HER2 (ERBB2) and are therefore no established candidates for targeted treatment options in BC, i.e., endocrine and anti-HER2 therapy. The aim of the present study was to use gene expression profiling and immunohistochemical (IHC) characterization to identify receptor tyrosine kinase (RTK) profiles that would allow patient stratification for the purposes of target-oriented personalized tumor therapy in TNBC. Methods: Twenty-nine cases of TNBC selected according to routine diagnostic IHC/cytogenetic criteria were examined by reverse transcription polymerase chain reaction (RT-PCR). RTK mRNA expression profiles were generated for a total of 31 tumor-relevant biomarkers, mainly belonging to the IGF- and EGF-receptor families but also including biomarkers related to downstream signaling. Protein expression of selected biomarkers was investigated by IHC. Results: Hierarchical cluster analysis revealed a dichotomous differentiation pattern amongst TNBCs. A significant difference in gene expression was observed for 16 of the 31 RTK-associated tumor relevant biomarkers between the two newly identified TNBC subgroups. The findings were verified at the posttranslational level by the IHC data. The RTKs HER4, IGF-1R and IGF-2R and the hormone receptors ER and PR below the IHC detection limit play a central role in the differentiation of the two TNBC subgroups. Observed survival was reported as Kaplan-Meier estimates and point towards an improved survival of patients with RTK-high with superior three-year survival rate of 100% compared to RTK-low gene signatures with superior three-year survival rate of 60% (log-rank test, p-value = 0.022). Conclusion: Gene-expression and IHC analysis of the EGF and IGF receptor families and biomarkers associated with downstream signaling point to the existence of two distinct TNBC subtypes. The RTKs HER4, IGF-1R, IGF-2R and the hormone receptors ER and PR appear to be of particular importance here. Based on survival analysis the differentiation of TNBC with RTK-high and RTK-low gene signatures seems to be of prognostic relevance. Additionally, correlation analysis of the relationship between RTKs and ER suggests co-regulatory mechanisms that may have potential significance in new therapeutic approaches.

Immunity drives TET1 regulation in cancer through NF-κB

Ten-eleven translocation enzymes (TET1, TET2, and TET3), which induce DNA demethylation and gene regulation by converting 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), are often down-regulated in cancer. We uncover, in basal-like breast cancer (BLBC), genome-wide 5hmC changes related to TET1 regulation. We further demonstrate that TET1 repression is associated with high expression of immune markers and high infiltration by immune cells. We identify in BLBC tissues an anticorrelation between TET1 expression and the major immunoregulator family nuclear factor κB (NF-κB). In vitro and in mice, TET1 is down-regulated in breast cancer cells upon NF-κB activation through binding of p65 to its consensus sequence in the TET1 promoter. We lastly show that these findings extend to other cancer types, including melanoma, lung, and thyroid cancers. Together, our data suggest a novel mode of regulation for TET1 in cancer and highlight a new paradigm in which the immune system can influence cancer cell epigenetics.

Breast cancer development and progression: Risk factors, cancer stem cells, signaling pathways, genomics, and molecular pathogenesis

As the most commonly occurring cancer in women worldwide, breast cancer poses a formidable public health challenge on a global scale. Breast cancer consists of a group of biologically and molecularly heterogeneous diseases originated from the breast. While the risk factors associated with this cancer varies with respect to other cancers, genetic predisposition, most notably mutations in BRCA1 or BRCA2 gene, is an important causative factor for this malignancy. Breast cancers can begin in different areas of the breast, such as the ducts, the lobules, or the tissue in between. Within the large group of diverse breast carcinomas, there are various denoted types of breast cancer based on their invasiveness relative to the primary tumor sites. It is important to distinguish between the various subtypes because they have different prognoses and treatment implications. As there are remarkable parallels between normal development and breast cancer progression at the molecular level, it has been postulated that breast cancer may be derived from mammary cancer stem cells. Normal breast development and mammary stem cells are regulated by several signaling pathways, such as estrogen receptors (ERs), HER2, and Wnt/β-catenin signaling pathways, which control stem cell proliferation, cell death, cell differentiation, and cell motility. Furthermore, emerging evidence indicates that epigenetic regulations and noncoding RNAs may play important roles in breast cancer development and may contribute to the heterogeneity and metastatic aspects of breast cancer, especially for triple-negative breast cancer. This review provides a comprehensive survey of the molecular, cellular and genetic aspects of breast cancer.

Pharmacophore modeling for identification of anti-IGF-1R drugs and in-vitro validation of fulvestrant as a potential inhibitor

Insulin-like growth factor 1 receptor (IGF-1R) is an important therapeutic target for breast cancer treatment. The alteration in the IGF-1R associated signaling network due to various genetic and environmental factors leads the system towards metastasis. The pharmacophore modeling and logical approaches have been applied to analyze the behaviour of complex regulatory network involved in breast cancer. A total of 23 inhibitors were selected to generate ligand based pharmacophore using the tool, Molecular Operating Environment (MOE). The best model consisted of three pharmacophore features: aromatic hydrophobic (HyD/Aro), hydrophobic (HyD) and hydrogen bond acceptor (HBA). This model was validated against World drug bank (WDB) database screening to identify 189 hits with the required pharmacophore features and was further screened by using Lipinski positive compounds. Finally, the most effective drug, fulvestrant, was selected. Fulvestrant is a selective estrogen receptor down regulator (SERD). This inhibitor was further studied by using both in-silico and in-vitro approaches that showed the targeted effect of fulvestrant in ER+ MCF-7 cells. Results suggested that fulvestrant has selective cytotoxic effect and a dose dependent response on IRS-1, IGF-1R, PDZK1 and ER-α in MCF-7 cells. PDZK1 can be an important inhibitory target using fulvestrant because it directly regulates IGF-1R.

Screen for MicroRNA and Drug Interactions in Breast Cancer Cell Lines Points to miR-126 as a Modulator of CDK4/6 and PIK3CA Inhibitors

Background: Breast cancer (BC) represents the most common cancer in women worldwide. Due to its heterogeneous nature, breast cancer management might benefit from differential treatments toward personalized medicine. Additionally, drug resistance is a common phenomenon. We systematically investigated the effect of 14 different drugs administered on BC cell lines in combination with microRNAs (miRNA, miR).

Methods: Thirty-eight miRNAs, all associated with BC by clinical and molecular parameters including progression, prognosis and subtypes, were tested for their effects on the viability of 12 different BC cell lines. Four miRNAs with the strongest impact on viability were further assayed in combination with 14 BC drugs. Mann–Whitney U-test with Bonferroni correction was used for statistical analysis.

Results: In a miRNA only pre-screen we observed effects on BC cell lines' viability for 34 out of 38 candidate miRNAs. We then identified 14 miRNA/drug combinations for which the combination IC₅₀ was lower than that of both miRNA and drug as single agents. miR-181a, paired with GSK1070916, Doxorubicin, XL765 and AMG511, was the only miRNA active on the triple negative (TNBC) MDA-MB-468 cell line. miR-126 was the only miRNA (in combination with CDK4/6 or PIK3CA inhibitors) with significant effects on cell lines from different subtypes: MCF7 (Luminal) and MDA-MB-453 (HER2⁺). Because of its activity on different BC subtypes, we investigated the genome wide effects of miR-126 using transcriptomics and confirmed that expression of miR-126 in BC cell lines affected cell cycle and mitosis.

Conclusion: Our results show that a combination treatment with miRNAs, in particular miR-181a, miR-326, miR-9 and miR-126, enhance the activity of specific BC drugs in vitro, even on the most aggressive BC subtypes, HER2+ and TNBC. Finally, as expected from its drug interactions, based on a whole transcriptome study we could confirm a role for miR-126 in cell cycle regulation.

Molecular Classification of Breast Cancer

Breast cancer is a heterogeneous disease, observed traditionally by morphology and protein expression but, more recently with the advent of modern molecular technologies, at the genomic and transcriptomic level. This review describes the association between the different molecular subtypes with the histologic subtypes of breast cancer alongside some of their major genomic characteristics and illustrates how these subtypes may affect the appearance of tumors on imaging studies. The authors aim to show how molecular stratification can be used to augment traditional methods to improve our understanding of breast cancers and their clinical management.

Neutrophil-lymphocyte ratio predicts response to chemotherapy in triple-negative breast cancer

Background

The neutrophil-lymphocyte ratio (nlr) has been reported to correlate with patient outcome in several cancers, including breast cancer. We evaluated whether the nlr can be a predictive factor for pathologic complete response (pcr) after neoadjuvant chemotherapy (nac) in patients with triple-negative breast cancer (tnbc).

Methods

We analyzed the correlation between response to nac and various factors, including the nlr, in 87 patients with tnbc who underwent nac. In addition, we analyzed the association between the nlr and recurrence-free survival (rfs) in patients with tnbc.

Results

Of the 87 patients, 25 (28.7%) achieved a pcr. A high Ki-67 index and a low nlr were significantly associated with pcr. The pcr rate was higher in patients having a high Ki-67 index (≥15%) than in those having a low Ki-67 index (35.7% vs. 0%, p = 0.002) and higher in patients having a low nlr (≤1.7) than in those having a high nlr (42.1% vs. 18.4%, p = 0.018). In multiple logistic analysis, a low nlr remained the only predictive factor for pcr (odds ratio: 4.274; p = 0.008). In the survival analysis, the rfs was significantly higher in the low nlr group than in the high nlr group (5-year rfs rate: 83.7% vs. 66.9%; log-rank p = 0.016).

Conclusions

Our findings that the nlr is a predictor of pcr to nac and also a prognosticator of recurrence suggest an association between response to chemotherapy and inflammation in patients with tnbc. The pretreatment nlr can be a useful predictive and prognostic marker in patients with tnbc scheduled for nac.

PHF5A Epigenetically Inhibits Apoptosis to Promote Breast Cancer Progression

Alternative splicing (AS) and its regulation play critical roles in cancer, yet the dysregulation of AS and its molecular bases in breast cancer development have not yet been elucidated. Using an in vivo CRISPR screen targeting RNA-binding proteins, we identified PHD finger protein 5A (PHF5A) as a key splicing factor involved in tumor progression. PHF5A expression was frequently upregulated in breast cancer and correlated with poor survival, and knockdown of PHF5A significantly suppressed cell proliferation, migration, and tumor formation. PHF5A was required for SF3b spliceosome stability and linked the complex to histones, and the PHF5A-SF3b complex modulated AS changes in apoptotic signaling. In addition, expression of a short truncated FAS-activated serine/threonine kinase (FASTK) protein was increased after PHF5A ablation and facilitated Fas-mediated apoptosis. This PHF5A-modulated FASTK-AS axis was widely present in breast cancer specimens, particularly those of the triple-negative subtype. Taken together, our findings reveal that PHF5A serves as an epigenetic suppressor of apoptosis and thus provides a mechanistic basis for breast cancer progression and may be a valuable therapeutic target.Significance: This study provides an epigenetic mechanistic basis for the aggressive biology of breast cancer and identifies a translatable therapeutic target. Cancer Res; 78(12); 3190-206. ©2018 AACR.

Post-operative radiotherapy is beneficial for T1/T2 triple negative breast cancer patients with four or more positive lymph nodes

The efficacy of adjuvant radiotherapy for the treatment of triple negative breast cancer patients with varying numbers of positive lymph nodes is not clear. We assessed the association between adjuvant radiotherapy and survival in 943 T1/T2 triple negative breast cancer patients treated at our institute between 2008 and 2012. We determined that post-operative radiotherapy improved overall survival (OS), disease-free survival (DFS), and local recurrence-free survival (LRFS) in patients with ≥ 4 positive nodes (p = 0.037, p = 0.035, and p = 0.012, respectively). Although Cox regression analysis demonstrated that radiotherapy was a significant prognostic factor in triple negative breast cancer with ≥ 4 positive nodes, post-operative radiotherapy had no clear effect on OS, DFS, or LRFS in patients with 1-3 positive nodes (p = 0.849, p = 0.860, and p = 0.162, respectively). The prognosis (i.e., OS, DFS, and LRFS) of triple negative breast cancer patients without lymph node metastasis who underwent breast-conserving surgery and post-operative radiotherapy was similar to that of patients who underwent mastectomy alone (p = 0.336, p = 0.537, and p = 0.978, respectively). Our findings demonstrate that post-operative radiotherapy is beneficial for T1/T2 triple negative breast cancer patients with ≥ 4 positive lymph nodes.

Squalene epoxidase as a promising metabolic target in cancer treatment

Oncogenic alteration of the cholesterol synthesis pathway is a recognized mechanism of metabolic adaptation. In the present review, we focus on squalene epoxidase (SE), one of the two rate-limiting enzymes in cholesterol synthesis, retracing its history since its discovery as an antimycotic target to its description as an emerging metabolic oncogene by amplification with clinical relevance in cancer. We review the published literature assessing the association between SE over-expression and poor prognosis in this disease. We assess the works demonstrating how SE promotes tumor cell proliferation and migration, and displaying evidence of cancer cell demise in presence of human SE inhibitors in in vitro and in vivo models. Taken together, robust scientific evidence has by now accumulated pointing out SE as a promising novel therapeutic target in cancer treatment.

18FDG-PET/CT and molecular markers to predict response to neoadjuvant chemotherapy and outcome in HER2-negative advanced luminal breast cancers patients

Background

The efficacy of neoadjuvant chemotherapy regimens in advanced luminal breast cancer patients is difficult to predict. Intrinsic properties of breast tumors, including altered gene expression profile and dynamic evaluation of metabolic properties of tumor cells using positron emission tomography/computed tomography (PET/CT) of tumor cells, have been identified to guide patient's prognosis. The aim of this study is to determine if both analyses may improve the prediction of response to neoadjuvant chemotherapy in ER-positive / HER2-negative breast cancers (BCs) patients.

Methods

We used metabolic PET parameters, at diagnosis and after two cycles of chemotherapy and proliferation gene expression profile on biopsy at diagnosis, in particular, the genomic grade index (GGI) analyzed by reverse transcription and quantitative polymerase chain reaction (RT-qPCR). The pathological response was the surrogate endpoint.

Results

The change of FDG uptake between baseline PET and interim PET after 2 cycles of neoadjuvant chemotherapy (ΔSUVmax) was highly associated with pCR (p=0.008). We also observed an ability of P53 mutated status (p=0.042), in addition to histological grade (p=0. 0004), and PR expression (p=0.01) to predict pCR in ER-positive BCs, whereas no proliferation marker predicted pCR (P=0.39 for GGI). Finally, only ΔSUVmax was significantly associated with event free survival (p=0.047).

Conclusions

Our results confirm the predictive and prognostic value of tumor ΔSUVmax in ER-positive /HER2-negative advanced BCs patients. These findings can be helpful to select high-risk patients within trials investigating novel treatment strategies.

Proteomic analysis defines kinase taxonomies specific for subtypes of breast cancer

Multiplexed small molecule inhibitors covalently bound to Sepharose beads (MIBs) were used to capture functional kinases in luminal, HER2-enriched and triple negative (basal-like and claudin-low) breast cancer cell lines and tumors. Kinase MIB-binding profiles at baseline without perturbation proteomically distinguished the four breast cancer subtypes. Understudied kinases, whose disease associations and pharmacology are generally unexplored, were highly represented in MIB-binding taxonomies and are integrated into signaling subnetworks with kinases that have been previously well characterized in breast cancer. Computationally it was possible to define subtypes using profiles of less than 50 of the more than 300 kinases bound to MIBs that included understudied as well as metabolic and lipid kinases. Furthermore, analysis of MIB-binding profiles established potential functional annotations for these understudied kinases. Thus, comprehensive MIBs-based capture of kinases provides a unique proteomics-based method for integration of poorly characterized kinases of the understudied kinome into functional subnetworks in breast cancer cells and tumors that is not possible using genomic strategies. The MIB-binding profiles readily defined subtype-selective differential adaptive kinome reprogramming in response to targeted kinase inhibition, demonstrating how MIB profiles can be used in determining dynamic kinome changes that result in subtype selective phenotypic state changes.

Apigenin, a dietary flavonoid, induces apoptosis, DNA damage, and oxidative stress in human breast cancer MCF-7 and MDA MB-231 cells

Apigenin is found in several dietary plant foods such as vegetables and fruits. To investigate potential anticancer properties of apigenin on human breast cancer, ER-positive MCF-7 and triple-negative MDA MB-231 cells were used. Moreover, toxicological safety of apigenin towards normal cells was evaluated in human lymphocytes. Cytotoxicity of apigenin towards cancer cells was evaluated by MTT assay whereas further genotoxic and oxidative stress parameters were measured by comet and lipid peroxidation assays, respectively. In order to examine the type of cell death induced by apigenin, several biomarkers were used. Toxicological safety towards normal cells was evaluated by cell viability and comet assays. After the treatment with apigenin, we observed changes in cell morphology in a dose- (10 to 100 μM) and time-dependent manner. Moreover, apigenin caused cell death in both cell lines leading to significant toxicity and dominantly to apoptosis. Furthermore, apigenin proved to be genotoxic towards the selected cancer cells with a potential to induce oxidative damage to lipids. Of great importance is that no significant cytogenotoxic effects were detected in normal cells. The observed cytogenotoxic and pro-cell death activities of apigenin coupled with its low toxicity towards normal cells indicate that this natural product could be used as a future anticancer modality. Therefore, further analysis to determine the exact mechanism of action and in vivo studies on animal models are warranted.