Basal-like Breast Cancer Subtype Research Articles

Evaluation of basal and luminal subtypes of urothelial carcinoma in African American and non-African American patients.

305 Background: African American (AA) patients with urothelial carcinoma (UC) have been known to have a worse prognosis even when corrected for variables such as tumor stage and grade. Analysis of gene expression of several malignancies has resulted in the discovery of molecular subtypes with well-defined intrinsic biology. Recent studies in high grade (HG), muscle-invasive UC have led to the identification of two intrinsic, molecular subsets termed “luminal” and “basal” with characteristics of stages of urothelial differentiation, and that remarkably reflect the luminal and basal-like molecular subtypes of breast cancer. Patients with basal-like UC have a significantly worse overall survival. Methods: A total of 215 HG muscle-invasive UC tumors from the MDACC (n=75) and TCGA (n=140) were used to make intrinsic subtype calls using gene expression profiling (MDACC: DASL [cDNA-mediated Annealing, Selection, extension, and Ligation] and TCGA: RNA seq). Basal and luminal subtype calls were derived using previously published subtype classifiers (Damrauer et. al. PNAS, 2014 and Choi et. al. Cancer Cell, 2014). Patients were classified into AA and non-AA (white, Hispanic, or Asian) based upon self-reported race. Results: In total there were 16 and 199 tumors from AA and non-AA patients respectively. In non-AA patients, the proportion of tumors that were classified as basal and luminal were approximately equal (93 and 106 respectively), while in AA patients, there was enrichment of basal tumors (12 basal and 4 luminal) (p=0.03735, Fisher’s exact test). Conclusions: AA patients are enriched in the basal molecular subtype of UC. Similar findings have been previously documented in AA women with breast cancer. The enrichment of basal UC in AAs suggests that a biological explanation may in part underlie the poor outcomes seen in AA patients. Future studies will explore the prognostic and predictive implications of basal subtype in AA patients with UC.

Pin1-based diagnostic and therapeutic strategies for breast cancer

Pin1 is the only known cis-to-trans isomerase that recognizes the phosphorylated pThr/pSer-Pro motifs in many signaling molecules, playing unique roles in the pathogenesis of breast cancer. First, Pin1 is prevalently over-expressed in kinds of breast cancer cell lines and tissues, such as MDA-MB-231 cell, MCF-7 cell, Her2+, ERα+, and basal-like breast cancer subtypes. Second, Pin1 amplifies many oncogenic signaling pathways, inhibits multiple tumor suppressors, promotes the angiogenesis and metastasis of breast cancer cells, and enhances the resistance of breast cancer cells to anti-tumor medicines. Third, inhibiting Pin1 blocks most of these detrimental effects in a great number of breast cancer cell lines. These findings suggest Pin1 as a promising diagnostic biomarker as well as an efficient therapeutic target for breast cancer. It is strongly expected that a Pin1-positive subtype of breast cancers should be extremely concerned and that the therapeutic efficacy of Pin1 inhibitors on breast cancer patients should be evaluated as soon as possible. Nonetheless, Pin1-based therapeutic strategies for breast cancer still deserve some debates. Hence, we give the predictions of several important issues, such as application precondition, side effects, and personalized medication, when Pin1 inhibitors are used in the breast cancer therapy. These proposals are meaningful for the further development of Pin1-based diagnostic and therapeutic strategies in order to conquer breast cancer.

Abstract PL01-01: Distinct immune and metabolic signatures in prostate and breast tumors of African American patients

Abstract PL01-01: Distinct immune and metabolic signatures in prostate and breast tumors of African American patients

Obesity-mediated regulation of HGF/c-Met is associated with reduced basal-like breast cancer latency in parous mice.

It is widely thought that pregnancy reduces breast cancer risk, but this lacks consideration of breast cancer subtypes. While a full term pregnancy reduces risk for estrogen receptor positive (ER+) and luminal breast cancers, parity is associated with increased risk of basal-like breast cancer (BBC) subtype. Basal-like subtypes represent less than 10% of breast cancers and are highly aggressive, affecting primarily young, African American women. Our previous work demonstrated that high fat diet-induced obesity in nulliparous mice significantly blunted latency in C3(1)-TAg mice, a model of BBC, potentially through the hepatocyte growth factor (HGF)/c-Met oncogenic pathway. Experimental studies have examined parity and obesity individually, but to date, the joint effects of parity and obesity have not been studied. We investigated the role of obesity in parous mice on BBC. Parity alone dramatically blunted tumor latency compared to nulliparous controls with no effects on tumor number or growth, while obesity had only a minor role in further reducing latency. Obesity-associated metabolic mediators and hormones such as insulin, estrogen, and progesterone were not significantly regulated by obesity. Plasma IL-6 was also significantly elevated by obesity in parous mice. We have previously reported a potential role for stromal-derived hepatocyte growth factor (HGF) via its cognate receptor c-Met in the etiology of obesity-induced BBC tumor onset and in both human and murine primary coculture models of BBC-aggressiveness. Obesity-associated c-Met concentrations were 2.5-fold greater in normal mammary glands of parous mice. Taken together, our studies demonstrate that, parity in C3(1)-TAg mice dramatically reduced BBC latency compared to nulliparous mice. In parous mice, c-Met is regulated by obesity in unaffected mammary gland and is associated with tumor onset. C3(1)-TAg mice recapitulate epidemiologic findings such that parity drives increased BBC risk and potential microenvironmental alterations in c-Met signaling may play a role in etiology.

Kallikrein-related peptidase 5 induces miRNA-mediated anti-oncogenic pathways in breast cancer

Kallikrein-related peptidase 5 (KLK5) displays aberrant expression in cancer. Recently, we showed KLK5 reconstitution in breast cancer cell lines suppresses malignancy. Present study aims to investigate the functional KLK5 mediated miRNA network on breast cancer progression, molecular subtype and survival. 28 miRNAs were up-regulated and 62 miRNAs were down-regulated upon KLK5 expression. Extracellular matrix (ECM) molecules and cell-adhesion pathways were the most significant KLK5-induced miRNA-mediated regulatory targets. Validation from The Cancer Genome Atlas (TCGA) database indicated KLK5 was specifically down-regulated in luminal B and basal-like breast cancer subtypes. There was a correlation between KLK5, miRNAs and their downstream ECM gene targets. Long-term patient survival correlated with dysregulation of KLK5 and interacting ECM target genes. It suggests biological differences between breast cancer molecular subtypes, patient survival, and their propensity for invasion and metastasis can be explained in part by altered miRNA networks induced by KLK5 dysregulation. We provide the first evidence that KLK5 can affect miRNA networks, which regulate MMPs and other novel ECM targets and a new compelling hypothesis of interplay between serine proteases and miRNAs. We developed a combined KLK5-(ITGB1+COL12A1) predictive score for recurrence-free survival that could be exploited in clinical applications.

Abstract 3306: Aberrant expression of ribosomal protein p1 and its pseudogene in breast tumors

Abstract Introduction: Ribosome biogenesis and translation control are essential cellular processes in growing cancer cells. Defects in ribosomal components can alter the pattern of gene expression, cell cycle progression and cell growth. Human ribosomes consist of four RNA species and 79 ribosomal proteins with 2090 processed and 16 duplicated pseudogenes. Specifically, 60S Acidic Ribosomal Protein P1 (RPLP1) is expressed in a tissue specific manner with multiple processed pseudogenes. We accidentally identified the expressed pseudogene 4 of RPLP1 (RPLP1P4) and determined genetic and molecular mechanism of RPLP1 and RPLP1P4 expression in breast cancer cells. Methods: Expression levels of RPLP1 and RPLP1P4 were quantified using qRT-PCR with total RNAs isolated from 7 normal tissues and 20 breast tumor tissues of 5 different subtypes. Cell cycle progression was analyzed cytofluorimetrically with the Beckman Coulter Gallios Flow Cytometer. Gene expression profiles were performed using Affymetrix GeneChip Human Genome U133 Plus 2.0 Array and analyzed using Partek Genomic Suite. Somatic copy number alterations (SCNA) of RPLP1/RPLP1P4 were detected with the custom designed TaqMan assays using ABI 7900HT real time PCR system. CopyCaller™ Software was used for the SCNA analysis with RNase P as a reference. Results: Because breast cancer subtypes have distinct origins and molecular characteristics, we compared expression of RPLP1 and RPLP1P4 in 5 subtypes of breast tumors. Although RPLP1/RPLP1P4 is ubiquitously expressed in normal and cancer tissues, their expression levels are significantly increased in the basal-like subtype of breast cancer compared to other subtypes with a 2.23 ± 1.06 fold increase in basal-like subtype compared to non-basal subtypes. Interfering RPLP1 expression with siRNA dramatically decreased cell proliferation up to the level of complete inhibition of cell proliferation. FACS data revealed reduced S phase cells in RPLP1 silencing-cells compared to control, suggesting that RPLP1-mediated regulation of cell proliferation is partly mediated through regulation of cell cycle progression. Analysis of gene expression profiles displayed down-regulation of genes involved in cellular metabolism and DNA replication. When we assessed 44 formalin fixed paraffin embedded breast tissues for SCNA of RPLP1/RPLP1P4, we observed RPLP1 amplifications in 44% of tumor DNAs with no amplification observed in normal tissues. The clear difference between tumors and normal tissues demonstrates frequent RPLP1 amplification events during tumorigenesis, which possibly drives an increase in RPLP1 expression and cell proliferation in cancer. Conclusion: Our data suggest a subtype-specific increased expression of a ribosomal protein and its pseudogene, potentially driven by copy number alterations in breast tumors. Future studies to understand the contributions of ribosomal protein genes and their pseudogenes to human neoplasia are warranted. Citation Format: Yoo J. Han, Olufunmilayo I. Olopade. Aberrant expression of ribosomal protein p1 and its pseudogene in breast tumors. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3306. doi:10.1158/1538-7445.AM2014-3306

Abstract 4871: Obesity-mediated regulation of HGF/c-Met and reduced basal-like breast cancer latency in parous mice

Abstract Background: Epidemiologic and experimental data have shown that a full term pregnancy reduces breast cancer risk. While a full term pregnancy reduces risk for estrogen receptor positive (ER+) and luminal breast cancers, parity is associated with increased risk of basal-like breast cancer (BBC) subtype. BBC represents <10% of breast cancers, are highly aggressive, affecting primarily young and African-American women. Experimental studies have examined parity and obesity individually, but to date, the independent and joint effects of parity and obesity have not been dissected. Our previous work demonstrated that high fat diet-induced obesity significantly blunted BBC latency in nulliparous C3(1)-Tag mice, potentially through the hepatocyte growth factor (HGF)/c-Met oncogenic pathway. Since obesity and post-partum weight gain are sometimes difficult to parse out, we investigated the role of obesity in parous mice on BBC. Methods: Seven week old female C3(1)-TAg mice were placed with male mice for breeding. Males were removed at pregnancy and pups were removed immediately after birth. The mothers were then randomly assigned to diet groups to model post-partum obesity. Mice were fed control low fat diet (10% kcal from fat) or high fat diet (45% or 60% kcal from fat) at 10 weeks until sacrifice. Mice were monitored for fat accretion, tumor onset, and tumor progression. Plasma measures of cytokines and metabolic parameters were assessed. Immunohistochemical analyses for HGF, c-Met and F4/80 macrophage markers were performed. Results: Mice on both 45% and 60% diets gained significantly greater fat mass compared to mice remaining lean on 10% diet. Compared with nulliparous mice fed the same diets, parity induced significant decreases in latency in C3(1)-TAg mice fed 10% and 45% diets. 60% diet reduced latency in parous mice to the same extent as nulliparous mice fed 60% diet. Tumor burden and tumor aggressiveness were not regulated by obesity in parous mouse. Obesity-associated metabolic mediators and hormones such as insulin, estrogen, and progesterone were not significantly regulated however, leptin levels were elevated in 45%-fed mice compared to other groups. Plasma IL-6 was significantly elevated by obesity in parous mice. Importantly, the HGF/c-Met axis in normal mammary gland was elevated significantly by obesity and correlated with reduced tumor latency. Conclusions: In summary, our studies demonstrate that, similar to epidemiologic reports, parity in C3(1)-TAg mice alone dramatically reduced BBC latency compared to nulliparous mice. Obesity in parous mice did not reduce latency further than obesity alone, indicating that obesity and parity may work through similar pathways. Finally, obesity induced c-Met expression in normal mammary gland in parous mice, similar to our reports in nulliparous mice, implicating an interaction between the HGF/c-Met signaling pathway and obesity in the etiology of BBC. Citation Format: Sneha Sundaram, Alex J. Freemerman, Erin L. Kirk, Joseph A. Galanko, Kirk K. McNaughton, Katharine M. Bendt, David B. Darr, Melissa A. Troester, Liza Makowski. Obesity-mediated regulation of HGF/c-Met and reduced basal-like breast cancer latency in parous mice. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4871. doi:10.1158/1538-7445.AM2014-4871

Molecular subtyping of serous ovarian tumors reveals multiple connections to intrinsic breast cancer subtypes.

ObjectiveTranscriptional profiling of epithelial ovarian cancer has revealed molecular subtypes correlating to biological and clinical features. We aimed to determine gene expression differences between malignant, benign and borderline serous ovarian tumors, and investigate similarities with the well-established intrinsic molecular subtypes of breast cancer.MethodsGlobal gene expression profiling using Illumina's HT12 Bead Arrays was applied to 59 fresh-frozen serous ovarian malignant, benign and borderline tumors. Nearest centroid classification was performed applying previously published gene profiles for the ovarian and breast cancer subtypes. Correlations to gene expression modules representing key biological breast cancer features were also sought. Validation was performed using an independent, publicly available dataset.Results5,944 genes were significantly differentially expressed between benign and malignant serous ovarian tumors, with cell cycle processes enriched in the malignant subgroup. Borderline tumors were split between the two clusters. Significant correlations between the malignant serous tumors and the highly aggressive ovarian cancer signatures, and the basal-like breast cancer subtype were found. The benign and borderline serous tumors together were significantly correlated to the normal-like breast cancer subtype and the ovarian cancer signature derived from borderline tumors. The borderline tumors in the study dataset, in addition, also correlated significantly to the luminal A breast cancer subtype. These findings remained when analyzed in an independent dataset, supporting links between the molecular subtypes of ovarian cancer and breast cancer beyond those recently acknowledged.ConclusionsThese data link the transcriptional profiles of serous ovarian cancer to the intrinsic molecular subtypes of breast cancer, in line with the shared clinical and molecular features between high-grade serous ovarian cancer and basal-like breast cancer, and suggest that biomarkers and targeted therapies may overlap between these tumor subsets. The link between benign and borderline ovarian cancer and luminal breast cancer may indicate endocrine responsiveness in a subset of ovarian cancers.

Molecular features of the basal-like breast cancer subtype based on BRCA1 mutation status.

BRCA1-mutated breast cancer is associated with basal-like disease; however, it is currently unclear if the presence of a BRCA1 mutation depicts a different entity within this subgroup. In this study, we compared the molecular features among basal-like tumors with and without BRCA1 mutations. Fourteen patients with BRCA1-mutated (nine germline and five somatic) tumors and basal-like disease, and 79 patients with BRCA1 non-mutated tumors and basal-like disease, were identified from the cancer genome atlas dataset. The following molecular data types were evaluated: global gene expression, selected protein and phospho-protein expression, global miRNA expression, global DNA methylation, total number of somatic mutations, TP53 and PIK3CA somatic mutations, and global DNA copy-number aberrations. For intrinsic subtype identification, we used the PAM50 subtype predictor. Within the basal-like disease, we observed minor molecular differences in terms of gene, protein, and miRNA expression, and DNA methylation variation, according to BRCA1 status (either germinal or somatic). However, there were significant differences according to average number of mutations and DNA copy-number aberrations, and four amplified regions (2q32.2, 3q29, 6p22.3, and 22q12.2), which are characteristic in high-grade serous ovarian carcinomas, were observed in both germline and somatic BRCA1-mutated breast tumors. These results suggest that minor, but potentially relevant, baseline molecular features exist among basal-like tumors according to BRCA1 status. Additional studies are needed to better clarify if BRCA1 genetic status is an independent prognostic feature, and more importantly, if BRCA1 mutation status is a predictive biomarker of benefit from DNA-damaging agents among basal-like disease.Electronic supplementary materialThe online version of this article (doi:10.1007/s10549-014-3056-x) contains supplementary material, which is available to authorized users.

Highlights of This Issue

Effective preventive drugs are declined by most women at high risk for breast cancer because of systemic toxicity, which may be decreased by the delivery of drugs through the breast skin. Lee and colleagues randomized women awaiting DCIS resection to 6-10 weeks of oral tamoxifen or 4-hyroxytamoxifen gel applied to the breast skin. The authors observed equivalent breast concentrations of 4-hydroxytamoxifen in both groups and similar reductions in the Ki67 labelling of DCIS cells, but far lower plasma concentrations in the transdermal group. Thus transdermal delivery appears to be a viable and potentially safer approach to breast cancer prevention, requiring further study.PARP inhibitors can potentiate the efficacy of temozolomide (TMZ) in multiple tumors; however, in previous animal studies, treatment of TMZ-resistant GBM xenograft models with veliparib and TMZ was ineffective in comparison with TMZ-sensitive models. By comparing isogenic TMZ-sensitive and –resistant GBM models, Gupta and colleagues report that resistant models in vitro are sensitized only by supratherapeutic concentrations of veliparib and TMZ. Using clinically relevant schedules in vivo, veliparib promotes TMZ-induced DNA damage signaling and survival benefit only in TMZ-sensitive models. These results highlight the importance of using clinically achievable drug levels in preclinical studies of PARP inhibitor combinations.Selective inhibition of CDK4/6 represents an area of considerable interest for anti-cancer therapy. To explore the in vivo quantitative pharmacology of LY2835219, a CDK4/6 inhibitor, an integrated pharmacokinetic/pharmacodynamic (PK/PD) model was developed by Tate and colleagues, relating plasma concentration to target engagement, cell cycle arrest, and growth inhibition of colo-205 and A375 xenograft tumors. Model simulations indicate that trough plasma concentrations of 200 ng/mL are associated with robust cell cycle arrest and that continuous dosing is required to achieve sustainable in vivo efficacy. These findings support and reinforce the continuous dosing strategy currently adopted in LY2835219 clinical studies.Tumor-infiltrating lymphocyte (TIL) prevalence predicts improved survival in breast and ovarian cancer. To explore the role of B-cell TILs by genomic subtype, Iglesia and colleagues assessed lymphocyte gene expression in breast and ovarian cancer mRNA-seq data. Furthermore, they developed a method to assess clonal diversity of B-cell populations from mRNA-seq. This work highlights the basal-like and HER2-enriched subtypes of breast cancer, and the immunoreactive subtype of ovarian cancer, as containing B-cell TILs that predict improved survival outcomes and are clonally restricted compared with TILs in other tumor subtypes.

Prognostic B-cell signatures using mRNA-seq in patients with subtype-specific breast and ovarian cancer.

Lymphocytic infiltration of tumors predicts improved survival in patients with breast cancer. Previous studies have suggested that this survival benefit is confined predominantly to the basal-like subtype. Immune infiltration in ovarian tumors is also associated with improved prognosis. Currently, it is unclear what aspects of the immune response mediate this improved outcome. Using The Cancer Genome Atlas mRNA-seq data and a large microarray dataset, we evaluated adaptive immune gene expression by genomic subtype in breast and ovarian cancer. To investigate B-cells observed to be prognostic within specific subtypes, we developed methods to analyze B-cell population diversity and degree of somatic hypermutation (SHM) from B-cell receptor (BCR) sequences in mRNA-seq data. Improved metastasis-free/progression-free survival was correlated with B-cell gene expression signatures, which were restricted mainly to the basal-like and HER2-enriched breast cancer subtypes and the immunoreactive ovarian cancer subtype. Consistent with a restricted epitope-driven response, a subset of basal-like and HER2-enriched breast tumors and immunoreactive ovarian tumors showed high expression of a low-diversity population of BCR gene segments. More BCR segments showed improved prognosis with increased expression in basal-like breast tumors and immunoreactive ovarian tumors compared with other subtypes. Basal-like and HER2-enriched tumors exhibited more BCR sequence variants in regions consistent with SHM. Taken together, these data suggest the presence of a productive and potentially restricted antitumor B-cell response in basal-like breast and immunoreactive ovarian cancers. Immunomodulatory therapies that support B-cell responses may be a promising therapeutic approach to targeting these B-cell infiltrated tumors.

MiR-221/222 promotes S-phase entry and cellular migration in control of basal-like breast cancer.

The miR-221/222 cluster has been demonstrated to function as oncomiR in human cancers. miR-221/222 promotes epithelial-to-mesenchymal transition (EMT) and confers tamoxifen resistance in breast cancer. However, the effects and mechanisms by which miR-221/222 regulates breast cancer aggressiveness remain unclear. Here we detected a much higher expression of miR-221/222 in highly invasive basal-like breast cancer (BLBC) cells than that in non-invasive luminal cells. A microRNA dataset from breast cancer patients indicated an elevated expression of miR-221/222 in BLBC subtype. S-phase entry of the cell cycle was associated with the induction of miR-221/222 expression. miRNA inhibitors specially targeting miR-221 or miR-222 both significantly suppressed cellular migration, invasion and G1/S transition of the cell cycle in BLBC cell types. Proteomic analysis demonstrated the down-regulation of two tumor suppressor genes, suppressor of cytokine signaling 1 (SOCS1) and cyclin-dependent kinase inhibit 1B (CDKN1B), by miR-221/222. This is the first report to reveal miR-221/222 regulation of G1/S transition of the cell cycle. These findings demonstrate that miR-221/222 contribute to the aggressiveness in control of BLBC.

Hypomethylation of the MMP7 promoter and increased expression of MMP7 distinguishes the basal-like breast cancer subtype from other triple-negative tumors.

Identification of novel targets for the treatment of basal-like breast cancer is essential for improved outcomes in patients with this disease. This study investigates the association of MMP7 expression and MMP7 promoter methylation with subtype and outcome in breast cancer patient cohorts. Immunohistochemical analysis was performed on a breast cancer tissue microarray and validated in independent histological samples. MMP7 expression significantly correlated with patient age, tumor size, triple-negative (TN) status, and recurrence. Analysis of publically available datasets confirmed MMP7 gene expression as a prognostic marker of breast cancer metastasis, particularly metastasis to the brain and lungs. Methylation of the MMP7 promoter was assessed by methylation-specific PCR in a panel of breast cancer cell lines and patient tumor samples. Hypomethylation of the MMP7 promoter significantly correlated with TN status in DNA from patient tumor samples, and this association was confirmed using The Cancer Genome Atlas (TCGA) dataset. Evaluation of a panel of breast cancer cell lines and data from the Curtis and TCGA breast carcinoma datasets revealed that elevated MMP7 expression and MMP7 promoter hypomethylation are specific biomarkers of the basal-like molecular subtype which shares considerable, but not complete, overlap with the clinical TN subtype. Importantly, MMP7 expression was identified as an independent predictor of pathological complete response in a large breast cancer patient cohort. Combined, these data suggest that MMP7 expression and MMP7 promoter methylation may be useful as prognostic biomarkers. Furthermore, MMP7 expression and promoter methylation analysis may be effective mechanisms to distinguish basal-like breast cancers from other triple-negative subtypes. Finally, these data implicate MMP7 as a potential therapeutic target for the treatment of basal-like breast cancers.

CUL4A contributes to the biology of basal-like breast tumors through modulation of cell growth and antitumor immune response.

The CUL4A E3 ubiquitin ligase is involved in the regulation of many cellular processes and its amplification and/or overexpression has been observed in breast cancer. The 13q34 amplification, which is associated with the basal-like breast cancer subtype, has been proposed as one of the mechanism behind CUL4A up-regulation. However, the specific contribution of CUL4A to the biology of basal-like breast tumors has not yet been elucidated. In this work, by using cellular models of basal phenotype, we show the inhibitory effect of CUL4A silencing in the proliferation and growth of breast cancer cells both, in vitro and in vivo. We also demonstrate the transforming capacity of CUL4A exogenous overexpression in the 184B5 human mammary epithelial cells in vitro. Our results suggest a synergistic effect between CUL4A high levels and the activation of the RAS pathway in the tumorigenesis of basal-like breast cancer tumors. In addition, by using a proteomics approach we have defined novel candidate proteins and pathways that might mediate the oncogenic effect of CUL4A. In particular, we report a putative role of CUL4A in bypassing the immune system in breast cancer through the down-regulation of several molecules involved in the immune surveillance. These findings provide insight into the oncogenic properties of CUL4A in basal-like breast cancer and highlight the therapeutic opportunities to target CUL4A.

Race and breast cancer survival by intrinsic subtype based on PAM50 gene expression.

To evaluate whether differences in PAM50 breast cancer (BC) intrinsic (Luminal A, Luminal B, Basal-like, and HER2-enriched) subtypes help explain the Black-White BC survival disparity. Utilizing a stratified case-cohort design, this study included 1,635 women from the Pathways and Life After Cancer Epidemiology cohorts, selecting women with tumors based upon IHC classification, recurrences, and deaths.One millimeter punches were obtained from tumor tissue, and expression of the PAM50 genes for molecular subtype was determined by RT-qPCR of extracted RNA. Cox proportional hazards models were used to analyze associations between race and BC outcomes, adjusted for PAM50 BC subtype. All tests of statistical significance were two-sided. Black women had a higher prevalence of the Basal-like BC subtype. Adjusted for potential confounding variables and disease characteristics at diagnosis, Black women had higher risks of recurrence (HR 1.65, 95 % CI 1.06-2.57) and breast cancer-specific mortality (HR 1.71, 95 % CI 1.02-2.86) than White women, but adjusting further for subtype did not attenuate survival disparities. By contrast, Hispanic women had a lower risk of recurrence (HR 0.54, 95 % CI 0.30-0.96) than Whites. Among those with the Basal-like subtype, Black women had a similar recurrence risk as women in other race groups but a higher recurrence risk for all other subtypes. Hispanic women had a lower recurrence risk within each subtype, though associations were not significant, given limited power. Although Black women had a higher risk of the Basal-like subtype, which has poor prognosis, this did not explain the Black-White BC survival disparity.

Radiation-Induced Gene Signature Predicts Pathologic Complete Response to Neoadjuvant Chemotherapy in Breast Cancer Patients

The identification of biomarkers predictive of neoadjuvant chemotherapy response in breast cancer patients would be an important advancement in personalized cancer therapy. In this study, we hypothesized that due to similarities between radiation- and chemotherapy-induced cellular response mechanisms, radiation-responsive genes may be useful in predicting response to neoadjuvant chemotherapy. Murine p53 null breast cancer cell lines representative of the luminal, basal-like and claudin-low human breast cancer subtypes were irradiated to identify radiation-responsive genes across subtypes. These murine tumor radiation-induced genes were then converted to their human orthologs, and subsequently tested as a predictor of pathologic complete response (pCR), which was validated on two independent published neoadjuvant chemotherapy datasets of genomic data with chemotherapy response. A radiation-induced gene signature consisting of 30 genes was identified on a training set of 337 human primary breast cancer tumor samples that was prognostic for survival. Mean expression of this signature was calculated for individual samples on two independent published datasets and was found to be significantly predictive of pCR. Multivariate logistic regression analysis in both independent datasets showed that this 30 gene signature added significant predictive information independent of that provided by standard clinical predictors and other gene expression-based predictors of pCR. This study provides new information for radiation-induced biology, as well as information regarding response to neoadjuvant chemotherapy and a possible means of improving the prediction of pCR.

Molecular features of the basal-like breast cancer subtype based on BRCA1 mutation status

Molecular features of the basal-like breast cancer subtype based on BRCA1 mutation status

Cyclin D1 induction of Dicer governs microRNA processing and expression in breast cancer

Cyclin D1 encodes the regulatory subunit of a holoenzyme that phosphorylates the pRB protein and promotes G1/S cell cycle progression and oncogenesis. Dicer is a central regulator of miRNA maturation, encoding an enzyme that cleaves double strand RNA or stem-loop-stem RNA into 20–25 nucleotide long small RNA, governing sequence specific gene silencing and heterochromatin methylation. The mechanism by which the cell cycle directly controls the non-coding genome is poorly understood. Here we show that cyclin D1−/− cells are defective in pre-miRNA processing which is restored by cyclin D1a rescue. Cyclin D1 induces Dicer expression in vitro and in vivo. Dicer is transcriptionally targeted by cyclin D1, via a cdk-independent mechanism. Cyclin D1 and Dicer expression significantly correlates in luminal A and basal-like subtypes of human breast cancer. Cyclin D1 and Dicer maintain heterochromatic histone modification (Tri-m-H3K9). Cyclin D1-mediated cellular proliferation and migration is Dicer-dependent. We conclude that cyclin D1 induction of Dicer coordinates microRNA biogenesis.

Triple-negative breast cancer: molecular characteristics and potential therapeutic approaches

The term triple-negative breast cancer (TNBC) defines breast tumors that do not express estrogen receptors, progesterone receptor or epidermal growth factor receptor HER2 on immunohistochemical analysis. TNBC accounts for 12-17% of all types of breast cancer. Molecular profiling indicated that triple-negative breast cancer represents a heterogeneous subgroup of breast cancer. Triple-negative breast cancer shares histological and genetic abnormalities with basal-like subtype of breast cancer; however, this overlap is incomplete. Breast cancer found in BRCA1 mutation carriers is also frequently TNBC. Triple-negative breast cancer does not benefit from hormonal therapies or treatments targeted against HER2. The results of ongoing studies as well as the results of clinical trials suggest that poly(ADP-ribose) polymerase inhibitors, EGFR, Hedgehog, Notch, Wnt/β-catenin, VEGF signaling inhibitors, and mTOR, Src, and Bcr/Abl kinase inhibitors used alone or in combination with other anticancer drugs might be effective in triple-negative breast cancer treatment. In this review, current knowledge on molecular characteristics of triple-negative breast cancer and its subtypes' treatment options is presented.

Abstract B8: Molecular subtyping of epithelial ovarian cancer reveals connections to intrinsic breast cancer subtypes

Abstract Aim: Epithelial ovarian cancer is one of the most lethal female cancers. It is a heterogeneous group of neoplasms and the different histologic subtypes are thought to constitute separate disease entities. Efforts have been made to characterize ovarian cancers further and molecular subgroups that correlate to clinical features have been reported, but are still not in clinical use (Tothill et al., Clin Cancer Res, 2008). The subgroups, called C1-C6, represent serous and endometrioid ovarian tumors with the C1-C2 and C4-C5 subgroups characterizing high-grade serous tumors and correlated to a worse prognosis. The C3 and C6 subtypes represent borderline and low-grade tumors and show a favorable prognosis. We aimed to further outline and refine the genetic differences between malignant, benign and borderline ovarian tumors and to investigate similarities between ovarian cancer and the well described intrinsic subtypes of breast cancer (Perou et al., Nature, 2000). Materials and methods: Global gene expression profiling (Illumina HT-12 bead arrays) was applied to 72 fresh-frozen serous ovarian tumors (37 adenocarcinomas, 17 adenomas, 5 borderline tumors,13 biological replicates) collected in the ovarian tumor tissue biobank at Skane University Hospital, Sweden (2004-2011). We performed nearest centroid classification of our tumors for the molecular subtypes of ovarian cancer (“C-signatures”) as well as for the intrinsic subgroups of breast cancer (luminal A, luminal B, basal-like, normal-like, and HER2) using the genes from Hu et al. (BMC Genomics, 2006). The results were validated by performing nearest centroid classification of the intrinsic breast cancer subtypes and the C-signatures on the ovarian tumors in the Tothill cohort as well. Results: Our malignant tumors correlated significantly to the basal-like breast cancer subtype (p<0.001) and to the ovarian C1, C2 and C4 signatures (p=0.020). The basal-like tumors, in turn, correlated significantly to the C2 and C4 signatures (p=0.019 and p=0.001, respectively), thus supporting a link between molecular subtypes of ovarian and breast cancers. The borderline and benign tumors showed a significant correlation to the normal-like breast cancer subtype and the ovarian C3 signature, and these signatures also correlated significantly with each other (p<0.001). These findings were supported when the breast cancer subtypes were applied to the Tothill cohort; the basal-like subtype correlated significantly to the C2 signature and the normal-like subtype to the C3 signature (p<0.001). Of interest, there was a tendency towards worse prognosis among malignant tumors that correlated to the basal-like breast cancer subtype compared to the other malignant tumors, which is in line with similar findings in breast cancer. All reported p-values are calculated using Fischer's Exact Test. Conclusion: Both epithelial ovarian cancers and breast cancers are heterogeneous diseases, nevertheless they share many similarities such as hormonal influence and varying long-term prognosis. Our novel findings support a link between previously reported molecular subtypes in ovarian cancer and the well-established intrinsic subtypes of breast cancer, which could potentially be of use for further investigations of biomarkers in ovarian cancer and new thinking regarding the use of chemotherapeutic agents as well as targeted treatments. Citation Format: Jenny-Maria Jönsson, Mev Dominguez-Valentin, Ida Johansson, Siker Kimbung, Mats Jönsson, Anna Måsbäck, Susanne Malander, Mef Nilbert. Molecular subtyping of epithelial ovarian cancer reveals connections to intrinsic breast cancer subtypes. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr B8.