Gene expression profiling of breast cancer

The role of talin2 in breast cancer tumorigenesis and metastasis

Recent studies show that talin2 has a higher affinity to β-integrin tails and is indispensable for traction force generation and cell invasion. However, its roles in cell migration, cancer cell metastasis and tumorigenesis remain to be determined. Here, we used MDA-MB-231 human breast cancer cells as a model to define the roles of talin2 in cell migration, invasion, metastasis and tumorigenesis. We show here that talin2 knockdown (KD) inhibited cell migration and focal adhesion dynamics, a key step in cell migration, and that talin2 knockout (KO) inhibited cell invasion and traction force generation, the latter is crucial for cell invasion. Re-expression of talin2^WT in talin2-KO cells restored traction force generation and cell invasion, but that of talin2^S339C, a β-integrin-binding deficient mutant, did not. Moreover, talin2 KO (or KD) suppressed tumorigenesis and metastasis in mouse xenograft models. However, surprisingly, re-expression of talin2^WT in talin2-KO cells did not rescue tumorigenesis. Thus, talin2 is required for breast cancer cell migration, invasion, metastasis and tumorigenesis, although exogenous expression of high levels of talin2 could inhibit tumorigenesis.

FKBPL: a marker of good prognosis in breast cancer

FK506-binding protein-like (FKBPL) has established roles as an anti-tumor protein, with a therapeutic peptide based on this protein, ALM201, shortly entering phase I/II clinical trials. Here, we evaluated FKBPL's prognostic ability in primary breast cancer tissue, represented on tissue microarrays (TMA) from 3277 women recruited into five independent retrospective studies, using immunohistochemistry (IHC). In a meta-analysis, FKBPL levels were a significant predictor of BCSS; low FKBPL levels indicated poorer breast cancer specific survival (BCSS) (hazard ratio (HR) = 1.30, 95% confidence interval (CI) 1.14–1.49, p < 0.001). The prognostic impact of FKBPL remained significant after adjusting for other known prognostic factors (HR = 1.25, 95% CI 1.07–1.45, p = 0.004). For the sub-groups of 2365 estrogen receptor (ER) positive patients and 1649 tamoxifen treated patients, FKBPL was significantly associated with BCSS (HR = 1.34, 95% CI 1.13–1.58, p < 0.001, and HR = 1.25, 95% CI 1.04–1.49, p = 0.02, respectively). A univariate analysis revealed that FKBPL was also a significant predictor of relapse free interval (RFI) within the ER positive patient group, but it was only borderline significant within the smaller tamoxifen treated patient group (HR = 1.32 95% CI 1.05–1.65, p = 0.02 and HR = 1.23 95% CI 0.99–1.54, p = 0.06, respectively). The data suggests a role for FKBPL as a prognostic factor for BCSS, with the potential to be routinely evaluated within the clinic.

Adenoviral vectors for prodrug activation-based gene therapy for cancer

Cancer cell heterogeneity is a common feature - both between patients diagnosed with the same cancer and within an individual patient's tumor - and leads to widely different response rates to cancer therapies and the potential for the emergence of drug resistance. Diverse therapeutic approaches have been developed to combat the complexity of cancer, including individual treatment modalities designed to target tumor heterogeneity. This review discusses adenoviral vectors and how they can be modified to replicate in a cancer-specific manner and deliver therapeutic genes under multi-tiered regulation to target tumor heterogeneity, including heterogeneity associated with cancer stem cell-like subpopulations. Strategies that allow for combination of prodrug-activation gene therapy with a novel replication-conditional, heterogeneous tumor-targeting adenovirus are discussed, as are the benefits of using adenoviral vectors as tumor-targeting oncolytic vectors. While the anticancer activity of many adenoviral vectors has been well established in preclinical studies, only limited successes have been achieved in the clinic, indicating a need for further improvements in activity, specificity, tumor cell delivery and avoidance of immunogenicity.

Clinical implication of p53 overexpression in breast cancer patients younger than 50 years with a triple-negative subtype who undergo a modified radical mastectomy

OBJECTIVE

The purpose of this study was to identify the clinicopathological characteristics and prognostic value of p53 overexpression in breast cancer patients treated with a modified radical mastectomy.

METHODS

The medical records of 197 patients who had undergone modified radical mastectomy between January 1991 and December 2008 were reviewed retrospectively. Breast cancer subtype and p53 overexpression were investigated using immunohistochemistry and/or fluorescent in situ hybridization analysis of surgical specimens.

RESULTS

The median follow-up after the modified radical mastectomy was 56.1 months (range, 14.7-232.7). The median age was 47 years (range, 31-72). p53 overexpression was noted in 73 patients (37.1%). Breast cancer-specific death rate (P = 0.011), cancer progression (P = 0.024), distant metastasis (P = 0.015), hormone receptor negativity (P < 0.001) and human epidermal growth factor receptor 2 positivity (P = 0.017) were detected more frequently in patients with p53 overexpression. The overall survival rates were significantly lower in the p53-overexpression group than in the non-p53-overexpression group (P = 0.021, log-rank test). In the multivariate analysis, p53 overexpression showed the strongest prognostic significance in patients aged <50 years (P = 0.039) and with the triple-negative subtype (P = 0.023).

CONCLUSIONS

p53 overexpression correlated with breast cancer-specific death rates and adverse prognostic factors in patients treated with modified radical mastectomy. p53 overexpression might be a more reliable prognosticator in patients aged <50 years and with the triple-negative subtype. More effective systemic treatments might be warranted for these patients exhibiting p53 overexpression. Further validation is required to make more definite conclusions.

Killer cell immunoglobulin-like receptor genes in patients with breast cancer

Killer cell immunoglobulin-like receptors (KIRs) contribute to the pathogenesis of diverse kind of diseases. Previous studies have shown associations between KIR genes, their ligands and either protection or susceptibility to leukemias or virally associated solid tumors. However, the possible roles of KIR gene polymorphisms in the development of breast cancer remain largely unknown. To investigate the association of KIR gene polymorphisms with breast cancer, we carried out the present study on 33 breast cancer patients and 77 healthy controls by means of sequence-specific oligonucleotide probes analysis, and then all data were statistically analyzed by Fisher exact test. Our results showed that the frame genes KIR2DL4, 3DL2, 3DL3, and 3DP1 were found in all patients and all controls. The rate of activating KIR2DS1 was much higher in patients with breast cancer than that in healthy controls (P = 0.032) while the allelic types of activating 2DS4 (2DS4 003/4/6/7) were lower in patients with breast cancer compared with healthy controls (P = 0.028). Additionally, there was a statistically significant negative correlation between 2DL1 genes and breast cancer development (P = 0.025). In conclusion, this study suggests that the activating KIR2DS1 may trigger breast cancer development, while 2DL1 gene and 2DS4 003/4/6/7 alleles are possibly protectors for breast cancer.

Identifying causal genes and dysregulated pathways in complex diseases

In complex diseases, various combinations of genomic perturbations often lead to the same phenotype. On a molecular level, combinations of genomic perturbations are assumed to dys-regulate the same cellular pathways. Such a pathway-centric perspective is fundamental to understanding the mechanisms of complex diseases and the identification of potential drug targets. In order to provide an integrated perspective on complex disease mechanisms, we developed a novel computational method to simultaneously identify causal genes and dys-regulated pathways. First, we identified a representative set of genes that are differentially expressed in cancer compared to non-tumor control cases. Assuming that disease-associated gene expression changes are caused by genomic alterations, we determined potential paths from such genomic causes to target genes through a network of molecular interactions. Applying our method to sets of genomic alterations and gene expression profiles of 158 Glioblastoma multiforme (GBM) patients we uncovered candidate causal genes and causal paths that are potentially responsible for the altered expression of disease genes. We discovered a set of putative causal genes that potentially play a role in the disease. Combining an expression Quantitative Trait Loci (eQTL) analysis with pathway information, our approach allowed us not only to identify potential causal genes but also to find intermediate nodes and pathways mediating the information flow between causal and target genes. Our results indicate that different genomic perturbations indeed dys-regulate the same functional pathways, supporting a pathway-centric perspective of cancer. While copy number alterations and gene expression data of glioblastoma patients provided opportunities to test our approach, our method can be applied to any disease system where genetic variations play a fundamental causal role.

Prospective randomized phase II study determines the clinical usefulness of genetic biomarkers for sensitivity to primary chemotherapy with paclitaxel in breast cancer

In patients with breast cancer, taxane as well as anthracycline play central roles in systemic chemotherapy. By evaluating the pathological response, we can gauge sensitivity to primary chemotherapy. However, biomarkers that would predict a response to taxane have not yet been established. We conducted a prospective randomized trial to evaluate whether selecting patients using sensitivity testing based on the gene expression of the tumor might enhance the probability of the pathological response. Five genes were identified as biomarkers derived from a microarray of DNA gene profiles from microdisected breast tumors. In the experimental arm (B1), 12 cycles of weekly paclitaxel, 80 mg/m(2) , were preoperatively given when the sensitivity test was positive and therefore judged to be sensitive to paclitaxel. When the test was negative, meaning insensitive to paclitaxel, four cycles of FEC100 were given (arm B2). In the control arm (A), paclitaxel was administered weekly without the use of the sensitivity test. A total of 92 patients were enrolled and 86 patients were analyzed. The pathological response rate (pRR) of each arm was 36.4% in B1 (expected sensitive to paclitaxel), 21.1% in A (control) and 12.5% in B2, respectively. Weekly paclitaxel-treated patients selected by the sensitivity test did not enhance the pRR. The study failed to validate sensitivity testing using five gene expressions for primary chemotherapy with paclitaxel in patients with breast cancer. However, this study suggests that a randomized phase II study is a robust tool for obtaining a rapid conclusion on the usefulness of biomarkers and could be the foundation for further large clinical trials.

Dual E1A oncolytic adenovirus: targeting tumor heterogeneity with two independent cancer-specific promoter elements, DF3/MUC1 and hTERT

The therapeutic utility of oncolytic adenoviruses controlled by a single, tumor-specific regulatory element may be limited by the intra- and inter-tumoral heterogeneity that characterizes many cancers. To address this issue, we constructed an oncolytic adenovirus that uses two distinct tumor-specific promoters (DF3/Muc1 and hTERT) to drive separate E1A expression cassettes, in combination with deletion of the viral E1B region, which confers additional tumor selectivity and increased oncolytic activity. The resultant virus, Adeno-DF3-E1A/hTERT-E1A, induced higher levels of E1A oncoprotein, enhanced oncolysis, and an earlier and higher apoptotic index in infected tumor cells than following infection with Adeno-hTERT-E1A, which harbors a single hTERT promoter-driven E1A cassette. In isolated U251 human gliosarcoma cell holoclones (putative cancer stem cells), where DF3/Muc1 expression is substantially enriched and hTERT expression is decreased compared to the parental U251 cell population, E1A production and oncolysis were strongly decreased following infection with Adeno-hTERT-E1A but not Adeno-DF3-E1A/hTERT-E1A. The strong oncolytic activity of Adeno-DF3-E1A/hTERT-E1A translated into superior anti-tumor activity over Adeno-hTERT-E1A in vivo in a U251 solid tumor xenograft model, where hTERT levels were >90% suppressed and the DF3/Muc1 to hTERT expression ratio was substantially increased compared to cultured U251 cells. The enhanced anti-tumor activity of the dual-targeted Adeno-DF3-E1A/hTERT-E1A was achieved despite premature viral host cell death and decreased production of functional viral progeny, which limited tumor cell spread of the viral infection. These findings highlight the therapeutic benefit of targeting oncolytic viruses to heterogeneous tumor cell populations.

Selection strategy and the design of hybrid oligonucleotide primers for RACE-PCR: cloning a family of toxin-like sequences from Agelena orientalis

BACKGROUND

The use of specific but partially degenerate primers for nucleic acid hybridisations and PCRs amplification of known or unknown gene families was first reported well over a decade ago and the technique has been used widely since then.

RESULTS

Here we report a novel and successful selection strategy for the design of hybrid partially degenerate primers for use with RT-PCR and RACE-PCR for the identification of unknown gene families. The technique (named PaBaLiS) has proven very effective as it allowed us to identify and clone a large group of mRNAs encoding neurotoxin-like polypeptide pools from the venom of Agelena orientalis species of spider. Our approach differs radically from the generally accepted CODEHOP principle first reported in 1998. Most importantly, our method has proven very efficient by performing better than an independently generated high throughput EST cloning programme. Our method yielded nearly 130 non-identical sequences from Agelena orientalis, whilst the EST cloning technique yielded only 48 non-identical sequences from 2100 clones obtained from the same Agelena material. In addition to the primer design approach reported here, which is almost universally applicable to any PCR cloning application, our results also indicate that venom of Agelena orientalis spider contains a much larger family of related toxin-like sequences than previously thought.

CONCLUSION

With upwards of 100,000 species of spider thought to exist, and a propensity for producing diverse peptide pools, many more peptides of pharmacological importance await discovery. We envisage that some of these peptides and their recombinant derivatives will provide a new range of tools for neuroscience research and could also facilitate the development of a new generation of analgesic drugs and insecticides.

Chromosome alterations associated with positive and negative lymph node involvement in breast cancer

Genetic heterogeneity is high in breast cancer, and hence it is difficult to link a specific chromosome alteration to a specific clinicopathologic feature. We examined clonal chromosome alterations in 45 breast carcinomas and statistically correlated the findings with clinical-histopathological parameters of the patients. The most common abnormalities were losses of chromosomes 19, 22, 21, X, and 17 and gains of chromosomes 9 and 18. A statistically significant correlation was found between clonal aberrations in chromosomes 17, 20, and 21 and positive lymph node involvement (LN+) and between clonal aberrations in chromosomes X and 6 and negative involvement (LN-). The average number of chromosome abnormalities was the same for both LN- and LN+ groups, and numerical and structural alterations were equally distributed. The mean number of chromosome aberrations did not differ significantly among tumor grades, but when aberrations were analyzed as monosomies, trisomies, and structural aberrations, a heterogeneous distribution was observed. Further cytogenetic investigation of breast tumors and their variable pathological features is undoubtedly necessary. The recognition and ultimately the molecular understanding of these abnormalities may improve breast cancer taxonomy and provide important prognostic information for both the patient and clinician.

Transcriptome profiling in clinical breast cancer: from 3D culture models to prognostic signatures

Early detection has been one of the most effective strategies to control the growing cancer burden. The power of earlier detection has been demonstrated by the impact of pap-smear, mammography, and PSA tests on cancer patient treatment and survival. These tests benefit patients independent of their genetic background or race. However, in many cases, we are still losing the battle against cancer because patients that initially presented with low-grade disease progress rapidly to aggressive forms of the disease. As of yet, we have limited means to predict a particular patient's fate or to specifically treat subtypes of cancer. A combination of earlier detection and targeted therapy, based on information from transcriptome analysis, could be a powerful ally in this battle. The theme of this review article is to briefly summarize innovative strategies using three-dimensional (3D) cell cultures of human mammary epithelial cells to predict clinical outcome in breast cancer. This strategy has the potential to further enhance our understanding of breast cancer biology and to contribute to the identification of biologically significant bio-markers that are also useful drug targets.

Regulatory networks: Linking microarray data to systems biology

Gene regulation and aging are intrinsically linked and these links often reach directly to transcription factors and their actions in gene regulation. However, it is very difficult to follow all the individual directions such factors can affect. Therefore, the opposite approach became more popular recently, i.e. observing the endpoints of all these actions. Microarrays are the preferred technology to monitor large-scale changes in transcripts across whole genomes. The trade-off for being able to survey whole genome transcriptomes is that the results are mere observations, which do not directly reveal the underlying mechanisms that represent the real link to transcription factors and their actions. Fortunately, a combination of knowledge mining (including but not restricted to literature mining) with genomics analyses can be harnessed to elucidate at least some of the regulatory networks orchestrating the transcriptional changes observed by microarray experiments. Thus, a considerable part of the functional system structure of cells and organisms can be revealed, which is a pivotal prerequisite for any meaningful systems biology approach towards aging related phenotypes.