Gene expression profile and response to trastuzumab-docetaxel-based treatment in breast carcinoma

Background:

Resistance to trastuzumab is often observed in women with human epidermal growth factor receptor 2 (HER2)-positive breast cancer and has been shown to involve multiple potential mechanisms. We examined the ability of microarray analyses to determine the potential markers of pathological complete response (pCR).

Methods:

We conducted an analysis of tumours from 38 patients with locally advanced HER2-positive breast cancer who had received trastuzumab combined with docetaxel. Quantitative reverse transcriptase (RT)–PCR was used to assess the expression of 30 key genes; microarray analyses were carried out on 25 tumours to identify a prognostic gene expression profile, with 13 blinded samples used to validate the identified profile.

Results:

No gene was found to correlate with response by RT–PCR. The microarray analysis identified a gene expression profile of 28 genes, with 12 upregulated in the pCR group and 16 upregulated in non-pCR. The leave-one-out cross-validation test exhibited 72% accuracy, 86% specificity, and 55% sensitivity. The 28-gene expression profile classified the 13 validation samples with 92% accuracy, 89% specificity, and 100% sensitivity.

Conclusion:

Our results suggest that genes not involved in classical cancer pathways such as apoptosis or DNA repair could be involved in responses to a trastuzumab–docetaxel-based regimen. They also describe for the first time a gene expression signature that predicts trastuzumab response.

Association of p53 gene alterations with the expression of antiapoptotic survivin splice variants in breast cancer

Survivin, a member of the inhibitory apoptosis protein family, gives rise, by an alternative splicing, to four variants with different functions. Many experimental studies indicate that p53 can regulate the expression of survivin and some of its splice variants. Although both the expression of survivin splice variants and the p53 gene were frequently altered in human cancers, nothing is known about their interactions in in vivo tumour samples. Here, we report that, in 162 breast carcinomas, p53 mutations are significantly associated with an increased expression of survivin and, in particular, its antiapoptotic splice variants (survivin-DeltaEx3 and survivin-3B). The upregulation of these variant expressions is particularly related to p53 mutations occurring in the residues belonging to the tetramerization domain. The loss of heterozygosity in the p53 gene is also associated with an increased expression of the survivin-DeltaEx3 variant. The expression of the proapoptotic variants (survivin-2B and survivin-2alpha) is not affected by any of these alterations. Our results provide for the first time in vivo evidence that, in human breast cancer, the survivin expression as well as its splicing depends on the p53 status. The results also suggest that the upregulation of antiapoptotic survivin variant expression by the mutant p53 may increase breast cancer cells survival and resistance to therapy.

Absence of genetic abnormalities in fibroadenomas of the breast determined at p53 gene mutations and microsatellite alterations

Genesis of breast cancer is a multistage process involving accumulation of genetic alterations, but little is known about the implication of genetic alterations in benign breast disease (BBD) lesions. Among benign lesions of the breast, one of the most common is fibroadenoma. The relationship between fibroadenoma and breast cancer is not clear. Some epidemiological studies show an association with breast cancer risk, whereas recent reports show no increased risk. In a previous study, we analyzed genetic alterations in a group of BBD lesions composed namely of fibroadenomas unaffected by breast cancer, and we found no evident implication of several loci by Southern blot method. However, genetic alterations, including p53 gene mutations, loss of heterozygosity, microsatellite instability, and cytogenetic chromosomal aberrations, have been reported recently to occur in fibroadenomas. Thus, we reexamined our BBD population for p53 gene mutations and for microsatellite alterations with 13 markers using a PCR-based method. Our results show that no molecular alterations were detected in these BBD lesions composed namely of fibroadenomas unaffected by breast cancer. Neither p53 gene mutations, determined at exons 5-9, nor microsatellite alterations tested with a very sensitive method were found in these lesions. Therefore, molecular results obtained in our study support recent epidemiological data showing that fibroadenoma does not constitute a significant increase in the relative risk of later contracting breast cancer.

Enhancement of mdr1 gene expression in normal tissue adjacent to advanced breast cancer

In the present study, mdr1 gene expression was investigated by a sensitive reverse transcriptase-PCR assay in advanced breast cancer and in corresponding adjacent normal tissues obtained before and after treatment with primary chemotherapy. Comparatively to normal tissues, a significant induction of mdr1 expression was observed in untreated tumors (p = 0.0222). Similarly, a significant induction of mdr1 expression was revealed when treated samples were compared to untreated counterparts (p = 0.0222), but no differences were detected between tumor and normal samples (p = 0.3199). Noteworthy, a significant induction of mdr1 gene expression occurred in treated normal samples comparatively to untreated ones (p = 0.0037), and this induction was even more important in normal than in tumoral tissue (p = 0.0627). However, neither the basal expression nor the induction of mdr1 were correlated with subsequent response to chemotherapy or with survival. Thus, in agreement with previous reports, our data show that chemotherapy induce mdr1 gene expression in breast cancer cells, but they also indicate that a similar phenomenon occurs in adjacent normal tissues. Therefore, our results strongly suggest that mdr1 gene overexpression is not a characteristic of breast malignant cells, but rather constitutes a general phenomenon occurring both in normal and tumor cells which could explain at least in part the absence of relationship between mdr1 expression and the clinical outcome of breast cancer patients.

Expression of the gadd153 gene in normal and tumor breast tissues by a sensitive RT-PCR method

The gadd153 gene belongs to the CCAAT/enhancer binding protein (C/EBP) family of transcription factors. The role of these proteins in the control of proliferation and differentiation have mostly been studied in vitro. The involvement of gadd153 gene expression in human disease, and most particularly in breast cancer, is largely unknown. Since gadd153 gene is normally expressed at very low levels in most cells, we developed a sensitive reverse transcriptase-polymerase chain reaction (RT-PCR) technique that permits the detection of low amounts of RNA. In these conditions, 24 breast tumors and 14 corresponding normal samples were analysed, and levels of expression between tumor and normal tissues were compared. Statistical analysis indicated a significant induction of gadd153 gene expression in tumor samples in comparison to normal ones (p<0. 01). Thus, overexpression of gadd153 may inhibit the cellular differentiation process and facilitate breast tumorigenesis. Further studies are needed with larger number of cases to determine the specific prognostic role of gadd153 in breast cancer.

MDR1 and thymidylate synthase (TS) gene expressions in advanced breast cancer: relationships to drug exposure, p53 mutations, and clinical outcome of the patients

To characterize the biological features of advanced breast cancer associated with poor chemotherapy response and worse prognosis, sequential tumor samples obtained from 75 patients receiving primary chemotherapy were analysed for MDR1 and TS gene expression before and after treatment. MDR1 gene expression was also analysed in 36 sequential normal samples. The levels of MDR1 and TS genes expression were determined by reverse transcription-PCR method, and examined in relation to p53 gene status, and the clinical outcome of the patients. After treatment, MDR1 expression levels were significantly enhanced in tumor (p = 0.0033) and normal (p = 0.0098) samples, whereas a significant decrease in TS expression was observed (p = 0.0054). There was no significant correlation between MDR1 or TS expressions and the presence of p53 mutations (detected in 24% of the cases), chemoresponsiveness, or survival. Only p53 mutations were associated with reduced disease-free survival (p = 0.0473). These results demonstrate that MDR1 and TS gene expressions were affected by drug exposure, but not by p53 gene status. Furthermore, the increase of MDR1 gene expression in normal and tumor tissues is in favor of an induced MDR1 expression rather than of a selection of resistant tumoral clones, which can be responsible for the absence of relationship of MDR1 expression with clinical outcome of advanced breast cancer patients.

Glutathione S-transferase M1 null genotype: lack of association with tumour characteristics and survival in advanced breast cancer

BACKGROUND

Glutathione S-transferase (GST)M1, a member of the mu class GST gene family, has been shown to be polymorphic because of a partial gene deletion. This results in a failure to express the GSTM1 gene in 50-60% of individuals. Several studies have demonstrated a possible link with the GSTM1-null genotype and susceptibility to cancer. Furthermore, a GSTM1 isoenzyme has been positively associated with protective effect against mutagenic drugs, such as alkylating agents and anthracyclines.

OBJECTIVES

To determine whether GSTM1 polymorphisms are associated with tumour characteristics and survival in advanced breast cancer patients, and whether it may constitute a prognostic factor.

METHODS

We genotyped 92 patients receiving primary chemotherapy, which included cyclophosphamide, doxorubicine and 5-fluorouracil. The relationships between allelism at GSTM1 and clinicopathological parameters including age, menopausal status, tumour size, grade hormone receptors, involved nodes and p53 gene mutations were analysed. Of the patients with GSTM1-positive genotype, tissue samples obtained before and after treatment were available from 28 cases, allowing RNA extraction and GSTM1 expression by reverse transcription polymerase chain reaction. Relationships with clinical response to chemotherapy, and disease-free and overall survival were also evaluated. The data obtained was analysed using logistic regression to estimate the odds ratio and 95% confidence interval.

RESULTS

Of 92 patients, 57.6% (n = 53) were classified as heritably GSTM1-deficient, and 42.4% (n = 39) were of the GSTM1-positive genotype. There were no statistically significant relationships between GSTM1-null genotype and the clinicopathological parameters analysed. No relationship was observed between GSTM1 RNA expression and objective clinical response to chemotherapy. Objective clinical response to chemotherapy was related only to clinical tumour size (P = 0.0177) and to the absence of intraductal carcinoma (P = 0.0013). GSTM1-null genotype had no effect on disease-free or overall survival. The absence of hormone receptors (P = 0.002), the presence of a mutated p53 gene (P = 0.0098) and lack of response to primary chemotherapy (P = 0.0086) were the only factors associated with reduced disease-free or overall survival.

CONCLUSIONS

GSTM1-null genotype alone had no effect on tumour characteristics and outcome of patients with advanced breast cancers. The lack of correlation of GSTM1 genotype with clinical tumour features, clinical response to chemotherapy and survival exclude a role for GSTM1 polymorphism as a prognostic factor in advanced breast cancer.

[Quantification of protein p53 expression by image analysis in 58 cases of colon carcinoma. Study of correlations between sex, age, histology, Dukes stage, DNA content and lymph node invasion]

The analysis of p53 expression has been performed on 58 cases of colonic carcinomas. p53 expression was revealed by immunohistochemistry with the monoclonal antibody DO.7, and its quantification was performed by image analysis on deparaffinized tissue sections treated by microwaves. p53 expression evaluated by images analysis has been compared to visual estimation performed under light microscopy, and an excellent correlation was found between the two methods. No statistical significant relationships were found between the proportion of tumours expressing p53, sex, age (< 70 or > 70 years), histology (well, intermediate or poorly differentiated) and DNA index (< 1.3 or > 1.3) whereas the proportion of tumors expressing p53 was significantly higher in case of metastatic behaviour as well as in the C stage of Dukes classification. p53 expression was also significantly more important in colonic carcinomas with DNA index higher than 1.3 and in case of metastatic behaviour. According to these data, the metastatic behaviour is correlated both with the proportion of tumors expressing p53 and with the level of p53 expression.

Loss of heterozygosity at the TP53 gene: independent occurrence from genetic instability events in node-negative breast cancer

TP53 abnormalities have been reported as an early event in the process of cellular transformation of human breast cancers, and involved in mammary-tumor evolution, from in situ to invasive disease. In this study, node-negative (N-) tumors were examined for TP53 allelic loss in relation to different genetic instability events, including allelic loss at chromosome 17p13.3 and c-H-ras-1 loci, as well as alteration of the c-myc and c-erbB-2/neu oncogenes. TP53 allelic loss was analyzed to determine whether such an abnormality was the more important, among other genetic events, in the N- tumors, whether it appeared independently of these genetic events, and whether accumulation of genetic events arises in this group of breast tumors. Clinicopathological parameters were also examined. Loss of heterozygosity (LOH) at the TP53 gene appears the most frequent alteration detected (26% vs. 13%, 8%, 9% and 3% for LOH at D17S30 and c-H-ras-1 loci, and amplification of c-myc and c-erbB-2/neu respectively). There was no association between LOH at the TP53 locus and other genetic events. Among clinicopathological parameters, significant associations were observed only with estrogen-receptor-negative tumors (p = 0.05). Our results demonstrate that LOH at TP53 arises more frequently in the N- breast cancer, thus supporting earlier findings suggesting that TP53 abnormality has a role early in the pathogenesis of breast lesions. Moreover, the data indicate that accumulation of many genetic events occurs at a low level in N- breast tumors, and that TP53 abnormality occurs independently of these genetic events.

Benign breast disease: absence of genetic alterations at several loci implicated in breast cancer malignancy

Benign breast disease (BBD) is a heterogeneous group of benign breast problems that has been associated with breast cancer risk by several investigators. Genetic alterations have been described in breast carcinomas under the headings of loss of heterozygosity (1p, 3p, 7q, 11p, 17p, 17 and 18q), mutations (p53, c-H-ras-1), and/or gene amplifications (c-myc, int-2/FGF3, and c-erbB-2/neu). In an attempt to determine whether these genetic alterations might also be involved in the development of BBD, we have analyzed such alterations in 50 BBD lesions. The histological types of samples studied were: 37 fibroadenomas; 8 benign phyllode tumors; and 5 fibrocytic diseases. Cellular DNA was extracted from tissues and from corresponding blood leukocytes according to standard techniques, digested with appropriate restriction endonucleases, and analyzed by Southern blot. The following are informative cases found in a total number of patients analyzed for each locus: 13 of 26 for L-myc (1p); 9 of 23 for THRB (3p); 11 of 29 for met (7q); 27 of 50 for c-H-ras-1 (11p); 3 of 13 for TP53 (17p); 14 of 50 for D17S30 (17p); 20 of 33 for D17S4 (17q); and 13 of 33 for D18S5 (18q). No loss of heterozygosity was detected at any of the examined loci. Alternatively, none of the 50 BBD cases displayed an amplification of the three genes tested (c-myc, int-2/FGF3, and c-erbB-2/neu). Our results show that molecular alterations, which are more frequently involved in malignant breast carcinomas, do not occur in BBD lesions. These results indicate that these molecular alterations could constitute late events in the pathogenesis of breast carcinomas.

Evaluation of multidrug resistant phenotype by flow cytometry with monoclonal antibodies and functional tests

Multidrug resistant (MDR) phenotype is characterized by a defect in drug accumulation caused by overexpression of a transmembrane glycoprotein, the P-glycoprotein (P-gp). MDR phenotype can be characterized either with monoclonal antibodies raised against P-gp or with functional tests, most often based on the incorporation of fluorescent compounds. In the present study, data obtained with the monoclonal antibodies C219, JSB1 and MRK16 are compared to those of functional tests performed by flow cytometry including uptake of daunorubicin (DNR), Rhodamine 123 (Rh 123) or Hoechst 33342. Sensitive and resistant cell lines K562S, K562R, KBA1 and KB31, derived either from a human chronic myeloid leukemia or from a human epithelial carcinoma, were used. In resistant cells, P-gp expression was revealed with either the monoclonal antibodies C219, JSB1 or MRK-16. The most specific results were obtained with MRK-16. With functional tests, no matter which dyes were used, the fluorescence was always stronger in sensitive than in resistant cells. However, with DNR and Hoechst 33342, an incorporation of these dyes was exhibited in resistant cells. This phenomenon was not observed with Rh 123, which makes it possible to distinguish clearly between sensitive and resistant cells and to detect as few as 1% of resistant cells. Because of its high sensitivity, the functional test involving incorporation of Rh 123 was successfully used in acute myeloid leukemia to detect multichemoresistant cells.

[Amplification of c-myc and c-erbbeta-2(HER-2/neu) in breast cancer without axillary lymph node metastasis: correlation with other prognostic parameters]

Amplification of c-myc and c-erb beta-2 (HER-2/neu) proto-oncogenes were analyzed in breast cancer tissues obtained from 100 patients without lymph node involvement (N-). An amplification of the c-myc gene was detected in four cases and a c-erb beta-2 (HER-2/neu) amplification in eight cases. The frequency of these abnormalities were compared to classical prognostic parameters as well as to new biological prognostic markers (cellular cycle, cathepsin-D and pS2 protein). Most of altered tumors were associated to some classical poor prognostic factors such as: steroid receptor-negative tumors, poorly differentiated tumors, high histoprognostic grade and tumor cell density. In contrast, no relation was found with new biological parameters. The analyses of these data in relation to clinical evolution will be of interest to evaluate their prognostic value.

Abnormal expression of neurofilament proteins in Ewing's sarcoma cell cultures

A neural origin of Ewing's sarcoma (ES) has often been suggested and we have demonstrated neurofilament protein expression in ES cells. However, only the 200-kD subunit has been revealed in all of the ES cells analyzed. The 160- and 68-kD subunits were always absent. For these reasons, we have attempted to induce neural differentiation in 3 ES cell lines with different types of inducers: tetradecanoylphorbol-13-acetate (TPA) retinoic acid and nerve growth factor. When the cell lines were cultured for 7 days with TPA (10(-9) M) or retinoic acid (10(-7) M), only the 68-kD neurofilament subunit was slightly induced. No inducation was obtained when nerve growth factor was used, even at a 21-day culture. These results are in agreement with the putative neural origin of ES and may indicate an abnormal expression of neurofilament proteins in this tumor.

Immunologic characterization of Ewing's sarcoma using mesenchymal and neural markers

The two most recent hypotheses about the histogenesis of Ewing's Sarcoma (ES) are that it has a mesenchymal or neuroectodermal origin. Immunologic markers specific to these two tissue origins were tested on cryostat sections from three primary tumors carrying the chromosomal translocation t(11;22)(q24;q12). Cell lines established in vitro from two of these three primary tumors were also analyzed. Using antibodies directed against neural components (neurone-specific-enolase [NSE], HNK-1, and neurofilament triplet proteins [NFTP]), positive reactions were observed in cells from two primary tumors and their corresponding cell lines. Results of electron microscopic examination of the primary tumors were compatible with the diagnosis of ES. When using antibodies directed against mesenchymal cell surface antigens (common leucocytes, Leu M1, Leu M2, and Leu M3), the weak positive reactions observed in the three primary tumors were attributed to lymphoid infiltrates within tumor cells. Six additional ES cell lines carrying the translocation t(11;22) were also analyzed by immunocytochemical and flow cytometry methods using antibodies directed against mesenchymal and neural components. Positive reactions were observed in all seven cell lines tested using antibodies directed against NSE, HNK-1, and 200 KD subunit of the NFTP, whereas negative reactions were obtained with Leu M2 antibody. These results are consistent with a neuroectodermal origin of ES cells.

Association of breakpoint 14q23 with uterine leiomyoma

A chromosomal study of short-term cultured tumor cells from a benign uterine leiomyoma showed a clonal insertion, dir ins(14;6)(q23;p23p25) as a unique change. This finding supports the hypothesis of a specific association of the breakpoint 14q23 with uterine leiomyoma.