Molecular profiling of breast cancer: clinical implications

Breast cancers are routinely subcategorised on the basis of clinical stage, cellular morphology and immunohistochemical analysis of a small number of markers. The recent development of gene expression microarray and related technologies provides an opportunity to perform more detailed profiling of the disease. It is anticipated that the molecular classification arising from such studies will be more powerful than its pathological predecessor at confining treatment to those patients who are most likely to benefit. It is likely that this will result in a much less frequent use of adjuvant chemotherapy. Furthermore, of those who do receive it, a higher proportion will benefit. If adopted, this will offer considerable patient benefits in terms of reducing unnecessary toxicity and have major health economic implications.     

Molecular profiling of platinum resistant ovarian cancer

The aim of this study is to discover a gene set that can predict resistance to platinum-based chemotherapy in ovarian cancer. The study was performed on 96 primary ovarian adenocarcinoma specimens from 2 hospitals all treated with platinum-based chemotherapy. In our search for genes, 24 specimens of the discovery set (5 nonresponders and 19 responders) were profiled in duplicate with 18K cDNA microarrays. Confirmation was done using quantitative RT-PCR on 72 independent specimens (9 nonresponders and 63 responders). Sixty-nine genes were differentially expressed between the nonresponders (n=5) and the responders (n=19) in the discovery phase. An algorithm was constructed to identify predictive genes in this discovery set. This resulted in 9 genes (FN1, TOP2A, LBR, ASS, COL3A1, STK6, SGPP1, ITGAE, PCNA), which were confirmed with qRT-PCR. This gene set predicted platinum resistance in an independent validation set of 72 tumours with a sensitivity of 89% (95% CI: 0.68-1.09) and a specificity of 59% (95% CI: 0.47-0.71)(OR=0.09, p=0.026). Multivariable analysis including patient and tumour characteristics demonstrated that this set of 9 genes is independent for the prediction of resistance (p<0.01). The findings of this study are the discovery of a gene signature that classifies the tumours, according to their response, and a 9-gene set that determines resistance in an independent validation set that outperforms patient and tumour characteristics. A larger independent multicentre study should further confirm whether this 9-gene set can identify the patients who will not respond to platinum-based chemotherapy and could benefit from other therapies.     

MicroRNA-494 inhibits cell proliferation and invasion of chondrosarcoma cells in vivo and in vitro by directly targeting SOX9

Accumulating evidence indicates that dysregulation of miRNAs could contribute to tumor growth and metastasis of chondrosarcoma by infuencing cell proliferation and invasion. In the current study, we are interested to examine the role of miRNAs in the carcinogenesis and progression of chondrosarcoma. Here, using comparative miRNA profiling of tissues and cells of chondrosarcoma and cartilage, we identified miR-494 as a commonly downregulated miRNA in the tissues of patients with chondrosarcoma and chondrosarcoma cancer cell line, and upregulation of miR-494 could inhibit proliferation and invasion of chondrosarcoma cancer cells in vivo and in vitro. Moreover, our data demonstrated that SOX9, the essential regulator of the process of cartilage differentiation, was the direct target and functional mediator of miR-494 in chondrosarcoma cells. And downregulation of SOX9 could also inhibit migration and invasion of chondrosarcoma cells. In the last, we identified low expression of miR-494 was significantly correlated with poor overall survival and prognosis of chondrosarcoma patients. Thus, miR-494 may be a new common therapeutic target and prognosis biomarker for chondrosarcoma.     

Gene expression profiling as a tool for basic analysis and clinical application of human cancer

The sequentiation of the human genome, together with the development of high throughput technologies, particularly gene-expression profiling, is giving us the opportunity to describe biological features in a quantitative manner. Here we review the use of global gene expression analyses in cancer research. Microarray analyses of tumor samples have allowed researchers the development of profiles that can distinguish, identify and classify discrete subsets of disease, predict the disease outcome, or the response to therapy. Profiling of experimental models with activation of certain oncogenic pathways could also be used to ascertain the molecular events involved in the establishment and development of tumors and, consequently, these models could be validated as tools for preclinical therapy. Furthermore, the detailed analysis of gene expression deregulation after response to the therapies in such models would allow us to predict the response to specific drugs, and to target the therapies to patients in search for individualized management of the disease.     

Gene expression profiling to identify markers associated with deregulated hTERT in HPV-transformed keratinocytes and cervical cancer

Although high-risk human papillomavirus (HPV) infection plays a major role in the development of cervical cancer, additive oncogenic events are involved as well. One key event involves increased activity of telomerase resulting from a deregulated expression of its catalytic subunit hTERT. Our previous microcell-mediated chromosome transfer studies revealed that introduction of human chromosome 6 in the HPV16-immortalized keratinocyte cell line FK16A and in the HPV16-containing cervical cancer cell line SiHa induced growth arrest, resulting from a repression of hTERT mRNA expression and telomerase activity. Here, this model was used to analyze expression profiles associated with hTERT deregulation in HPV-transformed cells. Microarray expression analysis of 12 FK16A/chromosome 6 hybrids, 4 of which were negative for endogenous hTERT and 8 of which were positive for endogenous hTERT, resulted in the identification of 164 differentially expressed genes. Differential expression of a selection of 5 genes was verified by real-time RT-PCR. Of these 164 genes, 32 were also differentially expressed in other HPV transformed cells with deregulated hTERT. For 2 of these genes, encoding AQP3 and MGP, altered expression in hTERT positive cervical carcinomas was confirmed by real-time RT-PCR and immunohistochemistry, respectively. Moreover, increased MGP protein expression was significantly more frequent in high-grade cervical premalignant lesions with elevated hTERT mRNA expression compared to those without. In summary, we identified 32 candidate biomarkers for deregulated hTERT mRNA expression, which may enable the identification of cervical premalignant lesions that are at highest risk to progress to invasive cancer.     

SOX家族在脑胶质瘤中的表达及作用

脑胶质瘤是神经系统常见的恶性肿瘤.SOX家族的许多基因与脑胶质瘤的发生发展密切相关,其中SOX2、SOX4、SOX7、SOX9基因在脑胶质瘤中均有异常表达.SOX2基因在脑胶质瘤组织中高表达,与脑胶质瘤的恶性分级呈正相关,并且与众多因子协调促进脑胶质瘤的发生、发展;SOX4基因在脑胶质瘤中既是致癌基因又是抑癌基因,且能对多种因子进行调控;SOX7作为一种肿瘤抑制基因,在脑胶质瘤组织中低表达,通过调节相关因子及信号通路抑制脑胶质瘤的发生;SOX9基因在脑胶质瘤组织中高表达,与多种因子协调促进脑胶质瘤的发生及转移,是判断脑胶质瘤患者预后的重要因素.     

Sox9 在人普通型与去分化型软骨肉瘤差异表达*

目的:探讨Sox9 在人普通软骨肉瘤,去分化软骨肉瘤和正常软骨中的表达。方法:取12例2003年1 月至2007年1 月在北京大学人民医院经病理切片确诊为软骨肉瘤（普通软骨肉瘤6 例,去分化软骨肉瘤6 例）及正常软骨组织（6 例）的新鲜冰冻标本,利用基因芯片的方法分析后,将Sox9 作为候选基因,而后利用Real-time PCR,Western blot和免疫组化的方法比较其在人普通软骨肉瘤,去分化软骨肉瘤和正常软骨组织中的差异表达。结果:基因芯片结果显示:与正常软骨组织相比,Sox9 在普通软骨肉瘤中上调约1.6 倍,在去分化软骨肉瘤中,其表达水平为正常软骨组织表达水平的0.082 倍;Real-time PCR检测结果显示:Sox9mRNA 在普通软骨肉瘤和去分化软骨肉瘤中表达水平分别为1.68± 0.119 和0.088 ± 0.017;Western blot分析表明Sox9 蛋白在人普通软骨肉瘤的表达量明显高于正常软骨组织,在去分化软骨肉瘤中的表达量显著低于正常软骨组织。免疫组化实验结果表明与正常软骨组织相比,6 例普通软骨肉瘤均有Sox9 表达,细胞染色呈较强的阳性,而去分化软骨肉瘤未发现较强阳性细胞出现,只有可疑的阳性细胞散在出现。结论:Sox9 在普通软骨肉瘤中的表达水平明显高于正常软骨组织,在去分化软骨肉瘤中的表达水平显著低于正常软骨组织。Sox9 在去分化软骨肉瘤中低水平表达与去分化软骨肉瘤疾病进展快,预后差呈正向相关。      

Gene expression profiling of human ovarian tumours

There is currently a lack of reliable diagnostic and prognostic markers for ovarian cancer. We established gene expression profiles for 120 human ovarian tumours to identify determinants of histologic subtype, grade and degree of malignancy. Unsupervised cluster analysis of the most variable set of expression data resulted in three major tumour groups. One consisted predominantly of benign tumours, one contained mostly malignant tumours, and one was comprised of a mixture of borderline and malignant tumours. Using two supervised approaches, we identified a set of genes that distinguished the benign, borderline and malignant phenotypes. These algorithms were unable to establish profiles for histologic subtype or grade. To validate these findings, the expression of 21 candidate genes selected from these analyses was measured by quantitative RT-PCR using an independent set of tumour samples. Hierarchical clustering of these data resulted in two major groups, one benign and one malignant, with the borderline tumours interspersed between the two groups. These results indicate that borderline ovarian tumours may be classified as either benign or malignant, and that this classifier could be useful for predicting the clinical course of borderline tumours. Immunohistochemical analysis also demonstrated increased expression of CD24 antigen in malignant versus benign tumour tissue. The data that we have generated will contribute to a growing body of expression data that more accurately define the biologic and clinical characteristics of ovarian cancers.     

Molecular pharmacology of cancer therapy in human colorectal cancer by gene expression profiling

Global gene expression profiling has potential for elucidating the complex cellular effects and mechanisms of action of novel targeted anticancer agents or existing chemotherapeutics for which the precise molecular mechanism of action may be unclear. In this study, decreased expression of genes required for RNA and protein synthesis, and for metabolism were detected in rectal cancer biopsies taken from patients during a 5-fluorouracil infusion. Our observations demonstrate that this approach is feasible and can detect responses that may have otherwise been missed by conventional methods. The results suggested new mechanism-based combination treatments for colorectal cancer and demonstrated that expression profiling could provide valuable information on the molecular pharmacology of established and novel drugs.     

Molecular markers for human colon cancer in stool and blood identified by RT-PCR

There is a need for sensitive and specific diagnostic and prognostic molecular markers which can monitor early patterns of gene expression in non-invasive exfoliated colonocytes shed in the stool, and aggression in carcinoma cells in blood of resected colorectal cancer patients. RNA-based detection methods are more comprehensive than either DNA- or protein-based methods. By routinely and systematically being able to perform quantitative gene expression studies on non-invasive samples using carefully selected tumor-specific colon cancer genes, we can quantitatively and accurately monitor changes at various stages in the neoplastic process, allowing for surgical and/or other therapies, and thus, decrease mortality from colorectal cancer.     

胃癌预后分子标志物

多种分子标志物与胃癌预后有关,如AT丰富结构域1A(ARID1A)基因的表达缺失、CD133和生存素的过表达均可致胃癌发生,且预后不良;瘦素、CD44、微小RNA(miRNA)则与胃癌侵袭转移密切相关;富含半胱氨酸的酸性分泌蛋白(SPARC)低表达有助于胃癌血管生成,但其表达与胃癌预后的相关性有待进一步研究;而核苷酸切除修复交叉互补基因1(ERCC1)在胃癌中的表达及其基因多态性则可能为用药选择提供依据.     

Molecular profiling of cervical cancer progression

Most cancer patients die of metastatic or recurrent disease, hence the importance to identify target genes upregulated in these lesions. Although a variety of gene signatures associated with metastasis or poor prognosis have been identified in various cancer types, it remains a critical problem to identify key genes as candidate therapeutic targets in metastatic or recurrent cancer. The aim of our study was to identify genes consistently upregulated in both lymph node micrometastases and recurrent tumours compared to matched primary tumours in human cervical cancer. Taqman Low-Density Arrays were used to analyse matched tumour samples, obtained after laser-capture microdissection of tumour cell islands for the expression of 96 genes known to be involved in tumour progression. Immunohistochemistry was performed for a panel of up- and downregulated genes. In lymph node micrometastases, most genes were downregulated or showed expressions equal to the levels found in primary tumours. In more than 50% of lymph node micrometastases studied, eight genes (AKT, BCL2, CSFR1, EGFR1, FGF1, MMP3, MMP9 and TGF-beta) were upregulated at least two-fold. Some of these genes (AKT and MMP3) are key regulators of epithelial-mesenchymal transition in cancer. In recurrent tumours, almost all genes were upregulated when compared to the expression profiles of the matched primary tumours, possibly reflecting their aggressive biological behaviour. The two genes showing a consistent downregulated expression in almost all lymph node metastases and recurrent tumours were BAX and APC. As treatment strategies are very limited for metastatic and recurrent cervical cancer, the upregulated genes identified in this study are potential targets for new molecular treatment strategies in metastatic or recurrent cervical cancer.     

Characterisation and protein expression profiling of annexins in colorectal cancer

The annexins are family of calcium-regulated phospholipid-binding proteins with diverse roles in cell biology. Individual annexins have been implicated in tumour development and progression, and in this investigation a range of annexins have been studied in colorectal cancer. Annexins A1, A2, A4 and A11 were identified by comparative proteomic analysis to be overexpressed in colorectal cancer. Annexins A1, A2, A4 and A11 were further studied by immunohistochemistry with a colorectal cancer tissue microarray containing primary and metastatic colorectal cancer and also normal colon. There was significant increase in expression in annexins A1 (P=0.01), A2 (P<0.001), A4 (P<0.001) and A11 (P<0.001) in primary tumours compared with normal colon. There was increasing expression of annexins A2 (P=0.001), A4 (P=0.03) and A11 (P=0.006) with increasing tumour stage. An annexin expression profile was identified by k-means cluster analysis, and the annexin profile was associated with tumour stage (P=0.01) and also patient survival. Patients in annexin cluster group 1 (low annexin expression) had a better survival (log rank=5.33, P=0.02) than patients in cluster group 2 (high annexins A4 and A11 expression). In conclusion, this study has shown that individual annexins are present in colorectal cancer, specific annexins are overexpressed in colorectal cancer and the annexin expression profile is associated with survival.     

Molecular markers associated with outcome and metastasis in human pancreatic cancer

ABSTRACT: BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is a heterogeneous cancer in which differences in survival rates might be related to a variety in gene expression profiles. Although the molecular biology of PDAC begins to be revealed, genes or pathways that specifically drive tumour progression or metastasis are not well understood. METHODS: We performed microarray analyses on whole-tumour samples of 2 human PDAC subpopulations with similar clinicopathological features, but extremely distinct survival rates after potentially curative surgery, i.e. good outcome (OS and DFS > 50 months, n = 7) versus bad outcome (OS < 19 months and DFS < 7 months, n = 10). Additionally, liver- and peritoneal metastases were analysed and compared to primary cancer tissue (n = 11). RESULTS: The integrin and ephrin receptor families were upregulated in all PDAC samples, irrespective of outcome, supporting an important role of the interaction between pancreatic cancer cells and the surrounding desmoplastic reaction in tumorigenesis and cancer progression. Moreover, some components such as ITGB1 and EPHA2 were upregulated in PDAC samples with a poor outcome, Additionally, overexpression of the non-canonical Wnt/beta-catenin pathway and EMT genes in PDAC samples with bad versus good outcome suggests their contribution to the invasiveness of pancreatic cancer, with beta-catenin being also highly upregulated in metastatic tissue. CONCLUSIONS: Components of the integrin and ephrin pathways and EMT related genes, might serve as molecular markers in pancreatic cancer as their expression seems to be related with prognosis.