Cancer Gene Expression Database Research Articles

Kinesin Family Member C1 (KIFC1/HSET) Underlies Aggressive Disease in Androgen Receptor-Low and Basal-Like Triple-Negative Breast Cancers.

Quadruple-negative breast cancer (QNBC) lacks traditional actionable targets, including androgen receptor (AR). QNBC disproportionately afflicts and impacts patients of African genetic ancestry. Kinesin family member C1 (KIFC1/HSET), a centrosome clustering protein that prevents cancer cells from undergoing centrosome-amplification-induced apoptosis, has been reported to be upregulated in TNBCs and African-American (AA) TNBCs. Herein, we analyzed KIFC1 RNA levels and their associations with clinical features and outcomes among AR-low and AR-high TNBC tumors in three distinct publicly available gene expression datasets and in the breast cancer gene expression database (bc-GenExMiner). KIFC1 levels were significantly higher in AR-low and basal-like TNBCs than in AR-high and non-basal-like TNBCs, irrespective of the stage, grade, tumor size, and lymph node status. KIFC1 levels were also upregulated in AR-low tumors relative to AR-high tumors among Black and premenopausal women with TNBC. High KIFC1 levels conferred significantly shorter overall survival, disease-free survival, and distant metastasis-free survival among AR-low and basal-like TNBC patients in Kaplan-Meier analyses. In conclusion, KIFC1 levels may be upregulated in AR-low tumors and, specifically, in those of African descent, wherein it may promote poor outcomes. KIFC1 may be an actionable cancer-cell-specific target for the AR-low TNBC subpopulation and could aid in alleviating racial disparities in TNBC outcomes.

A contrast set mining based approach for cancer subtype analysis

The task of detecting common and unique characteristics among different cancer subtypes is an important focus of research that aims to improve personalized therapies. Unlike current approaches mainly based on predictive techniques, our study aims to improve the knowledge about the molecular mechanisms that descriptively led to cancer, thus not requiring previous knowledge to be validated. Here, we propose an approach based on contrast set mining to capture high-order relationships in cancer transcriptomic data. In this way, we were able to extract valuable insights from several cancer subtypes in the form of highly specific genetic relationships related to functional pathways affected by the disease. To this end, we have divided several cancer gene expression databases by the subtype associated with each sample to detect which gene groups are related to each cancer subtype. To demonstrate the potential and usefulness of the proposed approach we have extensively analysed RNA-Seq gene expression data from breast, kidney, and colon cancer subtypes. The possible role of the obtained genetic relationships was further evaluated through extensive literature research, while its prognosis was assessed via survival analysis, finding gene expression patterns related to survival in various cancer subtypes. Some gene associations were described in the literature as potential cancer biomarkers while other results have been not described yet and could be a starting point for future research.

Abstract C065: Kinesin family member C1 (KIFC1/HSET) underlies aggressive disease course in androgen receptor-low triple negative breast cancers

Abstract Quadruple negative breast cancer (QNBC), which refers to triple negative breast cancers (TNBCs) lacking androgen receptor (AR) expression, is now considered to be a highly aggressive BC subtype, with no actionable therapeutic targets. QNBC disproportionately afflicts and impacts patients of African descent. Kinesin family member C1 (KIFC1/HSET), a centrosome clustering protein that prevents cancer cells from undergoing centrosome amplification-induced apoptosis, has been reported to be upregulated in TNBCs and African-American (AA) TNBCs, compared to non-TNBCs and European-American (EA) TNBCs. Herein, we analyzed KIFC1 mRNA levels and their associations with clinical features and outcomes among AR-low and AR-high TNBC patients in three distinct publicly-available gene expression datasets and the Breast cancer gene expression database (bc-GenExMiner). We discovered that KIFC1 levels were significantly higher (p<0.05) in AR-low and basal-like TNBCs compared to AR-high and luminal androgen receptor TNBCs, irrespective of stage, grade, tumor size, and lymph node status. We also observed that KIFC1 levels were upregulated in AR-low versus AR-high black and premenopausal TNBC patients (p<0.05). Furthermore, AR levels negatively correlated with KIFC1 levels among TNBC and basal-like TNBC patients (p<0.0001). High KIFC1 levels conferred significantly shorter overall survival (OS), disease-free survival, and distant metastasis-free survival among AR-low and basal-like TNBC patients in Kaplan-Meier analyses (p<0.05). In conclusion, KIFC1 levels may be upregulated in QNBCs and specifically QNBCs of African descent, wherein it may promote poorer outcomes. In addition, therapeutically targeting KIFC1 in these patient subpopulations could significantly mitigate racial disparities in TNBC outcomes. Citation Format: Nikita Wright, Yuan Yate-Ching, Tijana Talisman, Rama Natarajan, Mark LaBarge, Padmashree Rida, Victoria Seewaldt. Kinesin family member C1 (KIFC1/HSET) underlies aggressive disease course in androgen receptor-low triple negative breast cancers [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr C065.

Wnt-11 as a Potential Prognostic Biomarker and Therapeutic Target in Colorectal Cancer.

The expression of the secreted factor Wnt-11 is elevated in several types of cancer, including colorectal cancer, where it promotes cancer cell migration and invasion. Analysis of colorectal cancer gene expression databases associated WNT11 mRNA expression with increased likelihood of metastasis in a subset of patients. WNT11 expression was correlated with the expression of the Wnt receptors FZD6, RYK, and PTK7, and the combined expression of WNT11, FZD6 and RYK or PTK7 was associated with an increased risk of 5-year mortality rates. Immunohistochemical analysis of Wnt-11 in a cohort of 357 colorectal cancer patients found significantly higher Wnt-11 levels in tumors, compared with benign tissue. Elevated Wnt-11 levels occurred more frequently in rectal tumors than in colonic tumors and in tumors from women than men. In univariate analysis, increased Wnt-11 expression was also associated with tumor invasion and increased 5-year mortality. High Wnt-11 levels were not associated with high levels of nuclear β-catenin, suggesting Wnt-11 is not simply an indicator for activation of β-catenin-dependent signaling. Expression of Wnt-11 in colorectal cancer cell lines expressing low endogenous Wnt-11 inhibited β-catenin/Tcf activity and increased ATF2-dependent transcriptional activity. WNT11 gene silencing and antibody-mediated inhibition of Wnt-11 in colorectal cancer cell lines expressing high Wnt-11 reduced their capacity for invasion. Together, these observations suggest that Wnt-11 could be a potential target for the treatment of patients with invasive colorectal cancer.

Abstract 494: Intravital discovery of miRNA drivers of human cancer cell directional invasion

Abstract Metastatic cancer cells use directional ECM cues such as blood vessels or collagen fibers when invading through live tissue. Oncogenic miRNAs have been implicated as key regulators of cancer progression, yet the systemic discovery of miRNAs that drive directional cancer cell invasion has not been achieved. Here we describe the first in vivo quantitative whole human miRNAome screen for miRNA drivers of directional cancer cell invasion that is based on high-resolution intravital imaging. We identified several novel miRNAs that promote cancer cell invasion during the key rate-limiting step of cancer metastasis: the initiation of overt metastatic lesions. In vivo 4D cancer cell tracking revealed that these prometastatic miRNAs are required for successful invasion into collagen-rich tissue and for attachment to the outer surface of the vascular wall. Deregulation of these miRNAs led to formation of loose contacts with the vasculature and chaotic, nondirectional cancer cell invasion patterns in living tissue. Intravital SHG microscopy showed that inhibition of the expression of these miRNAs blocked the ability of cancer cells to rearrange the disorganized collagen network into collagen fiber bundles and stably protrude along these bundles. Further imaging analysis revealed that this miRNA expression specifically blocks vesicular transport of key cell invasion machinery proteins such as MT1-MMP to the cancer cell invadopodia. Human cancer gene expression database analysis showed that our top miRNA candidates are specifically deregulated in invasive pancreatic cancer. Indeed, intravital imaging analysis showed that blocking of metastatic miRNA function inhibited MT1-MMP secretion and ECM degradation by human pancreatic cancer cells. In summary, we identified a novel panel of human miRNAs that are functionally involved in the regulation of directional invasion and metastasis. This work establishes these miRNAs as promising therapeutic targets to block the metastatic spread of lethal cancers. Citation Format: Konstantin V. Stoletov, Lian Willetts, Juan Jovel, Emma Woolner, John D. Lewis. Intravital discovery of miRNA drivers of human cancer cell directional invasion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 494.

GPCRomics: GPCR Expression in Cancer Cells and Tumors Identifies New, Potential Biomarkers and Therapeutic Targets.

G protein-coupled receptors (GPCRs), the largest family of targets for approved drugs, are rarely targeted for cancer treatment, except for certain endocrine and hormone-responsive tumors. Limited knowledge regarding GPCR expression in cancer cells likely has contributed to this lack of use of GPCR-targeted drugs as cancer therapeutics. We thus undertook GPCRomic studies to define the expression of endoGPCRs (which respond to endogenous molecules such as hormones, neurotransmitters and metabolites) in multiple types of cancer cells. Using TaqMan qPCR arrays to quantify the mRNA expression of ∼340 such GPCRs, we found that human chronic lymphocytic leukemia (CLL) cells/stromal cells associated with CLL, breast cancer cell lines, colon cancer cell lines, pancreatic ductal adenocarcinoma (PDAC) cells, cancer associated fibroblasts (CAFs), and PDAC tumors express 50 to >100 GPCRs, including many orphan GPCRs (which lack known physiologic agonists). Limited prior data exist regarding the expression or function of most of the highly expressed GPCRs in these cancer cells and tumors. Independent results from public cancer gene expression databases confirm the expression of such GPCRs. We propose that highly expressed GPCRs in cancer cells (for example, GPRC5A in PDAC and colon cancer cells and GPR68 in PDAC CAFs) may contribute to the malignant phenotype, serve as biomarkers and/or may be novel therapeutic targets for the treatment of cancer.

Matrix metalloproteinase 12 promotes tumor propagation in the lung

ObjectivePast studies are inconsistent with regard to the role of matrix metalloproteinase 12 in lung tumorigenesis. This is due, in part, to differential tumorigenesis based on tumor-derived versus immune-derived matrix metalloproteinase 12 expression. Our study aims to thoroughly dissect the role of matrix metalloproteinase 12 in lung tumorigenesis. MethodsWe tested matrix metalloproteinase 12 expression and the association with prognosis using a tissue array and a published non–small cell lung cancer gene expression database. In addition, we characterized the contribution of matrix metalloproteinase 12 to tumor propagation in the lung using a series of in vitro and in vivo studies. ResultsTumor cells of a diverse set of human lung cancers stained positive for matrix metalloproteinase 12, and high matrix metalloproteinase 12 mRNA levels in the tumor were associated with reduced survival. The lung microenvironment stimulated endogenous production of matrix metalloproteinase 12 in lung cancer cells (human 460 lung cancer cell line, Lewis lung carcinoma). In vitro, matrix metalloproteinase 12 knockout Lewis lung carcinoma and Lewis lung carcinoma cells had the same proliferation rate, but Lewis lung carcinoma showed increased invasiveness. In vivo, deficiency of matrix metalloproteinase 12 in Lewis lung carcinoma cells, but not in the host, reduced tumor growth and invasiveness. ConclusionsWe suggest that tumor cell–derived matrix metalloproteinase 12 promotes tumor propagation in the lung and that in the context of pulmonary malignancies matrix metalloproteinase 12 should further be tested as a potential novel therapeutic target.

Abstract 1463: Intravital discovery of miRNA drivers of human cancer cell directional invasion

Abstract Metastatic cancer cells often use directional ECM cues such as blood vessels or collagen fibers when invading through live tissue. Oncogenic miRNAs have been implicated as key regulators of cancer progression yet the systemic discovery of miRNAs that drive directional cancer cell invasion has not been achieved. Here we describe the first in vivo quantitative whole human miRNAome screen for miRNA drivers of directional cancer cell invasion using an ex ovo avian embryo model of human cancer cell metastasis combined with high resolution intravital imaging. We identified more than twenty novel miRNAs that promote cancer cell invasion during the key rate-limiting step of cancer metastasis, the initiation and expansion of overt metastatic lesions. In silico miRNA target analysis (DIANA, Targetscan) showed significant enrichment in gene targets/pathways that control cancer cell-ECM adhesion and cancer cell contractility. These findings were further confirmed using Affymetrix gene expression analysis that showed significant changes in the expression of genes that regulate actin cytoskeleton rearrangement, cancer cell-ECM interaction and cell surface-receptor signaling. Public cancer gene expression database analysis (Oncoprint) showed that these miRNA-mRNA networks deregulated in several deadly cancers (pancreas, prostate, breast) and negatively correlate with the cancer patient survival. To elucidate potential mechanisms of these pro-metastatic miRNAs, we utilized an intravital imaging approach. In vivo 4D cancer cell tracking revealed that these pro-metastatic miRNAs are required for successful invasion into collagen-rich tissue and for attachment to the outer surface of the vascular wall. Deregulation of these miRNAs led to formation of loose contacts with the vasculature and chaotic, non-directional cancer cell invasion patterns in living tissue. Intravital second-harmonic microscopy analysis showed that inhibition of the expression of these miRNAs blocked the ability of cancer cells to rearrange the disorganized fine collagen fiber network into thicker collagen bundles that guide directional tumor cell invasion. In contrast to parental tumor cells that persistently moved along the collagen bundles, miRNA-deficient tumor cells were observed to transiently associate with multiple collagen fibers without establishing persistent collagen fiber-tumor cell protrusion contacts. Moreover, miRNA-deficient tumor cells failed to attach and protrude along preexisting perivascular collagen bundles, resulting in the complete abrogation of cancer cell/blood vessel co-option. In summary, we identified a novel panel of human miRNAs that are functionally involved in the regulation of directional invasion and metastasis. This work establishes these miRNAs as promising therapeutic targets to block the metastatic spread of lethal cancers. Citation Format: Konstantin V. Stoletov, Lian Willetts, Juan Jovel, Emma Woolner, John D. Lewis. Intravital discovery of miRNA drivers of human cancer cell directional invasion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1463. doi:10.1158/1538-7445.AM2017-1463

G9a drives hypoxia-mediated gene repression for breast cancer cell survival and tumorigenesis

G9a is an epigenetic regulator that methylates H3K9, generally causing repression of gene expression, and participates in diverse cellular functions. G9a is genetically deregulated in a variety of tumor types and can silence tumor suppressor genes and, therefore, is important for carcinogenesis. Although hypoxia is recognized to be an adverse factor in tumor growth and metastasis, the role of G9a in regulating gene expression in hypoxia has not been described extensively. Here, we show that G9a protein stability is increased in hypoxia via reduced proline hydroxylation and, hence, inefficient degradation by the proteasome. This inefficiency leads to an increase in H3K9me2 at its target promoters. Blocking the methyltransferase activity of G9a inhibited cellular proliferation and migration in vitro and tumor growth in vivo. Furthermore, an increased level of G9a is a crucial factor in mediating the hypoxic response by down-regulating the expression of specific genes, including ARNTL, CEACAM7, GATA2, HHEX, KLRG1, and OGN This down-regulation can be rescued by a small molecule inhibitor of G9a. Based on the hypothesis that the changes in gene expression would influence patient outcomes, we have developed a prognostic G9a-suppressed gene signature that can stratify breast cancer patients. Together, our findings provide an insight into the role G9a plays as an epigenetic mediator of hypoxic response, which can be used as a diagnostic marker, and proposes G9a as a therapeutic target for solid cancers.

Upregulation of Cyclooxygenase-2/Prostaglandin E2 (COX-2/PGE2) Pathway Member Multiple Drug Resistance-Associated Protein 4 (MRP4) and Downregulation of Prostaglandin Transporter (PGT) and 15-Prostaglandin Dehydrogenase (15-PGDH) in Triple-Negative Breast Cancer.

Elevated levels of cyclooxygenase-2 (COX-2) and prostaglandin E2 (PGE2) are indicators of a poor prognosis in breast cancer. Using several independent publicly available breast cancer gene expression databases, we investigated other members of the PGE2 pathway. PGE2 is produced by COX-2 and actively exported by multiple drug resistance-associated protein 4 (MRP4) into the extracellular microenvironment, where PGE2 can bind four cognate EP receptors (EP1–EP4) and initiate diverse biological signaling pathways. Alternatively, PGE2 is imported via the prostaglandin transporter (PGT) and metabolized by 15-prostaglandin dehydrogenase (15-PGDH/HPGD). We made the novel observation that MRP4, PGT, and 15-PGDH are differentially expressed among distinct breast cancer molecular subtypes; this finding was confirmed in independent datasets. In triple-negative breast cancer, the observed gene expression pattern (high COX-2, high MRP4, low PGT, and low 15-PGDH) would favor high levels of tumor-promoting PGE2 in the tumor microenvironment that may contribute to the overall poor prognosis of triple-negative breast cancer.

Abstract 233: Mining cancer gene expression databases for latent information on intronic microRNAs

Abstract In recent years, enormous effort has been dedicated to transcriptomic profiling of various physiological and pathological conditions, in particular in cancer biology field. Microarray gene expression (mRNA) datasets of thousands of human tumors are now publicly available and can be used to get insights of cancer processes by systems-based analysis and to identify biomarkers for improvement of cancer therapy. However, the high complexity of human transcriptome may be difficult to handle. In this regard, shifting the attention to the miRNome could be an advantage, since its complexity is at least 20-fold lower than that of a reference transcriptome (∼1000 miRNAs vs. ∼20,000 genes). Importantly, patterns of distinct miRNA expression profiles were observed in tumors and there is a growing interest in miRNAs, behaving as potential cancer determinants and biomarkers. Knowing that almost 50% of human miRNA genes are located within introns of coding genes and that they usually share transcriptional regulation, those publicly available datasets are likely to contain “latent” information on intronic-miRNA expression. In other words, it could be possible to predict the regulation of intronic-miRNA expression by simply analyzing their host genes profile (miR-HG). The aim of our work is to take advantage of cancer datasets, focusing mainly on breast cancer datasets, to provide proof of principle evidences that meta-analysis of miR-HG expression profiles can pinpoint intronic-miRNAs with a role in breast cancer cell biology, and a potential utility as cancer biomarkers. Using this approach, we successfully discovered a diagnostic microRNA signature enabling the identification of breast cancer molecular subtypes. Importantly, qRT-PCR analysis of just three intronic-miRNAs, using FFPE samples, was sufficient to identify more aggressive breast tumor subtypes (i.e. basal, HER2 and luminal B subtypes), with a ∼80% of accuracy, in patients with moderately differentiated breast cancer. Unexpectedly, in a number of cases, the regulation of expression of intronic-miRNAs was more relevant to cancer phenotypes than the expression of their host genes. In line with these encouraging results, we propose our data mining strategy as a valid tool for cancer research and other biomedical fields. Citation Format: Simona Monterisi, Giovanni D'Ario, Elisa Dama, Nicole Rotmensz, Stefano Confalonieri, Chiara Tordonato, Flavia Troglio, Giovanni Bertalot, Patrick Maisonneuve, Giuseppe Viale, Francesco Nicassio, Pier Paolo Di Fiore, Fabrizio Bianchi. Mining cancer gene expression databases for latent information on intronic microRNAs. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 233. doi:10.1158/1538-7445.AM2015-233

TRIM29 suppresses TWIST1 and invasive breast cancer behavior.

TRIM29 (ATDC) exhibits a contextual function in cancer, but seems to exert a tumor-suppressor role in breast cancer. Here, we show that TRIM29 is often silenced in primary breast tumors and cultured tumor cells as a result of aberrant gene hypermethylation. RNAi-mediated silencing of TRIM29 in breast tumor cells increased their motility, invasiveness, and proliferation in a manner associated with increased expression of mesenchymal markers (N-cadherin and vimentin), decreased expression of epithelial markers (E-cadherin and EpCAM), and increased expression and activity of the oncogenic transcription factor TWIST1, an important driver of the epithelial-mesenchymal transition (EMT). Functional investigations revealed an inverse relationship in the expression of TRIM29 and TWIST1, suggesting the existence of a negative regulatory feedback loop. In support of this relationship, we found that TWIST1 inhibited TRIM29 promoter activity through direct binding to a region containing a cluster of consensus E-box elements, arguing that TWIST1 transcriptionally represses TRIM29 expression. Analysis of a public breast cancer gene-expression database indicated that reduced TRIM29 expression was associated with reduced relapse-free survival, increased tumor size, grade, and metastatic characteristics. Taken together, our results suggest that TRIM29 acts as a tumor suppressor in breast cancer through its ability to inhibit TWIST1 and suppress EMT.

Expression of the Aldo-Ketoreductases AKR1B1 and AKR1B10 in Human Cancers

The American Cancer Society estimates that there will be more than 1.5 million new cases of cancer in 2011, underscoring the need for identification of new therapeutic targets and development of novel cancer therapies. Previous studies have implicated the human aldo-ketoreductases AKR1B1 and AKR1B10 in cancer, and therefore we examined AKR1B1 and AKR1B10 expression across all major human cancer types using the Oncomine cancer gene expression database (Compendia Biosciences, www.oncomine.com). Using this database, we found that expression of AKR1B1 and AKR1B10 varies greatly by cancer type and tissue of origin, including agreement with previous reports that AKR1B10 is significantly over-expressed in cancers of the lungs and liver. AKR1B1 is more broadly over-expressed in human cancers than AKR1B10, albeit at a generally lower magnitude. AKR1B1 over-expression was found to be associated with shortened patient survival in acute myelogenous leukemias and multiple myelomas. High AKR1B10 expression tends to predict less aggressive clinical course generally, notably within lung cancers, where it tends to be highly over-expressed compared to normal tissue. These findings suggest that AKR1B1 inhibitors in particular hold great potential as novel cancer therapeutics.

Lung cancer gene expression database analysis incorporating prior knowledge with support vector machine-based classification method

BackgroundA reliable and precise classification is essential for successful diagnosis and treatment of cancer. Gene expression microarrays have provided the high-throughput platform to discover genomic biomarkers for cancer diagnosis and prognosis. Rational use of the available bioinformation can not only effectively remove or suppress noise in gene chips, but also avoid one-sided results of separate experiment. However, only some studies have been aware of the importance of prior information in cancer classification.MethodsTogether with the application of support vector machine as the discriminant approach, we proposed one modified method that incorporated prior knowledge into cancer classification based on gene expression data to improve accuracy. A public well-known dataset, Malignant pleural mesothelioma and lung adenocarcinoma gene expression database, was used in this study. Prior knowledge is viewed here as a means of directing the classifier using known lung adenocarcinoma related genes. The procedures were performed by software R 2.80.ResultsThe modified method performed better after incorporating prior knowledge. Accuracy of the modified method improved from 98.86% to 100% in training set and from 98.51% to 99.06% in test set. The standard deviations of the modified method decreased from 0.26% to 0 in training set and from 3.04% to 2.10% in test set.ConclusionThe method that incorporates prior knowledge into discriminant analysis could effectively improve the capacity and reduce the impact of noise. This idea may have good future not only in practice but also in methodology.

What is hidden in the pannexin treasure trove: the sneak peek and the guesswork

Connexins had been considered to be the only class of the vertebrate proteins capable of gap junction formation; however, new candidates for this function with no homology to connexins, termed pannexins were discovered. So far three pannexins were described in rodent and human genomes: Panx1, Panx2 and Panx3. Expressions of pannexins can be detected in numerous brain structures, and now found both in neuronal and glial cells. Hypothetical roles of pannexins in the nervous system include participating in sensory processing, hippocampal plasticity, synchronization between hippocampus and cortex, and propagation of the calcium waves supported by glial cells, which help maintain and modulate neuronal metabolism. Pannexin also may participate in pathological reactions of the neural cells, including their damage after ischemia and subsequent cell death. Recent study revealed non-gap junction function of Panx1 hemichannels in erythrocytes, where they serve as the conduits for the ATP release in response to the osmotic stress. High-throughput studies produced some evidences of the pannexin involvement in the process of tumorigenesis. According to brain cancer gene expression database REMBRANDT, PANX2 expression levels can predict post diagnosis survival for patients with glial tumors. Further investigations are needed to verify or reject hypotheses listed.

Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues

Gene expression profiling of cancer tissues is expected to contribute to our understanding of cancer biology as well as developments of new methods of diagnosis and therapy. Our collaborative efforts in Japan have been mainly focused on solid tumors such as breast, colorectal and hepatocellular cancers. The expression data are obtained by a high-throughput RT–PCR technique, and patients are recruited mainly from a single hospital. In the cancer gene expression database (CGED), the expression and clinical data are presented in a way useful for scientists interested in specific genes or biological functions. The data can be retrieved either by gene identifiers or by functional categories defined by Gene Ontology terms or the Swiss-Prot annotation. Expression patterns of multiple genes, selected by names or similarity search of the patterns, can be compared. Visual presentation of the data with sorting function enables users to easily recognize of relationships between gene expression and clinical parameters. Data for other cancers such as lung and thyroid cancers will be added in the near future. The URL of CGED is http://cged.hgc.jp.