Characterization of C4-2 as a tumor-suppressor gene in human brain tumors

Oncogenic signaling pathways and deregulated target genes

A limited number of somatic mutations are known to trigger malignancy via chronic activation of cellular signaling pathways. High-throughput analysis of gene expression in cancer cells has revealed a plethora of deregulated genes by far exceeding the number of known genetic alterations. Targeted tumor therapy takes advantage of deregulated signaling in cancer. However, cancer cells may evade successful therapy, e.g., targeting oncogenic kinases, due to mutation of the target protein or to resistance mechanisms acting downstream of or parallel to the therapeutic block. To improve therapy and molecular diagnostics, we need detailed information on the wiring of pathway components and targets that ultimately execute the malignant properties of advanced tumors. Here we review work on Ras-mediated signal transduction and Ras pathway-responsive targets. We introduce the concept of signal-regulated transcriptional modules comprising groups of target genes responding to individual branches of the pathway network. Furthermore, we discuss functional approaches based on RNA interference for elucidating critical nodes in oncogenic signaling and the targets essential for malignancy.

Identification of differentially expressed genes in rheumatoid arthritis by a combination of complementary DNA array and RNA arbitrarily primed-polymerase chain reaction

OBJECTIVE

There is increasing evidence that T cell-independent pathways, such as the up-regulation of protooncogenes and the production of growth factors and matrix-degrading enzymes, lead to progressive destruction of affected joints. Therefore, identification of differentially regulated genes restricted to rheumatoid arthritis (RA) synovial fibroblasts is essential. A combination of RNA arbitrarily primed-polymerase chain reaction (RAP-PCR) and complementary DNA (cDNA) array with defined genes was used for a highly sensitive differential screening using small amounts of RNA.

METHODS

RNA was extracted from cultured synovial fibroblasts obtained from 6 patients with RA and 6 patients with osteoarthritis (OA). RAP-PCR was performed using different arbitrary primers for first- and second-strand synthesis. PCRs were hybridized to cDNA array membranes. RA samples were compared with OA samples for differentially expressed genes.

RESULTS

In contrast to standard cDNA array, the identification of 12 differentially expressed genes in RA compared with OA (approximately 6%) was possible. Differentially expressed genes of interest were confirmed using semiquantitative RT-PCR and in situ hybridization.

CONCLUSION

Numerous variants of the differential display method and continuous improvements, including RAP-PCR, have proven to be both efficient and reliable for examining differentially regulated genes. Our results show that RAP-PCR combined with cDNA arrays is a suitable method for identifying differentially expressed genes in rheumatoid synovial fibroblasts, using very small amounts of RNA.

The promise of transcription profiling for understanding the pathogenesis of scleroderma

Transcription profiling, expression fingerprinting, and microarray analysis are terms that describe the cataloging of mRNA levels in a given tissue. Recent profiling technologies allow the determination of thousands of mRNA transcript levels simultaneously. The application of this technology to scleroderma has already offered insights into the disease. This article reviews these recent findings and also describes the technology itself in its several variations, along with cost comparisons. Finally, the types of information we might derive from transcription profiling are reviewed and it is asked whether this technology will significantly advance our understanding of scleroderma.

The identification of novel therapeutic targets for the treatment of malignant brain tumors

A two-step strategy was developed consisting of differential display reverse transcriptase polymerase chain reaction (DDRT-PCR) with cultured normal human fetal astrocytes and U-373MG glioma cells followed by reverse Northern analysis of normal brain and primary tumor tissues. hu-dek, alpha-NAC, ribosomal proteins L7a and L35a, and five novel genes were identified. Since none of these genes has been previously shown to be associated with malignant brain tumor formation, this approach may be useful to identify novel targets for the diagnosis and treatment of brain tumors.

Identification of semaphorin E gene expression in metastatic human lung adenocarcinoma cells by mRNA differential display

Human lung adenocarcinoma cell lines HAL-8Luc and HAL-24Luc differ in their metastatic potential. HAL-8Luc cells metastasize to lungs when injected either intravenously or intramuscularly. in mice while HAL-24Luc cells do not. The differential display method is used to identify genes differentially expressed between the two cell lines and the findings are extensively discussed.

BACKGROUND

Lung cancer is the leading form of cancer in most countries, and metastasis is the main cause of death in oncological patients. The metastatic phenotype of tumor cells is the result of genetic events altering the RNA and protein expression of normal cells. Our objective was to identify genes expressed differentially between metastatic and nonmetastatic human lung adenocarcinoma cells that might be used as a prognostic factor.

METHODS

The differential display technique was used to compare the RNA expression patterns distinguishing metastatic (HAL-8Luc) and nonmetastatic (HAL-24Luc) human lung adenocarcinoma cells, two genetically close cell lines.

RESULTS

Differential expression of three cDNAs was confirmed by Northern blot analysis. Two sequences corresponding to a putative splicing factor and a proliferation-related factor cDNAs were underexpressed in the metastatic cells relative to the nonmetastatic ones. Interestingly, we found that human semaphorin E mRNA was several fold overexpressed in the metastatic cells. This recently identified gene encodes a protein whose expression has been related to several cell survival mechanisms as well as to immunosuppression.

CONCLUSION

Our results point to the relevance of semaphorin E in metastatic spread of human lung adenocarcinoma cells.

Cell adhesion molecule Nr-CAM is over-expressed in human brain tumors

Using the technique of differential display-polymerase chain reaction (DD-PCR), we isolated a cDNA fragment that is over-expressed in glioblastoma multiforme tissue as compared to normal brain tissue. Sequence analysis indicated that this sequence is identical to the previously isolated human neuron-glia-related cell adhesion molecule hNr-CAM. Gene-specific RT-PCR analysis indicated that hNr-CAM is over-expressed in high-grade astrocytomas, gliomas and glioblastoma tumor tissues as compared to normal brain tissue. High levels of hNr-CAM expression also were observed in cell lines derived from astrocytomas, gliomas and glioblastoma multiforme tumors. Low levels of hNr-CAM expression were observed in neuroblastoma, meningiomas, melanoma, normal breast and prostate tumor tissues. Northern blot analysis showed an alternatively spliced mRNA of 1.4 kb in several tumors as compared to the 7.5 kb transcript found in normal brain tissue. Genomic Southern blot analysis of DNA from 3 brain tumor cell lines showed that over-expression of hNr-CAM in brain tumors was not due to gene amplification. In situ hybridization analysis indicated that 11 of the 20 human brain tumor samples studied showed hNr-CAM over-expression. Our results suggest that hNr-CAM is over-expressed in malignant brain tumors and can serve as a novel marker for brain tumor detection and perhaps therapy.

Application of the differential hybridization of Atlas Human expression arrays technique in the identification of differentially expressed genes in human glioblastoma multiforme tumor tissue

BACKGROUND AND OBJECTIVES

Several molecular biology techniques are utilized to study changes in gene expression during the genesis of human tumors. Our objective was to identify genes that showed altered expression between normal brain tissue (NBT) and glioblastoma multiforme tumor tissue (GMTT).

METHODS

The technique of differential hybridization of two Atlas Human cDNA expression array was used. In this technique, dCTP32-labeled complimentary DNA from NBT and GMTT was hybridized to two identical human cDNA expression array membranes containing 588 known genes.

RESULTS

Autoradiographic analysis showed that of the 588 genes analyzed, 52 are overexpressed in GMTT and 57 in NBT. A gene-specific semiquantitative reverse transcription polymerase chain reaction (RT-PCR) method was used to confirm the expression pattern of seven known genes. RT-PCR results demonstrate that the expression pattern of a majority of genes agreed with the expression pattern observed on expression array. The known tumor suppressor genes retinoblastoma (RB) and p53 showed loss of expression in GMTT compared with NBT.

CONCLUSIONS

We conclude that the differential hybridization technique of Atlas Human cDNA expression array can be a useful method in identifying genes that are differentially expressed either in NBT or GMTT.

Molecular changes during the genesis of human gliomas

Neoplastic transformation in the normal human brain occurs as a result of the accumulation of a series of genetic alterations. These genetic alterations include the loss, gain or amplification of different chromosomes which lead to altered expression of proteins that play important roles in the regulation of cell proliferation. Several common genetic alterations at the chromosomal level (loss of 17p, 13q, 9p, 19, 10, 22q, 18q and amplification of 7 and 12q) have been observed. These alterations lead to changes in the expression of several genes; protein 53 (p53), retinoblastoma (RB), interferon (INF) alpha/beta, cyclic AMP dependent kinase number 2 (CDKN2), mutated in multiple advanced cancers 1 (MMAC1), deleted-in-colon carcinoma (DCC), epidermal growth factor receptor (EGFR), platelet derived growth factor (PDGF), platelet derived growth factor receptor (PDGFR), MDM2, GL1, CDK4 and SAS during the genesis and progression of human gliomas. Recent studies suggest that altered expression of several other genes [MET; MYC; transforming growth factor beta (TGF beta); CD44; vascular endothelial growth factor (VEGF); human neurological-related cell adhesion molecule (hNr-CAM); neuroglial cell adhesion molecule (NCAM L1); p21waf1/Cip1; TRKA; mismatch repair genes (MMR); C4-2; D2-2] and proteins [e.g., cathepsins, tenascin, matrix metalloproteases, tissue inhibitors of metalloproteases, nitric oxide synthase, integrins, interleukin-13 receptor (IL-13R), Connexin43, urokinase-type plasminogen activator receptors (uPARs), extracellular matrix proteins and heat shock proteins] are associated with the genesis of human gliomas. Taken together, these findings point to the accumulation of multiple genetic mutations coupled with extensive changes in gene expression in the etiology of human gliomas.

Cloning, sequence, and developmental expression analysis of C4-2, a potential brain tumor-suppressor gene

BACKGROUND

Previously, we reported the isolation of C4-2 as a potential tumor suppressor gene in human brain tumors. To understand the function of this gene, we investigated its molecular characterization and expression during development.

METHODS

Human fetal brain library screening and 5'RACE-PCR method was used to isolate the full-length cDNA. The coding region of C4-2 was used for in situ hybridization to study its expression during development.

RESULTS

We report here the complete sequence of this gene. Sequence analysis indicated that C4-2 has a 94% sequence identity to a family of cAMP-regulated phosphoproteins (ARPP-16/19) in the coding region. C4-2 has a 3.1 Kb long 3'UTR with variable identity to ARPP-16 and ARPP-19. Northern blot analysis indicated that C4-2 is expressed at high levels in normal brain compared to other tissues. Zoo blot analysis demonstrated that the coding region of C4-2 is highly conserved among different animals. In situ hybridization using C4-2 coding region demonstrated that it follows a unique expression pattern during mouse brain development. High level of C4-2 expression was also observed in the spinal cord and somites of the developing embryo.

CONCLUSION

Expression analysis during brain development strongly suggests that this family of proteins may play an important role not only in normal functioning of the brain, but also during brain development.