Isolation of differentially expressed cDNAs during ferret tracheal development: application of differential display PCR

Disrupted post-transcriptional regulation of the cystic fibrosis transmembrane conductance regulator (CFTR) by a 5'UTR mutation is associated with a CFTR-related disease

Cystic fibrosis (CF) is characterized as a single-gene disorder with a simple, autosomal recessive mode of inheritance. However, translation of cystic fibrosis transmembrane conductance regulator (CFTR) genotype into CF phenotype is influenced by nucleotide sequence variations at multiple genetic loci, and individuals heterozygous for CFTR mutations are predisposed to a range of CFTR-related conditions, such as disseminated bronchiectasis. CF disease severity and CFTR-related conditions are more akin to complex, multifactorial traits, which are increasingly being associated with mutations that perturb gene expression. We have identified a patient with disseminated bronchiectasis, who is heterozygous for a single-nucleotide substitution in the CFTR 5' untranslated region (UTR) (c.-34C>T). The c.-34C>T mutation creates an upstream AUG codon and upstream open reading frame that overlaps, and is out of frame with, the CFTR protein coding sequence. Using luciferase reporter constructs, we have shown that the c.-34C>T mutation decreases gene expression by 85-99%, by reducing translation efficiency and mRNA stability. This is the first CFTR regulatory mutation shown to act at a posttranscriptional level that reduces the synthesis of normal CFTR (Class V), and reaffirms the importance of regulatory mutations as a genetic basis of multifactorial phenotypes.

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.

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.

Rational primer design greatly improves differential display-PCR (DD-PCR)

Since its conception in 1992, differential display PCR (DD-PCR) has attracted widespread interest. Theoretically an attractive cloning approach, it combines the comparative analysis of several samples with the sensitivity of PCR. Although a large number of studies embracing this technology have been initiated, few novel genes of interest have been identified, suggesting that the method has not realised its potential. The present report shows that by modifying primer design, sampling of differentially expressed genes can be greatly enhanced and relevant genes can be isolated. Using our modified conditions DD-PCR efficiently screens a wide range of gene expression levels, in which differences are represented on a linear scale.

Isolation and characterization of a novel gene from human glioblastoma multiforme tumor tissue

Using the technique of DD-PCR (differential display-polymerase chain reaction) we isolated a novel gene (D2-2) that is overexpressed in glioblastoma multiforme tissue (GMT) as compared to normal brain tissue (NBT). D2-2 is also highly expressed in recurrent glioma, colon tumor metastatic to brain, breast tumors, prostate tumors and a prostate tumor cell line (LNCaP). Northern blot analysis showed that D2-2 is highly expressed in several tumor cell lines (MOLT lymphoblastic leukemia, SW480 colorectal adrenocarcinoma, A549 lung carcinoma, HL-60 promyelocytic leukemia, S3 HeLa cells, K-562 chronic myelogeneous leukemia and G361 melanoma) as compared to NBT. Additionally, D2-2 is very highly expressed in cell lines derived from glioblastomas, grade IV astrocytomas, normal human fetal astrocytes (NHFA) and glioma. D2-2 is moderately expressed in neuroblastoma, neuroectodermal and medulloblastoma tumor cell lines. D2-2 expression is localized to the frontal lobe, occipital lobe and the cerebellum in the normal brain. Normal tissues such as thyroid, stomach, adrenal cortex, small intestine and pancreas show high expression of D2-2. We also show that D2-2 is expressed 28-fold higher in fetal brain (20 weeks) than in adult brain. Sequence analysis of a 2.0-kb fragment for D2-2 shows no homology to known sequences in the data base.

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

BACKGROUND

Brain tumors claimed the lives of 13,300 people in 1995. Our objective was to isolate and characterize unique tumor-suppressor genes from human brain tumors derived from patients in the United States.

METHODS

Differential display-polymerase chain reaction was used to isolate tumor suppressor genes.

RESULTS

Clone C4-2 was isolated and is expressed in normal adult human brain, but not in brain tissue from glioblastoma multiforme tumors. C4-2 has 66% homology to the previously isolated ARPP-16 (cAMP-regulated phosphoprotein of Mr = 16,000) based on limited sequencing. C4-2 is expressed at high levels in normal brain and is not expressed or expressed at low levels in several brain tumor cell lines. Expression of C4-2 was also either not expressed or expressed at low levels in meningioma, B-cell lymphoma, recurrent glioma, LNCAP (prostate tumor cell line), breast tumor, or prostate tumor tissue.

CONCLUSION

We conclude that C4-2 may function as a potential tumor-suppressor gene.