Dysregulation of GIMAP genes in non-small cell lung cancer.

The GIMAP (GTPase of the immunity-associated protein) gene family includes seven functional members residing on human chromosome 7. GIMAP genes encode GTP-binding proteins that share a unique primary structure and whose function is largely unknown. However, gene ablation studies reveal that Gimap4 plays an important role in regulating the apoptosis of T cells. In a pilot microarray analysis on six cases of non-small cell lung cancer (NSCLC), we discovered that the expression of GIMAP family members, but not the neighboring non-GIMAP genes, was uniformly lower in the tumor tissues, compared to that in the adjacent nontumor tissues. This finding was subsequently confirmed by quantitative PCR assays in a total of twenty NSCLCs, and we found that GIMAP6 and GIMAP8 showed striking reduction of gene expression in the tumors. In contrast, GIMAP8 mRNA level was abnormally elevated in the adjacent nontumor tissues as compared to that in the control lung tissues. Such reciprocal expression of GIMAPs suggests that this unique gene family might contribute to the pathogenesis of and immune reactions to NSCLC.

Distant HNF1 site as a master control for the human class I alcohol dehydrogenase gene expression.

Gene duplication and divergence have contributed to the biochemical diversity of the alcohol dehydrogenase (ADH) family. Class I ADH is the major enzyme that catalyzes alcohol to acetaldehyde in the liver. To investigate the mechanism(s) controlling tissue-specific and temporal regulation of the three human class I ADH genes (ADH1A, ADH1B, and ADH1C), we compared genomic sequences for the human and mouse ADH loci and analyzed human ADH gene expression in BAC transgenic mice carrying different lengths of the upstream sequences of the class I ADH. A conserved noncoding sequence, located between the class I and class IV ADH (ADH7) genes, was found to be essential for directing class I ADH gene expression in fetal and adult livers. Within this region, a 275-bp fragment displaying liver-specific DNase I hypersensitivity was bound by HNF1. The HNF1-containing upstream sequence enhanced all three class I ADH promoters in an orientation-dependent manner, and the transcriptional activation depended on binding to the HNF1 site. Deletion of the conserved HNF1 site in the BAC led to the shutdown of human class I ADH gene expression in the transgenic livers, leaving ADH1C gene expression in the stomach unchanged. Moreover, interaction between the upstream element and the class I ADH gene promoters was demonstrated by chromosome conformation capture, suggesting a DNA looping mechanism is involved in gene activation. Taken together, our data indicate that HNF1 binding, at approximately 51 kb upstream, plays a master role in controlling human class I ADH gene expression and may govern alcohol metabolism in the liver.

Type II collagen gene variants and inherited osteonecrosis of the femoral head.

BACKGROUND: Avascular necrosis of the femoral head (ANFH) causes disability that often requires surgical intervention. Most cases of ANFH are sporadic, but we identified three families in which there was autosomal dominant inheritance of the disease and mapped the chromosomal position of the gene to 12q13. METHODS: We carried out haplotype analysis in the families, selected candidate genes from the critical interval for ANFH on 12q13, and sequenced the promoter and exonic regions of the type II collagen gene (COL2A1) from persons with inherited and sporadic forms of ANFH. RESULTS: We identified a G-->A transition in exon 50 of COL2A1 in affected members of a four-generation family with ANFH. This transition predicts the replacement of glycine with serine at codon 1170 in a GXY repeat of type II collagen. Another pedigree was shown to harbor the same transition, but the mutant allele occurred on a different haplotype background. In a third family, a G-->A transition in exon 33 of the gene, causing a glycine-to-serine change at codon 717, was detected. No mutation was found in the COL2A1 coding region in sporadic cases of ANFH. CONCLUSIONS: All the patients with familial ANFH whom we studied carried COL2A1 mutations. In families with ANFH, haplotype and sequence analysis of the COL2A1 gene can be used to identify carriers of the mutant allele before the onset of clinical symptoms, allowing the initiation of measures that may delay progression of the disease.

Novel mutations involving the NF1 gene coding sequence in neurofibromatosis type 1 patients from Taiwan.

Neurofibromatosis type 1 (NF1) is a common cancer predisposition syndrome affecting the nervous system. The disease is one of the most common autosomal dominant diseases in all ethnic groups. Although the gene was mapped to human chromosome 17 and isolated in 1990, the detection of NF1 mutation is still considered to be a challenge as the gene is large and contains multiple exons. Here we report the detection of three genomic mutations in three Chinese patients living in Taiwan. A DNA diagnosis procedure was established to investigate the NF1 gene mutation at both the transcript and genomic DNA levels. Mutations causing transcript alteration were uncovered in three patients. In the first case, we detected a deletion involving exons 39-45 (nucleotide 7260-8167 in GenBank accession No. M89914). In the second case, a 2199-2448 deletion resulted in skipping of exon 13. The third case skipped the exon 3 in the mutant transcript. We further investigated what caused the cDNA deletion by PCR using genomic DNA as a template. In the first patient, we identified an approximately 17.5 kbp deletion in the NF1 gene. In the other two patients, we identified a single-base substitution (IVS13+1G>A) at the splicing donor site in the second case, and an IVS3+1G>T substitution in the third case. We conclude that genomic deletion and alteration of splicing signal caused abnormal transcripts and truncated proteins in the three Taiwanese NF1 cases.