Original article
Genomic assessments of the frequent loss of heterozygosity region on 8p21.3∼p22 in head and neck squamous cell carcinoma

https://doi.org/10.1016/j.cancergencyto.2007.04.003Get rights and content

Abstract

Most human cancers are characterized by genetic instabilities. Chromosomal aberrations include segments of allelic imbalance identifiable by loss of heterozygosity (LOH) at polymorphic loci, which may be used to implicate regions harboring tumor suppressor genes. Here we performed whole-genome LOH profiling on 41 human head and neck squamous cell carcinoma (HNSCC) cell lines. Several frequent LOH regions were identified on chromosomal arms 3p, 4p, 4q, 5q, 8p, 9p, 10p, 11q, and 17p. A genomic region of ∼7 Mb located at 8p21.3∼p22 exhibits the most frequent LOH (87.9%), which suggests that this region harbors one or more important tumor suppressor genes. Mitochondrial tumor suppressor gene 1 (MTUS1) is a recently identified candidate tumor suppressor gene that resides in this region. Consistent downregulation in expression was observed in HNSCC for MTUS1 as measured by real-time quantitative reverse transcriptase-polymerase chain reaction. Sequence analysis of MTUS1 gene in HNSCC revealed several important sequence variants in the exon regions of this gene. Thus, our results suggest that MTUS1 is one of the candidate tumor suppressor genes for HNSCC residing at 8p21.3∼p22. The identification of these candidate genes will facilitate the understanding of tumorigenesis of HNSCC.

Introduction

Squamous cell carcinoma (SCC) of the head and neck is one of the most common cancers. In the United States, there are >31,000 new cases of head and neck or oral squamous cell carcinoma (HNSCC or OSCC) each year [1]. HNSCC will cause >8,000 deaths, killing ∼1 person per hour. Worldwide, the problem is much worse, with >270,000 new cases diagnosed each year [2]. In some parts of the world, including Melanesia, France, and the Indian subcontinent, HNSCC is a major health problem [3]. The overall 5-year survival rates for HNSCC have remained at ∼50%, considerably lower than for cervical cancer, Hodgkin's disease, or cancer of the brain, liver, testes, kidney, or skin (malignant melanoma) [2].

Tobacco, alcohol, and viral infections are common risk factors for HNSCC [4], [5], as are genetic polymorphisms on genes that metabolize carcinogens. Several chromosome regions have been identified as frequently altered in HNSCC, including 3p, 4q, 5q21∼q22, 8p21∼p23, 9p21∼p22, 11q13, 11q23, 13q, 14q, 17p, 18q, and 22q [6]. Significant improvement of functional mapping is needed to move forward research, diagnosis, and treatment of HNSCC.

Most human cancers are characterized by genetic instabilities [7]. Chromosomal aberrations include segments of allelic imbalance identifiable by loss of heterozygosity (LOH) at polymorphic loci, and may be used to implicate regions harboring tumor suppressor genes [8], [9], [10]. LOH patterns can be generated through allelotyping using polymorphic microsatellite markers. Only a modest number of microsatellite makers can be screened, however, because of the limited number of available microsatellite markers, the tedious and labor-intensive procedure, and the need for large amounts of DNA. Recent advances in high-density single-nucleotide polymorphism (SNP) array platforms provide unique opportunities for generating high-resolution LOH profiles. Our previous studies demonstrated the feasibility of using the 10K SNP mapping array (Affymetrix, Santa Clara, CA) for genome-wide LOH profiling [11], [12], [13].

In the present study, we used SNP array-based LOH profiling on a large panel of HNSCC cell lines to narrow the frequent LOH region at 8p to a region of ∼7 Mb, located at 8p21.3∼p22. Mitochondrial tumor suppressor gene 1 (MTUS1) is one of the candidate genes that reside in this genomic region. MTUS1 was initially identified as a potential tumor suppressor gene in pancreatic cancer [14]. Our recent study suggested that the reduction of MTUS1 expression may be associated with advanced oral tongue SCC [15]. Reduced expression of MTUS1 has been observed also in colon cancer, ovarian cancer, and pancreatic cancer [14], [16], [17]. In the present study, our expressional and sequence analyses on MTUS1 gene provide additional evidence in support of MTUS1 as a tumor suppressor for HNSCC.

Section snippets

Materials and methods

The SNP array assay was performed as described previously [11], [12], [13]. In brief, the genomic DNAs were isolated from cultured cell lines using a genomic DNA isolation kit (Qiagen, Valencia, CA). (For description of the 41 HNSCC and 4 reference cell lines, see Supplementary Table 1, available at http://www.elsevier.com.)

Labeling, hybridization, washing, and staining of the 10K SNP mapping array was performed according to the standard single primer GeneChip mapping assay protocol

Results and discussion

The SNP array-based LOH profiling was performed on 41 HNSCC cell lines. As reference, LOH profiles were also obtained for 2 immortalized normal oral keratinocyte, 1 normal oral keratinocyte primary culture (NHOK) and 1 immortalized skin keratinocyte (HaCaT). Although minimum allelic imbalance was observed for the normal keratinocytes, several frequent LOH regions were identified for HNSCC cases (Table 1). Chromosome arms 3p, 4p, 4q, 5q, 8p, 9p, 10p, 11q, and 17p exhibit frequent LOH, which is

Acknowledgments

This work was supported in part by National Institutes of Health Public Health Service (NIH-PHS) grants K22 DE014847, R03 DE016569, R03 CA114688 (to X.Z.), and R01 DE015970 (to D.T.W.). The 10K SNP mapping array hybridization and scanning were performed at the University of California Los Angeles (UCLA) DNA microarray facility. The sequence analyses performed at the University of Illinois at Chicago (UIC) Research Resource Center, DNA service facility. The primary NHOK cell and the 183 and 1483

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