Cancer Genetics and Cytogenetics最新文献

Amplification of the two oncogenes ERBB2 and MYC and deletion of the tumor suppressor gene TP53 are frequently encountered in cancerous tissues. The purpose of this study was to use the fluorescence in situ hybridization (FISH) technique for the assessment of ERBB2 and MYC amplification and TP53 deletion, and to relate these molecular markers to clinical and pathologic factors in Saudi patients with hepatocellular carcinoma. The study was conducted on 40 paraffin-embedded tissue samples originally taken from either hepatitis C virus (HCV)- or HBV-infected patients using the FISH technique. The level of ERBB2, MYC, and TP53 in the malignant group was significantly increased as compared to the control group. Of the 40 patients, 3 (7.5%) had amplification of ERBB2 gene, 4 (10%) different patients had amplification of MYC, and 26 patients (65%) had evidence of deletion of at least one allele on chromosome 17 for the TP53 gene in a high proportion of cells. There was a significant correlation between amplification of MYC oncogene and the number of tumor masses. Moreover, significant correlation was observed between poorly differentiated tumors when compared with moderate or well-differentiated tumors when MYC was analyzed. On the other hand, MYC failed to reveal any significant association between oncogene amplification and other clinicopathologic variables examined. Univariate analysis revealed a strong association between deletion of TP53 and multiple tumor mass (P< 0.001). No statistical correlation could be detected between deletion of TP53 and tumor size, grade, stage, and tumor differentiation. No significant difference could be detected in the mean survival time of patients positive for the alteration of the genes compared to the patients who showed no alterations for the same genes. However, when the stage of the tumor was analyzed, there was a significant difference in the mean survival time between patients who showed gene alterations compared to patients with no changes in the studied genes. When overall survival was analyzed, only patients with MYC amplification had a lower median survival (20.75 months) than patients without MYC amplification (35.82, P=0.009). Genetic alterations of ERBB2 and TP53 genes had no effect on survival 2 (see Results). The combination of ERBB2, MYC, and TP53 could be useful markers to stratify patients into different risk groups.

For most cases of colorectal cancer that arise without a family history of the disease, it is proposed that an appreciable heritable component of predisposition is the result of contributions from many loci. Although progress has been made in identifying single nucleotide variants associated with colorectal cancer risk, the involvement of low-penetrance copy number variants is relatively unexplored. We have used multiplex amplifiable probe hybridization (MAPH) in a fourfold multiplex (QuadMAPH), positioned at an average resolution of one probe per 2 kb, to screen a total of 1.56 Mb of genomic DNA for copy number variants around the genes APC, AXIN1, BRCA1, BRCA2, CTNNB1, HRAS, MLH1, MSH2, and TP53. Two deletion events were detected, one upstream of MLH1 in a control individual and the other in APC in a colorectal cancer patient, but these do not seem to correspond to copy number polymorphisms with measurably high population frequencies. In summary, by means of our QuadMAPH assay, copy number measurement data were of sufficient resolution and accuracy to detect any copy number variants with high probability. However, this study has demonstrated a very low incidence of deletion and duplication variants within intronic and flanking regions of these nine genes, in both control individuals and colorectal cancer patients.

Although aneuploidy has many possible causes, it often results from underlying chromosomal instability (CIN) leading to an unstable karyotype with cell-to-cell variation and multiple subclones. To test for the presence of CIN in high hyperdiploid acute lymphoblastic leukemia (HeH ALL) at diagnosis, we investigated 20 patients (10 HeH ALL and 10 non-HeH ALL), using automated four-color interphase fluorescence in situ hybridization (I-FISH) with centromeric probes for chromosomes 4, 6, 10, and 17. In HeH ALL, the proportion of abnormal cells ranged from 36.3% to 92.4%, and a variety of aneuploid populations were identified. Compared with conventional cytogenetics, I-FISH revealed numerous additional clones, some of them very small. To investigate the nature and origin of this clonal heterogeneity, we determined average numerical CIN values for all four chromosomes together and for each chromosome and patient group. The CIN values in HeH ALL were relatively high (range, 22.2–44.7%), compared with those in non-HeH ALL (3.2–6.4%), thus accounting for the presence of numerical CIN in HeH ALL at diagnosis. We conclude that numerical CIN may be at the origin of the high level of clonal heterogeneity revealed by I-FISH in HeH ALL at presentation, which would corroborate the potential role of CIN in tumor pathogenesis.

Carbohydrate N-acetylgalactosamine 4-0 sulfotransferase 9 (CHST9) belongs to the N-acetylgalactosamine 4-sulfotransferase (GalNAc4ST) family. A recent array-based study implicated the presence of copy-number variations (CNV) of the region encompassing CHST9 in the genomes of acute myelogenous leukemia. Most of the current studies, however, focused on the genome-wide screening of CNV, and the functional impact of such regions needs to be extensively investigated in large amounts of clinical samples. In our study, we collected 617 bone marrow samples from multi-types of hematologic malignancies, as well as healthy controls, and detected the CNV of CHST9 by real-time polymerase chain reaction (PCR). We found significant association between the CNV of CHST9 and these hematologic malignancies including acute lymphoblastic leukemia, acute myelogenous leukemia, chronic lymphocytic leukemia, chronic myelogenous leukemia, multiple myeloma, and myelodysplastic syndrome. We also examined CHST9 mRNA expression in the samples with one or two copies of DNA, and observed a weak yet positive correlation between the relative expression level and gene dosage. In general, the CNV of CHST9 have been shown to associate with hematologic malignancies. The functional consequences of CNV, however, need to be investigated extensively in the future.

Plexiform (multinodular) cellular schwannomas are rare tumors, not associated with neurofibromatosis type 1, that occur more often in children and can be congenital. Their biology is benign and is characterized by the tendency to recur locally without being metastatic. Cytogenetic studies in adult cases of schwannoma indicate a complete or partial loss of chromosome 22 as the most common abnormality. Only two cytogenetic studies describe cases in children, one of which concerned a congenital cellular plexiform schwannoma. Here, we report the cytogenetic analysis of a second case in an 8-month-old boy with recurrence of trisomy 17.

Most basal-like breast carcinomas are estrogen receptor negative, progesterone receptor negative, and cerb-B2/HER-2/neu negative—the so-called triple-negative breast carcinomas—with high epidermal growth factor receptor (EGFR) expression, which makes EGFR a target of treatment. We evaluated EGFR expression by immunohistochemistry (IHC) with two different clones (EGFR.31G7 and EGFR.25) and gene copy number by fluorescence in situ hybridization (FISH) with Locus specific identifier EGFR/CEP 7 dual probe in 62 triple-negative breast carcinomas. Any complete or incomplete membranous and/or cytoplasmic expression was regarded as IHC positive. Cases showing gene amplification (a ratio of EGFR gene to chromosome 7 of ≥2 or 15 copies per cell in ≥10% of cells) and high polysomy (≥4 copies in ≥40% of cells) were considered FISH positive. We detected EGFR.31G7 positivity in 38 of 62 cases (61.4%), which was composed of 12 of 62 (19.4%) cytoplasmic, 14 of 62 (22.6%) incomplete membranous, and 12 of 62 (19.4%) complete membranous staining. Among 38 of 49 (77.6%) EGFR.25-positive cases, 7 of 49 (14.3%) exhibited cytoplasmic, 10 of 49 (20.4%) exhibited incomplete membranous, and 21 of 49 (42.9%) exhibited complete membranous staining pattern. Ten of 62 (16.1%) FISH-positive cases were identified; 1 of 62 (1.6%) showed amplification, and the rest showed high polysomy. All FISH-positive cases were also found to be IHC positive (P = 0.01) by both EGFR clones. The amplified case displayed strong complete membranous staining with both clones. Among the high polysomic cases; 4 of 9 (44.4%) incomplete membranous, 4 of 9 (44.4%) complete membranous and 1 of 9 (11.1%) cytoplasmic expression of EGFR.31G7, and 6 of 8 (75%) complete membranous and 2 of 6 (25%) cytoplasmic expression of EGFR.25 were detected. Here, we report that membranous EGFR expression is associated with increased gene copy number (P = 0.035 for EGFR.31G7 and P = 0.026 for EGFR.25 clone). Because the markers to predict anti-EGFR treatment response in other system tumors such as EGFR mutation and amplification seem to be rare events in breast cancer, membranous staining pattern of EGFR might be the best way to decide the patient eligibility for anti-EGFR therapy.

To understand the influence of chromosomal alterations on gene expression in a genome-wide view, chromosomal imbalances detected by single nucleotide polymorphism (SNP) chips were compared with global gene expression in 16 cases of chronic lymphocytic leukemia (CLL). A strong concordance between chromosomal gain or loss and increased or reduced expression of genes in the affected regions was found, respectively. Regions of uniparental disomy (UPD) were rare and had usually no consistent influence on gene expression, but in one instance, a large UPD was associated with a downregulation of most genes in the affected chromosome. The frequently deleted miRNAs, MIRN15A and MIRN16-1, did not show a reduced expression in cases with monoallelic deletions. The BCL2 protein, considered to be downregulated by these miRNAs, was upregulated not only in CLL with biallelic deletion of MIRN15A and MIRN16-1, but also in cases with monoallelic deletion. This suggests a complex regulation of BCL2 levels in CLL cells. Taken together, in CLL, a global gene dosage effect exists for chromosomal gains and deletions and in some instances for UPDs. We did not confirm a consistent correlation between MIRN15A and MIRN16-1 expression levels and BCL2 protein levels, indicating a complex regulation of BCL2 expression.

Nasopharyngeal carcinoma (NPC) is one of the most common cancers in Malaysia, mainly occurring among the Chinese population. To detect common genetic alterations in NPC, we screened seven cases of NPC using the comparative genomic hybridization (CGH) technique. Before proceeding to the CGH technique, the tumors were first confirmed to consist of 75% tumor cells or more. In brief, the technique consists of binding tumor DNA with normal DNA and human Cot-1 DNA, which is then hybridized to normal metaphase spreads. The slides were then counterstained with 4,6 diamino-2-phenylindole (DAPI II) for detection. Analyses were performed using CGH software (Cytovision). We found genetic alterations in all seven NPC samples. The common chromosomal gains (57%, four cases) were found on chromosome arms 1q, 4p, 5, 7q, 11, 14p, 15q, 18p, and 21p, and common chromosomal losses (43%, three cases) were found on chromosome arm 16p. Our results showed chromosomal alterations in all seven NPC cases in the Malaysian population. This result provides the platform for further investigations to locate tumor suppressor genes and oncogenes at specific chromosomal regions in Malaysian NPC patients.