Integrative genomic approaches in cervical cancer: implications for molecular pathogenesis

Cervical cancer (CC) as a single diagnostic entity exhibits differences in clinical behavior and poor outcomes in response to therapy in advanced tumors. Although infection of high-risk human papillomavirus is recognized as an important initiating event in cervical tumorigenesis, stratification of CC into subclasses for progression and response to treatment remains elusive. Existing knowledge of genetic, epigenetic and transcriptional alterations is inadequate in addressing the issues of diagnosis, progression and response to treatment. Recent technological advances in high-throughput genomics and the application of integrative approaches have greatly accelerated gene discovery, facilitating the identification of molecular targets. In this article, we discuss the results obtained by preliminary integrative analysis of DNA copy number increases and gene expression, utilizing the two most common copy number-gained regions of 5p and 20q in identifying gene targets in CC. These analyses provide insights into the roles of genes such as RNASEN, POLS and SKP2 on 5p, KIF3B, RALY and E2F1 at 20q11.2 and CSE1L, ZNF313 and B4GALT5 at 20q13.13. Future integrative applications using additional datasets, such as mutations, DNA methylation and clinical outcomes, will raise the promise of accomplishing the identification of biological pathways and molecular targets for therapies for patients with CC

Re: Detection of Hypermethylated Genes in Women With and Without Cervical Neoplasia

Feng et al. (1) examined whether changes in DNA methylation of 20 genes, selected on the basis of their role in cervical cancer, could be used as markers of cervical intraepithelial neoplasia (CIN) and invasive cervical cancer (ICC). The authors found varying frequencies of promoter hypermethylation in these 20 genes in 319 exfoliated cell samples and matched tissue biopsy specimens. For four of these genes (DAPK1, RARB, TWIST1, and CDH13), increasing frequency of hypermethylation was statistically significantly associated with increasing severity of disease. The estimated specificity of the three-gene panel (DAPK, RARB, and TWIST1) was 95%, which is higher than specificities reported for cytology and human papillomavirus (HPV) testing. Although the study was well designed and a molecular genetic test with high specificity such as this one is needed, some of the findings are inconsistent with previously reported results and the conclusions may therefore not be valid

Molecular Cytogenetic Applications in Analysis of the Cancer Genome

Cancer cells exhibit nonrandom and complex chromosome abnormalities. The role of genomic changes in cancer is well established. However, the identification of complex and cryptic chromosomal changes is beyond the resolution of conventional banding methods. The fluorescence microscopy afforded by imaging technologies, developed recently, facilitates a precise identification of these chromosome alterations in cancer. The three most commonly utilized molecular cytogenetics methods comparative genomic hybridization, spectral karyotype, and fluorescence in situ hybridization, that have already become benchmark tools in cancer cytogenetics, are described in this chapter. Comparative genomic hybridization is a powerful tool for screening copy-number changes in tumor genomes without the need for preparation of metaphases from tumor cells. Multicolor spectral karyotype permits visualization of all chromosomes in one experiment permitting identification of precise chromosomal changes on metaphases derived from tumor cells. The uses of fluorescence in situ hybridization are diverse, including mapping of alteration in single copy genes, chromosomal regions, or entire chromosomes. The opportunities to detect genetic alterations in cancer cells continue to evolve with the use of these methodologies both in diagnosis and research

PCDH10, a novel p53 transcriptional target in regulating cell migration

Cell cycle arrest, senescence and apoptosis are commonly regarded as the major tumor suppression mechanisms of p53. However, accumulating evidence indicates that loss of these canonical functions is not sufficient for tumor formation, highlighting the complexity of p53-mediated tumor suppression. PCDH10 belongs to a proto cadherin protein family and is a potential tumor suppressor protein as the dysregulation of PCDH10 gene frequently existed in multiple human tumors. Here, we found that PCDH10 is a transcriptional target of p53 and that the levels of PCDH10 expression can be induced by wild type p53 but not mutant p53 in a number of human cancer cell lines. Moreover, we identified a p53 consensus binding site located in the PCDH10 promoter region that is responsive to p53 regulation. Although upregulation of PCDH10 has no obvious effect on growth arrest or apoptosis in human cells, PCDH10 exhibits inhibitory roles in cancer cell motility and cell migration. These results suggest an important role of p53 in regulating tumor cell migration through activating PCDH10 expression and support the notion that non-canonical activities of p53 may contribute to its tumor suppressor function in vivo

MLL/KMT2A translocations in diffuse large B-cell lymphomas

Translocations of the histone-lysine N-methyltransferase 2A (KMT2A) gene, formerly known as myeloid lymphoid leukemia/mixed-lineage leukemia gene, are commonly associated with high-risk de novo or therapy-associated B-cell and T-cell lymphoblastic leukemias and myeloid neoplasms. Rare B-cell non-Hodgkin lymphomas harboring KMT2A translocations have been reported, but information regarding the clinical behavior of such cases is limited. Here, we describe two extranodal diffuse large B-cell lymphomas (DLBCLs): a primary thyroid DLBCL and a large cell transformation of a splenic marginal zone lymphoma, which displayed complex karyotypes and translocations involving chromosome 11q23 targeting the KMT2A gene. The pathological and clinical characteristics of these cases are discussed in the context of previously reported lymphomas associated with different types of KMT2A genetic aberrations. In contrast to the poor clinical outcomes of patients with acute leukemias and myeloid neoplasms associated with KMT2A translocations, patients with B-cell non-Hodgkin lymphomas, exhibiting similar translocations, appear to respond well to immunochemotherapy. Our findings add to the growing list of histone methyltransferase genes deregulated in DLBCL and highlight the diversity of mechanisms, altering the function of epigenetic modifier genes in lymphomas

Unbalanced t(2;19) and t(2;16) in a neurofibroma

Neurofibromas are a benign heterogeneous group of tumors arising from peripheral nerve sheaths; they consist of a mixture of Schwann cells, fibroblasts, perineural cells, neuronal processes, and mast cells. Neurofibromas may present as dermal (cutaneous or subcutaneous) or plexiform (diffuse growths, spinal tumors, nodular or diffuse) tumors. They may present as isolated sporadic tumors in the general population or occur as a part of an autosomal dominant tumor diathesis in von Recklinghausen neurofibromatosis type 1 (NF1)

Variant translocation with a deletion of derivative (9q) in a case of Philadelphia chromosome positive (Ph +) essential thrombocythemia (ET), a variant of Chronic Myelogenous Leukemia (CML) with a poor prognosis

Patients presenting with thrombocytosis require thorough clinical and laboratory evaluation to determine whether they suffer from essential thrombocythemia or another myeloproliferative disorder. This distinction becomes increasingly relevant as targeted agents become available to treat specific myeloproliferative diseases. Cytogenetic testing plays a major role in this analysis. This study presents a patient with Philadelphia chromosome positive (Ph+) thrombocytosis and a cryptic der(9q)t(5;9)t(9;22) not found by conventional cytogenetics, whose disease progressed within 2 years to typical myeloblastic crisis of CML. It discusses the entity of Ph + ET, the utility of molecular cytogenetic testing in the diagnosis of this unusual disease entity and the importance of cytogenetic testing in the prognosis of ET

Double-minute chromosomes in the leukocytes of a patient with a previous history of cervical carcinoma

Double-minute chromosomes (DMs) were observed in repeated samples in the leukocytes of a patient with a previous history of cervical carcinoma. The most interesting cytogenetic finding was the coexistence of DMs and a dicentric chromosome along with chromosome- and chromatid-type breaks and gaps. This observation suggests that DMs might originate through the breakage of existing chromosomes. The presence of DMs in leukocytes may also indicate the possibility that certain common agents cause DMs in tumor cells as well as in normal cells

Assignment of the Human TYRP (brown) Locus to Chromosome Region 9p23 by Nonradioactive in Situ Hybridization

The TYRP (brown) locus determines pigmentation and coat color in the mouse. The human homolog of the TYRP locus has been recently identified and shown to encode a 75-KDA transmembrane melanosomal glycoprotein called gp75. The gp 75 glycoprotein is homologous to tyrosinase, an enzyme in evolved in the synthesis of melanin, forming a family of tyrosinase-related proteins. A genomic clone of human gp75 was used to map the human TYRP locus to chromosome 9, region 9p23, by nonradioactive fluorescent in situ hybridization. Specificity of hybridization was tested with a genomic fragment of hu- man tyrosinase that mapped to a distinct site on 1lq2 1. The 9p region has been reported to be nonrandomly altered in human melanoma, suggesting a role for the region near the TYRP locus in melanocyte transformation

Mapping common deleted regions on 5p15 in cervical carcinoma and their occurrence in precancerous lesions

BACKGROUND: Previous studies have shown that the short arm of chromosome 5 (5p) exhibit frequent genetic changes in invasive cervical carcinoma (CC), and that these changes arise early during the carcinogenesis, in precancerous lesions. These data therefore suggest that loss of candidate tumor suppressor genes located on 5p is associated with the development of CC. However, the precise location of 5p deletions is not known. RESULTS: We performed a detailed deletion mapping of 5p in 60 cases of invasive CC. We found that 60% of the tumors exhibit a 5p loss of heterozygosity (LOH). The patterns of LOH allowed us to identify two minimal regions of deletions, one at 5p15.3 spanning a 5.5 cM genetic distance and a second site of 7 cM at 5p15.2-15.3. In addition, we also identified 5p deletions in 16% lesions of high-grade cervical intraepithelial neoplasia (CIN). 5p LOH was found in 63% of HPV 16 positive tumors, while only 33% tumors with other HPV-types had 5p LOH. The differences in frequency of 5p LOH between tumors harboring HPV16 in combination with other HPV types and tumors harboring HPV16 DNA alone were significantly higher, suggesting a synergistic effect of high-risk types in causing genomic instability. CONCLUSION: These findings implicate the presence of tumor suppressor gene(s) on 5p relevant to CC tumorigenesis