Prognostic value of DNA alterations on chromosome 17p13.2 for intrahepatic cholangiocarcinoma

Pan-cancer driver copy number alterations identified by joint expression/CNA data analysis

Analysis of large gene expression datasets from biopsies of cancer patients can identify co-expression signatures representing particular biomolecular events in cancer. Some of these signatures involve genomically co-localized genes resulting from the presence of copy number alterations (CNAs), for which analysis of the expression of the underlying genes provides valuable information about their combined role as oncogenes or tumor suppressor genes. Here we focus on the discovery and interpretation of such signatures that are present in multiple cancer types due to driver amplifications and deletions in particular regions of the genome after doing a comprehensive analysis combining both gene expression and CNA data from The Cancer Genome Atlas.

Arrestins as regulatory hubs in cancer signalling pathways

Non-visual arrestins were initially appreciated for the roles they play in the negative regulation of G protein-coupled receptors through the processes of desensitisation and endocytosis. The arrestins are also now known as protein scaffolding platforms that act downstream of multiple types of receptors, ensuring relevant transmission of information for an appropriate cellular response. They function as regulatory hubs in several important signalling pathways that are often dysregulated in human cancers. Interestingly, several recent studies have documented changes in expression and localisation of arrestins that occur during cancer progression and that correlate with clinical outcome. Here, we discuss these advances and how changes in expression/localisation may affect functional outputs of arrestins in cancer biology.

An extended fluorescence in situ hybridization approach for the cytogenetic study of cholangiocarcinoma on endoscopic retrograde cholangiopancreatography brushing cytology preparations

The cytological diagnosis of cholangiocarcinoma has been significantly aided by applying a 4-probe fluorescence in situ hybridization system on endoscopic retrograde cholangiopancreatography brushing smears, aiming mainly at the detection of hyperdiploidy. However, this approach adds little to our understanding of the genetic background of the disease. With the prospect of obtaining additional data on chromosomal aberrations, we have extended the fluorescence in situ hybridization study, with the application of 4 independent 2-probe systems in 35 patients with documented cholangiocarcinoma. Fluorescence in situ hybridization assays were performed on endoscopic retrograde cholangiopancreatography brushing smears, with probes for the 7q31, 11q13 (CCND1), 17p53 (TP53), and 9p21 (INK4 locus) bands, together with the respective centromeric probe. Hyperdiploidy, involving at least 2 of the 4 chromosomes targeted, was found in 31 patients. 17p13 deletion was detected in 3, and 9p21 deletion, in 5 of the hyperdiploid cases, with the 2 aberrations concurrent in 1. CCND1 amplification was found in 1 case as the sole abnormality and in another together with hyperdiploidy, but in apparently unrelated clones. This work indicates that interphase fluorescence in situ hybridization is a practical and useful tool for the cytogenetic study of cholangiocarcinoma on endoscopic retrograde cholangiopancreatography brushing smears, which is often the only available tissue specimen of the tumor. Apart from hyperdiploidy, it provides additional data on the genetic profile of cholangiocarcinoma, especially regarding structural chromosomal aberrations and clonal diversity. This line of investigation may prove useful in the delineation of oncogenesis and the interpretation of the diverse clinical features of the disease.

Modern diagnostic approaches to cholangiocarcinoma

BACKGROUND

Cholangiocarcinoma is a very aggressive tumor with poor survival. Therefore, early diagnosis and surgical resection are of paramount importance. Its diagnosis is difficult because access to the tumor is not easy. Biopsy is possible only for intrahepatic cholangiocarcinoma, which accounts for 10% of cases. Routine brush cytology from endoscopic retrograde cholangiopancreatography (ERCP) has a high specificity of 100% but unfortunately a low sensitivity of 30%. In this review we briefly describe new diagnostic techniques applicable to ERCP brush cytology specimens and targeting the genetic background of the disease, in particular fluorescence in situ hybridization (FISH) and digital image analysis (DIA).

DATA SOURCES

The PubMed database up to 2011 was used for the retrieval of relevant articles. The search terms FISH, fluorescence in situ hybridization, DIA, digital image analysis and cholangiocarcinoma were used. Both original and review articles were used.

RESULTS

FISH identifies cells with chromosomal abnormalities, mainly numerical aberrations, using a mixture of fluorescence-labeled probes. FISH offers a higher sensitivity than routine cytology, retaining a high level of specificity. The DIA criterion for malignancy is demonstration of aneuploidy. This technique increases the sensitivity to 40%, but the specificity remains low. Preliminary data from application to other tumors suggest that combination of FISH and DIA may be of further benefit.

CONCLUSIONS

The new techniques offer a significantly enhanced diagnostic efficacy in the evaluation of ERCP brush specimens. Apart from contributing to a more timely diagnosis, their wider application to cholangiocarcinoma may also facilitate the genetic study of the disease and add to our understanding of oncogenesis at the molecular level, with the prospect of identifying targets for novel therapeutic interventions.

Allelic loss on chromosome 5q34 is associated with poor prognosis in hepatocellular carcinoma

PURPOSE

To identify and characterize novel genetic alterations in hepatocellular carcinoma (HCC).

METHODS

DNA was extracted from 29 HCC and corresponding normal tissues and amplified with 59 different 10-base arbitrary primers. A 550 bp DNA fragment amplified using primer Q-9 and which was present in 19 of 29 cases (66%) was cloned, sequenced, and compared with known nucleotide sequences deposited in Genome database, and quantified by real-time PCR.

RESULTS

DNA alterations were found on chromosomes 5q34, 6p25.2 and 8q12.1 in 11 of 29 cases (38%), 7 of 29 cases (24%), and 12 of 29 cases (41%), respectively. Multivariate analysis showed that the allelic loss on chromosome 5q34 was an independent prognostic factor for poor survival of HCC patients, with the median survival time of 19 weeks for allelic loss versus 109 weeks for no allelic loss (P = 0.001).

CONCLUSIONS

This study indicates that allelic loss on chromosome 5q34 may be involved in the development of HCC and could be used as a prognostic indicator in HCC patients.