Expression of CD44 splice variants in colorectal cancer

Identification of novel alternative splicing isoform biomarkers and their association with overall survival in colorectal cancer

BACKGROUND

Alternative splicing (AS) is an important mechanism of regulating eukaryotic gene expression. Understanding the most common AS events in colorectal cancer (CRC) will help developing diagnostic, prognostic or therapeutic tools in CRC.

METHODS

Publicly available RNA-seq data of 28 pairs of CRC and normal tissues and 18 pairs of metastatic and normal tissues were used to identify AS events using PSI and DEXSeq methods.

RESULT

The highly significant splicing events were used to search a database of The Cancer Genome Atlas (TCGA). We identified AS events in 9 genes in CRC (more inclusion of CLK1-E4, COL6A3-E6, CD44v8-10, alternative first exon regulation of ARHGEF9, CHEK1, HKDC1 and HNF4A) or metastasis (decrease of SERPINA1-E1a, CALD-E5b, E6). Except for CHEK1, all other 8 splicing events were confirmed by TCGA data with 382 CRC tumors and 51 normal controls. The combination of three splicing events was used to build a logistic regression model that can predict sample type (CRC or normal) with near perfect performance (AUC = 1). Two splicing events (COL6A3 and HKDC1) were found to be significantly associated with patient overall survival. The AS features of the 9 genes are highly consistent with previous reports and/or relevant to cancer biology.

CONCLUSIONS

The significant association of higher expression of the COL6A3 E5-E6 junction and HKDC1 E1-E2 with better overall survival was firstly reported. This study might be of significant value in the future biomarker, prognosis marker and therapeutics development of CRC.

Demonstration of a melanoma-specific CD44 alternative splicing pattern that remains qualitatively stable, but shows quantitative changes during tumour progression

The role of CD44 in the progression of human melanoma has mostly been characterised by qualitative changes in expression of its individual variable exons. These exons however, may be expressed to form a number of molecules, the alternative splice variants of CD44, which may be structurally and functionally different. Using real-time PCR measurements with variable exon specific primers we have determined that all are expressed in human melanoma. To permit comparison between different tumours we identified a stable CD44 variable exon (CD44v) expression pattern, or CD44 ‘fingerprint’. This was found to remain unchanged in melanoma cell lines cultured in different matrix environments. To evaluate evolution of this fingerprint during tumour progression we established a scid mouse model, in which the pure expression pattern of metastatic primary tumours, circulating cells and metastases, non-metastatic primary tumours and lung colonies could be studied. Our analyses demonstrated, that although the melanoma CD44 fingerprint is qualitatively stable, quantitative changes are observed suggesting a possible role in tumour progression.

Pathobiology of colorectal cancer hepatic metastases with an emphasis on prognostic factors

Colorectal cancer is the second leading cause of cancer related death in the United States. The majority of these deaths are due to metastasis, with the liver easily accounting as the most common site of deposit. While there are multiple steps in the CRC hepatic metastatic cascade, this review attempts to summarize the different processes involved, focusing on the most recent discoveries, as well as the associated effects in relation to prognosis.

Gene expression changes reveal patterns of aging in the rat digestive tract

Similarly to other organs, the human digestive system is adversely affected by aging presenting physiologic manifestations that include compromised absorption and secretion, decreased motility, weakened mucosal barrier and as well as a high incidence of colon cancer. As biomedical advances enable the population to live longer, our understanding of molecular events that govern aging and disease states is enhanced through methodical analyses of temporal tissue-specific gene expression profiles. Recently, DNA microarray analyses have been employed to examine age-associated transcriptional profiles in the mammalian digestive tract. Gene expression patterns revealed that the magnitude and trend of age-associated changes differ in the rat colon and duodenum. Interestingly, the expression of genes involved in energy-generating metabolic pathways was decreased in the duodenum and increased in the colon. Microarray analyses detected modulations in expression of genes associated with compromised intestinal function and propensity for colon cancer in the aged population. Furthermore, altered expression was observed for certain genes implicated in governance of aging and lifespan in other organisms suggesting intriguing commonalities across species. Thus, these studies demonstrated feasibility and usefulness of DNA microarrays for identifying pathways involved in the molecular pathophysiology of the aging process and lifespan control in complex organisms.

Levels of v5 and v6 CD44 splice variants in serum of patients with colorectal cancer are not correlated with pT stage, histopathological grade of malignancy and clinical features

AIM: This study was designed to compare the levels of v5 and v6 splice variants of CD44 evaluated using ELISA test in the serum of patients with colorectal cancer in different stages of progression of the disease estimated in pT stage according to WHO score, histopathological grade of malignancy and some clinicopathological features.

METHODS: The serum obtained from 114 persons with colorectal adenocarcinomas was examined using ELISA method. pT stage and grade of malignancy of the tumour were examined in formalin fixed and paraffin embedded materials obtained during operation.

RESULTS: Only the level of CD44 v5 in the serum of patients before operation with G2 pT4 tumour was lower than that in other probes and the difference was statistically significant. We did not find any other correlations between the level of v5 and v6 CD44 variants and other evaluated parameters.

CONCLUSION: The level of CD44 v5 and v6 estimated by ELISA test in the serum can not be used as a prognostic factor in colorectal cancer.

Expression of CD44 variants in colorectal carcinoma quantified by real-time reverse transcriptase-polymerase chain reaction

CD44 is a family of transmembrane glycoproteins that has been linked to carcinogenesis and metastasis. It serves as a major receptor for hyaluronate. The v3 isoform binds to growth factors through heparan sulfate side chains and targets these factors to their high-affinity signal transducing receptors. The purpose of this study was to analyze the expression of CD44 v3 and v4 in human colorectal carcinoma with real-time reverse transcriptase-polymerase chain reaction (RT-PCR). Our results show that 19 of 56 cases (33.9%) showed a greater than 2-fold increase in CD44 v3 expression in tumors as compared with matched normal mucosa, while 15 of 44 cases (34.1%) showed a greater than 2-fold increase in CD44 v4 expression. There was a marked variation in fold-differences of CD44 gene expression between tumor and normal samples (T/N ratios) among the tumors. This prompted us to correlate the T/N ratios of the tumors with clinicopathologic characteristics. Interestingly, overexpression of CD44 v3 mRNA was associated with the presence of vascular invasion (P <.05). Similarly, overexpression of CD44 v4 was significantly correlated to increased depth of invasion (P <.05). Results from the present study suggest that overexpression of CD44 v3 and v4 mRNA levels may be useful clinical markers for colorectal carcinoma invasiveness.

Age-associated changes in gene expression patterns in the duodenum and colon of rats

In humans, decreased intestinal motility, compromised nutritional status and increased risk of colon cancer are commonly associated with aging. Here, we used the cDNA microarray analysis to detect age-associated changes in duodenal and colonic gene expression in male Fischer 344 rats. The primary finding of this study is that the magnitude and direction of age-associated changes in gene expression differs in the colon and duodenum. In the colon, 56 genes showed altered expression, whereas expression of only 25 genes was altered in the duodenum. The magnitude of change was greater in the colon than in the duodenum. The direction of change also differed; in the aged colon, expression of 51 genes increased and only five genes decreased. In contrast, in the aged duodenum, only seven genes increased, whereas 18 genes decreased in expression. In the duodenum of aged rats, expression of genes involved in ATP-generating pathways is decreased. In contrast, in the colon of aged rats, expression of genes involved in energy generating pathways and in lipid oxidation is increased. In addition, in the aging colon, an increased expression of genes that show an aberrant regulation in colon cancer, including CD44, ras, and maspin is observed. Collectively, these findings provide clues to molecular events that may be related to compromised intestinal function and the high incidence of colon cancer in the aged population.

Molecular characterization of minimal residual cancer cells in patients with solid tumors

The failure to reduce the mortality of patients with solid tumors is mainly a result of the early dissemination of cancer cells to secondary sites, which is usually missed by conventional diagnostic procedures used for tumor staging. PCR was shown to be superior to conventional techniques in detecting circulating tumor cells and micrometastases allowing the identification of one tumor cell in up to 10(7) normal cells in various sources such as blood, bone marrow, lymph nodes, urine or stool. The methods used are based on the detection of either genomic alterations in oncogenes and tumor suppressor genes or on the mRNA expression of tissue-specific and tumor-associated genes. The additional implementation of techniques for cancer cell purification had a significant impact on analytical sensitivity and specificity of MRCC detection. For patients with e.g. melanoma, breast, colorectal or prostate cancer it was demonstrated that the presence of disseminated cancer cells defines a subgroup of patients with reduced time to recurrence. The possibility to use easily accessible body fluids as a source for MRCC detection enables longitudinal observations of the disease. In this review we discuss the potential of molecular characterization of MRCC as a tool to improve prognostication, therapy selection and drug targeting as well as therapy monitoring.

Molecular detection of cancer cells by competitive reverse transcription-polymerase chain reaction analysis of specific CD44 variant RNAs

BACKGROUND

CD44 is a cell surface glycoprotein implicated in such diverse biologic processes as lymphocyte activation and homing, extracellular matrix adhesion, and cellular migration. Primary transcripts of the CD44 gene can be alternatively spliced to produce a variety of messenger RNA (mRNA) species. The standard form of CD44 mRNA contains sequences from at least 20 genomic exons; variant mRNAs contain sequences from one or more additional exons (v1-10). Predominant expression of a specific CD44 variant, i.e., CD44v8-10, in several human carcinomas has been described previously. In this study, we developed a novel molecular approach for detecting cancer cells that overexpress CD44v8-10 mRNA.

METHODS

After finding that CD44v8-10 was predominantly expressed in non-small-cell lung and bladder carcinomas and that CD44v10 was predominantly expressed in leukocytes, we developed a competitive reverse transcription-polymerase chain reaction assay (CC-RT-PCR) that allows quantification of the relative expression of these two mRNA species in clinical specimens (i.e., determination of a v8-10/v10 ratio). CC-RT-PCR analysis was applied to pleural effusion specimens from patients with benign or malignant lung diseases as well as to spontaneously voided urine samples from patients with benign or malignant urologic diseases.

RESULTS

Fifty two of 54 samples from patients with benign diseases expressed CD44v10 predominantly (v8-10/v10 ratio < or = 0.65), whereas 46 of 61 samples from patients with malignant diseases expressed CD44v8-10 predominantly (v8-10/v10 ratio > 1.00) (two-sided P < .001). CC-RT-PCR detected predominant expression of CD44v8-10 in cytologically negative samples from 11 patients who were later diagnosed with malignant disease.

CONCLUSIONS

CC-RT-PCR analysis of CD44v8-10 expression could be an important adjunct to cytologic examination in cancer diagnosis, especially in detecting exfoliated cancer cells in pleural effusions and urine.