Mutational and expressional analyses of PTEN gene in colorectal cancer from Northern India

Rs12039395 Variant Influences the Expression of hsa-miR-181a-5p and PTEN Toward Colorectal Cancer Risk

BACKGROUND

Single nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes could alter miRNA expression levels or processing and, thus, may contribute to colorectal cancer (CRC) development. Therefore, this study aimed to examine whether the MIR181A1 genomic sequence possesses SNPs that can affect the expression of hsa-miR-181a-5p and, subsequently, impact its targets and associate with CRC risk.

METHODS

The NCBI dbSNP database was searched for possible SNPs associated with MIR181A1. One SNP with a minor allele frequency > 5%, rs12039395 G > T was identified. In silico analyses determined the effect of the SNP on the secondary structure of the miRNA and predicted the hsa-miR-181a-5p target genes. The SNP was genotyped using allelic discrimination assay, the relative hsa-miR-181a-5p expression level was determined using quantitative real-time PCR, and immunohistochemical staining was used to detect target genes in 192 paraffin-embedded specimens collected from 160 CRC patients and 32 healthy subjects.

RESULTS

The rs6505162 SNP conferred protection against CRC, and the G-allele presence provides may provide accessibility for the transcriptional machinery. Hsa-miR-181a-5p was significantly over-expressed in the CRC group compared to controls and in samples carrying the G-allele compared to those with T-allele. PTEN, identified as the only hsa-miR-181a-5p target implicated in CRC, was significantly diminished in the CRC group compared to controls and showed an inverse relationship with hsa-miR-181a-5p expression level as well as negatively associated with the G-allele presence in CRC.

CONCLUSION

This study highlights that rs12039395 G > T may protect against CRC by influencing the expression of hsa-mir-181a-5p and its target gene, PTEN.

Implication of alterations in Parkin gene among North Indian patients with colorectal cancer

BACKGROUND/AIMS

Alterations in Parkin (PRKN) have been described in many cancers; however, the molecular mechanism that contributes to loss of Parkin expression in colorectal cancer (CRC) remains unclear. The aim of this study was to investigate the involvement of PRKN mutation and loss of heterozygosity (LOH) in loss of Parkin expression. To understand the role of PRKN in cancer progression, we also evaluated the association of Parkin expression with clinicopathological parameters in North Indian population.

MATERIALS AND METHODS

We studied 219 CRC samples and their adjacent normal tissues (control) obtained from North Indian patients with CRC. The expression of Parkin was analyzed by immunohistochemistry (IHC). PRKN mutations were analyzed by single-stranded conformational polymorphism (SSCP) and sequencing. For loss of heterozygosity (LOH), we employed two intragenic, D6S305 and D6S1599, and one telomeric marker, D6S1008.

RESULTS

In our study, we found four novel somatic mutations, namely, C166G, K413N, R420P (exon 4), and V425E (exon 11). Both mutation in Parkin (p = 0.0014) and LOH (p = 0.0140) were significantly associated with loss of Parkin expression. Additionally, Parkin mutations were not associated with the clinicopathological parameters of the patients. Furthermore, both, LOH in Parkin and Parkin expression were significantly correlated with different clinicopathological variables (p<0.05).

CONCLUSION

Our results indicate that Parkin expression is not regulated by a single mechanism, but both mutation and LOH contribute to loss of Parkin expression. We also provide evidence of involvement of Parkin in metastasis and cancer progression. We, therefore, suggest Parkin as a potential prognostic marker and warrant further analysis in this direction.

PTEN Genetic and Epigenetic Alterations Define Distinct Subgroups in North Indian Breast Cancer Patients

Background:

Breast cancer is a heterogeneous disease that can be subdivided on the basis of histopathological features, genetic alterations, and gene-expression profiles. PTEN gene is considered an established tumor suppressor gene in different types of cancer including breast cancer. However, the role of PTEN alterations in north Indian breast cancer has not been explored especially in defining a group with distinct histological factors.

Methodology:

181 sporadic breast cancer and their adjacent normal tissues were included in the present study. We analyzed methylation and LOH through MS-PCR and microsatellite markers respectively. While, for PTEN protein expression, we used immunohistochemistry. All the molecular findings were correlated with the clinicopathological parameters of the patients to underline clinical relevance.

Results:

We found that LOH and methylation of the PTEN promoter were significantly associated with loss of PTEN protein expression, while, PTEN mutation was a rare event. Furthermore, out of 46 double hit cases (i.e., having both methylation and LOH), 70% (32/46) cases showed complete loss of PTEN expression (P= 0.0249). Both LOH and PTEN promoter methylation were associated significantly with age and clinical stage, while, methylation and loss of PTEN expression were associated with high grade and Her-2 negativity. In addition, a quadruple (ER/PR/Her-2 and PTEN) negative group with distinct features was found.

Conclusion:

The pattern of PTEN expression and its correlation with the clinical parameters indicates that loss of PTEN expression defines a clinical group with distinct features. Hence, PTEN expression provides differential therapeutic strategies for north Indian breast cancer.

Allelic loss at PTEN locus leads to progression of colorectal carcinoma among North Indian patients

We evaluated the loss of heterozygosity (LOH) at 10q^23.3 locus of microsatellite markers; D10S198, D10S192, and D10S541 of PTEN gene in 223 North Indian colorectal cancer (CRC) specimens. DNA was isolated and microsatellite-specific markers polymerase chain reaction was performed. Out of total 223 cases 102 showed LOH for at least one of the locus. In addition, thereto a significant association was found with the clinicopathologic features like grade of differentiation, clinical stage, invasion, lymph node invasion, and the clinical outcome (p < 0.05). These data argue that the given markers to check the possible LOH of PTEN gene at locus 10q^23.3 could be considered as one of the diagnostic markers in CRC.

Effects of PTEN gene alteration in patients with gallbladder cancer

Gallbladder cancer (GBC) is an aggressive malignancy usually diagnosed in an advanced stage. We investigated the effects of alterations of the phosphatase and tensin homologue (PTEN) gene on the occurrence and development of GBC, which has not been previously reported. A total 141 cases of GBC were analyzed for mutation, expression, and methylation across the nine exons of the PTEN gene. DNA sequencing methods were applied for mutation detection, whereas protein expression and methylation status were evaluated by immunohistochemical and methylation-specific PCR analysis, respectively. Novel PTEN mutations were observed in 6.3% of cases (9/141), and they included two silent mutations. In mutant cases, according to changes in codons, the respective amino acid sequences were also changed, which caused of proteins. A high percentage (72%) of loss of protein expression was observed more often in cases than in control samples. Interestingly, all nine cases with mutations showed loss of PTEN expression, whereas four of these nine cases showed positive promoter methylation. Hypermethylation was significantly more common in older patients than in younger ones (P<0.02). These findings suggest that PTEN mutations and inactivation may play an important role in the development and progression of gallbladder carcinoma.

Involvement of long non-coding RNA in colorectal cancer: From benchtop to bedside (Review)

Colorectal cancer (CRC) is one of the greatest threats to public health. Recent advances in whole-genome transcriptome analyses have enabled the identification of numerous members of a novel class of non-coding (nc)RNA, long ncRNA (lncRNA), which is broadly defined as RNA molecules that are >200 nt in length and lacking an open reading frame. In the present review, all lncRNAs associated with CRC are briefly summarized, with a particular focus on their potential roles as clinical biomarkers. CRC-associated lncRNAs involved in the underlying mechanisms of CRC progression are also initially included. This should benefit the development of novel markers and effective therapeutic targets for patients with CRC.

Can we accurately report PTEN status in advanced colorectal cancer?

BACKGROUND

Loss of phosphatase and tensin homologue (PTEN) function evaluated by loss of PTEN protein expression on immunohistochemistry (IHC) has been reported as both prognostic in metastatic colorectal cancer and predictive of response to anti-EGFR monoclonal antibodies although results remain uncertain. Difficulties in the methodological assessment of PTEN are likely to be a major contributor to recent conflicting results.

METHODS

We assessed loss of PTEN function in 51 colorectal cancer specimens using Taqman® copy number variation (CNV) and IHC. Two blinded pathologists performed independent IHC assessment on each specimen and inter-observer variability of IHC assessment and concordance of IHC versus Taqman® CNV was assessed.

RESULTS

Concordance between pathologists (PTEN loss vs no loss) on IHC assessment was 37/51 (73%). In specimens with concordant IHC assessment, concordance between IHC and Taqman® copy number in PTEN loss assessment was 25/37 (68%).

CONCLUSION

Assessment PTEN loss in colorectal cancer is limited by the inter-observer variability of IHC, and discordance of CNV with loss of protein expression. An understanding of the genetic mechanisms of PTEN loss and implementation of improved and standardized methodologies of PTEN assessment are required to clarify the role of PTEN as a biomarker in colorectal cancer.

Occipital anaplastic oligodendroglioma with multiple organ metastases after a short clinical course: a case report and literature review

Background

It is generally believed that malignant gliomas never metastasize outside the central nervous system (CNS). However, the notion that oligodendrogliomas (OGDs) cells cannot spread outside CNS is being challenged.

Methods

We described in detail the clinical story of one patient with anaplastic OGD, which metastasized to lymph nodes, bone marrowand bones Genetic analyses included detection of 1p and 19q chromosomal arms, methylation status of MGMT promoter, and PTEN exon mutations. A search of worldwide literature was conducted for reports of metastatic OGDs using NCBI-PubMed, with the keywords “extracranial”, “extraneural”, “oligodendroglioma”, “oligodendrogliomas”, “metastatic”, “metastasis”, and “metastases”, in different combinations.

Results

An open biopsy of the infiltrated bones in our patient revealed that malignant cells had replaced the patient’s marrow. Moreover, the diagnosis of multiple-organ metastases of anaplastic OGD was confirmed based on immunohistochemical staining. Genetic analyses showed that the tumors originated from previously resected brain lesions. None of the lesions had 1p and 19q deletions, but hypermethylation of MGMT promoter, and the G → A transversion at codon 234 of PTEN exon 2 were detected. Literatures review yielded 60 reports of metastatic OGDs from 1951 to the present, which with our patient makes 61 cases. Concerning these 61 patients, there were 110 infiltrated sites correlated closely with primary OGDs. The most frequent metastatic sites were bone and bone marrow (n = 47; 42.7%), lymph nodes (n = 22; 20.0%), liver (n = 7; 6.4%), scalp (n = 6; 5.5%), lung (n = 6; 5.5%), pleura (n = 4; 3.6%), chest wall (n = 3; 2.7%), iliopsoas muscle (n = 2; 1.8%), soft tissue (n = 2; 1.8%), and parotid gland (n = 2; 1.8%).

Conclusions

Extracranial metastases in anaplastic OGD are very rare but they do occur; bone and bone marrow may be the most common sites. Detection of certain molecular markers such as deletion of 1p and 19q chromosomal arms, hypermethylation of MGMT promoter, and characteristic PTEN exon mutations may help differentiate subtypes which are more prone to extracranial metastases.

Virtual slides

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/8749838611478560.