Analysis of the tumour suppressor genes, FHIT and WT-1, and the tumour rejection genes, BAGE, GAGE-1/2, HAGE, MAGE-1, and MAGE-3, in benign and malignant neoplasms of the salivary glands

Effect of DNMT3A R882H Hot Spot Mutations on DDX43 Promoter Methylation in Acute Myeloid Leukemia

Epigenetic alterations have been observed in many hematological malignancies, including acute myeloid leukemia (AML). Many of these alterations result from mutations in DNA methyl transferase (DNMT) enzymes, disabling them to methylate target genes in a proper way. In this case-control study, we investigated the association between R882H mutation in DNMT3A gene and DDX43 gene methylation in patients with AML. 47 AML patients and 6 controls were included in this study. After DNA extraction, amplification refractory mutation system (ARMS)-PCR was used to evaluate R882H mutations in DNMT3A gene. The high-resolution melting (HRM) method was used to determine the methylation changes of the DDX43 gene promoter. R882H mutation was only found in 10.6% (5 out of 47) of AML patients. The frequency of DDX43 gene methylation was significantly higher in patients without R882H mutations compared to patients with R882H mutations (P < 0.05). The DNMT3A R882H mutation is typically present in a minority of AML patients. Nevertheless, this mutation is associated with a reduced frequency of methylation in the DDX43 promoter region.

Aberrant Expression of PTPN-14 and Wilms’ Tumor 1 as Putative Biomarker for Locoregional Recurrence in Oral Squamous Cell Carcinoma

Objective Locoregional recurrence in oral squamous cell carcinoma (OSCC) is a major concern that leads to metastasis. Its detection at earliest stage is very important to increase the overall survival of the patient. There is no any biomarker for locoregional recurrence in oral squamous cell carcinoma (OSCC). The aim of this study was to find a biomarker for locoregional recurrence in tissue and serum at gene and protein level.

Methods This work studied the expression of protein tyrosine phosphatase nonreceptor type 14 (PTPN-14) and Wilms’ tumor 1 (WT-1) in patients and correlated their expression with locoregional recurrence and survival. Tissue expression was observed in formalin fixed tissue biopsies of 96 OSCC and 32 healthy controls by immunohistochemistry using antibody against PTPN-14 and WT-1 and serum level was estimated by enzyme-linked immunosorbent assay in pre- and post-chemoradiotherapy samples. mRNA expression was determined by using real-time polymerase chain reaction. Patients were followed for 3 years for locoregional recurrence.

Results Expression of PTPN-14 and WT-1 in OSCC was upregulated (aberrant) in tissue and sera in both gene and protein level as compared with healthy controls. Locoregional recurrence was observed in 10 (23.80%) patients and significantly associated with PTPN-14 (p < 0.047) and WT-1 expression (p < 0.031).

Conclusion PTPN-14 and WT-1 may be used as biomarker to identify patients for higher risk of locoregional recurrence. This study drove molecular aspect and phenotypic level to derive new emergent strategies in future for recurrent OSCC.

ImmunoBody®-HAGE derived vaccine induces immunity to HAGE and delays the growth and metastasis of HAGE-expressing tumours in vivo

The management of patients with triple-negative breast cancer (TNBC) continues to pose a significant clinical challenge. Less than 30% of women with metastatic TNBC survive 5 years, despite adjuvant chemotherapy and the initial higher rates of clinical response that can be achieved with neoadjuvant chemotherapy. ImmunoBody® is a plasmid DNA designed to encode a human antibody molecule with complementary determining regions (CDRs) engineered to express cytotoxic and helper T cell epitopes derived from the cancer antigen of interest. HAGE is a Cancer Testis Antigen, which is expressed in TNBC. Herein, we have identified a 30-amino-acid-long HAGE-derived sequence containing HLA-A2 and HLA-DR1 restricted epitopes and demonstrated that the use of this sequence as peptide (with CpG/IFA) or incorporated into an ImmunoBody® vaccine can generate specific IFNγ secreting splenocytes in HHDII/DR1 mice. T-cell responses elicited by the ImmunoBody®-HAGE vaccine were superior to peptide immunisation. Moreover, splenocytes from ImmunoBody®-HAGE vaccinated mice stimulated in vitro could recognise HAGE⁺ tumour cells and the human TNBC cell line MDA-MB-231. More importantly, the growth of implanted B16/HHDII/DR1/HAGE⁺ cells was significantly delayed by the ImmunoBody®-HAGE vaccine in both prophylactic and experimental metastasis settings. Overall, we demonstrate the potential of HAGE-derived vaccines for treating HAGE-expressing cancers and that such vaccines could be considered as therapeutic options for patients with HAGE⁺ TNBC after conventional treatment to prevent disease recurrence.

The expression of the cancer testis antigen MAGE A4: A favorable prognostic biomarker in salivary gland carcinomas related to low tumor grading

Background

Aim was to analyze the expression of different cancer testis antigens (CTA) and to assess its prognostic value in salivary gland carcinomas.

Methods

Patients with salivary gland carcinomas diagnosed 1994 to 2010 were included. Baseline characteristics, pathohistological, clinical, and outcome data were assessed. Tissue microarrays were constructed and immunohistochemistry for different CTA (NY-ESO1, NY-BR1, MAGE A1, MAGE A3, MAGE A4, MAGE C1/CT7, and MAGE C2/CT10) was performed. CTA expression was assessed and statistically correlated with pathological and outcome data.

Results

Expression rates of CTA in salivary gland tumors ranged from 0% to 40%. MAGE A4 expression was associated with a lower tumor grade tumor grading (P = .017), and a favorable recurrence-free (P = .003), disease-specific (P = .046) and overall survival (P = .028).

Conclusions

MAGE A4 is a highly significant prognostic marker in salivary gland carcinoma; its expression is associated with low-grade histology, a low rate of distant metastasis and a favorable survival.

Level of Evidence

4.

Identification of survivin as a promising target for the immunotherapy of adult B-cell acute lymphoblastic leukemia

B-cell acute lymphoblastic leukemia (B-ALL) is a rare heterogeneous disease characterized by a block in lymphoid differentiation and a rapid clonal expansion of immature, non-functioning B cells. Adult B-ALL patients have a poor prognosis with less than 50% chance of survival after five years and a high relapse rate after allogeneic haematopoietic stem cell transplantation. Novel treatment approaches are required to improve the outcome for patients and the identification of B-ALL specific antigens are essential for the development of targeted immunotherapeutic treatments.

We examined twelve potential target antigens for the immunotherapy of adult B-ALL. RT-PCR indicated that only survivin and WT1 were expressed in B-ALL patient samples (7/11 and 6/11, respectively) but not normal donor control samples (0/8). Real-time quantitative (RQ)-PCR showed that survivin was the only antigen whose transcript exhibited significantly higher expression in the B-ALL samples (n = 10) compared with healthy controls (n = 4)(p = 0.015). Immunolabelling detected SSX2, SSX2IP, survivin and WT1 protein expression in all ten B-ALL samples examined, but survivin was not detectable in healthy volunteer samples. To determine whether these findings were supported by the analyses of a larger cohort of patient samples, we performed metadata analysis on an already published microarray dataset. We found that only survivin was significantly over-expressed in B-ALL patients (n = 215) compared to healthy B-cell controls (n = 12)(p = 0.013).

We have shown that survivin is frequently transcribed and translated in adult B-ALL, but not healthy donor samples, suggesting this may be a promising target patient group for survivin-mediated immunotherapy.

A genomic approach to study down syndrome and cancer inverse comorbidity: untangling the chromosome 21

Down syndrome (DS), one of the most common birth defects and the most widespread genetic cause of intellectual disabilities, is caused by extra genetic material on chromosome 21 (HSA21). The increased genomic dosage of trisomy 21 is thought to be responsible for the distinct DS phenotypes, including an increased risk of developing some types of childhood leukemia and germ cell tumors. Patients with DS, however, have a strikingly lower incidence of many other solid tumors. We hypothesized that the third copy of genes located in HSA21 may have an important role on the protective effect that DS patients show against most types of solid tumors. Focusing on Copy Number Variation (CNV) array data, we have generated frequencies of deleted regions in HSA21 in four different tumor types from which DS patients have been reported to be protected. We describe three different regions of deletion pointing to a set of candidate genes that could explain the inverse comorbidity phenomenon between DS and solid tumors. In particular we found RCAN1 gene in Wilms tumors and a miRNA cluster containing miR-99A, miR-125B2 and miR-LET7C in lung, breast, and melanoma tumors as the main candidates for explaining the inverse comorbidity observed between solid tumors and DS.

Sperm associated antigen 9 (SPAG9) expression and humoral response in benign and malignant salivary gland tumors

Salivary gland cancers are highly aggressive epithelial tumor associated with metastatic potential and high mortality. The tumors are biologically diverse and are of various histotypes. Besides, the detection and diagnosis is a major problem of salivary gland cancer for available treatment modalities. In the present study, we have investigated the association of sperm associated antigen 9 (SPAG9) expression with salivary gland tumor (SGT). Clinical specimens of benign (n = 16) and malignant tumors (n = 86) were examined for the SPAG9 expression. In addition, the sera and adjacent non-cancerous tissues (n = 72) from available patients were obtained. Our in situ RNA hybridization and immunohistochemistry (IHC) analysis revealed significant difference (p = 0.0001) in SPAG9 gene and protein expression in benign (63%) and malignant tumor (84%) specimens. Further, significant association was also observed between SPAG9 expression and malignant tumors (P = 0.05). A cut-off value of >10% cells expressing SPAG9 protein designated as positive in IHC, predicted presence of malignant SGT with 83.72% sensitivity, 100% specificity, 100% PPV and 83.72% NPV. Humoral response against SPAG9 protein was generated in 68% of SGT patients. A cut-off value of 0.212 OD for anti-SPAG9 antibodies in ELISA predicted presence of malignant SGT with 69.23% sensitivity, 100% specificity, 100% PPV and 78.94% NPV. Collectively, our data suggests that the majority of SGT show significant difference and association among benign and malignant tumors for SPAG9 gene and protein expression and also exhibit humoral response against SPAG9 protein. Hence, SPAG9 may be developed as a biomarker for detection and diagnosis of salivary gland tumors.

Perturbations of RNA helicases in cancer

Helicases are implicated in most stages of the gene expression pathway, ranging from DNA replication, RNA transcription, splicing, RNA transport, ribosome biogenesis, mRNA translation, RNA storage and decay. These enzymes utilize energy derived from nucleotide triphosphate hydrolysis to remodel ribonucleoprotein complexes, RNA, or DNA and in this manner affect the information content or output of RNA. Several RNA helicases have been implicated in the oncogenic process--either through altered expression levels, mutations, or due to their role in pathways required for tumor initiation, progression, maintenance, or chemosensitivity. The purpose of this review is to highlight those RNA helicases for which there is significant evidence implicating them in cancer biology.

The methylation status of the DDX43 promoter in Chinese patients with chronic myeloid leukemia

Aberrant DNA methylation is a common epigenetic alteration and an important feature in human cancers. The DEAD box polypeptide 43 (DDX43) has been found to be overexpressed in various solid tumors and some hematologic malignancies. In the present study, we investigated the methylation status of the DDX43 promoter in 87 Chinese patients with chronic myeloid leukemia (CML) using real-time quantitative methylation-specific polymerase chain reaction and examined the DDX43 transcript in 35 patients using real-time quantitative polymerase chain reaction. DDX43 promoter hypomethylation was observed in 22 (25.3%) CML patients. No significant correlation was found between the hypomethylation of the DDX43 promoter with the age, sex, white blood cell counts, hemoglobin concentration, platelet counts, and chromosomal abnormalities of CML patients (p>0.05). The frequency of DDX43 hypomethylation in patients in the chronic phase, in the accelerated phase, and in blast crisis was 23.4% (15/64), 25.0% (2/8), and 33.3% (5/15), respectively (p>0.05). There was a significant correlation between DDX43 hypomethylation and DDX43 transcript (r=0.469, p=0.004). Our data suggest that hypomethylation of the DDX43 promoter may be an early and frequent molecular event in the development of CML in Chinese patients.

Expression of mucin (MUC) genes in mucoepidermoid carcinoma

OBJECTIVES/HYPOTHESIS

Mucoepidermoid carcinoma (MEC) is the most common malignant salivary gland tumor. The presence of mucin (MUC) genes has been correlated with patient prognosis using immunohistochemical techniques. This study was undertaken to 1) investigate the expression of newly discovered MUC genes in MEC specimens, 2) assess the correlation of this expression to prognosis, and 3) further investigate the correlation of previously identified MUC genes to prognosis using molecular techniques.

STUDY DESIGN

Retrospective chart review and sample isolation.

METHODS

Twenty-three patients with a diagnosis of MEC underwent mucin gene analysis of tumor and normal surrounding salivary gland tissue. Initial expression analysis of recently identified mucin genes MUC 12, 13, 17, 18, and 19 was performed using reverse transcription-polymerase chain reaction (RT-PCR) followed by quantitative assessment with quantitative PCR. Additional assessments of mucin genes MUC 1 and MUC 4, which have previously been associated with MEC, were also analyzed with real-time RT-PCR.

RESULTS

MEC was associated with MUC 19 expression in 65% of tumor samples compared to only 26% of normal tissue (P = .02). MUC 18 demonstrated equal expression in both tumor and normal tissue. MUC 12 and 17 were not expressed in either MEC or normal salivary gland. MUC 13 was found in 13% of tumors and 0% of normal samples. MUC 1 and MUC 4 were expressed 4.2- and 21-fold higher in stage I disease in tumor tissue compared to normal, respectively.

CONCLUSIONS

Presence of MUC 19 is suggestive of mucoepidermoid carcinoma, and higher expression of MUC 1 and MUC 4 is correlated with earlier stage disease.

Quantitative promoter methylation differentiates carcinoma ex pleomorphic adenoma from pleomorphic salivary adenoma

Background:

Potential epigenetic biomarkers for malignant transformation to carcinoma ex pleomorphic adenoma (Ca ex PSA) have been sought previously with and without specific comparison with the benign variant, pleomorphic salivary adenoma (PSA). Previous analysis has been limited by a non-quantitative approach. We sought to demonstrate quantitative promoter methylation across a panel of tumour suppressor genes (TSGs) in both Ca ex PSA and PSA.

Methods:

Quantitative methylation-specific real-time polymerase chain reaction (qMSP) analysis of p16^INK4A, CYGB, RASSF1, RARβ, human telomerase reverse transcriptase (hTERT), Wilms’ tumour 1 (WT1) and TMEFF2 gene promoters was undertaken on bisulphite-converted DNA, previously extracted from archival fixed tissue specimens of 31 Ca ex PSA and an unrelated cohort of 28 PSA. All target regions examined had formerly been shown to be hypermethylated in salivary and/or mucosal head and neck malignancies.

Results:

The qMSP demonstrated abnormal methylation of at least one target in 20 out of 31 (64.5%) Ca ex PSA and 2 out of 28 (7.1%) PSA samples (P<0.001). RASSF1 was the single gene promoter for which methylation is shown to be a statistically significant predictor of malignant disease (P<0.001) with a sensitivity of 51.6% and a specificity of 92.9%. RARβ, TMEFF2 and CYGB displayed no apparent methylation, while a combinatory epigenotype based on p16, hTERT, RASSF1 and WT1 was associated with a significantly higher chance of detecting malignancy in any positive sample (odds ratio: 24, 95% CI: 4.7–125, P<0.001).

Conclusions:

We demonstrate the successful application of qMSP to a large series of historical Ca ex PSA samples and report on a panel of TSGs with significant differences in their methylation profiles between benign and malignant variants of pleomorphic salivary adenoma. qMSP analysis could be developed as a useful clinical tool to differentiate between Ca ex PSA and its benign precursor.

HAGE, a cancer/testis antigen expressed at the protein level in a variety of cancers

The search for novel tumour antigens that are either uniquely expressed or over-expressed in a wide variety of tumours is still ongoing. Because of their expression in a broad spectrum of cancers and limited expression in normal tissues, cancer/testis antigens are considered to be potentially reliable targets for immunotherapy of cancer in general. The helicase antigen HAGE has been identified as a cancer/testis antigen. However, little is known about its expression in normal and cancer tissues. Using a newly developed antibody against HAGE, specific staining of its expression by immunohistochemistry was validated and optimised on murine tumours transfected to express the HAGE protein. The antibody was subsequently used to determine HAGE expression in normal human and cancer tissue microarrays. HAGE protein expression was confirmed in 75% (12/16) of carcinomas as compared to normal tissues, which either did not express HAGE at all or expressed HAGE at very low levels with the exception of testis. Interestingly, discrepancies were also found between mRNA analysis by real time quantitative PCR (RT-qPCR) and protein analysis by immunohistochemistry, emphasising the need to validate the expression of cancer/testis antigens at the protein level prior to the development of new vaccine strategies. HAGE is therefore proposed to be a valid candidate for designing a broad spectrum vaccine against cancer.

Immunotherapy for adenoid cystic carcinoma of salivary glands: cancer/testis antigens and 5-aza-2'-deoxycytidine

Adenoid cystic carcinoma of salivary glands is the epithelial tumor. There are amount of malignant occurrences of adenoid cystic carcinoma of salivary glands in the head and neck area. Cancer/testis antigens can be found in various malignant tumors, normal adult testis and occasionally placenta, but not in the other normal adult tissues. This characteristic makes Cancer/testis antigens as potential markers to be applied in immunotherapeutic strategies against cancer. It has been shown that in different tumors, the expression of certain Cancer/testis antigens is activated treated with 5-aza-CdR via the demethylation of their promoter CpG islands. It is logical that multiple Cancer/testis antigens may correlate with the clinicopathologic factors of adenoid cystic carcinoma of salivary glands and be the potential markers of prognosis treated with 5-aza-CdR. So the hypothesis will provide the new direction that we can use Cancer/testis antigens as candidate antigens for adenoid cystic carcinoma of salivary glands immunotherapy due to the high expression rate activated with 5-aza-CdR.

A hybrid machine learning-based method for classifying the Cushing's Syndrome with comorbid adrenocortical lesions

BACKGROUND

The prognosis for many cancers could be improved dramatically if they could be detected while still at the microscopic disease stage. It follows from a comprehensive statistical analysis that a number of antigens such as hTERT, PCNA and Ki-67 can be considered as cancer markers, while another set of antigens such as P27KIP1 and FHIT are possible markers for normal tissue. Because more than one marker must be considered to obtain a classification of cancer or no cancer, and if cancer, to classify it as malignant, borderline, or benign, we must develop an intelligent decision system that can fullfill such an unmet medical need.

RESULTS

We have developed an intelligent decision system using machine learning techniques and markers to characterize tissue as cancerous, non-cancerous or borderline. The system incorporates learning techniques such as variants of support vector machines, neural networks, decision trees, self-organizing feature maps (SOFM) and recursive maximum contrast trees (RMCT). These variants and algorithms we have developed, tend to detect microscopic pathological changes based on features derived from gene expression levels and metabolic profiles. We have also used immunohistochemistry techniques to measure the gene expression profiles from a number of antigens such as cyclin E, P27KIP1, FHIT, Ki-67, PCNA, Bax, Bcl-2, P53, Fas, FasL and hTERT in several particular types of neuroendocrine tumors such as pheochromocytomas, paragangliomas, and the adrenocortical carcinomas (ACC), adenomas (ACA), and hyperplasia (ACH) involved with Cushing's syndrome. We provided statistical evidence that higher expression levels of hTERT, PCNA and Ki-67 etc. are associated with a higher risk that the tumors are malignant or borderline as opposed to benign. We also investigated whether higher expression levels of P27KIP1 and FHIT, etc., are associated with a decreased risk of adrenomedullary tumors. While no significant difference was found between cell-arrest antigens such as P27KIP1 for malignant, borderline, and benign tumors, there was a significant difference between expression levels of such antigens in normal adrenal medulla samples and in adrenomedullary tumors.

CONCLUSIONS

Our frame work focused on not only different classification schemes and feature selection algorithms, but also ensemble methods such as boosting and bagging in an effort to improve upon the accuracy of the individual classifiers. It is evident that when all sorts of machine learning and statistically learning techniques are combined appropriately into one integrated intelligent medical decision system, the prediction power can be enhanced significantly. This research has many potential applications; it might provide an alternative diagnostic tool and a better understanding of the mechanisms involved in malignant transformation as well as information that is useful for treatment planning and cancer prevention.

HAGE, a cancer/testis antigen with potential for melanoma immunotherapy: identification of several MHC class I/II HAGE-derived immunogenic peptides

There remains a need to identify novel epitopes of potential tumour target antigens for use in immunotherapy of cancer. Here, several melanoma tissues and cell lines but not normal tissues were found to overexpress the cancer-testis antigen HAGE at the mRNA and protein level. We identified a HAGE-derived 15-mer peptide containing a shorter predicted MHC class I-binding sequence within a class II-binding sequence. However, only the longer peptide was found to be both endogenously processed and immunogenic for T cells in transgenic mice in vivo, as well as for human T cells in vitro. A different class I-binding peptide, not contained within a longer class II sequence, was subsequently found to be both immunogenic and endogenously processed in transgenic mice, as was a second class II epitope. These novel HAGE-derived epitopes may contribute to the range of immunotherapeutic targets for use in cancer vaccination programs.