Identification of a novel MAGE D2 antisense RNA transcript in human tissues

Integrated multigene expression panel to prognosticate patients with gastric cancer

Most of the proposed individual markers had limited clinical utility due to the inherent biological and genetic heterogeneity of gastric cancer. We aimed to build a new molecular-based model to predict prognosis in patients with gastric cancer. A total of 200 patients who underwent gastric resection for gastric cancer were divided into learning and validation cohorts using a table of random numbers in a 1:1 ratio. In the learning cohort, mRNA expression levels of 15 molecular markers in gastric tissues were analyzed and concordance index (C-index) values of all single and combinations of the 15 candidate markers for overall survival were calculated. The multigene expression panel was designed according to C-index values and the subpopulation index. Expression scores were determined with weighting according to the coefficient of each constituent. The reproducibility of the panel was evaluated in the validation cohort. C-index values of the 15 single candidate markers ranged from 0.506–0.653. Among 32,767 combinations, the optimal and balanced expression panel comprised four constituents (MAGED2, SYT8, BTG1, and FAM46) and the C-index value was 0.793. Using this panel, patients were provisionally categorized with scores of 1–3, and clearly stratified into favorable, intermediate, and poor overall survival groups. In the validation cohort, both overall and disease-free survival rates decreased incrementally with increasing expression scores. Multivariate analysis revealed that the expression score was an independent prognostic factor for overall survival after curative gastrectomy. We developed an integrated multigene expression panel that simply and accurately stratified risk of patients with gastric cancer.

The Expression of Melanoma-Associated Antigen D2 Both in Surgically Resected and Serum Samples Serves as Clinically Relevant Biomarker of Gastric Cancer Progression

BACKGROUND

Sensitive biomarkers are necessary for risk classification of patients with gastric cancer (GC), especially ones at risk of distant metastases. Melanoma-associated antigen (MAGE)-D2 has been reported to play a role in the process of cell adhesion and metastatic potential of tumor cells in colorectal cancer. The purpose of this study was to identify a novel clinically relevant biomarker of GC.

METHODS

Expression analysis of MAGE-D2 was conducted in GC cell lines and clinical samples (surgical specimen and serum) in both mRNA and protein level. Correlations between MAGE-D2 expression status and clinicopathological factors were evaluated.

RESULTS

MAGE-D2 mRNA expression levels were similar between GC tissues and the corresponding normal adjacent tissues and were independent of GC differentiation or subtype. In 101 (45 %) of 225 patients, the expression level of MAGE-D2 mRNA was increased in GC tissues compared with the corresponding normal adjacent tissues. Increased expression of MAGE-D2 mRNA in GC tissues was associated with distant metastasis and early recurrence and was an independent prognostic factor (hazard ratio 2.27, 95 % confidence interval 1.39-3.74, P = 0.001). There was a stepwise increase in serum MAGE-D2 level going from healthy volunteers to patients with localized GC and then to those with extended GC (stage IV). Patients with preoperative serum MAGE-D2 levels >130 pg/ml had a more unfavorable prognosis than those with levels ≤130 pg/ml.

CONCLUSION

MAGE-D2 was associated with metastatic potential of GC and may represent a promising biomarker, both in gastric tissues and serum samples, for malignant behavior of GC.

Aberrant expression of melanoma-associated antigen-D2 serves as a prognostic indicator of hepatocellular carcinoma outcome following curative hepatectomy

Hepatocellular carcinoma (HCC) is the most common cause of cancer-related mortality globally. Since the prognosis of advanced HCC patients is extremely poor, the development of novel molecular targets for diagnosis and therapy is urgently required. In the present study, the expression of the melanoma-associated antigen-D2 (MAGE-D2) gene was investigated to determine whether it affects the malignant phenotype of HCC and thus, may serve as a marker of prognosis. Therefore, the expression of MAGE-D2 mRNA and MAGE-D2 protein in nine HCC cell lines and 151 pairs of surgical tissues was analyzed. mRNA expression levels were analyzed using reverse transcription-quantitative polymerase chain reaction and immunohistochemistry was used to compare the clinicopathological parameters of the tumors. A significant difference in the level of MAGE-D2 expression was observed between the normal liver and chronic hepatitis tissues, however, no significant differences were identified among the levels of the chronic hepatitis, cirrhosis and HCC tissues. The expression patterns of the MAGE-D2 protein were consistent with those of its mRNA. The expression levels of MAGE-D2 mRNA in 66 of 151 (44%) patients were higher in the HCC tissues compared with the corresponding non-cancerous tissues. In addition, the disease-specific survival time was significantly shorter for patients with higher levels of MAGE-D2 mRNA expression. Multivariate analysis identified increased expression of MAGE-D2 mRNA as an independent prognostic factor for disease-specific survival (hazard ratio, 2.65; 95% confidence interval, 1.43–4.98; P=0.002). However, increased expression levels of MAGE-D2 mRNA were not significantly associated with other clinicopathological parameters, including extrahepatic recurrence. These results indicated that MAGE-D2 mRNA affects tumor progression and may serve as a prognostic indicator following curative resection. In addition, MAGE-D2 may provide a target for the therapy of HCC.

Comparative proteomics of pulmonary tumors with neuroendocrine differentiation

We aimed to evaluate neuroendocrine pulmonary tumors (NEPT) by a novel method involving map tree construction by comparing all of the protein spots. We performed a proteomics analysis to assess the similarities in protein expression between neuroendocrine pulmonary tumors (NEPT), including typical carcinoids (TC), atypical carcinoids (AC), large cell neuroendocrine carcinomas (LCNEC) and small cell carcinomas (SCLC). Total protein lysates were obtained from seven histologically confirmed frozen NEPT tissues, including 1TC, 2 SCLC, and 4 cases ranging from AC to LCNEC. 2-DE demonstrated that TC was similar to normal lung. AC, LCNEC, and SCLC were similar to each other, forming a group separate from TC, however, SCLC at an early stage showed a similarity to TC. MALDI analysis detected 9 surrogate endpoint biomarkers, including eIF5A1, GST M3, cytokeratin 18 (CK 18), FK506-binding protein p59, p63, MAGE-D2, mitochondrial short-chain enoyl-coenzyme A hydratase 1, tranferrin and poly (rC) binding protein 1. Immunohistochemical staining revealed a gradual decrease in expression rate of p63 and CK 18 with poor differentiation of NEPT. Our results demonstrate that (1) the comparative proteomics of NEPT match the WHO classification except for AC and LCNEC; (2) SCLC show differences in their proteomics according to tumor stage; and (3) CK 18 and p63 may be useful as diagnostically and prognostically available markers.

Expression profiling of antisense transcripts on DNA arrays

The majority of mouse genes are estimated to undergo bidirectional transcription; however, their tissue-specific distribution patterns and physiological significance are largely unknown. This is in part due to the lack of methodology to routinely assess the expression of natural antisense transcripts (NATs) on a large scale. Here we tested whether commercial DNA arrays can be used to monitor antisense transcription in mouse kidney and brain. We took advantage of the reversely annotated oligonucleotides on the U74 mouse genome array from Affymetrix that hybridize to NATs overlapping with the sense transcript in the area of the probe set. In RNA samples from mouse kidney and brain, 11.9% and 10.1%, respectively, of 5,652 potential NATs returned positive and about half of the antisense RNAs were detected in both tissues, which was similar to the fraction of sense transcripts expressed in both tissues. Notably, we found that the majority of NATs are related to the sense transcriptome since corresponding sense transcripts were detected for 92.5% (kidney) and 74.5% (brain) of the detected antisense RNAs. Antisense RNA transcription was confirmed by real-time PCR and included additional RNA samples from heart, thymus, and liver. The randomly selected transcripts showed tissue specific expression patterns and varying sense/antisense ratios. The results indicate that antisense transcriptomes are tissue specific, and although pairing of sense/antisense transcripts are known to result in rapid degradation, our data provide proof of principle that the sensitivity of commercial DNA arrays is sufficient to assess NATs in total RNA of whole organs.