Development of a Novel Output Value for Quantitative Assessment in Methylated DNA Immunoprecipitation-CpG Island Microarray Analysis

In DNA methylation microarray analysis, quantitative assessment of intermediate methylation levels in samples with various global methylation levels is still difficult. Here, specifically for methylated DNA immunoprecipitation-CpG island (CGI) microarray analysis, we developed a new output value. The signal log ratio reflected the global methylation levels, but had only moderate linear correlation (r = 0.72) with the fraction of DNA molecules immunoprecipitated. By multiplying the signal log ratio using a coefficient obtained from the probability value that took account of signals in neighbouring probes, its linearity was markedly improved (r = 0.94). The new output value, Me value, reflected the global methylation level, had a strong correlation also with the fraction of methylated CpG sites obtained by bisulphite sequencing (r = 0.88), and had an accuracy of 71.8 and 83.8% in detecting completely methylated and unmethylated CGIs. Analysis of gastric cancer cell lines using the Me value showed that methylation of CGIs in promoters and gene bodies was associated with low and high, respectively, gene expression. The degree of demethylation of promoter CGIs after 5-aza-2'-deoxycytidine treatment had no association with that of induction of gene expression. The Me value was considered to be useful for analysis of intermediate methylation levels of CGIs

Heterogeneous Tumor-Immune Microenvironments between Primary and Metastatic Tumors in a Patient with ALK Rearrangement-Positive Large Cell Neuroendocrine Carcinoma

Evolution of tumor-immune microenviroments (TIMEs) occurs during tumor growth and dissemination. Understanding inter-site tumor-immune heterogeneity is essential to harness the immune system for cancer therapy. While the development of immunotherapy against lung cancer with driver mutations and neuroendocrine tumors is ongoing, little is known about the TIME of large cell neuroendocrine carcinoma (LCNEC) or anaplastic lymphoma kinase (ALK) rearrangement-positive lung cancer. We present a case study of a 32-year-old female patient with ALK-rearrangement-positive LCNEC, who had multiple distant metastases including mediastinal lymph-node, bilateral breasts, multiple bones, liver and brain. Multiple biopsy samples obtained from primary lung and three metastatic tumors were analyzed by fluorescent multiplex immunohistochemistry. Tissue localizations of tumor-infiltrating lymphocytes in the tumor nest and surrounding stroma were evaluated. T cell and B cell infiltrations were decreased with distance from primary lung lesion. Although each tumor displayed a unique TIME, all tumors exhibited concomitant regression after treatment with an ALK-inhibitor. This study provides the first evidence of the coexistence of distinct TIME within a single individual with ALK-rearrangement-positive LCNEC. The present study contributes to our understanding of heterogeneous TIMEs between primary and metastatic lesions and provides new insights into the complex interplay between host-immunity and cancer cells in primary and metastatic lesions

Metal-Enhanced Fluorescence Platforms Based on Plasmonic Ordered Copper Arrays: Wavelength Dependence of Quenching and Enhancement Effects

Ordered arrays of copper nanostructures were fabricated and modified with porphyrin molecules in order to evaluate fluorescence enhancement due to the localized surface plasmon resonance. The nanostructures were prepared by thermally depositing copper on the upper hemispheres of two-dimensional silica colloidal crystals. The wavelength at which the surface plasmon resonance of the nanostructures was generated was tuned to a longer wavelength than the interband transition region of copper (>590 nm) by controlling the diameter of the underlying silica particles. Immobilization of porphyrin monolayers onto the nanostructures was achieved <i>via</i> self-assembly of 16-mercaptohexadecanoic acid, which also suppressed the oxidation of the copper surface. The maximum fluorescence enhancement of porphyrin by a factor of 89.2 was achieved as compared with that on a planar Cu plate (CuP) due to the generation of the surface plasmon resonance. Furthermore, it was found that while the fluorescence from the porphyrin was quenched within the interband transition region, it was efficiently enhanced at longer wavelengths. It was demonstrated that the enhancement induced by the proximity of the fluorophore to the nanostructures was enough to overcome the highly efficient quenching effects of the metal. From these results, it is speculated that the surface plasmon resonance of copper has tremendous potential for practical use as high functional plasmonic sensor and devices