High grade carcinoma ex pleomorphic adenoma of parotid gland: a case report.

Pleomorphic adenoma is the most prevalent benign tumor of the parotid gland, and shows potential malignancy. Carcinoma ex pleomorphic adenoma (CXPA) can occur in 3%-15% of pleomorphic adenoma cases. Owing to its clinical similarity to benign tumors, critical information related to CXPA can be easily overlooked, leading to frequent misdiagnosis of the condition. In this article, we report a rare case of CXPA found in the 55-year-old male patient with characteristic clinical, radiographic, and histological features, and subsequent treatment.

Application of NanoString technologies in angioimmunoblastic T cell lymphoma.

BACKGROUND: Angioimmunoblastic T-cell lymphoma (AITL) is an aggressive disease. Most cancer diagnoses are determined by anatomical histology. Therefore, many samples are stored in FFPE blocks for H&E staining. However, RNAs extracted from the FFPE block have a high level of fragmentation, making it difficult to perform accurate DEG analysis using RNA sequencing. OBJECTIVE: To overcome fragmented RNA's drawback in NGS application, we applied the NanoString nCounter® technique of hybridization method that can be used for DEG analysis without PCR amplification. METHODS: We characterized the gene expression profiling of AITLs though transcriptome analysis based on the nCounter® PanCancer IO 360™ Panel and NanoString platform. To perform the analysis of differential expression gene (DEG) profiles in AITLs, we compared the NanoString data from eight AITL patients with a healthy control donor. RESULTS: Ninety-one genes were up-regulated and six genes were down-regulated in AITLs compared to control. The Gene Ontology (GO) analysis of 97-DEGs revealed that they were closely related to cytokine, MAPK cascade, leukocyte differentiation, and immune response, suggesting that this affect the immune system. In addition, KEGG analysis revealed that AITL DEGs were found to be highly involved in cytokine-cytokine receptor interaction and PI3K-Akt signaling pathway. CONCLUSION: We believe that comprehensive multiplex studies, along with NanoString analysis, may be helpful to understand the molecular mechanisms of AITL, including mutations, gene expression, and protein expression studies.

Novel Discovery of LINE-1 in a Korean Individual by a Target Enrichment Method.

Long interspersed element-1 (LINE-1 or L1) is an autonomous retrotransposon, which is capable of inserting into a new region of genome. Previous studies have reported that these elements lead to genomic variations and altered functions by affecting gene expression and genetic networks. Mounting evidence strongly indicates that genetic diseases or various cancers can occur as a result of retrotransposition events that involve L1s. Therefore, the development of methodologies to study the structural variations and interpersonal insertion polymorphisms by L1 element-associated changes in an individual genome is invaluable. In this study, we applied a systematic approach to identify human-specific L1s (i.e., L1Hs) through the bioinformatics analysis of high-throughput next-generation sequencing data. We identified 525 candidates that could be inferred to carry non-reference L1Hs in a Korean individual genome (KPGP9). Among them, we randomly selected 40 candidates and validated that approximately 92.5% of non-reference L1Hs were inserted into a KPGP9 genome. In addition, unlike conventional methods, our relatively simple and expedited approach was highly reproducible in confirming the L1 insertions. Taken together, our findings strongly support that the identification of non-reference L1Hs by our novel target enrichment method demonstrates its future application to genomic variation studies on the risk of cancer and genetic disorders.

Mutational Analysis of Extranodal NK/T-Cell Lymphoma Using Targeted Sequencing with a Comprehensive Cancer Panel.

Extranodal natural killer (NK)/T-cell lymphoma, nasal type (NKTCL), is a malignant disorder of cytotoxic lymphocytes of NK or T cells. It is an aggressive neoplasm with a very poor prognosis. Although extranodal NKTCL reportedly has a strong association with Epstein-Barr virus, the molecular pathogenesis of NKTCL has been unexplored. The recent technological advancements in next-generation sequencing (NGS) have made DNA sequencing cost- and time-effective, with more reliable results. Using the Ion Proton Comprehensive Cancer Panel, we sequenced 409 cancer-related genes to identify somatic mutations in five NKTCL tissue samples. The sequencing analysis detected 25 mutations in 21 genes. Among them, KMT2D, a histone modification-related gene, was the most frequently mutated gene (four of the five cases). This result was consistent with recent NGS studies that have suggested KMT2D as a novel driver gene in NKTCL. Mutations were also found in ARID1A, a chromatin remodeling gene, and TP53, which also recurred in recent NGS studies. We also found mutations in 18 novel candidate genes, with molecular functions that were potentially implicated in cancer development. We suggest that these genes may result in multiple oncogenic events and may be used as potential bio-markers of NKTCL in the future.

Effect of fluorescent whitening agent on the transcription of cell damage-related genes in zebrafish embryos.

7-Diethylamino-4-methylcoumarin (DEMC) is a fluorescent whitening agent (FWAs). There have been some studies on DEMC's protective effects against biological activity but there are few papers about the in vivo toxicity of DEMC. In this study, we used wild-type zebrafish embryos 3 days post fertilization (dpf). Test solutions with DEMC concentrations were negative control (without vehicle), 0 (with vehicle, 0.01% v/v ethanol), 0.25, 0.5, 0.75, 1.0, 1.25, 1.5 and 2 ppm. Embryos and larvae were counted for survival rate and hatching rate. Heart rates were also counted at 2.5 and 3.0 dpf. At 3.0 dpf, quantitative RT-PCR was performed with some samples (0, 0.25, 0.75 and 1.25 ppm) to determine the toxic effect to DEMC by detecting the expression levels of toxic-responsive genes. We used 11 genes, which included oxidative stress-related genes [sod(Mn), sod(Cu,Zn) and hsp70], mitochondrial metabolism-related genes (coxI, pyc, cyt and cyclinG1) and apoptosis-related genes (c-jun, bcl2, bax and p53). High-concentration DEMC-treated groups showed significant different survival rate, hatching rate and heart rate compared with low-concentration DEMC-treated groups. The LC50 of this chemical, 0.959 ppm, was calculated. We also confirmed that some genes in the DEMC exposure groups showed significantly up-regulations in expression levels compared with control groups. We concluded that the fluorescence agent, DEMC, has possible developmental toxicities and alteration effect of gene expression, which are related to oxidative stress, mitochondrial metabolism and apoptosis in zebrafish embryos.

Low-temperature growth of ZnO nanorods by chemical bath deposition.

Aligned ZnO nanorod arrays were synthesized using a chemical bath deposition method at normal atmospheric pressure without any metal catalyst. A simple two-step process was developed for growing ZnO nanorods on a PET substrate at 90-95 degrees C. The ZnO seed precursor was prepared by a sol-gel reaction. ZnO nanorod arrays were fabricated on ZnO-seed-coated substrate. The ZnO seeds were indispensable for the aligned growth of ZnO nanorods. The ZnO nanorods had a length of 400-500 nm and a diameter of 25-50 nm. HR-TEM and XRD analysis confirmed that the ZnO nanorod is a single crystal with a wurtzite structure and its growth direction is [0001] (the c-axis). Photoluminescence measurements of ZnO nanorods revealed an intense ultraviolet peak at 378.3 nm (3.27 eV) at room temperature.