Validation of Customized Cancer Panel for Detecting Somatic Mutations and Copy Number Alterations

Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes. In terms of the limit of detection, more than 86% of target mutations with a mutant allele frequency (MAF) 3% MAF can be detected. When we applied this system for the analysis of Acrometrix Oncology Hotspot Control DNA, which contains more than 500 COSMIC mutations across 53 genes, 99% of the expected mutations were robustly detected. We also confirmed the high reproducibility of the detection of mutations in multiple independent analyses. When we explored copy number alterations (CNAs), the expected CNAs were successfully detected, and this result was confirmed by target-specific genomic quantitative polymerase chain reaction. Taken together, these results support the reliability and accuracy of our cancer panel in detecting mutations. This panel could be useful for key mutation profiling research in solid tumors and clinical translation

Overexpression of USF increases TGF-beta1 protein levels, but G1 phase arrest was not induced in FRTL-5 cells

Transforming growth factor-beta1 (TGF-beta1) is a potent inhibitor of cellular growth and proliferation by G1 phase arrest or apoptosis. We investigated the association of TGF-beta1 with the anti-proliferative effect of upstream stimulatory factor (USF) in Fischer rat thyroid cell line (FRTL-5) cells. [methyl-(3)H] thymidine uptake was measured after treatment of FRTL-5 cells with TGF-beta1 to identify its anti-proliferative effect. USF-1 and USF-2 proteins were in vitro translated, and an electrophoretic mobility shift assay was performed to identify the interaction between USF and the TGF-beta1 promoter. FRTL-5 cells were transfected with USF cDNA, and then the expression of TGF-beta1 was examined with Northern and Western blotting. The cell cycle-regulating proteins associated with TGF-beta1 were also measured. TGF-beta1 significantly inhibited [methyl-(3)H] thymidine uptake in FRTL-5 cells. Two specific binding sites for USF were found in the TGF-beta1 promoter: -1,846 approximately -1,841 (CACATG) and -621 approximately -616 (CATGTG). Overexpression of USF increased both the mRNA levels and protein levels of TGF-beta1. However, the expression of cyclin D1, CDK4, cyclin E, and CDK2, and the phosphorylation of retinoblastoma protein remained unchanged. Overexpression of USF in FRTL-5 cells increased the expression of TGF-beta10 through specific binding to TGF-beta1 promoter. However, the USF-induced expression of TGF-beta1 did not cause G1 arrest

Herbal Medication Aggravates Cataract Formation: A Case Report

We report a case of complicated cataract aggravated after taking herbal medication for atopic dermatitis. An 11-yr-old boy was referred for the evaluation of decreased visual acuity in both eyes for 2 months. Past history showed that he had been diagnosed with atopic dermatitis when he was 1 yr old. He had been treated only with herbal medication for a period of 8 months prior to visiting our clinic. He had his visual acuity checked in a local ophthalmic clinic one year before, and the visual acuity was 20/20 in both eyes at that time. When attending our clinic the ophthalmologic examination showed that his best corrected visual acuity was 20/200 in both eyes. Lenses of both eyes had severe posterior subcapsular and posterior capsular opacity. Phacoemulsification, posterior chamber intraocular lens implantation, and posterior continuous curvilinear capsulectomy were performed in both eyes. After 3 months postoperatively, the best corrected visual acuity was recovered to 20/20 in both eyes without any complication. Our case suggests that there may be a risk of aggravation of cataract or development of cataract after treatment with some unidentified herbal medication in a patient with atopic dermatitis

Pathological Classification of the Intramedullary Spinal Cord Tumors According to 2021 World Health Organization Classification of Central Nervous System Tumors, a Single-Institute Experience

According to the new 2021 World Health Organization (WHO) classification of tumors of the central nervous system (CNS) the classification of the primary intramedullary spinal cord tumors (IM-SCT) follows that of CNS tumors. However, since the genetics and methylation profile of ependymal tumors depend on the location of the tumor, the ‘spinal (SP)’ should be added for the ependymoma (EPN) and subependymoma (SubEPN). For an evidence-based review, the authors reviewed SCTs in the archives of the Seoul National University Hospital over the past decade. The frequent pathologies of primary IM-SCT were SP-EPN (45.1%), hemangioblastoma (20.0%), astrocytic tumors (17.4%, including pilocytic astrocytoma [4.6%] and diffuse midline glioma, H3 K27-altered [4.0%]), myxopapillary EPN (11.0%), and SP-subEPN (3.0%) in decreasing order. IDH-mutant astrocytomas, oligodendrogliomas, glioneuronal tumors, embryonal tumors, and germ cell tumors can occur but are extremely rare in the spinal cord. Genetic studies should support for the primary IM-SCT classification. In the 2021 WHO classifications, extramedullary SCT did not change significantly but contained several new genetically defined types of mesenchymal tumors. This article focused on primary IM-SCT for tumor frequency, age, sex difference, pathological features, and genetic abnormalities, based on a single-institute experience

Nasal Chondromesenchymal Hamartoma: CT and MR Imaging Findings

We report CT and MR imaging findings for a case of nasal chondromesenchymal hamartoma occurring in a 19-month-old boy. A nasal chondromesenchymal hamartoma is a rare benign pediatric hamartoma that can simulate malignancy. Although rare, knowledge of this entity is essential to avoid potentially harmful therapies

Regulation of autophagic cell death by glycogen synthase kinase-3 beta in adult hippocampal neural stem cells following insulin withdrawal

Background: Neural stem cells (NSCs) hold great potential for the treatment of neurodegenerative diseases. However, programmed cell death (PCD) provoked by the harsh conditions evident in the diseased brain greatly undermines the potential of NSCs. Currently, the mechanisms of PCD that effect NSCs remain largely unknown. Results: We have previously reported that hippocampal neural stem (HCN) cells derived from the adult rat brain undergo autopahgic cell death (ACD) following insulin withdrawal without hallmarks of apoptosis despite their normal apoptotic capabilities. In this study, we demonstrate that glycogen synthase kinase 3β (GSK-3β) induces ACD in insulin-deprived HCN cells. Both pharmacological and genetic inactivation of GSK-3β significantly decreased ACD, while activation of GSK-3β increased autophagic flux and caused more cell death without inducing apoptosis following insulin withdrawal. In contrast, knockdown of GSK-3α barely affected ACD, lending further support to the critical role of GSK-3β. Conclusion: Collectively, these data demonstrate that GSK-3β is a key regulator of ACD in HCN cells following insulin withdrawal. The absence of apoptotic indices in GSK-3β-induced cell death in insulin-deprived HCN cells corroborates the notion that HCN cell death following insulin withdrawal represents the genuine model of ACD in apoptosis-intact mammalian cells and identifies GSK-3β as a key negative effector of NSC survival downstream of insulin signaling. © 2015 Ha et al.; licensee BioMed Central.1

Gastrointestinal Complications Following Hematopoietic Stem Cell Transplantation in Children

Gastrointestinal system involvement is one of the principal complications seen in the recipients of hematopoietic stem cell transplantation (HSCT), and it is also a major cause of morbidity and death in these patients. The major gastrointestinal complications include typhlitis (neutropenic enterocolitis), pseudomembranous enterocolitis, viral enteritis, graft-versus-host disease, benign pneumatosis intestinalis, intestinal thrombotic microangiopathy, and post-transplantation lymphoproliferative disease. As these patients present with nonspecific abdominal symptoms, evaluation with using such imaging modalities as ultrasonography and CT is essential in order to assess the extent of gastrointestinal involvement and to diagnose these complications. We present here a pictorial review of the imaging features and other factors involved in the diagnosis of these gastrointestinal complications in pediatric HSCT recipients

Development of a Mobile Application, “Wild Flowers of Bukhansan National Park (version 1.0)”, for Identification of Plants in Bukhansan National Park

AbstractWe developed the educational purpose mobile application, named “Wild Flowers of Bukhansan National Park (version 1.0)”, aiming for easy identification of wildflowers for students and visitors in the park. When visitors find a flower or part of plant in the park, visitors can search for its name utilizing the pictures and characters provided in their own smartphone mobile devices or tablet PCs. The application provides pictures of wildflowers in the park and character-based searching system based on 12 diagnostic features (e.g., growth form, leaf arrangement, flower symmetry, petal color, petal number, sepal number, etc). We adopted the complete floristic survey of Chung and Lee (1962) and added species that we confirmed their distribution in the park during the development of this application. In summary, number of vascular plants in this park was estimated to be 428 taxa including 100 families, 280 genera, 327 species, 1 subspecies, 50 varieties, and 5 formas. We provided a total of 588 pictures representing 358 taxa and each taxon includes multiple pictures in many cases. Included identification quizzes can be an efficient educational tool as well as fun activity for students and visitors who are learning plant species in Korea. Our next step will include GPS function in the application for indicating visitor's location and for providing previously reported sites of the species that we interested in the map of the park. The future application which includes GPS function will be a valuable tool for the monitoring of rare plants, plant researches related to the climate changes, etc. We currently provide Korean iPhone version only, and English version and both of android versions will be serviced soon

Evaluation of an eight marker-panel including long mononucleotide repeat markers to detect microsatellite instability in colorectal, gastric, and endometrial cancers

Background Accurate determination of microsatellite instability (MSI) status is critical for optimal treatment in cancer patients. Conventional MSI markers can sometimes display subtle shifts that are difficult to interpret, especially in non-colorectal cases. We evaluated an experimental eight marker-panel including long mononucleotide repeat (LMR) markers for detection of MSI. Methods The eight marker-panel was comprised of five conventional markers (BAT-25, BAT-26, NR-21, NR-24, and NR-27) and three LMR markers (BAT-52, BAT-59 and BAT-62). MSI testing was performed against 300 specimens of colorectal, gastric, and endometrial cancers through PCR followed by capillary electrophoresis length analysis. Results The MSI testing with eight marker-panel showed 99.3% (295/297) concordance with IHC analysis excluding 3 MMR-focal deficient cases. The sensitivity of BAT-59 and BAT-62 was higher than or comparable to that of conventional markers in gastric and endometrial cancer. The mean shift size was larger in LMR markers compared to conventional markers for gastric and endometrial cancers. Conclusions The MSI testing with eight maker-panel showed comparable performance with IHC analysis. The LMR markers, especially BAT-59 and BAT-62, showed high sensitivity and large shifts which can contribute to increased confidence in MSI classification, especially in gastric and endometrial cancers. Further study is needed with large number of samples for the validation of these LMR markers

Pneumopericardium as a Complication of Pericardiocentesis

Pneumopericardium is a rare complication of pericardiocentesis, occurring either as a result of direct pleuro-pericardial communication or a leaky drainage system. Air-fluid level surrounding the heart shadow within the pericardium on a chest X-ray is an early observation at diagnosis. This clinical measurement and process is variable, depending on the hemodynamic status of the patient. The development of a cardiac tamponade is a serious complication, necessitating prompt recognition and treatment. We recently observed a case of pneumopericardium after a therapeutic pericardiocentesis in a 20-year-old man with tuberculous pericardial effusion