Generation and analysis of whole-genome sequencing data in human mammary epithelial cells

Breast cancer is the most common cancer worldwide, and advanced breast cancer with metastases is incurable mainly with currently available therapies. Therefore, it is essential to understand molecular characteristics during the progression of breast carcinogenesis. Here, we report a dataset of whole genomes from the human mammary epithelial cell system derived from a reduction mammoplasty specimen. This system comprises pre-stasis 184D cells, considered normal, and seven cell lines along cancer progression series that are immortalized or additionally acquired anchorage-independent growth. Our analysis of the whole-genome sequencing (WGS) data indicates that those seven cancer progression series cells have somatic mutations whose number ranges from 8,393 to 39,564 (with an average of 30,591) compared to 184D cells. These WGS data and our mutation analysis will provide helpful information to identify driver mutations and elucidate molecular mechanisms for breast carcinogenesis

Transcriptomic Analysis of Papillary Thyroid Cancer: A Focus on Immune-Subtyping, Oncogenic Fusion, and Recurrence

Objectives@#. Thyroid cancer is the most common endocrine tumor, with rapidly increasing incidence worldwide. However, its transcriptomic characteristics associated with immunological signatures, driver fusions, and recurrence markers remain unclear. We aimed to investigate the transcriptomic characteristics of advanced papillary thyroid cancer. @*Methods@#. This study included 282 papillary thyroid cancer tumor samples and 155 normal samples from Chungnam National University Hospital and Seoul National University Hospital. Transcriptomic quantification was determined by high-throughput RNA sequencing. We investigated the associations of clinical parameters and molecular signatures using RNA sequencing. We validated predictive biomarkers using the Cancer Genome Atlas database. @*Results@#. Through a comparison of differentially expressed genes, gene sets, and pathways in papillary thyroid cancer compared to normal tumor-adjacent tissue, we found increased immune signaling associated with cytokines or T cells and decreased thyroid hormone synthetic pathways. In addition, patients with recurrence presented increased CD8+ T-cell and Th1-cell signatures. Interestingly, we found differentially overexpressed genes related to immune-escape signaling such as CTLA4, IDO1, LAG3, and PDCD1 in advanced papillary thyroid cancer with a low thyroid differentiation score. Fusion analysis showed that the PI3K and mitogen-activated protein kinase (MAPK) signaling pathways were regulated differently according to the RET fusion partner genes (CCDC6 or NCOA4). Finally, we identified HOXD9 as a novel molecular biomarker that predicts the recurrence of thyroid cancer in addition to known risk factors (tumor size, lymph node metastasis, and extrathyroidal extension). @*Conclusion@#. We identified a high association with immune-escape signaling in the immune-hot group with aggressive clinical characteristics among Korean thyroid cancer patients. Moreover, RET fusion differentially regulated PI3K and MAPK signaling depending on the partner gene of RET, and HOXD9 was found to be a recurrence marker for advanced papillary thyroid cancer.

Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing

Currently, Illumina sequencers are the globally leading sequencing platform in the next-generation sequencing market. Recently, MGI Tech launched a series of new sequencers, including the MGISEQ-2000, which promise to deliver high-quality sequencing data faster and at lower prices than Illumina’s sequencers. In this study, we compared the performance of two major sequencers (MGISEQ-2000 and HiSeq 4000) to test whether the MGISEQ-2000 sequencer delivers high-quality sequence data as suggested. We performed RNA sequencing of four human colon cancer samples with the two platforms, and compared the sequencing quality and expression values. The data produced from the MGISEQ-2000 and HiSeq 4000 showed high concordance, with Pearson correlation coefficients ranging from 0.98 to 0.99. Various quality control (QC) analyses showed that the MGISEQ-2000 data fulfilled the required QC measures. Our study suggests that the performance of the MGISEQ-2000 is comparable to that of the HiSeq 4000 and that the MGISEQ-2000 can be a useful platform for sequencing.

Generation of Whole-Genome Sequencing Data for Comparing Primary and Castration-Resistant Prostate Cancer

Because castration-resistant prostate cancer (CRPC) does not respond to androgen deprivation therapy and has a very poor prognosis, it is critical to identify a prognostic indicator for predicting high-risk patients who will develop CRPC. Here, we report a dataset of whole genomes from four pairs of primary prostate cancer (PC) and CRPC samples. The analysis of the paired PC and CRPC samples in the whole-genome data showed that the average number of somatic mutations per patients was 7,927 in CRPC tissues compared with primary PC tissues (range, 1,691 to 21,705). Our whole-genome sequencing data of primary PC and CRPC may be useful for understanding the genomic changes and molecular mechanisms that occur during the progression from PC to CRPC.

ERRATUM: Acknowledgments Correction. Cell-Free miR-27a, a Potential Diagnostic and Prognostic Biomarker for Gastric Cancer

The funding acknowledgment in this article was partially omitted as published.

Cell-Free miR-27a, a Potential Diagnostic and Prognostic Biomarker for Gastric Cancer

MicroRNAs (miRNAs) have been demonstrated to play an important role in carcinogenesis. Previous studies revealed that miRNAs are present in human plasma in a remarkably stable form that is protected from endogenous RNase activity. In this study, we measured the plasma expression levels of three miRNAs (miR-21, miR-27a, and miR-155) to investigate the usefulness of miRNAs for gastric cancer detection. We initially examined plasma miRNA expression levels in a screening cohort consisting of 15 patients with gastric cancer and 15 healthy controls from Korean population, using TaqMan quantitative real-time polymerase chain reaction. We observed that the expression level of miR-27a was significantly higher in patients with gastric cancer than in healthy controls, whereas the miR-21 and miR-155a expression levels were not significantly higher in the patients with gastric cancer. Therefore, we further validated the miR-27a expression level in 73 paired gastric cancer tissues and in a validation plasma cohort from 35 patients with gastric cancer and 35 healthy controls. In both the gastric cancer tissues and the validation plasma cohort, the miR-27a expression levels were significantly higher in patients with gastric cancer. Receiver-operator characteristic (ROC) analysis of the validation cohort, revealed an area under the ROC curve value of 0.70 with 75% sensitivity and 56% specificity in discriminating gastric cancer. Thus, the miR-27a expression level in plasma could be a useful biomarker for the diagnosis and/or prognosis of gastric cancer.

Forensic Body Fluid Identification by Analysis of Multiple RNA Markers Using NanoString Technology

RNA analysis has become a reliable method of body fluid identification for forensic use. Previously, we developed a combination of four multiplex quantitative PCR (qRT-PCR) probes to discriminate four different body fluids (blood, semen, saliva, and vaginal secretion). While those makers successfully identified most body fluid samples, there were some cases of false positive and negative identification. To improve the accuracy of the identification further, we tried to use multiple markers per body fluid and adopted the NanoString nCounter system instead of a multiplex qRT-PCR system. After measuring tens of RNA markers, we evaluated the accuracy of each marker for body fluid identification. For body fluids, such as blood and semen, each body fluid-specific marker was accurate enough for perfect identification. However, for saliva and vaginal secretion, no single marker was perfect. Thus, we designed a logistic regression model with multiple markers for saliva and vaginal secretion and achieved almost perfect identification. In conclusion, the NanoString nCounter is an efficient platform for measuring multiple RNA markers per body fluid and will be useful for forensic RNA analysis.

Efficacy of Intracameral Lidocaine During Phacoemulsification in Vitrectomized Eye

PURPOSE: This study was designed to evaluate the efficacy of intracameral lidocaine injection on patient' s pain relief during phacoemulsification in vitrectomized eyes and the influence on the corneal endothelial cells. METHODS: A prospective, double blind clinical trial was performed on 60 eyes of 60 patients who had undergone phacoemulsification from October 2000 to February 2001 at Busan PAIK Hospital. Thirty eyes had prior vitrectomy. Before surgery specular microscopic examination was performed. The patients were divided into vitrectomized and nonvitrectomized groups, and the lidocaine or placebo (BSS) was injected into the anterior chamber of 15 eyes each in two subgroups within each group. Pain was assessed using a visual analogue scale before, during and after operation. Endothelial cells were examinined at one week, one month, and three months after operation with a specular microscope. RESULTS: In vitrectomized patients, intracameral lidocaine injection resulted in significantly lower intraoperative pain score. There were no significant differences in morphological changes of endothelium between lidocaine and placebo groups. CONCLUSIONS: Intracameral lidocaine injection with topical anesthesia had significant effect in intraoperative pain relief during phacoemulsification in vitrectomized eyes. There was no significant effects on corneal endothelium. We conclude that intracameral anesthesia is safe and reduces intraoperative pain in vitrectomized eyes.

A Clinical Study of the Rhegmatogenous Retinal Detachment

PURPOSE: This study aimed to analyze the clinical characteristics, results of operational method and causes of operational failure in rhegmatogenous retinal detachment except macula hole induced retinal detachment, and to analyze several factors of vision. METHOD: We reviewed the records of 720 patients, 743 eyes with regmatogenous retinal detachment who had undergone operation from January 1990 to December 1999, and followed up for at least 3 months or longer. RESULT: Scleral buckling (728 eyes, 98.0%), gas injection (9 eyes, 1.2%) and vitrctomy (6 eyes, 0.8%) were done as a primary operation. Anatomical success rate was 684 eyes(34.9%). A good visual acuity ( V A >or=0.5) was achieved in 239 eyes (34.9%), reasonable vision (VA 0.4~0.15) in 192 eyes(28.1%), ambulatory vision (VA 0.1~0.02) in 95 eyes (13.8%), whereas 158 eyes (23.2%) became blind (VA

The Clinical Analysis of Surgical Methods in Intermittent Exotropia

PURPOSE: The outcome after operations for intermittent exotropia were frequently unsatisfactory because of high incidence of postoperative undercorrection, overcorrection or recurrence. The author studied surgical outcome of each operation method in intermittent exotropia. METHODS: The results of surgical treatment in 90 patients with intermittent exotropia were reviewed. The operative procedure were devided into 3 groups-bilateral rectus muscle recessions, unilateral lateral rectus muscle recession and medial rectus muscle resection and medial rectus muscle resection of dominant eye and lateral rectus muscle recession of non-dominant eye. The success of operation was defined as a final alignment of orthotropia, esotropia less than 5 prism diopter or exotropia less than 10 prism diopter in primary position at postoperative 6 months. RESULTS: The method of of operation in medial rectus muscle resection of dominant eye and lateral rectus muscle recession of non-dominant eye lead to higher success rate than other surgical method (96.7%) and the difference with statistically significant (p=0.03). The success rate of bilateral rectus muscle recessions group was 76.6%, and that of unilateral lateral rectus muscle recession and medial rectus muscle resection group was 80.0%. CONCLUSIONS: This result suggested that medial rectus muscle resection of dominant eye and lateral rectus muscle recession of non-dominant eye might be a most effective surgical method for intermittent exotropia.