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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
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A wave of new technologies has created opportunities for the cost-effective generation of high-throughput profiles of biological systems, foreshadowing a "data-driven science" era. The large variety of data available from biological research is also a rich resource that can be used for innovative endeavors. However, we are facing considerable challenges in big data deposition, integration, and translation due to the complexity of biological data and its production at unprecedented exponential rates. To address these problems, in 2020, the Korean government officially announced a national strategy to collect and manage the biological data produced through national R&D fund allocations and provide the collected data to researchers. To this end, the Korea Bioinformation Center (KOBIC) developed a new biological data repository, the Korea BioData Station (K-BDS), for sharing data from individual researchers and research programs to create a data-driven biological study environment. The K-BDS is dedicated to providing free open access to a suite of featured data resources in support of worldwide activities in both academia and industry.
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Objectives@#This study examined the associations between Internet addiction and suicide and non-suicidal self-injury (NSSI) among South Korean adolescents. @*Methods@#We conducted a cross-sectional study of 1694 Korean adolescents. The suicidal Ideation Questionnaire and Deliberate SelfHarm Inventories were used to identify high-risk suicide and NSSI groups, respectively. Internet addiction was assessed using the Internet Addiction Scale. Other questionnaires included sociodemographic data, perceived academic stress, and daily life-related factors. We also performed a logistic regression analysis using the high suicide risk and NSSI groups as dependent variables. @*Results@#The high suicide risk and NSSI prevalence rates among participants were 11.8% and 28.3%, respectively. A multivariable logistic regression analysis revealed that Internet addiction is associated with higher suicide risk and NSSI. Additionally, being female and academic stress were significant suicide risk factors, while male participants had a higher NSSI prevalence. @*Conclusion@#Our results suggest that monitoring adolescents’ Internet use and providing education to prevent Internet addiction would lower high suicide and NSSI risk. Moreover, suicide and NSSI risk screening in adolescents with Internet addiction and providing suitable interventions will be essential for the preventing suicide and NSSI.
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Objective@#The aim of the study was to develop a checklist for mental health clinicians to predict and manage suicidality. @*Methods@#A literature review of the risk and protective factors for suicide was conducted to develop a checklist for evaluating suicidality. @*Results@#The fixed risk factors included sex (male), age (older individuals), history of childhood adversity, and a family history of suicide. Changeable risk factors included marital status (single), economic status (poverty), physical illness, history of psychiatric hospitalization, and history of suicide attempts. Recent discharge from a mental hospital and a recent history of suicide attempts were also included. Manageable risk factors included depression (history and current), alcohol problems (frequent drinking and alcohol abuse), hopelessness, agitation, impulsivity, impaired reality testing, and command hallucinations. Protective factors included responsibility to family, social support, moral objections to suicide, religiosity, motivation to get treatment, ability to cope with stress, and a healthy lifestyle. A final score was assigned based on the sum of the risk and protective factor scores. @*Conclusion@#We believe that the development of this checklist will help mental health clinicians to better assess those at risk for suicidal behavior. Further studies are necessary to validate the checklist.
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BACKGROUND/OBJECTIVES@#(Cheonggukjang) is a traditional fermented soybean paste with significant health-promoting effects. On the other hand, there have been insufficient studies on the safety and efficacy of (Cheonggukjang), which is produced using traditional methods containing toxins and biogenic amines (BAs). This study compared the laxative effect of (Cheonggukjang), containing high or low levels of toxins and BAs (HTBC or LTBC) in a loperamide (Lop)-induced constipation mouse model.MATERIALS/METHODS: To induce constipation, Lop (5 mg/kg) was administered orally to ICR mice twice a day for 4 days, and the dose was increased to 8 mg/kg after a 3-day rest period. (Cheonggukjang) (500 mg/kg, HTBC, or LTBC respectively) was administered for four weeks before the Lop treatment. @*RESULTS@#The number of stools, fecal weight, water contents, gastrointestinal transit, and histological alterations were recovered significantly in the HTBC or LTBC groups. HTBC and LTBC administration did not induce significant changes in body weight, dietary intake, and behavior. The opioid-receptor downstream signaling pathway in colon tissues was also evaluated. The c-Kit, stem cell kinase, and mitogen-activated protein kinases subfamilies, including extracellular signal-regulated kinase 1/2, c-Jun N-terminal kinases, and p38, were all downregulated in the HTBC or LTBC-administered mice colon compared to the Lop group. @*CONCLUSION@#These results show that (Cheonggukjang), containing high levels of toxins and BAs, have a similar laxative effect in a mouse model of Lop-induced constipation.
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Conduction block or temporal dispersion on motor nerve conduction studies (NCSs) are known as key features of chronic inflammatory demyelinating polyneuropathy. Some types of CharcotMarieTooth disease (CMT) have been also reported to show conduction block or temporal dispersion on NCS. We experienced a case who presented with slowly progressive motor weakness, sensory loss, foot deformity, and segmental demyelination on NCS. We confirmed her and her mother harboring CMT1B with a novel p.Arg98Leu MPZ variant.
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Objectives@#Demoralization, which results from the inability to cope, is characterized by hopelessness, helplessness, and loss of the meaning and purpose of life. Although demoralization is prevalent in patients with chronic illness, including cancer, a Korean version of the scale has not been developed and validated. Thus, we translated into Korean and validated a version of the Demoralization Scale-II (DS-II-Kr) for cancer patients. @*Methods@#This cross-sectional study recruited cancer patients and survivors who visited a mental health clinic in a cancer hospital. Internal consistency, test-retest reliability, and concurrent validity of DS-II-Kr were assessed. Additionally, the construct validity of two sub-factors was evaluated using confirmatory factor analysis. The optimal DS-II-Kr cut-off point was determined by logistic regression analysis based on the distress cut-off in the Hospital Anxiety-Depression Scale (HADS). @*Results@#This study included 105 participants. The mean and standard deviation for total DS-IIKr scores were 11.9 and 7.6, respectively. The scale demonstrated good internal consistency and test-retest reliability. Goodness-of-fit analysis was moderate for the Meaning and Purpose subscale, and a good fit was found for the Distress and Coping Ability subscale. The DS-II-Kr cut-off value based on HADS was 10 (≤10 vs. >10). @*Conclusion@#The DS-II-Kr is a useful tool for assessing demoralization in clinical and research settings. However, further studies are needed to confirm the optimal DS-II-Kr cut-off score. External validation in other populations is also needed.
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Background@#Non-palpable splenomegaly in patients with polycythemia vera (PV) has seldom been addressed. In this retrospective study, we evaluated non-palpable, volumetric splenomegaly defined based on age- and body surface area (BSA)–matched criteria in patients with PV diagnosed according to the 2016 World Health Organization diagnostic criteria. @*Methods@#Patients with PV who underwent abdominal computed tomography (CT) and who had palpable splenomegaly at diagnosis from January 1991 to December 2020 at Chungnam National University Hospital were enrolled. The spleen volume of each patient was determined by volumetric analysis of abdominal CT and adjusted for the patient’s age and BSA. Then the degree of splenomegaly was classified as no splenomegaly, borderline volumetric splenomegaly, overt volumetric splenomegaly, or palpable splenomegaly. @*Results@#Of the 87 PV patients enrolled, 15 (17.2%) had no splenomegaly, whereas 17 (19.5%), 45 (51.7%), and 10 (11.5%) had borderline volumetric, overt volumetric, and palpable splenomegaly, respectively. The degree of splenomegaly did not affect the cumulative incidence of thrombotic vascular events (10-year incidence: 7.7%, 0%, 22.3%, and 50.7%, respectively, P = 0.414). By contrast, splenomegaly tended to adversely affect myelofibrotic transformation (10-year cumulative incidence: 0%, 0%, 7.1%, and 30.3%, respectively, P = 0.062). Moreover, the cumulative incidence of myelofibrotic transformation was significantly higher in patients with overt volumetric or palpable splenomegaly than those with no or borderline volumetric splenomegaly (10-year incidence: 0% vs. 10.3%, respectively; 15-year incidence: 0% vs. 26.3%, respectively, P = 0.020). Overall survival (OS) differed among patients with different degrees of splenomegaly (15-year OS: 100%, 78.6%, 71.7%, and 51.9%, respectively, P = 0.021). @*Conclusion@#The degree of splenomegaly, including volumetric splenomegaly, based on ageand BSA-matched reference spleen volumes at diagnosis reflects disease progression in PV patients. Therefore, volumetric splenomegaly should be evaluated at the time of diagnosis and taken into consideration when predicting the prognosis of patients with PV.
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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.
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Background@#Information on myelofibrotic and leukemic transformations in Korean Philadelphia chromosome-negative myeloproliferative neoplasms (Ph ‒ MPNs) is limited. @*Methods@#This study retrospectively analyzed transformations in patients diagnosed with essential thrombocythemia (ET), polycythemia vera (PV) prefibrotic/early primary myelofibrosis (pre-PMF), or overt primary myelofibrosis (PMF) based on the 2016 World Health Organization criteria between January 1996 and December 2020 at Chungam National University Hospital, Daejeon, Korea. @*Results@#A total of 351 patients (144 with ET, 131 with PV, 45 with pre-PMF, and 31 with PMF;204 men and 147 women) with a median age of 64 years (range, 15‒91 years) were followed for a median of 4.6 years (range, 0.2‒24.8 years). The 10-year incidence of overt myelofibrosis was higher in pre-PMF than in ET (31.3% and 13.7%, respectively; P =0.031) and PV (12.2%; P =0.003). The 10-year incidence of leukemic transformation was significantly higher in PMF than in ET (40.0% and 7.9%, respectively; P =0.046), pre-PMF (4.7%; P =0.048), and PV (3.2%; P =0.031). The 5-year incidence of leukemic transformation was higher in patients with secondary myelofibrosis (SMF) than in those with PMF (19.0% and 11.4%, respectively; P =0.040). The 5-year overall survival of patients with SMF was significantly worse than that of patients with pre-PMF (74% and 93%, respectively; P =0.027) but did not differ from that of patients with PMF (57%; P =0.744). @*Conclusion@#The rates and clinical courses of myelofibrotic and leukemic transformations in Korean patients with Ph ‒ MPN did not differ from those in Western populations.
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The Say–Barber–Biesecker–Young–Simpson variant of Ohdo syndrome (SBBYSS) (Online Mendelian Inheritance in Man #603736) is a rare autosomal dominant disorder and clinically features blepharophimosis with ptosis, a mask-like facial appearance, cryptorchidism, congenital heart defect, long thumbs/great toes, and thyroid dysfunction. The etiology of SBBYSS has been shown to be due to heterozygous KAT6B gene mutation. Here we report a case of a neonate with SBBYSS identified a novel mutation in KAT6B gene. The patient showed typical dysmorphic facies, cryptorchidism with micropenis, overriding fingers, and long thumbs and toes at birth. He had also hypothyroidism, large atrial septal defect, and sensorineural hearing loss. The next generation sequencing identified a heterozygous novel variant, c.5206C>T (p.Gln1736Ter) in KAT6B gene. At the 9 months of age, he underwent patch closure for atrial septal defect. Until the 12-month follow-up, he was under-developed.
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Tamoxifen (TAM) is an anticancer drug used to treat estrogen receptor (ER)‒positive breast cancer. However, its ER-independent cytotoxic and antifungal activities have prompted debates on its mechanism of action. To achieve a better understanding of the ER-independent antifungal action mechanisms of TAM, we systematically identified TAM-sensitive genes through microarray screening of the heterozygous gene deletion library in fission yeast (Schizosaccharomyces pombe). Secondary confirmation was followed by a spotting assay, finally yielding 13 TAM-sensitive genes under the drug-induced haploinsufficient condition. For these 13 TAM-sensitive genes, we conducted a comparative analysis of their Gene Ontology (GO) ‘biological process’ terms identified from other genome-wide screenings of the budding yeast deletion library and the MCF7breast cancer cell line. Several TAM-sensitive genes overlapped between the yeast strains and MCF7 in GO terms including ‘cell cycle’ (cdc2, rik1, pas1, and leo1), ‘signaling’ (sck2, oga1, and cki3), and ‘vesicle-mediated transport’ (SPCC126.08c, vps54, sec72, and tvp15), suggesting their roles in the ER-independent cytotoxic effects of TAM. We recently reported that the cki3 gene with the ‘signaling’ GO term was related to the ER-independent antifungal action mechanisms of TAM in yeast. In this study, we report that haploinsufficiency of the essential vps54 gene, which encodes the GARP complex subunit, significantly aggravated TAM sensitivity and led to an enlarged vesicle structure in comparison with the SP286 control strain. These results strongly suggest that the vesicle-mediated transport process might be another action mechanism of the ER-independent antifungal or cytotoxic effects of TAM.
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Hypokalemic periodic paralysis (hypoPP) is a disorder characterized by episodic, short-lived, and hypo-reflexive skeletal muscle weakness. HypoPP is a rare disease caused by genetic mutations related to expression of sodium or calcium ion channels. Most mutations are associated with autosomal dominant inheritance, but some are found in patients with no relevant family history. A 28-year-old man who visited the emergency room for paralytic attack was assessed in this study.He exhibited motor weakness in four limbs. There was no previous medical history or family history. The initial electrocardiogram showed a flat T wave and QT prolongation. His blood test was delayed, and sudden hypotension and bradycardia were observed. The blood test showed severe hypokalemia. After correcting hypokalemia, his muscle paralysis recovered without any neurological deficits. The patient’s thyroid function and long exercise test results were normal. However, because of the history of high carbohydrate diet and exercise, hypoPP was suspected. Hence, next-generation sequencing (NGS) was performed, and a mutation of Arg669His was noted in the SCN4A gene. Although hypoPP is a rare disease, it can be suspected in patients with hypokalemic paralysis, and iden tification of this condition is important for preventing further attacks and improving patient outcomes. Diagnosing hypoPP through targeted NGS is a cost-effective and useful method.
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Background/Aims@#Recent changes in the diagnostic criteria for myeloproliferative neoplasms (MPNs) and increasing patient numbers necessitate updating of the data on vascular events in patients with such disorders. @*Methods@#In this single-center study, thrombotic and hemorrhagic events were retrospectively analyzed in patients diagnosed with essential thrombocythemia (ET), polycythemia vera (PV) prefibrotic/early primary myelofibrosis (pre-PMF), or PMF, based on the 2016 World Health Organization diagnostic criteria. @*Results@#Of a total of 335 consecutive patients (139 ET, 42 pre-PMF, 124 PV, and 30 PMF patients; 192 males and 143 females) of median age 64 years (range, 15 to 91), 112 (33.4%) experienced a total of 126 thrombotic events before diagnosis, at the time of diagnosis, or during follow-up over a median of 4.6 years (range, 0.1 to 26.5). Cerebrovascular thrombosis (18.8%) was the most common initial event, followed by coronary heart disease (10.1%) and splanchnic (1.5%) and peripheral thrombosis (1.5%). Arterial thrombosis was more common than venous thrombosis (31.3% vs. 2.1%, respectively; p = 0.001). Thrombosis was most frequent in PV patients (39.5%), followed by patients with pre-PMF (38.1%), ET (30.9%), and PMF (13.3%). Of the 112 patients who experienced thromboses, 53 (47%) and 39 (33.9%) had thrombotic events before and at the time of MPN diagnosis, respectively. Twenty-seven patients (8.1%) experienced 29 hemorrhagic events, of which gastrointestinal bleeding (n = 20) was the most common. @*Conclusions@#Most thrombotic events occurred before or at the time of diagnosis, and the prevalence of arterial thrombosis was markedly higher than that of venous thrombosis in patients with MPN.
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Background/Aims@#Recent changes in the diagnostic criteria for myeloproliferative neoplasms (MPNs) and increasing patient numbers necessitate updating of the data on vascular events in patients with such disorders. @*Methods@#In this single-center study, thrombotic and hemorrhagic events were retrospectively analyzed in patients diagnosed with essential thrombocythemia (ET), polycythemia vera (PV) prefibrotic/early primary myelofibrosis (pre-PMF), or PMF, based on the 2016 World Health Organization diagnostic criteria. @*Results@#Of a total of 335 consecutive patients (139 ET, 42 pre-PMF, 124 PV, and 30 PMF patients; 192 males and 143 females) of median age 64 years (range, 15 to 91), 112 (33.4%) experienced a total of 126 thrombotic events before diagnosis, at the time of diagnosis, or during follow-up over a median of 4.6 years (range, 0.1 to 26.5). Cerebrovascular thrombosis (18.8%) was the most common initial event, followed by coronary heart disease (10.1%) and splanchnic (1.5%) and peripheral thrombosis (1.5%). Arterial thrombosis was more common than venous thrombosis (31.3% vs. 2.1%, respectively; p = 0.001). Thrombosis was most frequent in PV patients (39.5%), followed by patients with pre-PMF (38.1%), ET (30.9%), and PMF (13.3%). Of the 112 patients who experienced thromboses, 53 (47%) and 39 (33.9%) had thrombotic events before and at the time of MPN diagnosis, respectively. Twenty-seven patients (8.1%) experienced 29 hemorrhagic events, of which gastrointestinal bleeding (n = 20) was the most common. @*Conclusions@#Most thrombotic events occurred before or at the time of diagnosis, and the prevalence of arterial thrombosis was markedly higher than that of venous thrombosis in patients with MPN.
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Psychiatric side effects of oseltamivir can result in accident-proneness and suicide. Reportedly, such adverse psychiatric events are more common in children than in adults, but other risk factors are not known. We present a 13-year-old girl with influenza infection who developed manic symptoms after taking oseltamivir and receiving the human papillomavirus vaccination. While other research has found that psychiatric side effects associated with oseltamivir generally occur within 48 hours after beginning administration, in this case the manic symptoms developed on the fourth day after cessation of 5-day course of oseltamivir administration. Based on our review of this case, we recommend that clinicians should carry out vigilant monitoring of each patient’s mental state when the patient is young, has a family history of psychiatric disorder, has drug sensitivity and has received medical treatments such as vaccination before or after taking oseltamivir. In addition, as side effects of oseltamivir may occur more than 48 hours after administration, it will be necessary to observe patients for several days after the prescription of oseltamivir.
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We used a heterozygous gene deletion library of fission yeasts comprising all essential and non-essential genes for a microarray screening of target genes of the antifungal terbinafine, which inhibits ergosterol synthesis via the erg1 enzyme. We identified 14 heterozygous strains corresponding to 10 non-essential [7 ribosomal-protein (RP) coding genes, spt7, spt20, and elp2] and 4 essential genes (tif302, rpl2501, rpl31, and erg1). Expectedly, their erg1 mRNA and protein levels had decreased compared to the control strain SP286. When we studied the action mechanism of the non-essential target genes using cognate haploid deletion strains, knockout of SAGA-subunit genes caused a down-regulation in erg1 transcription compared to the control strain ED668. However, knockout of RP genes conferred no susceptibility to ergosterol-targeting antifungals. Surprisingly, the RP genes participated in the erg1 transcription as components of repressor complexes as observed in a comparison analysis of the experimental ratio of erg1 mRNA. To understand the action mechanism of the interaction between the drug and the novel essential target genes, we performed isobologram assays with terbinafine and econazole (or cycloheximide). Terbinafine susceptibility of the tif302 heterozygous strain was attributed to both decreased erg1 mRNA levels and inhibition of translation. Moreover, Tif302 was required for efficacy of both terbinafine and cycloheximide. Based on a molecular modeling analysis, terbinafine could directly bind to Tif302 in yeasts, suggesting Tif302 as a potential off-target of terbinafine. In conclusion, this genome-wide screening system can be harnessed for the identification and characterization of target genes under any condition of interest.
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A clinical practice guideline for patients in the dying process in general wards and their families, developed through an evidence-based process, is presented herein. The purpose of this guideline is to enable a peaceful death based on an understanding of suitable management of patients’ physical and mental symptoms, psychological support, appropriate deci-sion-making, family care, and clearly-defined team roles. Although there are limits to the available evidence regarding medical issues in patients facing death, the final recommendations were determined from expert advice and feedback, considering values and preferences related to medical treatment, benefits and harms, and applicability in the real world. This guideline should be applied in a way that takes into account specific health care environments, including the resources of medical staff and differences in the available resources of each institution. This guideline can be used by all medical institutions in South Korea.
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We present a rare case of urothelial carcinoma in situ (CIS), which invades the prostate and seminal vesicle (SV). A 70-year-old man underwent transurethral resection of bladder (TURB), and the pathologic examination revealed multiple CIS. Although the patient received intravesical bacillus Calmette-Guerin (BCG) therapy following TURB, recurrence of CIS was confirmed in the bladder and left distal ureter at 3 months following BCG. Radical cystectomy was performed due to BCG-refractory CIS. Microscopically, CIS was found throughout the mucosa of the bladder, left ureter, prostatic duct, and both SVs. Next-generation sequencing revealed significant differences in tumor clonality between bladder and SV CIS cells. Among 101 (bladder CIS) and 95 (SV CIS) somatic mutations, only two were shared, and only one gene (ARHGAP23) was common exon coding region gene. In conclusion, multicentric genetic changes, in line with the field-cancerization effect, may result in SV involvement by CIS of the bladder.
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The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. In Korea, the amount of genomic data has been increasing rapidly in the recent years. Leveraging these big data requires researchers to use large-scale computational resources and analysis pipelines. A promising solution for addressing this computational challenge is cloud computing, where CPUs, memory, storage, and programs are accessible in the form of virtual machines. Here, we present a cloud computing-based system, Bio-Express, that provides user-friendly, cost-effective analysis of massive genomic datasets. Bio-Express is loaded with predefined multi-omics data analysis pipelines, which are divided into genome, transcriptome, epigenome, and metagenome pipelines. Users can employ predefined pipelines or create a new pipeline for analyzing their own omics data. We also developed several web-based services for facilitating downstream analysis of genome data. Bio-Express web service is freely available at https://www.bioexpress.re.kr/.