Depression and suicide risk prediction models using blood-derived multi-omics data

More than 300 million people worldwide experience depression; annually, ~800,000 people die by suicide. Unfortunately, conventional interview-based diagnosis is insufficient to accurately predict a psychiatric status. We developed machine learning models to predict depression and suicide risk using blood methylome and transcriptome data from 56 suicide attempters (SAs), 39 patients with major depressive disorder (MDD), and 87 healthy controls. Our random forest classifiers showed accuracies of 92.6% in distinguishing SAs from MDD patients, 87.3% in distinguishing MDD patients from controls, and 86.7% in distinguishing SAs from controls. We also developed regression models for predicting psychiatric scales with R2 values of 0.961 and 0.943 for Hamilton Rating Scale for Depression???17 and Scale for Suicide Ideation, respectively. Multi-omics data were used to construct psychiatric status prediction models for improved mental health treatment

The dual role of transforming growth factor-beta signatures in human B viral multistep hepatocarcinogenesis: early and late responsive genes

Background/Aim Transforming growth factor-beta (TGF-β) has a dichotomous role, functioning as a tumor suppressor and tumor promoter. TGF-β signatures, explored in mouse hepatocytes, have been reported to predict the clinical outcomes of hepatocellular carcinoma (HCC) patients; HCCs exhibiting early TGF-β signatures showed a better prognosis than those with late TGF-β signatures. The expression status of early and late TGF-β signatures remains unclear in defined lesions of human B-viral multistep hepatocarcinogenesis. Methods The expression of TGF-β signatures, early and late responsive signatures of TGF-β were investigated and analyzed for their correlation in cirrhosis, low-grade dysplastic nodules (DNs), high-grade DNs, early HCCs and progressed HCCs (pHCCs) by real-time PCR and immunohistochemistry. Results The expression levels of TGF-β signaling genes (TGFB1, TGFBR1, TGFBR2 and SMAD4) gradually increased with the progression of hepatocarcinogenesis, peaking in pHCCs. The expression of early responsive genes of TGF-β (GADD45B, FBP1, CYP1A2 and CYP3A4) gradually decreased, and that of the late TGF-β signatures (TWIST and SNAI1) significantly increased according to the progression of multistep hepatocarcinogenesis. Furthermore, mRNA levels of TWIST and SNAI1 were well correlated with those of stemness markers, with upregulation of TGF-β signaling, whereas FBP1 expression was inversely correlated with that of stemness markers. Conclusions The enrichment of the late responsive signatures of TGF-β with induction of stemness is considered to be involved in the progression of the late stage of multistep hepatocarcinogenesis, whereas the early responsive signatures of TGF-β are suggested to have tumor-suppressive roles in precancerous lesions of the early stage of multistep hepatocarcinogenesis

Letter to the Editor: Detection of EML4-ALK and Other ALK Fusion Genes in Lung Cancer: A Lesson from the Leukemia Fusion Gene Analysis and Future Application

We read with interest the article “EML4-ALK Fusion Gene in Korean Non-Small Cell Lung Cancer ” in a recent issue of the Journal of Korean Medical Science by Jin et al. (1). In this study, EML4-ALK fusion gene was detected in 10 of 167 non-small cell lung cancer (NSCLC) patients by using reverse transcriptase-polymerase chain reaction (RT-PCR) as a basic screening technique instead of fluorescence in situ hybridization (FISH) method. The frequency of EML4-ALK fusion gene in this study (6.0%) was not largely different from a previous study that used the FISH method on Korean NSCLC patients (4.2%) (2), while it did not diverge from the results in previous studies on a general NSCLC patient population that yielded 3%-7 % ratios as well. Based on the experience of detecting leukemia fusion genes with several new molecular methods during the diagnosis of leukemia (3-6), we would like to mention the pros and cons of such methods i

Prognostic Significance of HER2 Gene Amplification According to Stage of Breast Cancer

It is well known that the amplification of the HER2 gene is closely associated with poor prognosis of breast cancer. However, there is controversy about the clinical significance of HER2 according to lymph node status in breast cancer. The aim of this study was to identify the differences in the prognostic significance of HER2 gene amplification according to the stages of breast cancer. We prepared a tissue array for fluorescence in situ hybridization (FISH) with breast cancer specimens from the surgery in 1994 to 1999. Total 338 cases of breast cancer were enrolled and the median follow-up period was 6.3 yr. The detection rates of HER2 gene amplification were as follows: 10.3% in stage I, 22.3% in stage II, and 43.8% in stage III. On survival analyses HER2-positive groups showed worse prognosis in stage III of breast cancer, but not in stage I or II. Multivariate analyses with a Cox-regression model also revealed that HER2 amplification was an independent prognostic factor only in stage III breast cancer. Regarding HER2 gene amplification as a prognostic factor of breast cancer, the clinical significance of the gene was found to be confined to advanced breast cancer

Association Between Parkinsonism and Participation in Agriculture in Korea

BACKGROUND AND PURPOSE: Environmental factors might influence the pathogenesis of Parkinson's disease (PD) or multiple-system atrophy (MSA), and previous examinations of pesticide exposure, well-water drinking, and farming have produced inconclusive results. Because agriculture has been of considerable importance to Korean society, and hence the risk of exposure to pesticides was high in Korea, this study investigated whether such exposure is associated with elevated risks of developing PD and MSA. METHODS: Two hundred and thirty-five PD patients, 133 MSA patients, and 77 normal control subjects were examined. Data concerning environmental factors were collected by face-to-face interviews using a structured questionnaire. Odds ratios (ORs) were calculated by binary logistic regression. RESULTS: ORs for environmental risk factors for developing PD were 1.06 [95% confidence interval (CI) = 1.02-1.10] for age and 2.37 (95% CI = 1.32-4.27) for rural well-water drinking for >10 years. Smoking >10 pack-years (OR = 0.31; 95% CI = 0.11-0.64) was a preventable factor for developing PD in this study. However, no significant risk factors were identified for MSA. CONCLUSIONS: These results suggest that exposure to certain environmental risk factors plays a role in the development of PD. However, the development of MSA appears to be independent of environmental risk factors in Korean patients

Treatment Outcome and Mortality among Patients with Multidrug-resistant Tuberculosis in Tuberculosis Hospitals of the Public Sector

This study was conducted to evaluate treatment outcome, mortality, and predictors of both in patients with multidrug-resistant tuberculosis (MDR-TB) at 3 TB referral hospitals in the public sector of Korea. We included MDR-TB patients treated at 3 TB referral hospitals in 2004 and reviewed retrospectively their medical records and mortality data. Of 202 MDR-TB patients, 75 (37.1%) had treatment success and 127 (62.9%) poor outcomes. Default rate was high (37.1%, 75/202), comprising 59.1% of poor outcomes. Male sex (adjusted odds ratio [aOR], 2.91; 95% confidence interval [CI], 1.13-7.49), positive smear at treatment initiation (aOR, 5.50; 95% CI, 1.22-24.90), and extensively drug-resistant TB (aOR, 10.72; 95% CI, 1.23-93.64) were independent predictors of poor outcome. The all-cause mortality rate was 31.2% (63/202) during the 3-4 yr after treatment initiation. In conclusion, the treatment outcomes of patients with MDR-TB at the 3 TB hospitals are poor, which may reflect the current status of MDR-TB in the public sector of Korea. A more comprehensive program against MDR-TB needs to be integrated into the National Tuberculosis Program of Korea