Deep learning imaging phenotype can classify metabolic syndrome and is predictive of cardiometabolic disorders

BACKGROUND

Cardiometabolic disorders pose significant health risks globally. Metabolic syndrome, characterized by a cluster of potentially reversible metabolic abnormalities, is a known risk factor for these disorders. Early detection and intervention for individuals with metabolic abnormalities can help mitigate the risk of developing more serious cardiometabolic conditions. This study aimed to develop an image-derived phenotype (IDP) for metabolic abnormality from unenhanced abdominal computed tomography (CT) scans using deep learning. We used this IDP to classify individuals with metabolic syndrome and predict future occurrence of cardiometabolic disorders.

METHODS

A multi-stage deep learning approach was used to extract the IDP from the liver region of unenhanced abdominal CT scans. In a cohort of over 2,000 individuals the IDP was used to classify individuals with metabolic syndrome. In a subset of over 1,300 individuals, the IDP was used to predict future occurrence of hypertension, type II diabetes, and fatty liver disease.

RESULTS

For metabolic syndrome (MetS) classification, we compared the performance of the proposed IDP to liver attenuation and visceral adipose tissue area (VAT). The proposed IDP showed the strongest performance (AUC 0.82) compared to attenuation (AUC 0.70) and VAT (AUC 0.80). For disease prediction, we compared the performance of the IDP to baseline MetS diagnosis. The models including the IDP outperformed MetS for type II diabetes (AUCs 0.91 and 0.90) and fatty liver disease (AUCs 0.67 and 0.62) prediction and performed comparably for hypertension prediction (AUCs of 0.77).

CONCLUSIONS

This study demonstrated the superior performance of a deep learning IDP compared to traditional radiomic features to classify individuals with metabolic syndrome. Additionally, the IDP outperformed the clinical definition of metabolic syndrome in predicting future morbidities. Our findings underscore the utility of data-driven imaging phenotypes as valuable tools in the assessment and management of metabolic syndrome and cardiometabolic disorders.

A novel approach of kinship determination based on the physical length of genetically shared regions of chromosomes

BACKGROUND

Determination of genetic relatedness between individuals plays a crucial role in resolving numerous civil cases involving familial relationships and in forensic investigation concerning missing persons. Short tandem repeats (STRs), known for their high degree of DNA polymorphism, have traditionally been the primary choice of DNA markers in genetic testing, but their application for kinships testing is limited to cases involving close kinship. SNPs have emerged as promising supplementary markers for kinship determination. Nevertheless, the challenging remains in discriminating between third-degree or more distant relatives, such as first cousins, using SNPs.

OBJECTIVE

To investigate a kinship analysis method for distant degree of familial relationships using high-density SNP data.

METHODS

A high-density SNP data from 337 individuals of Korean families using Affymetrix Axiom KORV1.0-96 Array was obtained for this study. SNPs were aligned by chromosomal positions, and identity-by-state (IBS) was determined, and then shared regions as consecutive SNPs with IBS of 1 or 2 were investigated. The physical lengths of these IBS segments were measured and summed them to create an Index, as a measure of kinship.

RESULTS

The kinship was determined by the physical length of shared chromosomal regions that are distinguished by each kinship. Using this method, the relationship was able be distinguished up to the fourth degree of kinship, and non-relatives were clearly distinguished from true relatives. We also found a potential for this approach to be used universally, regardless of microarray platforms for SNP genotyping and populations.

CONCLUSION

This method has a potential to determine the different degree of kinship between individuals and to distinguish non-relatives from true relatives, which can be of great help for practical applications in kinship determination.

Genome-wide association study of metabolic dysfunction-associated fatty liver disease in a Korean population

Genome-wide association studies have identified several genetic variants associated with nonalcoholic fatty liver disease. To emphasize metabolic abnormalities in fatty liver, metabolic (dysfunction)-associated fatty liver disease (MAFLD) has been introduced; thus, we aimed to investigate single-nucleotide polymorphisms related to MAFLD and its subtypes. A genome-wide association study was performed to identify genetic factors related to MAFLD. We used a Korean population-based sample of 2282 subjects with MAFLD and a control group of 4669. We replicated the results in a validation sample which included 639 patients with MAFLD and 1578 controls. Additionally, we categorized participants into three groups, no MAFLD, metabolic dysfunction (MD)-MAFLD, and overweight/obese-MAFLD. After adjusting for age, sex, and principal component scores, rs738409 [risk allele G] and rs3810622 [risk allele T], located in the PNPLA3 gene, showed significant associations with MAFLD (P-values, discovery set = 1.60 × 10-15 and 4.84 × 10-10; odds ratios, 1.365 and 1.284, validation set = 1.39 × 10-4, and 7.15 × 10-4, odds ratios, 1.299 and 1.264, respectively). An additional SNP rs59148799 [risk allele G] located in the GATAD2A gene showed a significant association with MAFLD (P-values, discovery set = 2.08 × 10-8 and validation set = 0.034, odds ratios, 1.387 and 1.250). rs738409 was significantly associated with MAFLD subtypes ([overweight/obese-MAFLD; odds ratio (95% confidence interval), P-values, 1.515 (1.351-1.700), 1.43 × 10-12 and MD-MAFLD: 1.300 (1.191-1.416), 2.90 × 10-9]. There was a significant relationship between rs3810622 and overweight/obese-MAFLD and MD-MAFLD [odds ratios (95% confidence interval), P-values, 1.418 (1.258, 1.600), 1.21 × 10-8 and 1.225 (1.122, 1.340), 7.06 × 10-6, respectively]; the statistical significance remained in the validation set. PNPLA3 was significantly associated with MAFLD and MAFLD subtypes in the Korean population. These results indicate that genetic factors play an important role in the pathogenesis of MAFLD.

Genetic and Metabolic Characteristics of Lean Nonalcoholic Fatty Liver Disease in a Korean Health Examinee Cohort

Background/Aims

The pathophysiology of lean nonalcoholic fatty liver disease (NAFLD) is unclear but has been shown to be associated with more diverse pathogenic mechanisms than that of obese NAFLD. We investigated the characteristics of genetic or metabolic lean NAFLD in a health checkup cohort.

Methods

This retrospective cross-sectional study analyzed single nucleotide polymorphism data for 6,939 health examinees. Lean individuals were categorized according to a body mass index cutoff of 23 kg/m2. Single nucleotide polymorphisms were analyzed using genotyping arrays.

Results

The prevalence of lean NAFLD was 21.6% among all participants with NAFLD, and the proportion of lean NAFLD was 18.5% among lean participants. The prevalence of metabolic syndrome and diabetes among lean patients with NAFLD was 12.4% and 10.4%, respectively. Lean NAFLD appeared to be metabolic-associated in approximately 20.1% of patients. The homozygous minor allele (GG) of PNPLA3 (rs738409) and heterozygous minor alleles (CT, TT) of TM6SF2 (rs58542926) were associated with lean NAFLD. However, the prevalence of fatty liver was not associated with the genetic variants MBOAT7 (rs641738), HSD17B13 (rs72613567), MARC1 (rs2642438), or AGXT2 (rs2291702) in lean individuals. Lean NAFLD appeared to be associated with PNPLA3 or TM6SF2 genetic variation in approximately 32.1% of cases. Multivariate risk factor analysis showed that metabolic risk factors, genetic risk variants, and waist circumference were independent risk factors for lean NAFLD.

Conclusions

In a considerable number of patients, lean NAFLD did not appear to be associated with known genetic or metabolic risk factors. Further studies are required to investigate additional risk factors and gain a more comprehensive understanding of lean NAFLD.

The association between platelet-related parameters and nonalcoholic fatty liver disease in a metabolically healthy nonobese population

Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease characterized by subclinical inflammation and is related to obesity and metabolic syndrome (MS), but it is also frequently observed in nonobese populations. We aimed to evaluate the relationship between the white blood cell count-to-mean platelet volume ratio (WBC/MPV), platelet-to-lymphocyte count ratio (PLR) and lymphocyte-monocyte ratio (LMR) in association with NAFLD, considering the presence of obesity and MS. Additionally, we aimed to investigate whether these parameters exhibited similar correlations in metabolic dysfunction-associated steatotic liver disease (MASLD) as observed in NAFLD. This cross-sectional study included subjects who underwent a comprehensive health evaluation, including blood tests and abdominal ultrasonography. Subgroup analyses were conducted based on obesity and MS. Out of a total 5929 subjects (3271 males, mean age 49.7 ± 10.6 years), 2253 (38.0%) had NAFLD. WBC/MPV was significantly higher, and PLR was significantly lower in subjects with NAFLD. In the analysis restricted to the nonobese (BMI < 25 kg/m2) population without MS, both WBC/MPV and PLR were independently associated with NAFLD: WBC/MPV (adjusted OR 3.366; 95% CI 2.238-5.066) and PLR (adjusted OR 0.997; 95% CI 0.996-0.999). When assessing the risk of NAFLD based on the WBC/MPV and PLR quartiles, the adjusted OR and 95% CI for the lowest quartile compared to the highest were 2.055 (95% CI 1.626-2.602) for WBC/MPV and 0.660 (95% CI 0.523-0.832) for PLR in the nonobese, metabolically healthy group. The levels of WBC/MPV and PLR were independently associated with NAFLD. Furthermore, in MASLD, an association with WBC/MPV, PLR and LMR was identified, similar to the results observed in NAFLD, even after adjusting for confounding variables. In conclusion, the present study demonstrated a significant association between NAFLD and platelet-related parameters, especially in nonobese, metabolically healthy subjects.

Clinical Strategies in Gene Screening Counseling for the Healthy General Population

The burgeoning interest in precision medicine has propelled an increase in the use of genome tests for screening purposes within the healthy population. Gene screening tests aim to pre-emptively identify those individuals who may be genetically predisposed to certain diseases. However, as genetic screening becomes more commonplace, it is essential to acknowledge the unique challenges it poses. A prevalent issue in this regard is the occurrence of falsepositive results, which can lead to unnecessary additional tests or treatments, and psychological distress. Additionally, the interpretation of genomic variants is based on current research evidence, and can accordingly change as new research findings emerge, potentially altering the clinical significance of these variants. Conversely, a further prominent concern regards false assurances in genetic testing, as genetic tests can yield false-negative results, potentially posing a significant clinical risk. Moreover, the results obtained for the same disease can vary among different genetic testing services, due to differences in the types of variants assessed, the scope of tests, analytical methods, and the algorithms used for predicting diseases. Consequently, whereas genetic testing holds significant promise for the future of medicine, it poses unique challenges. If conducted without a full understanding of its implications, genetic testing may fail to achieve its purpose potentially hindering effective health management. Therefore, to ensure a comprehensive understanding of the implications of genetic testing within the general population, sufficient discussion and careful consideration should be given to counseling based on gene test results.

Genome-wide polygenic risk scores for hypertensive disease during pregnancy can also predict the risk for long-term cardiovascular disease

BACKGROUND

Hypertensive disorders during pregnancy are associated with the risk of long-term cardiovascular disease after pregnancy, but it has not yet been determined whether genetic predisposition for hypertensive disorders during pregnancy can predict the risk for long-term cardiovascular disease.

OBJECTIVE

This study aimed to evaluate the risk for long-term atherosclerotic cardiovascular disease according to polygenic risk scores for hypertensive disorders during pregnancy.

STUDY DESIGN

Among UK Biobank participants, we included European-descent women (n=164,575) with at least 1 live birth. Participants were divided according to genetic risk categorized by polygenic risk scores for hypertensive disorders during pregnancy (low risk, score ≤25th percentile; medium risk, score 25th∼75th percentile; high risk, score >75th percentile), and were evaluated for incident atherosclerotic cardiovascular disease, defined as the new occurrence of one of the following: coronary artery disease, myocardial infarction, ischemic stroke, or peripheral artery disease.

RESULTS

Among the study population, 2427 (1.5%) had a history of hypertensive disorders during pregnancy, and 8942 (5.6%) developed incident atherosclerotic cardiovascular disease after enrollment. Women with high genetic risk for hypertensive disorders during pregnancy had a higher prevalence of hypertension at enrollment. After enrollment, women with high genetic risk for hypertensive disorders during pregnancy had an increased risk for incident atherosclerotic cardiovascular disease, including coronary artery disease, myocardial infarction, and peripheral artery disease, compared with those with low genetic risk, even after adjustment for history of hypertensive disorders during pregnancy.

CONCLUSION

High genetic risk for hypertensive disorders during pregnancy was associated with increased risk for atherosclerotic cardiovascular disease. This study provides evidence on the informative value of polygenic risk scores for hypertensive disorders during pregnancy in prediction of long-term cardiovascular outcomes later in life.

Investigation of optimal convolutional neural network conditions for thyroid ultrasound image analysis

Neural network models have been used to analyze thyroid ultrasound (US) images and stratify malignancy risk of the thyroid nodules. We investigated the optimal neural network condition for thyroid US image analysis. We compared scratch and transfer learning models, performed stress tests in 10% increments, and compared the performance of three threshold values. All validation results indicated superiority of the transfer learning model over the scratch model. Stress test indicated that training the algorithm using 3902 images (70%) resulted in a performance which was similar to the full dataset (5575). Threshold 0.3 yielded high sensitivity (1% false negative) and low specificity (72% false positive), while 0.7 gave low sensitivity (22% false negative) and high specificity (23% false positive). Here we showed that transfer learning was more effective than scratch learning in terms of area under curve, sensitivity, specificity and negative/positive predictive value, that about 3900 images were minimally required to demonstrate an acceptable performance, and that algorithm performance can be customized according to the population characteristics by adjusting threshold value.

Long-term cardiovascular outcomes of gestational diabetes mellitus: a prospective UK Biobank study

BACKGROUND

Previous studies showed that gestational diabetes mellitus (GDM) can be a risk factor for subsequent atherosclerotic cardiovascular disease. However, there is a paucity of information regarding diverse cardiovascular outcomes in elderly women after GDM. In the current study, we examined whether women with a history of GDM have an increased risk for long-term overall cardiovascular outcomes.

METHODS

Among the UK participants, we included 219,330 women aged 40 to 69 years who reported at least one live birth. The new incidence of diverse cardiovascular outcomes was compared according to GDM history by multivariable Cox proportional hazard models. In addition, causal mediation analysis was performed to examine the contribution of well-known risk factors to observed risk.

RESULTS

After enrollment, 13,094 women (6.0%) developed new overall cardiovascular outcomes. Women with GDM history had an increased risk for overall cardiovascular outcomes [adjusted HR (aHR) 1.36 (95% CI 1.18-1.55)], including coronary artery disease [aHR 1.31 (1.08-1.59)], myocardial infarction [aHR 1.65 (1.27-2.15)], ischemic stroke [aHR 1.68 (1.18-2.39)], peripheral artery disease [aHR 1.69 (1.14-2.51)], heart failure [aHR 1.41 (1.06-1.87)], mitral regurgitation [aHR 2.25 (1.51-3.34)], and atrial fibrillation/flutter [aHR 1.47 (1.18-1.84)], after adjustment for age, race, BMI, smoking, early menopause, hysterectomy, prevalent disease, and medication. In mediation analysis, overt diabetes explained 23%, hypertension explained 11%, and dyslipidemia explained 10% of the association between GDM and overall cardiovascular outcome.

CONCLUSIONS

GDM was associated with more diverse cardiovascular outcomes than previously considered, and conventional risk factors such as diabetes, hypertension, and dyslipidemia partially contributed to this relationship.

Impaired migration of autologous induced neural stem cells from patients with schizophrenia and implications for genetic risk for psychosis

Stem cell technologies have presented explicit evidence of the neurodevelopmental hypothesis of schizophrenia. However, few studies investigated relevance of the schizophrenia genetic liability and the use of genetic reprogramming on pluripotent stem cells to the impaired neurodevelopment shown by stem cells. Therefore, this study sought to investigate the cellular phenotypes of induced neural stem cells (iNSCs) derived without genetic modification from patients with schizophrenia and from genetic high risk (GHR) individuals. Three patients with a diagnosis of schizophrenia, 3 GHR individuals who had two or more relatives with schizophrenia, and 3 healthy volunteers participated. iNSCs were derived using a small molecule-based lineage switch method, and their gene expression levels and migration capabilities were examined. Demographic characteristics were not different among the groups (age, χ² = 5.637, P = .060; education, χ² = 2.111, P = .348). All participants stayed well during the follow-up except one GHR individual who developed psychosis 1.5 years later. Migration capacity was impaired in iNSCs from patients with schizophrenia (SZ-iNSCs) compared to iNSCs from GHR individuals or controls (P < .001). iNSCs from a GHR individual who later developed schizophrenia showed migratory impairment that was similar to SZ-iNSCs. Gene expression levels of Sox2 in SZ-iNSCs were significantly lower than those in controls (P = .028). Defective migration in genetically unmodified SZ-iNSCs is the first direct demonstration of neurodevelopmental abnormalities in schizophrenia. Additionally, alterations in gene expression in SZ-iNSCs suggest mechanisms by which genetic liability leads to aberrant neurodevelopment.

Dissecting the clinical relevance of polygenic risk score for obesity-a cross-sectional, longitudinal analysis

BACKGROUND

Obesity is a global pandemic disease whose prevalence is increasing worldwide. The clinical relevance of a polygenic risk score (PRS) for obesity has not been fully elucidated in Asian populations.

METHOD

We utilized a comprehensive health check-up database from the Korean population in conjunction with genotyping to generate PRS for BMI (PRS-BMI). We conducted a phenome-wide association (PheWAS) analysis and observed the longitudinal association of BMI with PRS-BMI.

RESULTS

PRS-BMI was generated by PRS-CS. Adding PRS-BMI to a model predicting ten-year BMI based on age, sex, and baseline BMI improved the model's accuracy (p = 0.003). In a linear mixed model of longitudinal change in BMI with aging, higher deciles of PRS were directly associated with changes in BMI. In the PheWAS, significant associations were observed for metabolic syndrome, bone density, and fatty liver. In the lean body population, those having the top 20% PRS-BMI had higher BMI and body fat mass along with better metabolic trait profiles compared to the bottom 20%. A bottom-20% PRS-BMI was a risk factor for metabolically unhealthy lean body (odds ratio 3.092, 95% confidence interval 1.707-6.018, p < 0.001), with adjustment for age, sex and BMI.

CONCLUSIONS

Genetic predisposition to obesity as defined by PRS-BMI was significantly associated with obesity-related disease or trajectory of obesity. Low PRS-BMI might be a risk factor associated with a metabolically unhealthy lean body. Better understanding the mechanisms of these relationships may allow tailored intervention in obesity or early selection of populations at risk of metabolic disease.

Development and validation of a novel strong prognostic index for colon cancer through a robust combination of laboratory features for systemic inflammation: a prognostic immune nutritional index

BACKGROUND

Systemic inflammation is associated with survival outcomes in colon cancer. However, it is not well-known which systemic inflammatory marker is a powerful prognostic marker in patients with colon cancer.

METHODS

A total of 4535 colon cancer patients were included in this study. We developed a novel prognostic index using a robust combination of seven systemic inflammation-associated blood features of the discovery set. The predictability and generality of the novel prognostic index were evaluated in the discovery, validation and replication sets.

RESULTS

Among all combinations, the combination of albumin and monocyte count was the best candidate expression. The final formula of the proposed novel index is named the Prognostic Immune and Nutritional Index (PINI). The concordance index of PINI for overall and progression-free survival was the highest in the discovery, validation and replication sets compared to existing prognostic inflammatory markers. PINI was found to be a significant independent prognostic factor for both overall and progression-free survival.

CONCLUSIONS

PINI is a novel prognostic index that has improved discriminatory power in colon cancer patients and appears to be superior to existing prognostic inflammatory markers. PINI can be utilised for decision-making regarding personalised treatment as the complement of the TNM staging system.

NETMAGE: A human disease phenotype map generator for the network-based visualization of phenome-wide association study results

BACKGROUND

Disease complications, the onset of secondary phenotypes given a primary condition, can exacerbate the long-term severity of outcomes. However, the exact cause of many of these cross-phenotype associations is still unknown. One potential reason is shared genetic etiology-common genetic drivers may lead to the onset of multiple phenotypes. Disease-disease networks (DDNs), where nodes represent diseases and edges represent associations between diseases, can provide an intuitive way of understanding the relationships between phenotypes. Using summary statistics from a phenome-wide association study (PheWAS), we can generate a corresponding DDN where edges represent shared genetic variants between diseases. Such a network can help us analyze genetic associations across the diseasome, the landscape of all human diseases, and identify potential genetic influences for disease complications.

RESULTS

To improve the ease of network-based analysis of shared genetic components across phenotypes, we developed the humaN disEase phenoType MAp GEnerator (NETMAGE), a web-based tool that produces interactive DDN visualizations from PheWAS summary statistics. Users can search the map by various attributes and select nodes to view related phenotypes, associated variants, and various network statistics. As a test case, we used NETMAGE to construct a network from UK BioBank (UKBB) PheWAS summary statistic data. Our map correctly displayed previously identified disease comorbidities from the UKBB and identified concentrations of hub diseases in the endocrine/metabolic and circulatory disease categories. By examining the associations between phenotypes in our map, we can identify potential genetic explanations for the relationships between diseases and better understand the underlying architecture of the human diseasome. Our tool thus provides researchers with a means to identify prospective genetic targets for drug design, using network medicine to contribute to the exploration of personalized medicine.

Leveraging deep phenotyping from health check-up cohort with 10,000 Korean individuals for phenome-wide association study of 136 traits

The expanding use of the phenome-wide association study (PheWAS) faces challenges in the context of using International Classification of Diseases billing codes for phenotype definition, imbalanced study population ethnicity, and constrained application of the results in research. We performed a PheWAS utilizing 136 deep phenotypes corroborated by comprehensive health check-ups in a Korean population, along with trans-ethnic comparisons through using the UK Biobank and Biobank Japan Project. Meta-analysis with Korean and Japanese population was done. The PheWAS associated 65 phenotypes with 14,101 significant variants (P < 4.92 × 10-10). Network analysis, visualization of cross-phenotype mapping, and causal inference mapping with Mendelian randomization were conducted. Among phenotype pairs from the genotype-driven cross-phenotype associations, we evaluated penetrance in correlation analysis using a clinical database. We focused on the application of PheWAS in order to make it robust and to aid the derivation of biological meaning post-PheWAS. This comprehensive analysis of PheWAS results based on a health check-up database will provide researchers and clinicians with a panoramic overview of the networks among multiple phenotypes and genetic variants, laying groundwork for the practical application of precision medicine.

Genetic Determinants of Visit-to-Visit Lipid Variability: Genome-Wide Association Study in Statin-Naïve Korean Population

Background and Aim

There is a growing evidence that fluctuation in lipid profiles is important in cardiovascular outcomes. We aimed to identify single nucleotide polymorphism (SNP) variants associated with low-density lipoprotein-cholesterol (LDL-C) and high-density lipoprotein-cholesterol (HDL-C) variability in statin-naïve Korean subjects and evaluate their associations with coronary atherosclerosis.

Methods

In statin-naïve subjects from Gene-Environment of Interaction and phenotype cohort, we performed genome-wide association studies of lipid variability; the discovery (first) and replication (second) sets included 4,287 and 1,086 subjects, respectively. Coronary artery calcium (CAC) score and degree of coronary artery stenosis were used as outcome measures. Cholesterol variability was determined by standard deviation and average successive variability, and significant coronary atherosclerosis was defined as CAC score ≥400 or coronary stenosis ≥70%.

Results

Mean HDL-C and LDL-C level were 54 ± 12 and 123 ± 30 mg/dL in the first set and 53 ± 12 and 126 ± 29 mg/dL in the second set. APOA5 rs662799 and APOA5 rs2266788 were associated with LDL-C variability and PXDNL rs80056520, ALDH2 rs671, HECTD4 rs2074356, and CETP rs2303790 were SNPs associated for HDL-C variability. APOA5 rs662799 passed Bonferroni correction with p-value of 1.789 × 10⁻⁹. Among the SNPs associated with cholesterol variability, rs80056520 and rs2266788 variants were associated with CACS ≥400 and coronary stenosis ≥70% and rs662799 variant was associated with coronary stenosis ≥70%.

Conclusion

Two SNPs associated with LDL-C variability (APOA5 rs662799 and rs2266788) and one SNP associated with HDL-C variability (PXDNL rs80056520) were significantly associated with advanced coronary artery stenosis. Combining GWAS results with imaging parameters, our study may provide a deeper understanding of underlying pathogenic basis of the link between lipid variability and coronary atherosclerosis.

Long-term Survival of 10,116 Korean Live Liver Donors

OBJECTIVE

To evaluate the long-term mortality of Korean live liver donors using data from a national donor registry by comparing it with the mortality of the general population.

SUMMARY OF BACKGROUND DATA

Although live liver donors generally have a healthy status, their long-term mortality has not been properly addressed in a large donor registry.

METHODS

Data of 10,116 live liver donors were drawn from a mandated national registry of Korean live liver donors between 2000 and 2015. Matched controls were selected from the Korean National Health Insurance System-National Sample Cohort (NHIS-NSC). Median (range) follow-up of liver donors was 5.7 (0-15.9) years. Donors were 1:3 individually matched to controls by sex and 5-year age group; potential controls were from the whole NHIS-NSC (Control 1) or from NHIS-NSC after excluding people with contraindications to be organ donors (Control 2) (donor, n = 7538; Control 1, n = 28,248; Control 2, n = 28,248).

RESULTS

Fifty-three deaths occurred after donation. Ten-year cumulative mortality of live liver donors was 0.9%. The most common cause of death was suicide (n = 19) followed by cancer (n = 9) and traffic accident (n = 7). In the matched control analysis, overall risk of death was significantly lower in donors than in Control 1 (P < 0.001), but higher than in Control 2 (P < 0.001).

CONCLUSIONS

Liver donors have increased long-term mortality risk compared to similar healthy controls without contraindications to be organ donors. Therefore, long-term follow-up, including psychosocial support, is needed for live liver donors.

Prognostic Effect of Inflammatory Genes on Stage I-III Colorectal Cancer-Integrative Analysis of TCGA Data

Simple Summary

Research interest in the role of inflammation in the progression and prognosis of colorectal cancer (CRC) is growing. In this study, we evaluated the expression and DNA methylation levels of inflammation-related genes in CRC tissues using the TCGA-COREAD dataset by integratively combining multi-omics features using machine learning. Statistical analysis was additionally performed to allow for interpretable, understandable, and clinically practical results. An integrative model combining expression, methylation, and clinical features had the highest performance. In multivariate analysis, the methylation levels of CEP250, RAB21, and TNPO3 were significantly associated with overall survival. Our study results implicate the importance of integrating expression and methylation information along with clinical information in the prediction of survival. CEP250, RAB21, and TNPO3 in the prediction model might have a crucial role in CRC prognosis and further improve our understanding of potential mechanisms linking inflammatory reactions and CRC progression.

Abstract

Background inflammatory status indicators have been reported as prognostic biomarkers of colorectal cancer (CRC). However, since inflammatory interactions with the colon involve various modes of action, the biological mechanism linking inflammation and CRC prognosis has not been fully elucidated. We comprehensively evaluated the predictive roles of the expression and methylation levels of inflammation-related genes for CRC prognosis and their pathophysiological associations. Method. An integrative analysis of 247 patients with stage I-III CRC from The Cancer Genome Atlas was conducted. Lasso-penalized Cox proportional hazards regression (Lasso-Cox) and statistical Cox proportional hazard regression (CPH) were used for the analysis. Results. Models to predict overall survival were designed with respective combinations of clinical variables, including age, sex, stage, gene expression, and methylation. An integrative model combining expression, methylation, and clinical features performed better (median C-index = 0.756) than the model with clinical features alone (median C-index = 0.726). Based on multivariate CPH with features from the best model, the methylation levels of CEP250, RAB21, and TNPO3 were significantly associated with overall survival. They did not share any biological process in functional networks. The 5-year survival rate was 29.8% in the low methylation group of CEP250 and 79.1% in the high methylation group (p < 0.001). Conclusion. Our study results implicate the importance of integrating expression and methylation information along with clinical information in the prediction of survival. CEP250, RAB21, and TNPO3 in the prediction model might have a crucial role in CRC prognosis and further improve our understanding of potential mechanisms linking inflammatory reactions and CRC progression.

Multi-layered network-based pathway activity inference using directed random walks: application to predicting clinical outcomes in urologic cancer

MOTIVATION

To better understand the molecular features of cancers, a comprehensive analysis using multiomics data has been conducted. Additionally, a pathway activity inference method has been developed to facilitate the integrative effects of multiple genes. In this respect, we have recently proposed a novel integrative pathway activity inference approach, iDRW, and demonstrated the effectiveness of the method with respect to dichotomizing two survival groups. However, there were several limitations, such as a lack of generality. In this study, we designed a directed gene-gene graph using pathway information by assigning interactions between genes in multiple layers of networks.

RESULTS

: As a proof-of-concept study, it was evaluated using three genomic profiles of urologic cancer patients. The proposed integrative approach achieved improved outcome prediction performances compared with a single genomic profile alone and other existing pathway activity inference methods. The integrative approach also identified common/cancer-specific candidate driver pathways as predictive prognostic features in urologic cancers. Furthermore, it provides better biological insights into the prioritized pathways and genes in an integrated view using a multi-layered gene-gene network. Our framework is not specifically designed for urologic cancers and can be generally applicable for various datasets.

AVAILABILITY

iDRW is implemented as the R software package. The source codes are available at https://github.com/sykim122/iDRW.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

The association of genetic polymorphisms with nonalcoholic fatty liver disease in a longitudinal study

Background

Several genetic variants are known to be associated with nonalcoholic fatty liver disease (NAFLD). We aimed to evaluate the longitudinal associations between genetic variants and NAFLD.

Methods

We performed a genome-wide association study (GWAS) in Korean individuals who underwent repeated health check-ups. NAFLD was defined by ultrasonography and exclusion of secondary causes.

Results

The subjects had a median age of 50.0 years, and 54.8% were male. The median follow-up duration was 39 months. Among the 3905 subjects without NAFLD at baseline, 874 (22.4%) subjects developed NAFLD, and among the 1818 subjects with NAFLD at baseline, NAFLD regressed in 336 (18.5%) subjects during the follow-up period. After adjusting for age, sex and body mass index, no single-nucleotide polymorphism (SNP) passed Bonferroni correction for genome-wide significance in the development or regression of NAFLD. Among the SNPs that passed the genome-wide suggestiveness threshold (p = 1E-04) in the discovery set in the GWAS, only 1 SNP (rs4906353) showed an association with the development of NAFLD, with marginal significance in the validation set (p-value, discovery set = 9.68E-5 and validation set = 0.00531).

Conclusions

This exploratory study suggests that longitudinal changes in NAFLD are not associated with genetic variants in the Korean population. These findings provide new insight into genetic mechanisms in the pathogenesis of NAFLD.

Liver imaging features by convolutional neural network to predict the metachronous liver metastasis in stage I-III colorectal cancer patients based on preoperative abdominal CT scan

Background

Introducing deep learning approach to medical images has rendered a large amount of un-decoded information into usage in clinical research. But mostly, it has been focusing on the performance of the prediction modeling for disease-related entity, but not on the clinical implication of the feature itself. Here we analyzed liver imaging features of abdominal CT images collected from 2019 patients with stage I – III colorectal cancer (CRC) using convolutional neural network (CNN) to elucidate its clinical implication in oncological perspectives.

Results

CNN generated imaging features from the liver parenchyma. Dimension reduction was done for the features by principal component analysis. We designed multiple prediction models for 5-year metachronous liver metastasis (5YLM) using combinations of clinical variables (age, sex, T stage, N stage) and top principal components (PCs), with logistic regression classification. The model using “1^st PC (PC1) + clinical information” had the highest performance (mean AUC = 0.747) to predict 5YLM, compared to the model with clinical features alone (mean AUC = 0.709). The PC1 was independently associated with 5YLM in multivariate analysis (beta = − 3.831, P < 0.001). For the 5-year mortality rate, PC1 did not contribute to an improvement to the model with clinical features alone. For the PC1, Kaplan-Meier plots showed a significant difference between PC1 low vs. high group. The 5YLM-free survival of low PC1 was 89.6% and the high PC1 was 95.9%. In addition, PC1 had a significant correlation with sex, body mass index, alcohol consumption, and fatty liver status.

Conclusion

The imaging features combined with clinical information improved the performance compared to the standardized prediction model using only clinical information. The liver imaging features generated by CNN may have the potential to predict liver metastasis. These results suggest that even though there were no liver metastasis during the primary colectomy, the features of liver imaging can impose characteristics that could be predictive for metachronous liver metastasis.

The prognoses and postoperative outcomes of patients with both colorectal cancer and liver cirrhosis based on a nationwide cohort in Korea

Purpose

The management of patients with colorectal cancer (CRC) who have liver cirrhosis (LC) requires a thorough understanding of both diseases; however, the prognoses and postoperative outcomes of such patients remain understudied. We investigated the effect of LC on surgical and oncologic outcomes in patients with CRC, and identified prognostic factors.

Methods

We analyzed 453 patients with CRC and LC (CRC-LC group), 906 with CRC only (CRC group), 906 with LC only (LC group), and 1,812 healthy subjects using health insurance claim data (2008–2013).

Results

The CRC-LC group had a higher frequency of intensive care unit admission than the CRC group; there were no differences between the 2 groups in terms of early and late postoperative small bowel obstruction and incisional hernia. However, the 30-day, 60-day, and 90-day mortality rates were all significantly higher in the CRC-LC group. The higher Charlson comorbidity index (hazard ratio [HR], 1.127) and the lower socioeconomic status (HR, 0.985) were significant worse predictors of 5-year survival. Patients with underlying LC had a significantly higher HR in both the advanced CRC (HR, 1.858) and nonadvanced CRC (HR, 1.799) subgroups. However, the nonadvanced CRC subgroup showed a lower HR than the LC group (HR, 0.730).

Conclusion

Patients with CRC who had underlying LC had a lower survival rate than did those without LC, although the incidence rates of postoperative complications were not significantly different. The presence of LC was associated with a significantly lower survival rate regardless of CRC presence.

ERRATUM: Correction of Figure 1: Outcomes of surgical treatments for rectovaginal fistula and prognostic factors for successful closure: a single-center tertiary hospital experiences

[This corrects the article on p. 149 in vol. 97, PMID: 31508396.].

The exploration of feature extraction and machine learning for predicting bone density from simple spine X-ray images in a Korean population

OBJECTIVE

Osteoporosis is hard to detect before it manifests symptoms and complications. In this study, we evaluated machine learning models for identifying individuals with abnormal bone mineral density (BMD) through an analysis of spine X-ray features extracted by deep learning to alert high-risk osteoporosis populations.

MATERIALS AND METHODS

We retrospectively used data obtained from health check-ups including spine X-ray and dual-energy X-ray absorptiometry (DXA). Consecutively, we selected people with normal and abnormal bone mineral density. From the regions of interest of X-ray images, deep convolutional networks were used to generate image features. We designed prediction models for abnormal BMD using the image features trained by machine learning classification algorithms. The performances of each model were evaluated.

RESULTS

From 334 participants, 170 images of abnormal (T scores < - 1.0 standard deviations (SD)) and 164 of normal BMD (T scores > = - 1.0 SD) were used for analysis. We found that a combination of feature extraction by VGGnet and classification by random forest based on the maximum balanced classification rate (BCR) yielded the best performance in terms of the area under the curve (AUC) (0.74), accuracy (0.71), sensitivity (0.81), specificity (0.60), BCR (0.70), and F1-score (0.73).

CONCLUSION

In this study, we explored various machine learning algorithms for the prediction of BMD using simple spine X-ray image features extracted by three deep learning algorithms. We identified the combination for the best performance in predicting high-risk populations with abnormal BMD.

A Novel Susceptibility Locus Near GRIK2 Associated With Erosive Esophagitis in a Korean Cohort

INTRODUCTION

The male-predominant sex difference through the spectrum of erosive esophagitis to Barrett's esophagus is widely known. We conducted a genome-wide association study (GWAS) stratified by sex for identifying factors that can predict the endoscopically diagnosed erosive esophagitis.

METHODS

Erosive esophagitis was diagnosed by endoscopy and assessed for severity. We identified genetic factors associated with erosive esophagitis that accounted for the sex differences in a cohort of 4,242 participants via a GWAS. After quality control and imputation, genetic associations with erosive esophagitis were investigated by multivariate linear regression in 3,620 subjects. Single-nucleotide polymorphisms (SNPs) with P < 5.0 × 10 were considered significant genome wide, and a genetic risk score was constructed for the prediction of erosive esophagitis risk.

RESULTS

Six genome-wide significant SNPs near the GRIK2 gene on chromosome 6 were found to be associated with erosive esophagitis only in male subjects. These were predictive of severity through a genetic risk score (P < 0.05), and the findings were validated in a cohort of 622 subjects (P < 0.05).

DISCUSSION

This is the first GWAS of erosive esophagitis, and we identified 6 genome-wide significant SNPs in male subjects. These SNPs could help explain the pathogenesis of erosive esophagitis and contribute to the understanding of sex differences. Further genetic investigation could allow for the prediction of high risk for erosive esophagitis and development of new treatment options.

Outcomes of surgical treatments for rectovaginal fistula and prognostic factors for successful closure: a single-center tertiary hospital experiences

Purpose

Rectovaginal fistula can result from various causes and diverse surgical procedures have developed as a result. We investigated the outcomes of surgical treatments for rectovaginal fistula according to causes and procedures.

Methods

Between 1998 and 2016, 92 patients underwent 128 operations for rectovaginal fistula. Prospectively collected data were recorded, and a retrospective review was conducted.

Results

The median age was 49 years, and low fistula occurred in 58 patients (63.0%). The most common cause was radiation therapy, followed by pelvic operation, birth injury, perineal operation, cancer invasion, and trauma. The most common procedure during the first operation was diverting ostomy alone, followed by transanal rectal advancement flap, sphincteroplasty with perineoplasty, bowel resection, fistulectomy with seton placement, and Martius flap. Thirty-one patients (33.7%) experienced successful closure after the first operation. Repeated operations were performed in 16 patients (17.4%), including gracilis muscle transpositions, stem cell injections, and Martius flaps. The overall success rate was 42.4% (n = 39). Radiation therapy and pelvic operation as cause of fistula were significantly poor prognostic factors (P = 0.010, P = 0.045) and Crohn disease had a tendency for poor prognostic factors (P = 0.058).

Conclusion

Radiation therapy and pelvic operation for cancer were more common causes than birth injury, and these causes of rectovaginal fistula were the most important prognostic factors. An individualized approach and repeated surgeries with complex or newly developed procedures, even among high-risk causes of fistula, may be necessary to achieve successful closure.

Genome-wide association study of right-sided colonic diverticulosis in a Korean population

Diverticulosis results from complex interactions related to aging, environmental factors and genetic predisposition. Despite epidemiologic evidence of genetic risk factors, there has been no attempt to identify genes that confer susceptibility to colonic diverticulosis. We performed the first genome-wide association study (GWAS) on susceptibility to diverticulosis in a Korean population. A GWAS was carried out in 7,948 healthy individuals: 893 patients and 1,075 controls comprised the test set, and 346 patients and 305 controls comprised the replication set. Diverticulosis was diagnosed by colonoscopy during comprehensive medical check-ups, and single-nucleotide polymorphisms (SNPs) related to diverticulosis were detected with the Affymetrix Axiom KORV1.1-96 Array. In all, 9 SNPs were identified in three SNP aggregates in the test set (P < 10⁻³, within 200 kb) after adjusting for sex. All the SNPs were replicated in the replication set (P < 0.05). Three SNPs were near the WNT4 gene, four near the RHOU gene, and two in the OAS1/3 genes. The top SNP associated with right-sided colonic diverticulosis was rs22538787, located near the WNT4 gene [combined set, P-value = 3.128 × 10⁻⁶, odds ratio = 1.415 (95% confidence interval: 1.223–1.637)]. These 9 novel SNP alleles associated with the WNT4, RHOU, and OAS1/3 genes are possibly involved in the underlying genetic susceptibility to right-sided diverticulosis. Our results provide basic knowledge about the development of diverticulosis in an Asian population.

Association between CT-Measured Abdominal Skeletal Muscle Mass and Pulmonary Function

A relationship between lung function and sarcopenia has been suggested. This study aimed to evaluate the association between lung function and abdominal skeletal muscle mass, as measured by computed tomography (CT). The clinical records of 1907 subjects (1406 males, mean age 53.1 ± 9.2 years), who underwent routine health check-ups, including spirometry and abdominal CT, were retrospectively reviewed. The CT-measured skeletal muscle index (SMI_CT, cm²/(kg/m²) was defined as the skeletal muscle area of the third lumbar vertebrae (L3) level that is normalized by the body mass index. The mean values of forced vital capacity (FVC) and forced expiratory volume in one second (FEV1) gradually increased as the SMI_CT quartiles increased (all p for trend < 0.05). The proportions of subjects with less than 80% of the predicted FVC (%) and predicted FEV1 (%) significantly decreased as the SMI_CT quartiles increased (all p for trend < 0.05). The β regression coefficients for FVC and FEV1 significantly increased as the SMI_CT quartiles increased after adjusting for other confounding variables (p for trend < 0.05). This study showed that abdominal muscle mass, which was precisely measured by CT, independently affected lung function proportionally after adjusting for confounding factors in relatively healthy adults.

Upregulation of SLC2A3 gene and prognosis in colorectal carcinoma: analysis of TCGA data

BACKGROUND

Upregulation of SLC2A genes that encode glucose transporter (GLUT) protein is associated with poor prognosis in many cancers. In colorectal cancer, studies reporting the association between overexpression of GLUT and poor clinical outcomes were flawed by small sample sizes or subjective interpretation of immunohistochemical staining. Here, we analyzed mRNA expressions in all 14 SLC2A genes and evaluated the association with prognosis in colorectal cancer using data from the Cancer Genome Atlas (TCGA) database.

METHODS

In the present study, we analyzed the expression of SLC2A genes in colorectal cancer and their association with prognosis using data obtained from the TCGA for the discovery sample, and a dataset from the Gene Expression Omnibus for the validation sample.

RESULTS

SLC2A3 was significantly associated with overall survival (OS) and disease-free survival (DFS) in both the discovery sample (345 patients) and validation sample (501 patients). High SLC2A3 expression resulted in shorter OS and DFS. In multivariate analyses, high SLC2A3 levels predicted unfavorable OS (adjusted HR 1.95, 95% CI 1.22-3.11; P = 0.005) and were associated with poor DFS (adjusted HR 1.85, 95% CI 1.10-3.12; P = 0.02). Similar results were found in the discovery set.

CONCLUSION

Upregulation of the SLC2A3 genes is associated with decreased OS and DFS in colorectal cancer patients. Therefore, assessment of SLC2A3 gene expression may useful for predicting prognosis in these patients.

Genome-wide association study of coronary artery calcification in asymptomatic Korean populations

Epidemiologic evidence indicates that the prevalence and severity of coronary artery disease vary depending on ethnicity. In this study, a genome-wide association study for coronary artery calcification (CAC) was performed in a Korean population-based sample of 400 subjects without prior coronary artery disease and replicated in another of 1,288 subjects. CAC score, as assessed by multi-detector computed tomography, was evaluated in volunteers for screening purposes as part of a routine health examination. CAC score greater than the 90th percentile across the age in each sex group was considered severe CAC. Single nucleotide polymorphisms (SNPs) associated with severe CAC after adjusting for age, sex, hypertension, and diabetes were investigated using the additive model of logistic regression. One SNP (rs10757272 in the intronic region of the CDKN2B-AS1 gene in chromosome 9p21.3) met Bonferroni correction in the discovery set (p = 7.55E-08) and was also significant in the validation set by TaqMan assay (p = 0.036). Subjects with rs10757272 were found to have an increased odds ratio (OR) of having severe CAC in multivariate logistic regression analysis after adjusting for age, sex, hypertension, and diabetes (adjusted OR 3.24 and 95% CI 2.11–4.97). In conclusion, SNP rs10757272 in chromosome 9p21.3 was associated with severe CAC based on age and sex in an asymptomatic community-based Korean population. Therefore, it was associated with promotion of coronary artery calcification in subclinical state.

Oncologic evaluation of obesity as a factor in patients with rectal cancer undergoing laparoscopic surgery: a propensity-matched analysis using body mass index

Purpose

This study evaluated the oncologic impact of obesity, as determined by body mass index (BMI), in patients who underwent laparoscopic surgery for rectal cancer.

Methods

The records of 483 patients with stage I-III rectal cancer who underwent laparoscopic surgery between June 2003 and December 2011 were reviewed. A matching model based on BMI was constructed to balance obese and nonobese patients. Cox hazard regression models for overall survival (OS) and disease-free survival (DFS) were used for multivariate analyses. Additional analysis using visceral fat area (VFA) measurement was performed for matched patients. The threshold for obesity was BMI ≥ 25 kg/m² or VFA ≥ 130 cm².

Results

The score matching model yielded 119 patients with a BMI ≥ 25 kg/m² (the obese group) and 119 patients with a BMI < 25 kg/m² (the nonobese group). Surgical outcomes including operation time, estimated blood loss, nil per os periods, and length of hospital stay did not differ between the obese and the nonobese group. The retrieved lymph node numbers and pathologic CRM positive rate were also similar in between the 2 groups. After a median follow-up of 48 months (range, 3-126 months), OS and DFS rates were similar between the 2 groups. A tumor location-adjusted model for overall surgical complications showed that a BMI ≥ 25 kg/m² were not risk factors. Multivariable analyses for OS and DFS showed no significant association with a BMI ≥ 25 kg/m².

Conclusion

Obesity was not associated with long-term oncologic outcomes in patients undergoing laparoscopic surgery for rectal cancer in the Asian population.

Prognostic nomogram of hypoxia-related genes predicting overall survival of colorectal cancer-Analysis of TCGA database

Hypoxia-related gene (HRG) expression is associated with survival outcomes of colorectal cancer (CRC). Our aim was developing a nomogram predicting CRC overall survival (OS) with HRGs and clinicopathological factors. The Cancer Genome Atlas (TCGA) database was used as discovery cohort and two Gene Expression Omnibus databases (GSE39582 and GSE41258) served as validation cohorts. A genetic risk score model prognosticating OS was developed using mRNA expression level of HRGs. Nomogram predicting OS was developed using genetic risk score model and clinicopathological variables. The genetic risk score model included four HRGs (HSPA1L, PUM1, UBE2D2, and HSP27) and successfully prognosticated OS of discovery and two validation cohorts (p < 0.001 for TCGA discovery set, p < 0.003 for the GSE39582 and p = 0.042 for the GSE41258 datasets). Nomogram included genetic risk score, age, and TNM stage. Harrell’s concordance indexes of the nomogram were higher than those of TNM stage alone in the discovery set (0.77 vs. 0.69, p < 0.001), GSE39582 (0.65 vs. 0.63, p < 0.001), and GSE41258 datasets (0.78 vs. 0.77, p < 0.001). Our nomogram successfully predicted OS of CRC patients. The mRNA expression level of the HRGs might be useful as an ancillary marker for prognosticating CRC outcome.

Exploration of Machine Learning for Hyperuricemia Prediction Models Based on Basic Health Checkup Tests

BACKGROUND

Machine learning (ML) is a promising methodology for classification and prediction applications in healthcare. However, this method has not been practically established for clinical data. Hyperuricemia is a biomarker of various chronic diseases. We aimed to predict uric acid status from basic healthcare checkup test results using several ML algorithms and to evaluate the performance.

METHODS

We designed a prediction model for hyperuricemia using a comprehensive health checkup database designed by the classification of ML algorithms, such as discrimination analysis, K-nearest neighbor, naïve Bayes (NBC), support vector machine, decision tree, and random forest classification (RFC). The performance of each algorithm was evaluated and compared with the performance of a conventional logistic regression (CLR) algorithm by receiver operating characteristic curve analysis.

RESULTS

Of the 38,001 participants, 7705 were hyperuricemic. For the maximum sensitivity criterion, NBC showed the highest sensitivity (0.73), and RFC showed the second highest (0.66); for the maximum balanced classification rate (BCR) criterion, RFC showed the highest BCR (0.68), and NBC showed the second highest (0.66) among the various ML algorithms for predicting uric acid status. In a comparison to the performance of NBC (area under the curve (AUC) = 0.669, 95% confidence intervals (CI) = 0.669⁻0.675) and RFC (AUC = 0.775, 95% CI 0.770⁻0.780) with a CLR algorithm (AUC = 0.568, 95% CI = 0.563⁻0.571), NBC and RFC showed significantly better performance (p < 0.001).

CONCLUSIONS

The ML model was superior to the CLR model for the prediction of hyperuricemia. Future studies are needed to determine the best-performing ML algorithms based on data set characteristics. We believe that this study will be informative for studies using ML tools in clinical research.

Colorectal Cancer Prognosis is Not Associated with BRAF and KRAS Mutations-A STROBE Compliant Study

Background: We investigated the associations between v-Raf murine sarcoma viral oncogene homolog B1 (BRAF^V600E, henceforth BRAF) and v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations and colorectal cancer (CRC) prognosis, using The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GSE39582) datasets. Materials and Methods: The effects of BRAF and KRAS mutations on overall survival (OS) and disease-free survival (DFS) of CRC were evaluated. Results: The mutational status of BRAF and KRAS genes was not associated with overall survival (OS) or DFS of the CRC patients drawn from the TCGA database. The 3-year OS and DFS rates of the BRAF mutation (+) vs. mutation (−) groups were 92.6% vs. 90.4% and 79.7% vs. 68.4%, respectively. The 3-year OS and DFS rates of the KRAS mutation (+) vs. mutation (−) groups were 90.4% vs. 90.5% and 65.3% vs. 73.5%, respectively. In stage II patients, however, the 3-year OS rate was lower in the BRAF mutation (+) group than in the mutation (−) group (85.5% vs. 97.7%, p < 0.001). The mutational status of BRAF genes of 497 CRC patients drawn from the GSE39582 database was not associated with OS or DFS. The 3-year OS and DFS rates of BRAF mutation (+) vs. mutation (−) groups were 75.7% vs. 78.9% and 73.6% vs. 71.1%, respectively. However, KRAS mutational status had an effect on 3-year OS rate (71.9% mutation (+) vs. 83% mutation (−), p = 0.05) and DFS rate (66.3% mutation (+) vs. 74.6% mutation (−), p = 0.013). Conclusions: We found no consistent association between the mutational status of BRAF nor KRAS and the OS and DFS of CRC patients from the TCGA and GSE39582 databases. Studies with longer-term records and larger patient numbers may be necessary to expound the influence of BRAF and KRAS mutations on the outcomes of CRC.

Composition Characterization of Fatty Acid Zinc Salts by Chromatographic and NMR Spectroscopic Analyses on Their Fatty Acid Methyl Esters

To implement EU REACH- (Registration, Evaluation, and Authorization of Chemicals-) like chemical legislations in various countries of which the purpose is human and environment safety, the first step is substance identification followed by the hazard and risk assessments. Although both structural and composition identifications are required, the latter can more importantly result in the essential data to fill out the required substance information such as purity and concentrations of constituents, as well as impurities. With fatty acid zinc salts (FAZSs) as an exemplary industrial chemical of which chromatographic and nuclear magnetic resonance (NMR) analyses were impossible due to their insolubility in water and any organic solvents, the composition characterization was tried by preparing their fatty acid methyl esters (FAMEs) using the conc. HCl/methanol/toluene method. This acid-catalyzed methyl esterification was optimized with zinc stearate as a surrogate substance. Gas chromatography-mass spectrometry (GC-MS) and NMR analyses on methyl-esterified products revealed that the optimum conditions were at 90°C for 10 min or 45°C for 30 min with two equivalent HCl as well as at 45°C for 10 min with five equivalent HCl. Almost all zinc stearates were converted into the corresponding fatty acids with 97-99% conversion rates. Free fatty acids (FFAs) were detected in extracted ion chromatograms of pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS) in the methyl-esterified products with incomplete conversions of 73∼79%. The optimized conc. HCl/methanol/toluene method of direct one-step reaction from FAZSs was compared with the two-step NaOH saponification/BF₃-methanol method after acidic hydrolysis of FAZSs. The mechanism of fatty acid zinc salts into free fatty acids and fatty acid methyl esters was suggested with the evidence of the formation of Zn(OH)₂.

Metabolic Syndrome Prediction Using Machine Learning Models with Genetic and Clinical Information from a Nonobese Healthy Population

The prevalence of metabolic syndrome (MS) in the nonobese population is not low. However, the identification and risk mitigation of MS are not easy in this population. We aimed to develop an MS prediction model using genetic and clinical factors of nonobese Koreans through machine learning methods. A prediction model for MS was designed for a nonobese population using clinical and genetic polymorphism information with five machine learning algorithms, including naïve Bayes classification (NB). The analysis was performed in two stages (training and test sets). Model A was designed with only clinical information (age, sex, body mass index, smoking status, alcohol consumption status, and exercise status), and for model B, genetic information (for 10 polymorphisms) was added to model A. Of the 7,502 nonobese participants, 647 (8.6%) had MS. In the test set analysis, for the maximum sensitivity criterion, NB showed the highest sensitivity: 0.38 for model A and 0.42 for model B. The specificity of NB was 0.79 for model A and 0.80 for model B. In a comparison of the performances of models A and B by NB, model B (area under the receiver operating characteristic curve [AUC] = 0.69, clinical and genetic information input) showed better performance than model A (AUC = 0.65, clinical information only input). We designed a prediction model for MS in a nonobese population using clinical and genetic information. With this model, we might convince nonobese MS individuals to undergo health checks and adopt behaviors associated with a preventive lifestyle.

Genetic Polymorphisms of PNPLA3 and SAMM50 Are Associated with Nonalcoholic Fatty Liver Disease in a Korean Population

Background/Aims

The development of nonalcoholic fatty liver disease (NAFLD) is associated with multiple genetic and environmental factors.

Methods

We performed a genome-wide association study to identify the genetic factors related to NAFLD in a Korean population-based sample of 1,593 subjects with NAFLD and 2,816 controls. We replicated the data in another sample that included 744 NAFLD patients and 1,137 controls. We investigated single-nucleotide polymorphisms (SNPs) that were related to NAFLD.

Results

After adjusting for age, sex and body mass index, rs738409, rs12483959 and rs2281135, located in the PNPLA3 gene, were validated in our population (p<8.56×10⁻⁸) in the same linkage disequilibrium block. Additionally, rs2143571, rs3761472, and rs2073080 in the SAMM50 gene showed significant associations with NAFLD (p<8.56×10⁻⁸). Furthermore, these six SNPs showed significant associations with the severity of fatty liver (all p<2.0×10⁻¹⁰ in the discovery set and p<2.0×10⁻⁶ in the validation set) and NAFLD, with elevated levels of alanine aminotransferase (all p<2.0×10⁻¹⁰ in the discovery set and p<2.0×10⁻⁶ in the validation set).

Conclusions

We demonstrated that the PNPLA3 and SAMM50 genes are significantly associated with the presence and severity of NAFLD in a Korean population. These findings confirm the important roles of genetic factors in the pathogenesis of NAFLD.

Health and Prevention Enhancement (H-PEACE): a retrospective, population-based cohort study conducted at the Seoul National University Hospital Gangnam Center, Korea

PURPOSE

The Health and Prevention Enhancement (H-PEACE) study was designed to investigate the association of diagnostic imaging results, biomarkers and the predisease stage of non-communicable diseases (NCDs), such as malignancies and metabolic diseases, in an average-risk population in Korea.

PARTICIPANTS

This study enrolled a large-scale retrospective cohort at the Healthcare System Gangnam Center, Seoul National University Hospital, from October 2003 to December 2014.

FINDINGS TO DATE

The baseline and follow-up information collected in the predisease stage of NCDs allows for evaluation of an individual's potential NCD risk, which is necessary for establishing personalised prevention strategies. A total of 91 336 health examinees were included in the cohort, and we repeatedly measured and collected information for 50.9% (n=46 484) of the cohort members. All participants completed structured questionnaires (lifestyle, medical history, mini-dietary assessment index, sex-specific variables and psychiatric assessment), doctors' physical examinations, laboratory blood and urine tests and digital chest X-ray imaging. For participants with available data, we also obtained information on specific diagnostic variables using advanced diagnostic tests, including coronary CT for coronary calcium scores, colonoscopy and brain MRI. Furthermore, 17 455 of the participants who provided informed consent and donated blood samples were enrolled into the Gene-environmental interaction and phenotype study, a subcohort of the H-PEACE, from October 2013, and we analysed genome-wide single-nucleotide polymorphism array data for 6579 of these blood samples.

FUTURE PLANS

The data obtained from this cohort will be used to facilitate advanced and accurate diagnostic techniques related to NCDs while considering various phenotypes. Potential collaborators can access the dataset after receiving approval from our institutional review board. Applications can be submitted on the study homepage (http://en-healthcare.snuh.org/HPEACEstudy).

Osteoporosis and fracture after gastrectomy for stomach cancer: A nationwide claims study

This study was planned to evaluate the incidence and risk factors of osteoporosis and fracture after gastrectomy for stomach cancer using a nationwide claims database in South Korea.Data from 41,512 patients (50-79 years) who underwent gastrectomy for stomach cancer from 2008 to 2010 with at least 5 years of follow-up were obtained from the Health Insurance Review and Assessment Service database. Patients diagnosed with osteoporosis and prescribed bisphosphonate or raloxifene or who experienced osteoporotic fractures after gastrectomy were operationally defined as osteoporosis. Osteoporotic fracture was defined as a fracture at common osteoporotic fracture sites (spine, pelvis, hip, forearm, or rib).In total, 37,076 patients were included in the final analysis. The incidences of postgastrectomy osteoporosis and osteoporotic fractures were 41.9 and 27.6 cases per 1000 person-years, respectively. Multivariate analysis showed that older age (hazard ratio [HR] 1.88; 95% confidence interval [CI] 1.79-1.96), female gender (HR 2.46; 2.35-2.58), total gastrectomy (HR 1.10; 1.04-1.16), and diabetes (HR 1.16; 1.11-1.22) were significantly associated with osteoporosis and that older age (HR 1.90; 95% CI 1.80-2.01), female gender (HR 1.50; 1.41-1.58), total gastrectomy (HR 1.17; 1.10-1.25), chemotherapy (HR 1.06; 1.00-1.12), and diabetes (HR 1.26; 1.19-1.33) were significantly associated with fractures. Osteoporotic fractures occurred a median 3.1 years after gastrectomy. Among the 5175 fracture patients, 780 (15.1%) experienced multisite fractures, mostly in the elderly and chemotherapy groups.The osteoporosis and osteoporotic fracture incidences are high in patients within a relatively short timeframe after gastrectomy for stomach cancer. Systematic management of osteoporosis is necessary after this surgery.

Oncologic and surgical outcomes in colorectal cancer patients with liver cirrhosis: A propensity-matched study

The management of colorectal cancer in patients with liver cirrhosis requires a thorough understanding of both diseases. This study evaluated the effect of liver cirrhosis on oncologic and surgical outcomes and prognostic factors in colorectal cancer patients. Fifty-five consecutive colorectal cancer patients with liver cirrhosis underwent colorectal resection (LC group). Using a prospectively maintained database, these patients were matched 1:4 using propensity scoring with R programming language, package "MatchIt" and "optmatch" by sex, age, cancer location, and tumor stage with 220 patients without liver cirrhosis (non-LC group), resulting in 275 patients. The 5-year overall survival (OS) was significantly worse in the LC group than in the non-LC group (46.7% vs. 76.2% respectively, P < 0.001); however, the 5-year proportion of recurrence free (PRF) rates were similar (73.1% vs. 84.5% respectively, P = 0.094). On multivariate analysis of the LC group, tumor-node-metastasis (TNM) stage ≥III disease, venous invasion, and a model for end-stage liver disease plus serum sodium (MELD-Na) score >10 were prognostic factors for OS. However, the OS was not different between the LC group with MELD-Na score ≤10 and the non-LC group (5-year OS rate, TNM stage ≤II, 85.7 vs 89.5%, p = 0.356; TNM stage ≥III, 41.1 vs 66.2%, p = 0.061). Colorectal cancer patients with liver cirrhosis have poorer OS compared to those without liver cirrhosis; however, the PRF rates are similar. It might be due to the mortality from the liver, and surgical treatment should be actively considered for patients with MELD-Na score <10.

Long-Term Surgical Outcome of Trocar Site Hernia Repair

Port site hernias are emerging as a problematic complication of laparoscopic surgery. The aim of this study was to elucidate the characteristics of port site hernias and determine the long-term outcomes based on the interval between primary surgery and hernia occurrence. Twenty-four patients were surgically treated for trocar site hernia between 1997 and 2013. The patients were grouped into early-onset group (EOG; less than one month) and late-onset group (LOG; more than one month) based on the interval between laparoscopic surgery and hernia onset. A retrospective analysis was performed. There were seven patients in the EOG and 17 patients in the LOG. The body mass index was significantly higher (P = 0.033) in the LOG. In the EOG, primary closure was performed, and there were no recurrences. In the LOG, mesh reinforcement was applied in 58.8 per cent of patients, and 29.4 per cent of patients had recurrences. This recurrence rate was higher than the recurrence rate after primary repair of incisional hernia after open laparotomy (P = 0.088). In conclusion, In the EOG, small bowel resection was more frequent, but once repaired, there were no recurrences. Although mesh reinforcement was applied in the LOG, the recurrence rate was not less than the EOG.

Long-Term Surgical Outcome of Trocar Site Hernia Repair

Port site hernias are emerging as a problematic complication of laparoscopic surgery. The aim of this study was to elucidate the characteristics of port site hernias and determine the long-term outcomes based on the interval between primary surgery and hernia occurrence. Twenty-four patients were surgically treated for trocar site hernia between 1997 and 2013. The patients were grouped into early-onset group (EOG; less than one month) and late-onset group (LOG; more than one month) based on the interval between laparoscopic surgery and hernia onset. A retrospective analysis was performed. There were seven patients in the EOG and 17 patients in the LOG. The body mass index was significantly higher (P = 0.033) in the LOG. In the EOG, primary closure was performed, and there were no recurrences. In the LOG, mesh reinforcement was applied in 58.8 per cent of patients, and 29.4 per cent of patients had recurrences. This recurrence rate was higher than the recurrence rate after primary repair of incisional hernia after open laparotomy (P = 0.088). In conclusion, In the EOG, small bowel resection was more frequent, but once repaired, there were no recurrences. Although mesh reinforcement was applied in the LOG, the recurrence rate was not less than the EOG.

Prognostic Impact of Changes in Adipose Tissue Areas after Colectomy in Colorectal Cancer Patients

There have been few studies assessing the changes in the body components of patients after colectomy in colorectal cancer (CRC). The purpose of this study was to verify the trends in the adipose tissue areas of CRC patients before and after surgery and to determine their clinical relevance. Computed tomography (CT)-assessed subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) areas were recorded before and after curative resection in stage I to III CRC patients. Changes in the adipose tissue were assessed by calculating the difference in the adipose tissue area between preoperative CT and the most recent postoperative CT, which is disease-free state. Regarding obesity before surgery, there were no prognostic effect of body mass index (BMI), VAT and SAT, and 47.3% of patients had increases in VAT after colectomy. By multivariate analysis, adjusting sex, age, stage, differentiation, VAT change was the only obesity related factor to predict the prognosis, that patients who had increase in VAT after colectomy had better overall survival (HR, 0.557; 95% CI, 0.317-0.880) and disease-free survival (HR, 0.602; 95% CI, 0.391-0.927). BMI and SAT change had no significant association. In subgroup analysis of stage III CRC patients, VAT change had significance for prognosis only in patients who had adjuvant chemotherapy but not in those who did not receive postoperative chemotherapy. Increase in visceral adipose tissue after surgery is a favorable predictor of prognosis for CRC patients.

High-Dose Radiation-Induced Changes in Murine Small Intestinal Motility: Are the Changes in the Interstitial Cells of Cajal or in the Enteric Nervous System?

Murine small intestinal motility consists of phasic contraction from interstitial cells of Cajal (ICC) and migrating motor complexes (MMCs) from the enteric nervous system. The number of ICC is reduced in various gastrointestinal disorders, and this effect can be reversed once the disorder is resolved through cellular and tissue remodelling. Exposure to high-dose radiation can induce inflammation and alter intestinal motility. In this study, we investigated the changes in the small intestinal motility of 8- to 10-week-old male C3H/HeN mice after high-dose (13 Gy) irradiation. The aim of this study was to determine whether those changes are caused by changes in the ICC or enteric nervous system. After irradiation, the small intestine was dissected and stored in oxygenated Krebs-Ringer bicarbonate solution. The tension of contractions and intracellular membrane potentials were recorded at day 0, 1, 3 and 5 after irradiation and compared with those of sham-irradiated mice. Histological evaluation was performed by immunohistochemistry and apoptosis was evaluated. Quantitative real-time polymerase chain reaction (qPCR) for c-kit mRNA was also performed. Phasic contractions were not changed at day 0, 1, 3 and 5 after irradiation and did not significantly differ from those in the control mice. Slow waves were also sustained after irradiation. However, the frequency of migrating motor complexes (MMCs) was significantly higher at day 0 and 1 after exposure and the amplitude and area under the curve were significantly lower at day 3 after exposure compared with control mice. MMCs were recovered at day 5 with no difference from those of the control mice. ICC were detected after irradiation by immunohistochemistry for c-kit, and c-kit mRNA levels did not differ between sham-irradiated and irradiated mice. Histological evaluation showed that the most severe inflammation was detected at day 3 after irradiation, and apoptosis was detected only in the mucosa. Acetylcholine increased the contractility after irradiation, and tetrodotoxin decreased the number of MMCs in sham-irradiated and irradiated mice. N(w)-oxide-l-arginine (L-NA) increased the number of MMCs. MMCs were recovered after L-NA treatment at day 3 after irradiation. Sodium nitroprusside decreased the MMCs in sham-irradiated and irradiated mice. Exposure to high-dose radiation did not alter phasic contractions and slow waves in the small intestine of mice, which suggests that ICC and their functions may be sustained after high-dose irradiation. Mucosal inflammation was severe after irradiation and there were some changes in MMCs related to the enteric nervous system.

Electrophysiological and Mechanical Characteristics in Human Ileal Motility: Recordings of Slow Waves Conductions and Contractions, In vitro

Little human tissue data are available for slow waves and migrating motor complexes, which are the main components of small bowel motility. We investigated the electrophysiological and mechanical characteristics of human ileal motility, in vitro. Ileum was obtained from patients undergoing bowel resection. Electrophysiological microelectrode recordings for membrane potential changes and mechanical tension recordings for contraction from smooth muscle strips and ileal segments were performed. Drugs affecting the enteric nervous system were applied to measure the changes in activity. Slow waves were detected with a frequency of 9~10/min. There were no cross-sectional differences in resting membrane potential (RMP), amplitude or frequency between outer and inner circular muscle (CM), suggesting that electrical activities could be effectively transmitted from outer to inner CM. The presence of the interstitial cell of Cajal (ICC) at the linia septa was verified by immunohistochemistry. Contractions of strips and segments occurred at a frequency of 3~4/min and 1~2/min, respectively. The frequency, amplitude and area under the curve were similar between CM and LM. In segments, contractions of CM were associated with LM, but propagation varied with antegrade and retrograde directions. Atropine, N^W-oxide-L-arginine, and sodium nitroprusside exhibited different effects on RMP and contractions. There were no cross-sectional differences with regard to the characteristics of slow waves in CM. The frequency of contractions in smooth muscle strips and ileal segments was lower than slow waves. The directions of propagation were diverse, indicating both mixing and transport functions of the ileum.