Supplementary Material for: Analysis of Gene-Gene Interactions Using Gene-Trait Similarity Regression

<b><i>Objective:</i></b> Gene-gene interactions (G×G) are important to study because of their extensiveness in biological systems and their potential in explaining missing heritability of complex traits. In this work, we propose a new similarity-based test to assess G×G at the gene level, which permits the study of epistasis at biologically functional units with amplified interaction signals. <b><i>Methods:</i></b> Under the framework of gene-trait similarity regression (SimReg), we propose a gene-based test for detecting G×G. SimReg uses a regression model to correlate trait similarity with genotypic similarity across a gene. Unlike existing gene-level methods based on leading principal components (PCs), SimReg summarizes all information on genotypic variation within a gene and can be used to assess the joint/interactive effects of two genes as well as the effect of one gene conditional on another. <b><i>Results:</i></b> Using simulations and a real data application to the Warfarin study, we show that the SimReg G×G tests have satisfactory power and robustness under different genetic architecture when compared to existing gene-based interaction tests such as PC analysis or partial least squares. A genome-wide association study with approx. 20,000 genes may be completed on a parallel computing system in 2 weeks

Supplementary Material for: Effects of Music Intervention on the Physical and Mental Status of Patients with Breast Cancer: A Systematic Review and Meta-Analysis

Background: The aim of this review was to evaluate the effects of music intervention on the physical and mental status of patients with breast cancer. Methods: 9 databases were searched; 30 randomized controlled trials that compared the effects of music plus standard care and standard care alone in patients with breast cancer were included. Methodological quality was assessed using the Jadad scale. Results: The results of the metaanalysis suggested that music intervention was significantly effective in lowering systolic blood pressure (standardized mean difference (SMD) –0.63, 95% confidence interval (CI) –0.85 to –0.42; p < 0.00001), diastolic blood pressure (SMD –0.64, 95% CI –1.06 to –0.22; p = 0.003), and heart rate (SMD –0.45, 95% CI –0.66 to –0.24; p < 0.0001), and in relieving anxiety (Hamilton Scale: mean difference (MD) –7.04, 95% CI –9.31 to –4.78; p < 0.00001; Self-Rating Anxiety Scale: MD –7.40, 95% CI –10.28 to –4.52; p < 0.00001; State Anxiety Inventory: MD –12.40, 95% CI –21.86 to –2.94; p = 0.01), and depression (MD –7.39, 95% CI –8.35 to –6.43; p < 0.00001). Conclusion: This review provides clues that music intervention might partially improve the physiological and psychological health of patients with breast cancer

Supplementary Material for: Fasting Plasma Glucose Levels Predict Steroid-Induced Abnormal Glucose Metabolism in Patients with Non-Diabetic Chronic Kidney Disease: A Prospective Cohort Study

<b><i>Background/Aims:</i></b> Glucocorticoids-induced abnormal glucose metabolism (AGM) is a common medical problem in patients with non-diabetic chronic kidney disease (CKD). However, little information is available regarding the prediction of steroid-induced AGM in this patient population. <b><i>Methods:</i></b> In this prospective cohort study, we consecutively enrolled 303 non-diabetic CKD patients with fasting plasma glucose (FPG) levels <5.6 mmol/l and normal oral glucose tolerance test (OGTT). OGTT was performed every 3 months during glucocorticoid treatment to identify new-onset AGM, and patients were followed for 12 months post steroid withdrawal. <b><i>Results:</i></b> During 593 person-years, there were 107 incident cases of steroid-induced AGM (18/100 person-year), including 55 (51.4%) diabetes and 52 (48.6%) pre-diabetes. In a multivariate model, each millimole increase per liter in FPG enhanced the risk of AGM by 4.6-fold (hazard ratio 4.58, 95% confidence interval, 2.67-7.83). After adjusting other risk factors, a progressively increased risk of AGM or DM was observed in patients with FPG levels ≥4.8 mmol/l, as compared with those whose levels were ≤4.3 mmol/l (p for trend <0.001). Furthermore, a greater increase in FPG level (≥0.3 mmol/l) during the first 3 months of glucocorticoid treatment was associated with an increased risk for future diabetes. For predicting steroid-induced diabetes, the area under the receiver-operating characteristic curve was 0.90 for the combination of FPG and changes in FPG levels at month 3. <b><i>Conclusion:</i></b> Higher-normal FPG and a greater increase in FPG levels during glucocorticoid treatment may help to identify non-diabetic CKD patients at increased risk of steroid-induced AGM or diabetes

Supplementary Material for: Genome-Wide Identification and Analysis of the Type-B Authentic Response Regulator Gene Family in Peach (Prunus persica)

<p>The type-B authentic response regulator (ARR-B) family members serve as DNA-binding transcriptional regulators, whose activities are probably regulated by phosphorylation/dephosphorylation, resulting in the rapid induction of type-A ARR genes. Type-B ARRs are believed to be involved in many biological processes, including cytokinin signaling, plant growth, and stress responses through a chaperone or by isomerization of proline residues during protein folding. The public availability of complete peach genome sequences allows the identification of 23 ARR-B genes by HMMER and blast analysis. Scaffold locations of these genes in the peach genome were determined, and the protein domain and motif organization of peach type-B ARRs were analyzed. The phylogenetic relationships between peach type-B ARRs were also assessed. The expression profiles of peach ARR-B genes revealed that most of the type-B ARRs showed high expression levels in tissues undergoing rapid cell division and may engage more cytokinins, like half-opened flowers, fruits at expansion stages, and young leaves. These findings not only contribute to a better understanding of the complex regulation of the peach ARR-B gene family, but also provide valuable information for future research in peach functional genomics.</p

Supplementary Material for: Life's Essential 8 and Mortality in US Adults with Chronic Kidney Disease

Introduction: The current prevalence of chronic kidney disease (CKD) is substantial, and CKD individuals face a heightened risk of mortality, encompassing both all-cause and cause-specific outcomes. The current study aims to investigate the potential impact of adhering to Life Essential 8 (LE8) on reducing mortality among CKD individuals. Methods: Using the National Health and Nutrition Survey (NHANES) data from 2005 to 2018, we analyzed 22,420 United States adults (≥20 years old). CKD is defined by urinary albumin-to-creatinine ratio (≥30 mg/g or 3 mg/mmol) and estimated glomerular filtration rate (<60 ml/min/1.73m2). The components of LE8, including diet, physical activity (PA), nicotine exposure, sleep, Body Mass Index, blood lipids, blood glucose, and blood pressure (BP) were measured and given a score of 0-100. The total LE8 score was the unweighted average of all components and was divided into low cardiovascular health (CVH) (0-49), moderate CVH (50-79), and high CVH (80-100). Cox proportional hazards regression model was used to explore the associations of LE8 with all-cause, cardiovascular disease (CVD), and cancer mortality, which were followed prospectively by the National Center for Health Statistics until December 31, 2019. Results: In the overall population, individuals with moderate CVH had a 47% lower risk of CKD, while high CVH was linked to a 55% lower risk compared to low CVH. During a median follow-up of 7.58 years, CKD individuals had a 93% higher all-cause mortality rate and a 149% higher CVD mortality rate compared to those without CKD. Among the CKD individuals, every 10-point increase in LE8 score was associated with reduced risks of 17% for all-cause mortality (especially PA, nicotine exposure, blood glucose, and BP), 18% for CVD mortality (especially PA), and 12% for cancer mortality (especially PA and sleep health). In additional and sensitivity analysis, the results remained significant after further consideration of potential confounding of renal function. Additionally, LE8 demonstrated superior risk stratification for CVD mortality among CKD patients compared with LS7. Interaction was observed between LE8 and age, education level, marital status, and drinking status. Conclusions: The current study demonstrates that adherence to higher LE8 levels within CKD individuals is associated with a reduced risk of both all-cause and cause-specific mortality

Supplementary Material for: Life's Essential 8 and Mortality in US Adults with Chronic Kidney Disease

Introduction: The current prevalence of chronic kidney disease (CKD) is substantial, and CKD individuals face a heightened risk of mortality, encompassing both all-cause and cause-specific outcomes. The current study aims to investigate the potential impact of adhering to Life Essential 8 (LE8) on reducing mortality among CKD individuals. Methods: Using the National Health and Nutrition Survey (NHANES) data from 2005 to 2018, we analyzed 22,420 United States adults (≥20 years old). CKD is defined by urinary albumin-to-creatinine ratio (≥30 mg/g or 3 mg/mmol) and estimated glomerular filtration rate (<60 ml/min/1.73m2). The components of LE8, including diet, physical activity (PA), nicotine exposure, sleep, Body Mass Index, blood lipids, blood glucose, and blood pressure (BP) were measured and given a score of 0-100. The total LE8 score was the unweighted average of all components and was divided into low cardiovascular health (CVH) (0-49), moderate CVH (50-79), and high CVH (80-100). Cox proportional hazards regression model was used to explore the associations of LE8 with all-cause, cardiovascular disease (CVD), and cancer mortality, which were followed prospectively by the National Center for Health Statistics until December 31, 2019. Results: In the overall population, individuals with moderate CVH had a 47% lower risk of CKD, while high CVH was linked to a 55% lower risk compared to low CVH. During a median follow-up of 7.58 years, CKD individuals had a 93% higher all-cause mortality rate and a 149% higher CVD mortality rate compared to those without CKD. Among the CKD individuals, every 10-point increase in LE8 score was associated with reduced risks of 17% for all-cause mortality (especially PA, nicotine exposure, blood glucose, and BP), 18% for CVD mortality (especially PA), and 12% for cancer mortality (especially PA and sleep health). In additional and sensitivity analysis, the results remained significant after further consideration of potential confounding of renal function. Additionally, LE8 demonstrated superior risk stratification for CVD mortality among CKD patients compared with LS7. Interaction was observed between LE8 and age, education level, marital status, and drinking status. Conclusions: The current study demonstrates that adherence to higher LE8 levels within CKD individuals is associated with a reduced risk of both all-cause and cause-specific mortality

Supplementary Material for: Myopic vascular changes revealed by optical tomography angiography and their association with myopic fundus manifestations

Abstract Introduction: We aimed to quantify and evaluate fundal vascular changes at different severities of myopia using optical tomography angiography (OCTA) and explore their association with fundus changes captured by ultra-widefield (UWF) fundus cameras. Methods: Seventy-four participants with myopia were enrolled in the study and underwent basic ophthalmic examination, OCTA, and UWF fundus photography. Multiple parameters were obtained using OCTA (flow area, structure thickness, and vessel density) and UWF fundus cameras (tessellation and parapapillary atrophy (PPA)). Results: The right eye of 30 participants with low and moderate myopia (LMM) and 44 participants with high myopia (HM) were included. Patients with HM had a larger flow area in the outer retina (FA-OR) and a smaller thickness of choroid (TC). Axial length was significantly correlated with retinal and choroidal flow area and thickness in the different zones. The PPA area was positively correlated with FA-OR and negatively correlated with TC. Tessellation exhibited different levels of correlation with OCTA parameters regarding the flow area, thickness, and vessel density of the fundal layers, mainly in the inner retina. Conclusion: FA-OR and TC exhibited sensitive changes in patients with HM and axial elongation; therefore, they could serve as predictive OCTA biomarkers. The PPA and tessellation were connected to the vascular and structural changes revealed by OCTA

Supplementary Material for: Aberrant Expression of Long Non-Coding RNAs in Newly Diagnosed Type 2 Diabetes Indicates Potential Roles in Chronic Inflammation and Insulin Resistance

<b><i>Background/Aims:</i></b> Long non-coding RNAs (lncRNAs) have emerged as key players in several biological processes and complex diseases. The risk of type 2 diabetes (T2D) is determined by a combination of environmental factors and genetic susceptibility. The purpose of this study was to identify aberrant lncRNAs involved in T2D pathogenesis. <b><i>Methods:</i></b> Microarray analysis was performed using whole blood samples from patients newly diagnosed with T2D and healthy controls. Pathway and Gene Ontology (GO) analyses were utilized to annotate the target genes. Coding non-coding co-expression (CNC) analysis was performed to construct a co-expression network. <b><i>Results:</i></b> We found 55 lncRNAs and 202 mRNAs were differentially expressed in the T2D group compared to the healthy control group. Pathway and GO analyses demonstrated that dysregulated mRNAs were mainly associated with immune regulation, inflammation, and insulin resistance, whereas CNC analysis identified 10 pairs of co-expressed lncRNA-mRNAs in our patient cohort (R > 0.99). Furthermore, expression of the top three upregulated lncRNAs in the T2D group was correlated with measures of glycometabolism (<i>P</i> < 0.05). <b><i>Conclusion:</i></b> This study identified aberrantly expressed lncRNAs and mRNAs in Han Chinese patients with T2D, and demonstrated that dysregulated lncRNAs may have roles in T2D pathogenesis through regulation of inflammation and insulin resistance

Supplementary Material for: Resveratrol Inhibits Proliferation and Induces Apoptosis through the Hedgehog Signaling Pathway in Pancreatic Cancer Cell

<p><i>Purpose:</i> To investigate the effect and possible mechanisms of resveratrol on pancreatic cancer cells in vitro. <i>Methods:</i> After being treated with resveratrol, cell viability, cell cycle phase distribution and apoptosis rate of pancreatic cancer cells were measured by CCK-8 assay and flow cytometer, respectively. The effects of resveratrol on the Hedgehog pathway were studied by real-time RT-PCR and Western blotting. By interfering Gli1 expression in PANC-1 cells and overexpressing Gli1 in BxPC-3 cells, we detected the expressions of Gli1-targeted genes, such as Ptc1, CCND1 and BCL-2, compared with resveratrol experimental group. We further used the luciferase reporter assay to explore the correlation between resveratrol and Gli1. <i>Results:</i> Resveratrol inhibited the growth of pancreatic cancer cells in a dose- and time-dependent manner. Compared with control group, the cells in the G0/G1 phase and the apoptosis rate were significantly increased. Low concentration of resveratrol decreased the expression of the Hedgehog pathway members including Gli1, Ptc1 and Smo. The expression of downstream target genes of the Hedgehog pathway such as Gli1, Ptc1, CCND1 and BCL-2 were significantly decreased after 12.5 µ<i>M</i> resveratrol treatment, which demonstrated a similar change of gene expression when Gli1 was knocked down by the RNAi technique in PANC-1 cells. Resveratrol also downregulated the expression of Gli1, Ptc1, CCND1 and BCL-2 in Gli1-overexpressed BxPC-3 cells. Results of the luciferase assay showed that resveratrol did not act on the Gli1 promoter directly. <i>Conclusion:</i> Resveratrol can inhibit pancreatic cancer cell survival and its mechanisms might be partly via the Hedgehog signaling pathway.</p

Supplementary Material for: Deferoxamine-Induced Migration and Odontoblast Differentiation via ROS-Dependent Autophagy in Dental Pulp Stem Cells

<b><i>Background/Aims:</i></b> As a vital degradation and recycling system, autophagy plays an essential role in regulating the differentiation of stem cells. We previously showed that iron chelator deferoxamine (DFO) could promote the repair ability of dental pulp stem cells (DPSCs). Here, we investigated the effect of DFO in autophagy and the role of autophagy in regulating the migration and odontoblast differentiation of DPSCs. <b><i>Methods:</i></b> Transmission electron microscopy, immunofluorescence staining and western blotting were performed to evaluate the autophagic activity of DPSCs. Transmigration assay, alkaline phosphatase staining/activity, alizarin red S staining and quantitative PCR were performed to examine the migration and odontoblast differentiation of DPSCs. Reactive oxygen species (ROS) levels and the effects of ROS scavenger in autophagy induction were also detected. Autophagy inhibitors (3-MA and bafilomycin A1) and lentiviral vectors carrying ATG5 shRNA sequences were used for autophagy inhibition. <b><i>Results:</i></b> Early exposure to DFO promoted the mineralization of DPSCs and increased autophagic activity. Autophagy inhibition suppressed DFO-induced DPSC migration and odontoblast differentiation. Furthermore, DFO treatment could induce autophagy partly through hypoxia-inducible factor 1α/B cell lymphoma 2/adenovirus E1B 19K-interacting protein 3 (HIF-1α/BNIP3) pathway in a ROS-dependent manner. <b><i>Conclusion:</i></b> DFO increased DPSC migration and differentiation, which might be modulated through ROS-induced autophagy