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Abstract Background Chronic kidney disease (CKD) is prevalent among elderly patients with type 2 diabetes mellitus (T2DM). The association between dietary patterns and CKD in elderly T2DM patients remains understudied. This study aimed to investigate the relationship between dietary patterns and CKD in elderly Chinese patients with T2DM. Methods This community-based cross-sectional study included 5,713 elderly T2DM patients (aged ≥ 65 years) from Xiangcheng District, Suzhou, China. Dietary intake was assessed using a validated food frequency questionnaire, and dietary patterns were identified using factor analysis. Each participant was assigned a score for each identified dietary pattern, with higher scores indicating a greater alignment of their diet with the respective pattern. Quartiles of these pattern scores were utilized as the primary exposures in the analysis. CKD was defined as albuminuria, reduced estimated glomerular filtration rate (eGFR), or both. Logistic regression models assessed CKD prevalence across quartiles of dietary pattern scores, expressed as adjusted odds ratios (ORs) with 95% confidence intervals (CIs). Results CKD prevalence was 45.7%. Four dietary patterns were identified: “traditional southern”, “high-protein”, “balanced” and “imbalanced”. A balanced dietary pattern, featured with high intake of fruits, dairy products, eggs, snacks, crab and shellfish, and fish and shrimp, was associated with lower CKD prevalence. The adjusted ORs for CKD across ascending quartiles were 0.99 (95% CI: 0.85–1.16), 0.89 (95% CI: 0.76–1.04), and 0.73 (95% CI: 0.62–0.86). The imbalanced dietary pattern, characterized by high intake of green leafy vegetables, refined grains, and red meat but low dietary diversity, was associated with increased CKD prevalence, with ORs of 1.01 (95% CI: 0.86–1.18), 1.15 (95% CI: 0.98–1.35), and 1.25 (95% CI: 1.07–1.46) across quartiles. No significant associations were observed for “traditional southern” or “high-protein” dietary patterns. Conclusions Dietary patterns were associated with CKD prevalence in elderly Chinese T2DM patients. A “balanced dietary pattern”, consistent with local dietary customs, was associated with a lower risk of CKD. Further longitudinal and intervention studies are needed to confirm these associations. Graphical Abstract

Abstract Assessing marker genes from all cell clusters can be time-consuming and lack systematic strategy. Streamlining this process through a unified computational platform that automates identification and benchmarking will greatly enhance efficiency and ensure a fair evaluation. We therefore developed a novel computational platform, cellMarkerPipe ( https://github.com/yao-laboratory/cellMarkerPipe ), for automated cell-type specific marker gene identification from scRNA-seq data, coupled with comprehensive evaluation schema. CellMarkerPipe adaptively wraps around a collection of commonly used and state-of-the-art tools, including Seurat, COSG, SC3, SCMarker, COMET, and scGeneFit. From rigorously testing across diverse samples, we ascertain SCMarker’s overall reliable performance in single marker gene selection, with COSG showing commendable speed and comparable efficacy. Furthermore, we demonstrate the pivotal role of our approach in real-world medical datasets. This general and opensource pipeline stands as a significant advancement in streamlining cell marker gene identification and evaluation, fitting broad applications in the field of cellular biology and medical research.

IntroductionAutoimmune thyroid diseases (AITDs) are prevalent disorders, primarily encompassing Graves’ disease (GD) and Hashimoto’s thyroiditis (HT). Despite their common occurrence, the etiology of AITDs remains elusive. Th9 cells, a new subset of CD4+T cells with immunomodulatory properties, have been linked to the development of various autoimmune diseases. However, research on the role of Th9 cells in AITDs is limited. MethodsWe investigated the expression of Th9 cells,their functional cytokine IL-9, and transcription factor IRF4 in peripheral blood mononuclear cells (PBMCs) and plasma of AITD patients and healthy controls. Additionally, we explored the genetic association between four loci polymorphisms (rs31564, rs2069879, rs1859430, and rs2069868) of the IL-9 gene and AITDs.ResultsWe reported, for the first time, that refractory GD patients exhibited elevated mRNA levels of IL-9 and IRF4 in PBMCs, increased IL-9 protein levels in plasma, and a higher proportion of Th9 cells in peripheral blood when compared to normal controls. Furthermore, human recombinant IL-9 protein was found to enhance IFN-g secretion in PBMCs from both GD patients and normal controls. At the genetic association level, after adjusting for age and sex, the rs2069879 polymorphism exhibited a significant association with AITDs under an additive model (P

Members of the calcium-dependent protein kinase (CDPK/CPK) and SNF-related protein kinase (SnRK) superfamilies are commonly found in plants and some protists. Our knowledge of client specificity of the members of this superfamily is fragmentary. As this family is represented by over 30 members in Arabidopsis thaliana, the identification of kinase-specific and overlapping client relationships is crucial to our understanding the nuances of this large family of kinases as directed towards signal transduction pathways. Herein, we used the kinase client (KiC) assay—a relative, quantitative, high-throughput mass spectrometry-based in vitro phosphorylation assay—to identify and characterize potential CPK/SnRK targets of Arabidopsis. Eight CPKs (1, 3, 6, 8, 17, 24, 28, and 32), four SnRKs (subclass 1 and 2), and PPCK1 and PPCK2 were screened against a synthetic peptide library that contains 2095 peptides and 2661 known phosphorylation sites. A total of 625 in vitro phosphorylation sites corresponding to 203 non-redundant proteins were identified. The most promiscuous kinase, CPK17, had 105 candidate target proteins, many of which had already been discovered. Sequence analysis of the identified phosphopeptides revealed four motifs: LxRxxS, RxxSxxR, RxxS, and LxxxxS, that were significantly enriched among CPK/SnRK clients. The results provide insight into both CPK- and SnRK-specific and overlapping signaling network architectures and recapitulate many known in vivo relationships validating this large-scale approach towards discovering kinase targets.

Small proteins, encoded by small open reading frames, are only beginning to emerge with the current advancement of omics technology and bioinformatics. There is increasing evidence that small proteins play roles in diverse critical biological functions, such as adjusting cellular metabolism, regulating other protein activities, controlling cell cycles, and affecting disease physiology. In prokaryotes such as bacteria, the small proteins are largely unexplored for their sequence space and functional groups. For most bacterial species from a natural community, the sample cannot be easily isolated or cultured, and the bacterial peptides must be better characterized in a metagenomic manner. The bacterial peptides identified from metagenomic samples can not only enrich the pool of small proteins but can also reveal the community-specific microbe ecology information from a small protein perspective. In this study, metaBP (Bacterial Peptides for metagenomic sample) has been developed as a comprehensive toolkit to explore the small protein universe from metagenomic samples. It takes raw sequencing reads as input, performs protein-level meta-assembly, and computes bacterial peptide homolog groups with sample-specific mutations. The metaBP also integrates general protein annotation tools as well as our small protein-specific machine learning module metaBP-ML to construct a full landscape for bacterial peptides. The metaBP-ML shows advantages for discovering functions of bacterial peptides in a microbial community and increases the yields of annotations by up to five folds. The metaBP toolkit demonstrates its novelty in adopting the protein-level assembly to discover small proteins, integrating protein-clustering tool in a new and flexible environment of RBiotools, and presenting the first-time small protein landscape by metaBP-ML. Taken together, metaBP (and metaBP-ML) can profile functional bacterial peptides from metagenomic samples with potential diverse mutations, in order to depict a unique landscape of small proteins from a microbial community.

Background: Graves’ disease (GD) is a common autoimmune disease, and its pathogenesis is unclear. Studies have found that the occurrence of GD is related to the immune disorder caused by the interaction of genetic susceptibility and environmental factors. The CD4+ T cell subset is closely related to the immune disorder of GD. LncRNAs are RNA molecules with a length of more than 200 nt and are involved in a variety of autoimmune diseases. However, the roles of lncRNAs in recurrent GD are still elusive. The purpose of this study is to identify lncRNA and mRNA expression profile in relapsed Graves’ disease.Method: CD4+ T cells from 12 recurrent GD and 8 healthy controls were collected for high-throughput sequencing. The gene-weighted co-expression network analysis (WGCNA) was used to construct the co-expression module relevant to recurrent GD, and the key genes in the module were verified by RT-PCR.Results: There are 602 upregulated lncRNAs and 734 downregulated lncRNAs in CD4+ T cells in recurrent GD patients compared with the healthy controls. The module most relevant to GD recurrence was constructed using WGCNA, and the key genes in the module were verified by RT-PCR. We found that the expression of RPL8, OAS2, NFAT5, DROSHA, NONHSAT093153.2, NONHSAT118924.2, and NONHSAT209004.1 was significantly decreased in GD group (p < 0.001, p < 0.001, p < 0.01, p < 0.05, p < 0.001, p < 0.05, and p < 0.01, respectively).Conclusion: LncRNAs are closely related to the recurrence of GD. For the first time, we constructed the expression profile of lncRNAs and mRNAs in CD4+ T cells in recurrent GD patients.

Objective. Rheumatoid arthritis (RA) is a complex disease with unknown pathogenesis. In recent years, fewer have paid attention to the broad spectrum of systemic markers of RA. The aim of this study was to identify exosomal candidate proteins in the pathogenesis of RA. Methods. Totally, 12 specimens of plasma from 6 RA patients and 6 age- and gender-matched controls from the Chinese population were obtained for nanoscale liquid chromatography coupled to tandem mass spectrometry (nano-LC-MS/MS) analysis to identify exosomal profiles. Results. A total of 278 exosomal proteins were detected. Among them, 32 proteins were significantly upregulated (FC≥2.0 and P

Abstract CRISPR/Cas9 pooled screening permits parallel evaluation of comprehensive guide RNA libraries to systematically perturb protein coding sequences in situ and correlate with functional readouts. For the analysis and visualization of the resulting datasets, we develop CRISPRO, a computational pipeline that maps functional scores associated with guide RNAs to genomes, transcripts, and protein coordinates and structures. No currently available tool has similar functionality. The ensuing genotype-phenotype linear and three-dimensional maps raise hypotheses about structure-function relationships at discrete protein regions. Machine learning based on CRISPRO features improves prediction of guide RNA efficacy. The CRISPRO tool is freely available at gitlab.com/bauerlab/crispro.

Background/Aims: The IKZF3 gene encodes a zinc-finger protein that plays an important role in the proliferation and differentiation of B lymphocytes. Autoimmune thyroid diseases (AITDs), mainly include Graves’ disease (GD) and Hashimoto’s thyroiditis (HT), are probably caused by the aberrant proliferation of B cells. The objective of this study was to explore the association between IKZF3 polymorphisms and AITDs. Methods: We examined 915 AITD patients (604 GD and 311 HT) and 814 healthy controls. IKZF3 variants (rs2941522, rs907091, rs1453559, rs12150079 and rs2872507) were tested by PCR-ligase detection reaction. Results: It was manifested that that the minor alleles of the five loci increased susceptibility to GD (p

Abstract Glomerular basement membrane (GBM) damage plays a pivotal role in pathogenesis of albuminuria in diabetic nephropathy (DN). Heparan sulfate (HS) degradation induced by podocyte heparanase is the major cause of GBM thickening and abnormal perm-selectivity. In the present study, we aimed to examine the prophylactic effect of hyperoside on proteinuria development and GBM damage in DN mouse model and the cultured mouse podocytes. Pre-treatment with hyperoside (30 mg/kg/d) for four weeks could significantly decrease albuminuria, prevent GBM damage and oxidative stress in diabetes mellitus (DM) mice. Immunofluorescence staining, Real time PCR and Western blot analysis showed that decreased HS contents and increased heparanase expression in DN mice were also significantly improved by hyperoside pre-treatment. Meanwhile, transmission electron microscope imaging showed that hyperoside significantly alleviated GBM thickening in DN mice. In addition, hyperoside pre-treatment inhibited the increased heparanase gene (HPR1) promoter activity and heparanase expression induced by high glucose or reactive oxidative species (ROS) in cultured podocytes. Our data suggested that hyperoside has a prophylactic effect on proteinuria development and GBM damage in DM mice by decreasing podocyte heparanase expression.

Abstract Background Selenium is an essential trace and there is a high selenium concentration in the thyroid gland. Selenium deficiency may impair the thyroid function. The aim of this study was to investigate the association between three selenoprotein genes polymorphisms and autoimmune thyroid diseases. Methods We genotyped six single-nucleotide polymorphisms (SNPs), rs6865453 in selenoprotein P gene (SELENOP), rs713041 rs2074451 rs3746165 in glutathione peroxidase 4 gene (GPX4) and rs28665122 and rs7178239 in selenoprotein S gene (SELENOS) by MassARRAY system using the chip-based matrix-assisted laser desorption ionization time-of-flight mass spectrometry technology in 1060 patients with autoimmune thyroid diseases and 938 healthy controls. Results Major alleles in rs6865453 of SELENOP, rs713041, rs2074451, rs3746165 of GPX4 decreased while the major allele C in rs28665122 of SELENOS increased in AITD patients than in the control. The allele C and genotype CC in rs7178239 of SELENOS showed different trend in GD and HT patients when compared with the control. All the distribution difference showed nonsignificant. Analysis according to clinical features including ophthalmopathy, hypothyroidism and family history came out to be negative either. Conclusions Our findings suggest non-association between three selenoprotein genes and AITD, conflicting to the positive result in another population. Different selenium nutrition status in different populations may contribute to conflicting results, the contribution of genetic variants in AITD mechanism may be another reason.

Stable isotope probing (SIP) enables tracking the nutrient flows from isotopically labeled substrates to specific microorganisms in microbial communities. In proteomic SIP, labeled proteins synthesized by the microbial consumers of labeled substrates are identified with a shotgun proteomics approach. Here, proteomic SIP was combined with targeted metagenomic binning to reconstruct metagenome-assembled genomes (MAGs) of the microorganisms producing labeled proteins. This approach was used to track carbon flows from 13CO2 to the rhizosphere communities of Zea mays, Triticum aestivum, and Arabidopsis thaliana. Rhizosphere microorganisms that assimilated plant-derived 13C were capable of metabolic and signaling interactions with their plant hosts, as shown by their MAGs containing genes for phytohormone modulation, quorum sensing, and transport and metabolism of nutrients typical of those found in root exudates. XoxF-type methanol dehydrogenases were among the most abundant proteins identified in the rhizosphere metaproteomes. 13C-methanol proteomic SIP was used to test the hypothesis that XoxF was used to metabolize and assimilate methanol in the rhizosphere. We detected 7 13C-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 13C-labeled microorganisms, which supported the hypothesis. These two studies demonstrated the capability of proteomic SIP for functional characterization of active microorganisms in complex microbial communities.

Purpose: Sjögren’s syndrome (SS) is an autoimmune disease characterized by dry mouth and eyes. To date, the exact molecular mechanisms of its etiology are still largely unknown. The aim of this study was to identify SS related key genes and functionally enriched pathways using the weighted gene co-expression network analysis (WGCNA).Materials and Methods: We downloaded the microarray data of 190 SS patients and 32 controls from Gene Expression Omnibus (GEO). Gene network was constructed and genes were classified into different modules using WGCNA. In addition, for the hub genes in the most related module to SS, gene ontology analysis was applied. The expression profile and diagnostic capacity (ROC curve) of interested hub genes were verified using a dataset from the GEO. Moreover, gene set enrichment analysis (GSEA) was also performed.Results: A total of 1483 differentially expressed genes were filtered. Weighted gene coexpression network was constructed and genes were classified into 17 modules. Among them, the turquoise module was most closely associated with SS, which contained 278 genes. These genes were significantly enriched in 10 Gene Ontology terms, such as response to virus, immune response, defense response, response to cytokine stimulus, and the inflammatory response. A total of 19 hub genes (GBP1, PARP9, EPSTI1, LOC400759, STAT1, STAT2, IFIH1, EIF2AK2, TDRD7, IFI44, PARP12, FLJ20035, PARP14, ISGF3G, XAF1, RSAD2,LY6E, IFI44L, and DDX58) were identified. The expression levels of the five interested genes including EIF2AK2, GBP1, PARP12, PARP14, and TDRD7 were also confirmed. ROC curve analysis determined that the above five genes’ expression can distinguish SS from controls (the area under the curve is all greater than 0.7). GSEA suggests that the SS samples with highly expressed EIF2AK2 or TDRD7 genes are correlated with inflammatory response, interferon α response, and interferon γ response.Conclusion: The present study applied WGCNA to generate a holistic view of SS and provide a basis for the identification of potential pathways and hub genes that may be involved in the development of SS.

Recently, abnormal expression of interleukin-32 (IL-32) has been involved in various inflammatory or autoimmune diseases, but the level of IL-32 expression in Graves' disease (GD) is still unknown. This study is aimed to explore the human IL-32 expression in GD and the association of IL-32 expression with the disease activity of GD. A total of 125 GD patients and 97 normal controls (NC) were recruited in this study. We examined IL-32 mRNA level in peripheral blood mononuclear cells (PBMCs) of 43 GD patients and 41 controls using real-time polymerase chain reaction (RT-PCR). Serum IL-32 level of 40 GD patients and 34 controls was measured by enzyme linked immunosorbent assay (ELISA). In another cohort including 42 GD patients and 22 controls, we detected the percentages of IL-32α+ cells, CD4+IL-32α+T cells, and CD4−IL-32α+ cells in PBMCs by flow cytometry. In GD patients, IL-32 mRNA expression was dramatically higher than that in controls (P < 0.001) and positively associated with FT3 (P = 0.036, r = 0.321). Subgroup analysis revealed that IL-32 mRNA level was elevated in both newly onset GD and refractory GD group (P < 0.01, P < 0.001, respectively) compared with controls. Furthermore, in refractory GD group, the IL-32 mRNA expression also positively correlated with FT3 (P = 0.019, r = 0.560). In addition, serum IL-32 level was notably higher in GD patients than that of controls (P < 0.01). Subgroup analysis also indicated that serum IL-32 level in both newly onset GD and refractory GD group was higher in comparison with controls (P = 0.015, P = 0.023, respectively) and serum IL-32 level in refractory GD patients positively correlated with TRAb (P = 0.043, r = 0.481). The percentages of IL-32α+ cells, CD4+IL-32α+ T cells, and CD4−IL-32α+ cells were all significantly enhanced in GD patients compared with controls (P = 0.005, P = 0.017, P = 0.016, respectively). IL-32 and IL-32α+ cells may be associated with the pathogenesis of GD. IL-32 may become a promising target for the treatment of GD.

ABSTRACT Objective In the present study, we aimed to assess the associations of C1q gene polymorphisms with autoimmune thyroid diseases (AITD) susceptibility. Subjects and methods A set of 1,003 AITD patients (661 with Graves’ disease and 342 with Hashimoto’s thyroiditis) and 880 ethnically- and geographically-matched controls from Chinese Han population were included. Five common single nucleotide polymorphisms (SNPs) (rs294185, rs292001, rs682658, rs665691 and rs294179) in C1q gene locus were genotyped. Frequencies of genotypes and alleles were compared between patients and controls, and haplotype analysis was also performed. Results There was no statistically significant difference between AITD patients and controls in the frequencies of alleles of rs294185 (P = 0.41), rs292001 (P = 0.71), rs682658 (P = 0.68), rs665691 (P = 0.68) and rs294179 (P = 0.69). There was also no statistically significant difference between AITD patients and controls in the frequencies of genotypes of rs294185 (P = 0.72), rs292001 (P = 0.89), rs682658 (P = 0.83), rs665691 (P = 0.90) and rs294179 (P = 0.43). Stratified analyses showed that none of those five SNPs in C1q gene were associated with Graves’ disease or Hashimoto’s thyroiditis (all P values > 0.05). Haplotype analysis revealed that there were no obvious genetic associations of C1q gene polymorphisms with AITD susceptibility. Conclusions We, for the first time, identified the associations between C1q gene SNPs and AITD, and our findings suggested that five common SNPs in C1q gene were not associated with AITD susceptibility in Chinese Han population.

Co-signaling molecules include co-stimulatory and co-inhibitory molecules and play important roles in modulating immune responses. The roles of co-signaling molecules in autoimmune diseases have not been clearly defined. We assessed the expressions of co-stimulatory and co-inhibitory molecules in autoimmune diseases through a bioinformatics-based study. By using datasets of whole-genome transcriptome, the expressions of 54 co-stimulatory or co-inhibitory genes in common autoimmune diseases were analyzed using Robust rank aggregation (RRA) method. Nineteen array datasets and 6 RNA-seq datasets were included in the RRA discovery study and RRA validation study, respectively. Significant genes were further validated in several autoimmune diseases including Graves' disease (GD). RRA discovery study suggested that CD160 was the most significant gene aberrantly expressed in autoimmune diseases (Adjusted P = 5.9E-12), followed by CD58 (Adjusted P = 5.7E-06) and CD244 (Adjusted P = 9.5E-05). RRA validation study also identified CD160 as the most significant gene aberrantly expressed in autoimmune diseases (Adjusted P = 5.9E-09). We further found that the aberrant expression of CD160 was statistically significant in multiple autoimmune diseases including GD (P < 0.05), and CD160 had a moderate role in diagnosing those autoimmune diseases. Flow cytometry confirmed that CD160 was differentially expressed on the surface of CD8+ T cells between GD patients and healthy controls (P = 0.002), which proved the aberrant expression of CD160 in GD at the protein level. This study suggests that CD160 is the most significant co-signaling gene aberrantly expressed in autoimmune diseases. Treatment strategy targeting CD160-related pathway may be promising for the therapy of autoimmune diseases.

Autoimmune thyroid diseases (AITDs) are chronic organ-specific autoimmune diseases and mainly include Graves' disease (GD) and Hashimoto's thyroiditis (HT). CD14 is an important component of the immune system as a receptor for gram-negative lipopolysaccharide (LPS). The genetic polymorphisms of CD14 have been confirmed to be associated with a variety of autoimmune diseases. However, its relationship with AITDs is still unclear. The study was aimed to determine whether four single nucleotide polymorphisms (rs2915863, rs2569190, rs2569192, and rs2563298) of CD14 are associated with AITDs and its subgroups of GD and HT. The results showed significant association of rs2915863 and rs2569190 with GD. The frequencies of rs2915863 genotypes and T allele in patients with GD differed significantly from their controls (P = 0.007 and P = 0.021, respectively). For rs2569190, frequencies of genotypes and G allele in GD patients also showed positive P-values (P = 0.038 and P = 0.027, respectively). The correlations between these two loci and GD are more pronounced in female GD patients and patients with a family history. In genetic model analysis, the allele model, recessive model, and homozygous model of rs2569190 and rs2915863 embodied strong correlations with GD after the adjusting of age and gender (P = 0.014, P = 0.015, P = 0.009, and P = 0.014, P = 0.001, P = 0.006, respectively). However, these four sites are not related to HT. We firstly discovered the relationship between CD14 gene polymorphism and GD, and the results indicate that CD14 is an important risk locus for AITD and its SNPs may contribute to host's genetic predisposition to GD.

The objective of this study was to investigate whether IRF7 polymorphisms are associated with autoimmune thyroid diseases (AITDs). We selected three single nucleotide polymorphisms (SNPs) of IRF7, namely, rs1061501, rs1131665, and rs1061502 for genotyping using PCR-based ligase detection reaction (LDR) method in a total of 1659 participants (592 with Graves’ disease, 297 with Hashimoto’s thyroiditis, and 770 healthy controls). Gene-disease and genotype-clinical phenotype associations were evaluated for the three SNPs. Our results showed that the AG genotype and the minor allele G frequency of rs1131665 and rs1061502 in AITD patients were both higher than those of the controls (rs1131665: AG genotype: P=0.017, OR=1.968; allele G: P=0.018, OR=1.946; rs1061502: AG genotype: P=0.029, OR=1.866; allele G: P=0.031, OR=1.847). Subgroup analysis also showed that the AG genotype and the minor allele G frequency of rs1131665 and rs1061502 in Graves’ disease patients were both higher than those of the controls (rs1131665: AG genotype: P=0.015, OR=2.074; allele G: P=0.016, OR=2.048; rs1061502: AG genotype: P=0.034, OR=1.919; allele G: P=0.035, OR=1.898). Furthermore, the allele G frequency of rs1061501 was associated with Graves’ ophthalmopathy (P=0.035, OR=1.396). No significant difference in IRF7 polymorphisms was found between Hashimoto’s thyroiditis patients and controls. Our study has revealed for the first time that IRF7 is a susceptibility gene for AITD, especially for Graves’ disease and Graves’ ophthalmopathy.

Previous studies investigating the association of circulating 25-hydroxyvitamin D level with prognosis of prostate cancer yielded controversial results. We conducted a dose–response meta-analysis to elucidate the relationship. PubMed and EMBASE were searched for eligible studies up to July 15, 2018. We performed a dose–response meta-analysis using random-effect model to calculate the summary hazard ratio (HR) and 95% CI of mortality in patients with prostate cancer. Seven eligible cohort studies with 7808 participants were included. The results indicated that higher vitamin D level could reduce the risk of death among prostate cancer patients. The summary HR of prostate cancer-specific mortality correlated with an increment of every 20 nmol/L in circulating vitamin D level was 0.91, with 95% CI 0.87–0.97, P = 0.002. The HR for all-cause mortality with the increase of 20 nmol/L vitamin D was 0.91 (95% CI: 0.84–0.98, P = 0.01). Sensitivity analysis suggested the pooled HRs were stable and not obviously changed by any single study. No evidence of publications bias was observed. This meta-analysis suggested that higher 25-hydroxyvitamin D level was associated with a reduction of mortality in prostate cancer patients and vitamin D is an important protective factor in the progression and prognosis of prostate cancer.

There is an intensive link between obesity and thyroid dysfunction, but this relationship in Asians is still unclear. This study was conducted to define the impact of obesity on risk of hypothyroidism and thyroid autoimmunity among Chinese adults. A population-based, cross-sectional study was carried out, which enrolled a total of 2,808 Chinese adults. To assess the associations of obesity with hypothyroidism and thyroid autoimmunity, odds ratio (ORs) with 95% confidence intervals (95%CIs) were calculated through logistic regression model, and the correlations of body mass index (BMI) with TPOAb and TGAb were also analyzed. Obese females had higher risk of hypothyroidism (22.7 vs. 15.0%; OR = 1.66, 95%CI 1.10–2.53; P = 0.02) and higher risk of subclinical hypothyroidism (22.1 vs. 13.4%; OR = 1.83, 95%CI 1.20–2.80; P = 0.005) than non-obese females. Multivariate logistic regression analysis found significant associations of obesity with hypothyroidism (Adjusted OR = 1.54, 95%CI 1.00–2.38; P = 0.05) and subclinical hypothyroidism (Adjusted OR = 1.69, 95%CI 1.09–2.63; P = 0.02) in females after adjustment for confounding factors. No association between obesity and hypothyroidism was observed in male participants. Spearman's correlation analysis suggested BMI was significantly and positively correlated with TPOAb (Spearman's r = 0.062, P = 0.022) in men but not in women. Linear regression analysis suggested an obviously positive correlation of BMI with TPOAb in men (β = 0.018, P = 0.015) and an obviously negative correlation of BMI with TGAb in women (β = −0.025, P = 0.012), respectively. The study suggests sex differences in the associations of obesity with hypothyroidism and thyroid autoimmunity among Chinese adults. Further studies are needed to better understand the exact mechanism of sex difference in the obesity-thyroid relationship.

BackgroundPrevious studies propose that hypothyroidism might play a crucial role in the pathogenesis of non-alcoholic fatty liver disease (NAFLD), but findings from published studies on the relationship between hypothyroidism and NAFLD are still controversial. Our study aimed to make a comprehensive evaluation of the relationship between hypothyroidism and NAFLD through a meta-analysis.MethodsPubMed, China Dissertation Database, and EMBASE databases were searched to find observational studies assessing the relationship between hypothyroidism and NAFLD. The pooled odds ratios (ORs) with 95% confidence intervals (95% CIs) were calculated to evaluate the strength of the relationship between hypothyroidism and NAFLD through meta-analysis.ResultsThirteen articles were ultimately included in our meta-analysis. Meta-analysis of the 13 studies found a high correlation between hypothyroidism and NAFLD (OR = 1.52, 95% CI 1.24–1.87, P

A number of studies have previously assessed the impact of antibiotic exposure in early life on the risk of childhood obesity, but no systematic assessment is currently available. A systematic review and meta-analysis was performed to comprehensively and quantitatively elucidate the risk of childhood obesity caused by antibiotic exposure in early life. Literature search was performed in PubMed, Embase, and Web of Science. Random-effect meta-analysis was used to pool the statistical estimates. Fifteen cohort studies involving 445,880 participants were finally included, and all those studies were performed in developed countries. Antibiotic exposure in early life significantly increased risk of childhood overweight [relative risk (RR) = 1.23, 95% confidence interval (CI) 1.13–1.35, P

Drought and flooding are two major causes of severe yield loss in soybean worldwide. A lack of knowledge of the molecular mechanisms involved in drought and flood stress has been a limiting factor for the effective management of soybeans; therefore, it is imperative to assess the expression of genes involved in response to flood and drought stress. In this study, differentially expressed genes under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. A total of 2,724 and 3,498 differentially expressed genes (DEGs) were identified under drought and flooding treatments, respectively. These genes comprise 289 Transcription Factors (TFs) representing Basic Helix-loop Helix (bHLH), Ethylene Response Factors (ERFs), myeloblastosis (MYB), No apical meristem (NAC), and WRKY amino acid motif (WRKY) type major families known to be involved in the mechanism of stress tolerance. The expression of photosynthesis and chlorophyll synthesis related genes were significantly reduced under both types of stresses, which limit the metabolic processes and thus help prolong survival under extreme conditions. However, cell wall synthesis related genes were up-regulated under drought stress and down-regulated under flooding stress. Transcript profiles involved in the starch and sugar metabolism pathways were also affected under both stress conditions. The changes in expression of genes involved in regulating the flux of cell wall precursors and starch/sugar content can serve as an adaptive mechanism for soybean survival under stress conditions. This study has revealed the involvement of TFs, transporters, and photosynthetic genes, and has also given a glimpse of hormonal cross talk under the extreme water regimes, which will aid as an important resource for soybean crop improvement.

Small proteins, encoded by small open reading frames, are only beginning to emerge with the current advancement of omics technology and bioinformatics. There is increasing evidence that small proteins play roles in diverse critical biological functions, such as adjusting cellular metabolism, regulating other protein activities, controlling cell cycles, and affecting disease physiology. In prokaryotes such as bacteria, the small proteins are largely unexplored for their sequence space and functional groups. For most bacterial species from a natural community, the sample cannot be easily isolated or cultured, and the bacterial peptides must be better characterized in a metagenomic manner. The bacterial peptides identified from metagenomic samples can not only enrich the pool of small proteins but can also reveal the community-specific microbe ecology information from a small protein perspective. In this study, metaBP (Bacterial Peptides for metagenomic sample) has been developed as a comprehensive toolkit to explore the small protein universe from metagenomic samples. It takes raw sequencing reads as input, performs protein-level meta-assembly, and computes bacterial peptide homolog groups with sample-specific mutations. The metaBP also integrates general protein annotation tools as well as our small protein-specific machine learning module metaBP-ML to construct a full landscape for bacterial peptides. The metaBP-ML shows advantages for discovering functions of bacterial peptides in a microbial community and increases the yields of annotations by up to five folds. The metaBP toolkit demonstrates its novelty in adopting the protein-level assembly to discover small proteins, integrating proteinclustering tool in a new and flexible environment of RBiotools, and presenting the firsttime small protein landscape by metaBP-ML. Taken together, metaBP (and metaBP-ML) can profile functional bacterial peptides from metagenomic samples with potential diverse mutations, in order to depict a unique landscape of small proteins from a microbial community. [ABSTRACT FROM AUTHOR]

Background: Iodine status has long been regarded as an environmental determinant for thyroid dysfunction, but its relationship with thyroid autoimmunity (TAI) is still controversial. Our study aimed to elucidate the relationship between iodine status and TAI through both a population-based study and a dose-response meta-analysis of eligible epidemiological studies. Methods: A population-based, cross-sectional study was firstly carried o ut, which enrolled a total of 2808 Chinese adults. Odds ratio (OR) with 95% confidence interval (95% CI) wa s calculated through logistic regression analysis. A dose-response meta-analysis of eligible epidemiological studies was also carried out. Results: The cross-sectional study showed an U-shaped relationship between iodine intake and TAI in adults. Compared with those with more than adequate iodine status, individuals w ith iodine deficiency, adequate iodine status and iodine excess all had higher risk of TAI, and the adjusted ORs were 1.50 (95% CI 1.03-2.17, P = 0.032), 1.50 (95% CI 1.09-2.07, P = 0.013) and 1.68 (95% CI 1.11-2.53, P = 0.014), respectively. The dose-response meta-analysis included 22 epidemiological studies with a total of 69,987 participants and further validated the U-shaped relationship between iodine intake and TAI in adults, which proved the significantly increased risk of TAI among individuals with either iodine deficiency or iodine excess. Stratified analysis of studie s with low risk of confounding bias also identified similar findings. Conclusion: The study suggests an U-shaped relationship between iodine intake and TAI in adults, and both iodine deficiency and iodine excess are risk factors of TAI in adults. The underlying mechanisms need to be elucidated in future studies. [ABSTRACT FROM AUTHOR]

Protein phosphorylation is widely recognized as the most widespread, enzyme-catalyzed post-translational modification in eukaryotes. In particular, plants have appropriated this signaling mechanism as evidenced by the twofold higher frequency of protein kinases within the genome compared to other eukaryotes. While all aspects of plant protein phosphorylation research have grown in the past 10 years; phosphorylation site mapping using high-resolution mass spectrometry has grown exponentially. In Arabidopsis alone there are thousands of experimentally determined phosphorylation sites. To archive these events in a user-intuitive format we have developed P³DB, the Plant Protein Phosphorylation Database (p3db.org). This database is a repository for plant protein phosphorylation site data, currently hosting information on 32,963 non-redundant sites collated from 23 experimental studies from six plant species. These data can be queried for a protein-of-interest using an integrated BLAST module to query similar sequences with known phosphorylation sites among the multiple plants currently investigated. The paper demonstrates how this resource can help identify functionally conserved phosphorylation sites in plants using a multi-system approach. [ABSTRACT FROM AUTHOR]

Although protein phosphorylation sites can be reliably identified with high-resolution mass spectrometry, the experimental approach is time-consuming and resource-dependent. Furthermore, it is unlikely that an experimental approach could catalog an entire phosphoproteome. Computational prediction of phosphorylation sites provides an efficient and flexible way to reveal potential phosphorylation sites and provide hypotheses in experimental design. Musite is a tool that we previously developed to predict phosphorylation sites based solely on protein sequence. However, it was not comprehensively applied to plants. In this study, the phosphorylation data from Arabidopsis thaliana, B. napus, G. max, M. truncatula, O. sativa, and Z. mays were collected for cross-species testing and the overall plant-specific prediction as well. The results show that the model for A. thaliana can be extended to other organisms, and the overall plant model from Musite outperforms the current plant-specific prediction tools, Plantphos, and PhosphAt, in prediction accuracy. Furthermore, a comparative study of predicted phosphorylation sites across orthologs among different plants was conducted to reveal potential evolutionary features. A bipolar distribution of isolated, non-conserved phosphorylation sites, and highly conserved ones in terms of the amino acid type was observed. It also shows that predicted phosphorylation sites conserved within orthologs do not necessarily share more sequence similarity in the flanking regions than the background, but they often inherit protein disorder, a property that does not necessitate high sequence conservation. Our analysis also suggests that the phosphorylation frequencies among serine, threonine, and tyrosine correlate with their relative proportion in disordered regions. Musite can be used as a web server () or downloaded as an open-source standalone tool (). [ABSTRACT FROM AUTHOR]

Autoimmune thyroid disease (AITD) comprises Graves' disease (GD) and Hashimoto's thyroiditis (HT). IL37 has been recently proved to be a natural suppressor for innate immunity and acquired immunity. Therefore, this study was conducted to identify the association of IL37 genetic polymorphisms with AITD in Chinese Han population. Polymorphisms of rs3811046/rs3811047/rs2723176/rs272186 in the IL37 gene were assessed in a case-control study comprising 701 GD patients, 301 HT patients and 939 controls. Genetic variants were genotyped by multiplex polymerase chain reaction and ligase detection reaction. The frequencies of the minor allele A of rs2723176 and A of rs2723186 were significantly lower in the GD patients than in the controls (PZ0.014, ORZ0.774; PZ0.014, ORZ0.777). After gender stratification, the rs3811046 G allele and the rs3811047/rs2723186 A allele were both significantly associated with a decreased risk of GD in female patients (PZ0.030, ORZ0.777; PZ0.023, ORZ0.774; PZ0.029, ORZ0.761). However, none of the four single nucleotide polymorphisms of IL37 gene showed any significant association with HT. Moreover, haplotype analysis revealed the GCG haplotype conferred increased risk for GD as a whole and in female GD patients (ORZ1.213; ORZ1.320). The ACG haplotype was associated with an increased risk of HT as a whole (ORZ1.567) and in male GD patients (ORZ1.820). In contrast, the AAA haplotype showed a protective role for GD as a whole (ORZ0.760) and in female GD patients (ORZ0.765). Our study strongly supports that the IL37 gene variants are associated with the susceptibility to AITD. [ABSTRACT FROM AUTHOR]