Comprehensive review and annotation of susceptibility SNPs associated with obesity-related traits

We aimed to summarize the results of genetic association studies for obesity and provide a comprehensive annotation of all susceptibility single nucleotide polymorphisms (SNPs). A total of 72 studies were summarized, resulting in 90,361 susceptibility SNPs (738 index SNPs and 89,623 linkage disequilibrium SNPs). Over 90% of the susceptibility SNPs are located in non-coding regions, and it is challenging to understand their functional significance. Therefore, we annotated these SNPs by using various functional databases. We identified 24,623 functional SNPs, including 4 nonsense SNPs, 479 missense SNPs, 399 untranslated region SNPs which might affect microRNA binding, 262 promoter and 5,492 enhancer SNPs which might affect transcription factor binding, 7 splicing sites, 76 SNPs which might affect gene methylation levels, 1,839 SNPs under natural selection and 17,351 SNPs which might modify histone binding. Expression quantitative trait loci analyses for functional SNPs identified 98 target genes, including 69 protein coding genes, 27 long non-coding RNAs and 3 processed transcripts. The percentage of protein coding genes that could be correlated with obesity-related pathways directly or through gene-gene interaction is 75.36 (52/69). Our results may serve as an encyclopaedia of obesity susceptibility SNPs and offer guide for functional experiments.

Nano liquid metal for the preparation of a thermally conductive and electrically insulating material with high stability

Dielectric materials typically demonstrate poor thermal conductivity, which limits their application in emerging technologies in integrated circuits, computer chips, light-emitting diode lamps, and other electronic packaging areas. Using liquid metal microdroplets as inclusions to develop thermal interface materials has been shown to effectively improve thermal pathways, but this type of material may become electroconductive with the application of a concentrated compressive stress. In this study, an isotropic nano-liquid metal thermally-conductive and electrically-insulating material (nLM-THEM) is developed by combining a modified polymer and well-dispersed nanoparticles, achieving an ∼50× increase in thermal conductivity over the base polymer. In addition, the thermal conductivity of nLM-THEMs exhibits no significant change with varying humidity and a stable anti-corrosion effect even in direct contact with aluminum. More importantly, nLM-THEMs demonstrate a stable electrical insulating property upon compressive stress, while conventional micro-LM-THEMs exude liquid metal. This exceptional combination of thermal and electrical insulation properties is enabled by the interconnection of uniform and spherical liquid metal nanoparticles to create more thermally-conductive pathways, and surfactant modified nanoparticles ensure excellent electric insulation. Moreover, this material can achieve passive heat exchange through rapid heat dissipation, which demonstrates its great application potential in the electronic packaging area.

Compared to liquid metal (LM) microdroplets based thermally conductive materials (micro-LM-THEMs), nano LM-THEMs (nLM-THEMs) presents a more stable electric insulating property even upon stress, achieving ~50-fold thermal conductivity over base polymer.

Downregulation of heat shock protein B8 decreases osteogenic differentiation potential of dental pulp stem cells during in vitro proliferation

OBJECTIVES

Tissue-derived stem cells, such as dental pulp stem cells (DPSCs), reduce differentiation capability during in vitro culture. We found that cultured DPSCs reduce expression of heat shock protein B8 (HspB8) and GIPC PDZ domain containing family member 2 (Gipc2). Our objectives were to evaluate the changes in DPSC composition during in vitro proliferation and to determine whether HspB8 and Gipc2 have function in differentiation potential of DPSCs.

MATERIALS AND METHODS

Different passages of rat DPSCs were evaluated for changes in CD90+ and/or CD271+ stem cells and changes in osteogenic potential. Real-time RT-PCR and immunostaining were conducted to determine expression of HspB8 and Gipc2. Expression of the genes in DPSCs was knocked down by siRNA, followed by osteogenic induction to evaluate the function of the genes.

RESULTS

About 90% of cells in the DPSC cultures were CD90+ and/or CD271+ cells without dramatic change during in vitro proliferation. The DPSCs at passages 3 to 5 (P3 to P5) possess strong osteogenic potential, but such potential was greatly reduced at later passages. Expression of HspB8 and Gipc2 was significantly reduced at P11 versus P3. Knock-down of HspB8 expression abolished osteogenic potential of the DPSCs, but knock-down of Gipc2 had no effect.

CONCLUSIONS

CD90+ and CD271+ cells are the major components of DPSCs in in vitro culture. High-level expression of HspB8 was critical for maintaining differentiation potential of DPSCs.

Hemispheric asymmetry of the frontolimbic cortex in young adults with borderline personality disorder

OBJECTIVE

Although the frontolimbic cortex has been implicated in borderline personality disorder (BPD), information about possible asymmetries in this region in patients with BPD is limited. This study aimed to examine whether frontolimbic cortex asymmetries differ between patients with BPD and healthy individuals.

METHODS

The brains of 30 young adult patients with BPD and 32 healthy control subjects were scanned with magnetic resonance imaging (MRI). The participants completed self-report scales assessing impulsivity, affect intensity and other psychological variables. Gray matter volume, surface area, and cortical thickness in regions of interest (ROIs), namely anterior insula (AI) and anterior cingulate cortex (ACC) were determined and the data were probed for hemisphere-group interactions.

RESULTS

Relative to controls, patients with BPD had reduced cortical thickness in left ACC and less surface area and gray matter volume in left AI. Significant group-hemisphere interactions were observed for gray matter volume and surface area of AI and for cortical thickness of ACC. Post hoc analysis showed that the BPD patients had greater frontolimbic cortex asymmetry than healthy controls; furthermore, greater asymmetry of AI&ACC correlated with a higher score in attention subscale of Barratt Impulsiveness Scale.

CONCLUSION

Patients with BPD have greater frontolimbic asymmetry than healthy individuals.

Genetic and environmental aspects in the association between attention-deficit hyperactivity disorder symptoms and binge-eating behavior in adults: a twin study

BACKGROUND

Prior research demonstrated that attention-deficit hyperactivity disorder (ADHD) is associated with binge-eating behavior, binge-eating disorder (BED), and bulimia nervosa (BN). The aim of this study was to investigate these associations in an adult twin population, and to determine the extent to which ADHD symptoms and binge-eating behavior share genetic and environmental factors.

METHODS

We used self-reports of current ADHD symptoms and lifetime binge-eating behavior and associated characteristics from a sample of over 18 000 adult twins aged 20-46 years, from the population-based Swedish Twin Registry. Mixed-effects logistic regression was used to examine the association between ADHD and lifetime binge-eating behavior, BED, and BN. Structural equation modeling was used in 13 773 female twins to determine the relative contribution of genetic and environmental factors to the association between ADHD symptoms and binge-eating behavior in female adult twins.

RESULTS

ADHD symptoms were significantly associated with lifetime binge-eating behavior, BED, and BN. The heritability estimate for current ADHD symptoms was 0.42 [95% confidence interval (CI) 0.41-0.44], and for lifetime binge-eating behavior 0.65 (95% CI 0.54-0.74). The genetic correlation was estimated as 0.35 (95% CI 0.25-0.46) and the covariance between ADHD and binge-eating behavior was primarily explained by genetic factors (91%). Non-shared environmental factors explained the remaining part of the covariance.

CONCLUSIONS

The association between adult ADHD symptoms and binge-eating behavior in females is largely explained by shared genetic risk factors.

Gene expression profiles indicate tissue-specific obesity regulation changes and strong obesity relevant tissues

BACKGROUND

With the growing evidence that other tissues, apart from adipose, could have strong relevance to obesity, it is necessary to comprehensively understand the relationship between obesity and other tissues, and to point out the most relevant tissues.

METHODS

There were 549 participants with 20 different tissue types involved in this study. We firstly employed both Spearman's correlation test and WGCNA (weighted correlation network analysis) to identify body mass index (BMI)-related genes. Subsequently, we performed enrichment analyses with obesity genes and pathways to see the different regulation patterns among tissues. In addition, we compared obesity genes identified by genome-wide association studies (GWAS) with BMI-related genes to find the overlapping proportion in each tissue. Finally, we integrated preceding results to identify six strong obesity relevant tissues and indicate three categories to represent different obesity relevant tissues.

RESULTS

Statistical analyses revealed diverse BMI-related genes and tissue-specific enrichment patterns among tissues. Comparison between BMI-related genes and GWAS findings showed tissue-specific expression changes of GWAS genes. Ultimately, six tissues that showed predominant performance in enrichment analyses and significantly embraced GWAS genes were referred to as strong obesity relevant tissues, including adipose, esophagus, nerve, pancreas, pituitary and skin. We also proposed three categories to represent different obesity relevant tissues.

CONCLUSIONS

We performed the first study to investigate the BMI-related gene expression changes across 20 tissues at the same time. With valid data analyses and comparison with GWAS findings, our study provides a holistic view of how different tissues correlate with obesity, and proposes target tissues for obesity pathogenesis investigation.

Transient receptor potential melastatin 4 channel is required for rat dental pulp stem cell proliferation and survival

OBJECTIVES

Investigate the role of the transient receptor potential melastatin 4 (TRPM4) channel in rat dental pulp stem cell (DPSC) proliferation and survival.

MATERIALS AND METHODS

Immunofluorescence and FACS analysis were used to detect the stem cell marker CD90. Alizarin Red S and Oil Red O staining were used to identify osteoblast and adipocyte differentiation, respectively. To characterize TRPM4, patch-clamp recordings were obtained from single cells in the whole-cell configuration mode. The significance of TRPM4 for proliferation and survival was examined with 9-phenanthrol, a TRPM4 inhibitor during a 96-hour period of culture. Real-time Ca²⁺ imaging analysis with Fura-2AM was used to investigate the impact of TRPM4 on intracellular Ca²⁺ signals.

RESULTS

DPSCs were CD90-positive and differentiated into osteoblasts. Patch-clamp recordings revealed currents typical of TRPM4 that were Ca²⁺ -activated, voltage-dependent and Na⁺ -conducting. Inhibition of TRPM4 resulted in a significant reduction in the cell population after a 96-hr period of culture and transformed the biphasic pattern of intracellular Ca²⁺ signalling into sustained oscillations.

CONCLUSIONS

Rat DPSCs have stem cell characteristics and functional TRPM4 channels that are required for proliferation and survival. These data suggest that the shape and frequency of intracellular Ca²⁺ signals may mediate stem cell proliferation and survival.

More improvement than progression of liver fibrosis following antiretroviral therapy in a longitudinal cohort of HIV-infected patients with or without HBV and HCV co-infections

We examined the effect of combination antiretroviral therapy (cART) on liver fibrosis among HIV-infected patients with or without hepatitis B (HBV) or C virus (HCV) co-infection. This was a retrospective cohort study of HIV-infected patients receiving cART during 2004-2016. Liver fibrosis was assessed using Fibrosis-4 (FIB-4) score with three classifications: Class 1, <1.45; Class 2, 1.45-3.25; Class 3, >3.25. Of 3900 participants, 68.6% were HIV mono-infected, 5.3% were HIV/HBV co-infected, 23.8% were HIV/HCV co-infected and 2.3% were HIV/HBV/HCV co-infected. Participants received follow-up treatment (median was 3.3 years). Improvement to a lower class was observed in Class 2 (52.6%) and Class 3 (74.2%), respectively. Progression to a higher class was observed in 12.8% and 5.0% in Class 1 and Class 2, respectively, and with a median time of 5.7 months. For improvement to lower classes, older age, male, Dai ethnicity, injection drug use, HCV co-infection and tenofovir for treatment were negative predictors, but in Class 3 of FIB-4 and time-updated increases in CD4 count from baseline were positive predictors. For progression to higher classes, older age, male, Jingpo ethnicity and HCV co-infection were positive predictors, while baseline CD4 count and in Class 2 of FIB-4 were negative predictors. Improvement to lower class linked with decreased mortality risk among patients in Class 3. Early cART initiation for HIV-infected patients with and without hepatitis co-infections may mitigate or slow down some of liver fibrosis, but special attention should be given to those who are older, male, co-infected with HCV.

An integrated analysis identifies STAT4 as a key regulator of ovarian cancer metastasis

Epithelial ovarian cancer (EOC) is one of the most common gynecological cancers, with diagnosis often at a late stage. Metastasis is a major cause of death in patients with EOC, but the underlying molecular mechanisms remain obscure. Here, we utilized an integrated approach to find potential key transcription factors involved in ovarian cancer metastasis and identified STAT4 as a critical player in ovarian cancer metastasis. We found that activated STAT4 was overexpressed in epithelial cells of ovarian cancer and STAT4 overexpression was associated with poor outcome of ovarian cancer patients, which promoted metastasis of ovarian cancer in both in vivo and in vitro. Although STAT4 mediated EOC metastasis via inducing epithelial-to-mesenchymal transition (EMT) of ovarian cancer cells in vivo, STAT4 failed to induce EMT directly in vitro, suggesting that STAT4 might mediate EMT process via cancer-stroma interactions. Further functional analysis revealed that STAT4 overexpression induced normal omental fibroblasts and adipose- and bone marrow-derived mesenchymal stem cells to obtain cancer-associated fibroblasts (CAF)-like features via induction of tumor-derived Wnt7a. Reciprocally, increased production of CAF-induced CXCL12, IL6 and VEGFA within tumor microenvironment could enable peritoneal metastasis of ovarian cancer via induction of EMT program. In summary, our study established a model that STAT4 promotes ovarian cancer metastasis via tumor-derived Wnt7a-induced activation of CAFs.

RNF168 cooperates with RNF8 to mediate FOXM1 ubiquitination and degradation in breast cancer epirubicin treatment

The forkhead box M1 (FOXM1) transcription factor has a central role in genotoxic agent response in breast cancer. FOXM1 is regulated at the post-translational level upon DNA damage, but the key mechanism involved remained enigmatic. RNF168 is a ubiquitination E3-ligase involved in DNA damage response. Western blot and gene promoter-reporter analyses showed that the expression level and transcriptional activity of FOXM1 reduced upon RNF168 overexpression and increased with RNF168 depletion by siRNA, suggesting that RNF168 negatively regulates FOXM1 expression. Co-immunoprecipitation studies in MCF-7 cells revealed that RNF168 interacted with FOXM1 and that upon epirubicin treatment FOXM1 downregulation was associated with an increase in RNF168 binding and conjugation to the protein degradation-associated K48-linked polyubiquitin chains. Consistently, RNF168 overexpression resulted in an increase in turnover of FOXM1 in MCF-7 cells treated with the protein synthesis inhibitor cycloheximide. Conversely, RNF168, knockdown significantly enhanced the half-life of FOXM1 in both absence and presence of epirubicin. Using a SUMOylation-defective FOXM1-5x(K>R) mutant, we demonstrated that SUMOylation is required for the recruitment of RNF168 to mediate FOXM1 degradation. In addition, clonogenic assays also showed that RNF168 mediates epirubicin action through targeting FOXM1, as RNF168 could synergise with epirubicin to repress clonal formation in wild-type but not in FOXM1-deficient mouse embryo fibroblasts (MEFs). The physiological relevance of RNF168-mediated FOXM1 repression is further emphasized by the significant inverse correlation between FOXM1 and RNF168 expression in breast cancer patient samples. Moreover, we also obtained evidence that RNF8 recruits RNF168 to FOXM1 upon epirubicin treatment and cooperates with RNF168 to catalyse FOXM1 ubiquitination and degradation. Collectively, these data suggest that RNF168 cooperates with RNF8 to mediate the ubiquitination and degradation of SUMOylated FOXM1 in breast cancer genotoxic response.

Latrophilin receptors: novel bronchodilator targets in asthma

Background

Asthma affects 300 million people worldwide. In asthma, the major cause of morbidity and mortality is acute airway narrowing, due to airway smooth muscle (ASM) hypercontraction, associated with airway remodelling. However, little is known about the transcriptional differences between healthy and asthmatic ASM cells.

Objectives

To investigate the transcriptional differences between asthmatic and healthy airway smooth muscle cells (ASMC) in culture and investigate the identified targets using in vitro and ex vivo techniques.

Methods

Human asthmatic and healthy ASMC grown in culture were run on Affymetrix_Hugene_1.0_ST microarrays. Identified candidates were confirmed by PCR, and immunohistochemistry. Functional analysis was conducted using in vitro ASMC proliferation, attachment and contraction assays and ex vivo contraction of mouse airways.

Results

We suggest a novel role for latrophilin (LPHN) receptors, finding increased expression on ASMC from asthmatics, compared with non-asthmatics in vivo and in vitro, suggesting a role in mediating airway function. A single nucleotide polymorphism in LPHN1 was associated with asthma and with increased LPHN1 expression in lung tissue. When activated, LPHNs regulated ASMC adhesion and proliferation in vitro, and promoted contraction of mouse airways and ASMC.

Conclusions

Given the need for novel inhibitors of airway remodelling and bronchodilators in asthma, the LPHN family may represent promising novel targets for future dual therapeutic intervention.

Optimization of a protective medium for freeze-dried Pichia membranifaciens and application of this biocontrol agent on citrus fruit

AIMS

To optimize a protective medium for freeze-dried Pichia membranifaciens and to evaluate biocontrol efficacies of agents against blue and green mould and anthracnose in citrus fruit.

METHODS AND RESULTS

Based on the screening assays of saccharides and antioxidants, response surface methodology was used to optimize sucrose, sodium glutamate and skim milk to improve viability of freeze-dried Pi. membranifaciens. Biocontrol assays were conducted between fresh and freeze-dried Pi. membranifaciens against Penicillium italicum, Penicillium digitatum and Colletotrichum gloeosporioides in citrus fruit. Solving the regression equation indicated that the optimal protective medium was 6·06% (w/v) sucrose combined with 3·40% (w/v) sodium glutamate and 5·43% (w/v) skim milk. Pi. membranifaciens freeze-dried in the optimal protective medium showed 76·80% viability, and retained biocontrol efficacy against Pe. italicum, Pe. digitatum and Co. gloeosporioides in citrus fruit.

CONCLUSIONS

The optimal protective medium showed more effective protective properties than each of the three protectants used alone. The viability of freeze-dried Pi. membranifaciens finally reached 76·80%. Meanwhile, the biocontrol efficacies showed no significant difference between fresh and freeze-dried yeast against Pe. italicum, Pe. digitatum and Co. gloeosporioides in citrus fruit.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results showed the potential value of Pi. membranifaciens CICC 32259 for commercialization.

Analysis of QTLs for panicle exsertion and its relationship with yield and yield-related traits in rice (Oryza sativa L.)

Panicle exsertion (PE) is an important morphological trait that is closely associated with spikelet fertility and grain yield. To understand the genetic basis of PE and its relationships with yield and yield-related traits, a recombinant inbred population consisting of 240 lines derived from a cross between an Indica cultivar 'Kasalath' and a Japonica germplasm 'TD70', was studied over two years. PE was significantly correlated with plant height, heading date (HD), panicle length (PL), and panicle characteristics such as primary branch number, spikelet number per panicle, and spikelet density, but showed poor correlation with yield components. Based on linkage mapping of 141 SSR markers, a total of 38 quantitative trait loci (QTLs) were located for 12 investigated traits, with the contribution varying from 6.51 to 8.61%. Among these, four QTL clusters were identified on chromosomes 1, 2, 3, and 6, suggesting the existence of pleiotropic alleles. In some intervals, two loci for PE were collocated with several traits, which is consistent with the correlations observed with phenotypic variations. The PE QTLs with 'Kasalath' alleles and without pleiotropic effects would be valuable for the improvement of PE in 'TD70' and in other rice varieties.