An unexpected role for p53 in regulating cancer cell-intrinsic PD-1 by acetylation

Cancer cell-intrinsic programmed cell death protein-1 (PD-1) has emerged as a tumor regulator in an immunity-independent manner, but its precise role in modulating tumor behaviors is complex, and how PD-1 is regulated in cancer cells is largely unknown. Here, we identified PD-1 as a direct target of tumor suppressor p53. Notably, p53 acetylation at K120/164 played a critical role in p53-mediated PD-1 transcription. Acetylated p53 preferentially recruited acetyltransferase cofactors onto PD-1 promoter, selectively facilitating PD-1 transcription by enhancing local chromatin acetylation. Reexpression of PD-1 in cancer cells inhibited tumor growth, whereas depletion of cancer cell-intrinsic PD-1 compromised p53-dependent tumor suppression. Moreover, histone deacetylase inhibitor (HDACi) activated PD-1 in an acetylated p53-dependent manner, supporting a synergistic effect by HDACi and p53 on tumor suppression via stimulating cancer cell-intrinsic PD-1. Our study reveals a mechanism for activating cancer cell-intrinsic PD-1 and indicates that p53-mediated PD-1 activation is critically involved in tumor suppression in an immunity-independent manner.

Genomic scan revealed KIT gene underlying white/gray plumage color in Chinese domestic geese

Goose is an important type of domesticated poultry. The wild geese that are regarded as the ancestors of modern domestic geese present gray plumage. Domesticated, geese have both white and gray feathers. To elucidate the genetic mechanisms underlying the formation of white and gray plumage in geese, we resequenced the whole genome of 18 geese from six populations including white and gray goose breeds. The average sequencing depth per individual was 9.81× and the average genome coverage was 96.8%. A total of 346 genes were detected in the top 1% of F_ST scores of gray- and white-feathered geese, and a significant F_ST site was located in the intron region within the KIT gene, the 18 bp deletion in KIT having the strongest potential association with white feathers. It has been reported that a number of genes are associated with plumage colors in birds. However, no studies have identified the relationship between KIT and plumage color in birds at present, although the white coat can be attributed to mutations in KIT in some mammals. Our study showed that that KIT is a plausible candidate gene for white/gray plumage color in Chinese domestic geese.

Optimization of Tilmicosin-Loaded Nanostructured Lipid Carriers Using Orthogonal Design for Overcoming Oral Administration Obstacle

Tilmicosin (TMS) is widely used to treat bacterial infections in veterinary medicine, but the clinical effect is limited by its poor solubility, bitterness, gastric instability, and intestinal efflux transport. Nanostructured lipid carriers (NLCs) are nowadays considered to be a promising vector of therapeutic drugs for oral administration. In this study, an orthogonal experimental design was applied for optimizing TMS-loaded NLCs (TMS-NLCs). The ratios of emulsifier to mixed lipids, stearic acid to oleic acid, drugs to mixed lipids, and cold water to hot emulsion were selected as the independent variables, while the hydrodynamic diameter (HD), drug loading (DL), and entrapment efficiency (EE) were the chosen responses. The optimized TMS-NLCs had a small HD, high DL, and EE of 276.85 ± 2.62 nm, 9.14 ± 0.04%, and 92.92 ± 0.42%, respectively. In addition, a low polydispersity index (0.231 ± 0.001) and high negative zeta potential (-31.10 ± 0.00 mV) indicated the excellent stability, which was further demonstrated by uniformly dispersed spherical nanoparticles under transmission electron microscopy. TMS-NLCs exhibited a slow and sustained release behavior in both simulated gastric juice and intestinal fluid. Furthermore, MDCK-chAbcg2/Abcb1 cell monolayers were successfully established to evaluate their absorption efficiency and potential mechanism. The results of biodirectional transport showed that TMS-NLCs could enhance the cellular uptake and inhibit the efflux function of drug transporters against TMS in MDCK-chAbcg2/Abcb1 cells. Moreover, the data revealed that TMS-NLCs could enter the cells mainly via the caveolae/lipid raft-mediated endocytosis and partially via macropinocytosis. Furthermore, TMS-NLCs showed the same antibacterial activity as free TMS. Taken together, the optimized NLCs were the promising oral delivery carrier for overcoming oral administration obstacle of TMS.

Nonconservative integration and diversity of a new family of integrative and conjugative elements associated with antibiotic resistance in zoonotic pathogen Streptococcus suis

Macrolide and tetracycline resistance in streptococci is mainly caused by acquisition of integrative and conjugative elements (ICEs) of the ICESa2603 family carrying erm(B) and tet(O). But the characteristics about the transferability and physiological consequences of ICEs with triplet serine integrases are still rare. This study tested the transferability of ICESsuYZDH1_SSU0877, a novel erm(B)- and tet(O)-carrying ICESa2603 family-like ICE with triplet serine integrases, and evaluated the physiological consequences after ICE transferred and integrated into recipient. The prevalence of ICESsuYZDH1-like ICEs in S. suis was analyzed based on 1334 genomic sequences available in GenBank and examined in 330 clinical isolates in China. Nonconservative transfer was observed by integrating of ICESsuYZDH1 into SSU1797 gene besides the primary SSU0877 site. Imperfect direct repeats of 2-/4-nt (5'-TC-3'/5'-TCCC-3') and (5'-GC-3'/5'-TCCC-3') were observed at SSU0877 and SSU1797 sites, respectively. The transconjugant suffered a weak fitness cost with stunted growth and less competition with recipient strain. Successive passages indicate the ICESsuYZDH1 could be persist and endued stable resistant phenotype. Comprehensive analysis of the ICESsuYZDH1-like ICEs from both public genome database and our clinical isolates revealed the widespread and diversity of the ICEs by integration at the sites of SSU0877, SSU0468, SSU1262, and SSU1797. The ICESsuYZDH1-like ICEs could stably co-exist within the host chromosome at more than one attachment sites, which is probably mediated by the triplet serine integrases. Nonconservative integration and diversity of the ICESsuYZDH1 family of ICEs might have contributed to the evolution of ICEs and the dissemination of macrolide and tetracycline resistance in S. suis.

MicroRNA-26b-5p alleviates cerebral ischemia-reperfusion injury in rats via inhibiting the N-myc/PTEN axis by downregulating KLF10 expression

MicroRNAs plays important role in cerebral ischemia-reperfusion (CIR). However, the role of miR-26b-5p in CIR injury remains unclear. PC12 cells were treated with oxygen-glucose deprivation (OGD) for 0 h, 2 h, 4 h, 6 h, and then reoxygenated for 24 h to construct an in vitro I/R model. Then, miR-26b-5p mimic, small interfering RNA of KLF10 and KLF10 overexpression plasmid were transfected into cells respectively for mechanism study. Our results showed that miR-26b-5p was downregulated in OGD/R-induced PC12 cells. After overexpression of miR-26b-5p, cell proliferation ability was enhanced, apoptosis, ROS and inflammatory mediators were inhibited. Bioinformatics analysis indicated that miR-26b-5p was directly bound to the 3' UTR of KLF10, and downregulated the expression of KLF10. KLF10 was upregulated in OGD/R cells, and transfection with si-KLF10 promoted cell proliferation and reduced apoptosis, NO concentration and inflammatory factor secretion. Moreover, pcDNA-KLF10 reversed the inhibitory effects of miR-26b-5p mimic on apoptosis, NO content and inflammatory factor secretion, as well as the downregulation of N-myc and PTEN expression. Meanwhile, I/R rat models were constructed and divided into sham operation group (femoral artery isolation only), model group (middle cerebral artery occlusion model of rats was prepared by thread embolization), treatment group (200 µL of miR-26b-5p mimic was injected into the brain of model rats). We observed that the infarct size of brain tissue was reduced, KLF10 expression was downregulated, and apoptosis and inflammatory response were reduced. These results suggest that miR-26b-5p had protective effects on CIRI and it may be a potential treatment target.

Phosphoinositide 3-kinase γ deficiency attenuates kidney injury and fibrosis in angiotensin II-induced hypertension

BACKGROUND

We have shown that the CXCL16/CXCR6 axis plays a critical role in recruiting inflammatory cells and bone marrow-derived fibroblasts into the kidney leading to renal injury and fibrosis. However, the underlying signaling mechanisms are not known.

METHODS

In the present study, we examined the role of phosphoinositide-3 kinase γ (PI3Kγ) signaling in the recruitment of inflammatory cells and bone marrow-derived fibroblasts into the kidney and development of renal injury and fibrosis in an experimental model of hypertension induced by angiotensin II.

RESULTS

Blood pressure was comparable between wild-type (WT) and PI3Kγ knockout (KO) mice at baseline. Angiotensin II treatment led to an increase in blood pressure that was similar between WT and PI3Kγ KO mice. Compared with WT mice, PI3Kγ KO mice were protected from angiotensin II-induced renal dysfunction and injury and developed less proteinuria. PI3Kγ deficiency suppressed bone marrow-derived fibroblast accumulation and myofibroblast formation in the kidney and inhibited total collagen deposition and extracellular matrix protein production in the kidney in response to angiotensin II. PI3Kγ deficiency inhibited the infiltration of F4/80+ macrophages and CD3+ T cells into the kidney and reduced gene expression levels of pro-inflammatory cytokines in the kidney following angiotensin II treatment. Finally, inhibition of PI3Kγ suppressed CXCL16-induced monocyte migration in vitro.

CONCLUSION

These results indicate that PI3Kγ mediates the influx of macrophages, T cells and bone marrow-derived fibroblasts into the kidney resulting in kidney injury and fibrosis.

Simultaneous immobilization of As and Cd in a mining site soil using HDTMA-modified zeolite

Arsenic (As) and cadmium (Cd) co-contamination has been a typical problem in Chinese agricultural land adjacent to historical metal mining and smelting activities. Remediation of As and Cd in soil has encountered many difficulties owing to the distinct nature of the two metal(loid)s. In this study, we developed a remediation scheme by adding a hexadecyltrimethylammonium (HDTMA)-modified zeolite to a mining site soil and evaluated the immobilization effect. The result of the increased surface zeta potential indicates that the HDTMA modification conferred the zeolite with adsorbability towards As through the cationic surfactant head. The addition of the highest dosage of HDTMA-modified zeolite (10%) to the contaminated soil greatly improved soil organic matter by 1.4 times, partly due to the elevated C loading on the zeolite from HDTMA. Sequential extraction results show that the addition of HDTMA-modified zeolite not only increased the residual fraction of As (by 2.7-5.9%) but also reduced the toxicity-related fraction (by 2.3-2.7%) when compared to the unmodified zeolite and blank treatments. The oxidizable fractions of Cd in the modified zeolite treatment were significantly higher than that in the blank soil. Besides, the exchangeable fractions of Cd were all significantly reduced in the zeolite treatments. Enzyme activity assays show that the HDTMA-modified zeolite treatment could greatly improve soil microbial environment. The physiologically based extraction test (PBET) also proved that the bioavailability of As and Cd was reduced after the modified zeolite treatment.

[Application value of high-throughput gene copy number variation detection in the diagnosis of enlarged vestibular aqueduct]

Objective: To explore the application value of high-throughput gene detection method of copy number variations (CNV) in the diagnosis of enlarged vestibular aqueduct (EVA). Methods: A total of 46 nonsyndromic hearing loss patients with EVA were recruited between May 2014 and December 2016 from Department of Otolaryngology of Xiangya Hospital, Central South University. A high-throughput multiplex analysis method based on double ligation and multiple fluorescent PCR was designed and performed to detect CNV in the three EVA-related genes (SLC26A4, FOXI1 and KCNJ10). The data were analyzed by GeneMapper v4.1. Healthy volunteers (n=100) were selected as normal controls. Results: A total of 46 EVA patients were detected (32 males, 14 females, aged 1 to 26 years). In 4 EVA patients, deletions of exons 1-3 of SLC26A4 gene (4/46, 8.7%) were detected, which were not reported in the database of genomic variants (DGV), and were absent in 100 normal controls. There was no CNV detected in FOXI1 and KCNJ10 in the study. Conclusions: In the current study, three known EVA-related genes were designed as the target area for CNV detection by high-throughput ligation-dependent probe amplification (HLPA) analysis. This method can be used as a supplementary analysis of point mutation detection of hearing loss, which helps achieve the accurate genetic diagnosis of EVA.

Mobilization or immobilization? The effect of HDTMA-modified biochar on As mobility and bioavailability in soil

Biochar plays an essential role in soil remediation, but its effect on the arsenic remediation has been controversial. In this study, hexadecyl trimethyl ammonium bromide (HDTMA-Br) modified or unmodified biochar on As mobility and bioavailability in soil were studied. The sequential extraction experiment showed that As in the original soil mainly existed in the occluded form (78.24%), followed by Fe‒As (20.72%) and Al‒As (0.88%) forms. With the addition of the modified and unmodified biochars, the contents of Ca‒As and Fe‒As increased by 0.36 - 0.95% and 2.06 - 3.36%, respectively, suggesting the increased potential toxicity of As. The NaH₂PO₄ extraction result showed that the unmodified biochar increased the As availability by 3.23 - 22.76%, whereas the HDTMA-modified biochar reduced the As availability by 4.80 - 13.41%. Pot experiment showed that the unmodified and modified biochar increased the biomass of Brassica pekinensis, and the modified biochar (HB5) decreased the uptake of As by plants by 80.77% compared to the unmodified biochar. In particular, the plant achieved better growth in the modified biochar treatment (average height 8.31 cm) than in the unmodified biochar treatment (average height 6.97 cm). Therefore, both biochars facilitated phase transformation of As from the stable to the mobile states in the soil. Nevertheless, the HDTMA-modified biochar had an effect on alleviating As bioavailability and toxicity.

MACC1 Contributes to the Development of Osteosarcoma Through Regulation of the HGF/c-Met Pathway and Microtubule Stability

Osteosarcoma (OS) is the most prevalent human bone malignancy, and presents a global annual morbidity of approximately five cases per million. Notably, precise and efficient targeted therapy has become the most promising strategy for the treatment of OS; however, there is still an urgent need for the identification of suitable therapeutic targets. Metastasis-associated in colon cancer 1 (MACC1) was first identified in colon tumors by differential display RT-PCR, and was shown to be involved in the regulation of colon tumor growth and metastasis through the hepatocyte growth factor (HGF)/c-Met signaling pathway. Additionally, MACC1 overexpression has been reported to induce the growth of several types of cancers, including glioblastoma multiforme and gastric cancer. However, whether MACC1 also plays a role in the progression of OS remains unclear. In this study, we found that MACC1 was highly expressed in human OS tissues, as well as in U-2OS and MG-63 cells, when compared with normal tissues and osteoblasts, respectively. Our data further indicated that MACC1 expression was correlated with several clinicopathological features of OS. Through in vitro assays, we found that MACC1 depletion markedly suppressed the proliferative ability of both OS cells and endothelial cells, and inhibited the angiogenic capacity of endothelial cells. Similarly, MACC1 depletion inhibited tumor growth, metastasis, and angiogenesis in mice. Mechanistically, we found that MACC1 could bind to the MET promoter, and enhanced the proliferation of both OS cells and endothelial cells through the HGF/c-Met signaling pathway. Furthermore, we show that MACC1 also promoted angiogenesis by regulating microtubule dynamics, thereby promoting the progression of OS. Our results indicate that MACC1 may be a new and promising therapeutic target for the treatment of OS.

Ice-interface assisted large-scale preparation of polypyrrole/graphene oxide films for all-solid-state supercapacitors

In this paper, large-scale, self-standing polypyrrole/graphene oxide (PPy/GO) nanocomposite films were prepared by an environmentally friendly and easy-to-operate confined polymerization method, and were also assembled as electrode materials for symmetric all-solid-state supercapacitors. In this paper, large-scale, self-standing polypyrrole/graphene oxide (PPy/GO) nanocomposite films were prepared by an environmentally friendly and easy-to-operate confined polymerization method, and were also assembled as electrode materials for symmetric all-solid-state supercapacitors. The morphology, chemical structure and electrochemical property were characterized by field emission scanning electron microscope (FESEM), Fourier transform infrared spectroscopy (FTIR), cyclic voltammetry (CV), galvanostatic charge-discharge (GCD), and electrochemical impedance spectroscopy (EIS), respectively. The lamellar structure of GO and both strong interaction with ice and pyrrole could promote polymerization of pyrrole and improve the compactness of the film. With the aid of GO, the conjugation length of PPy increased, the resistance of the material decreased, and the electrochemical energy storage of the composite film was significantly enhanced. In the case of 2.5 wt% GO, the prepared PPy/GO nanocomposite supercapacitor exhibited a high area specific capacitance of 97.3 mF cm^-2 at 1 mA cm^-2. Furthermore, the PPy/GO film supercapacitor also showed excellent cycling stability and good flexibility.

[Establishment of nutrition literacy core items for Chinese preschool children]

Objective: To establish the nutrition literacy core items for preschool children in China. Methods: The framework system and preliminary items of nutrition literacy were established through literature review and experts consultation. E-Delphi method was used to determine the nutrition literacy items. Nine experts in the field of nutrition, child and adolescent health, health education were invited to score the importance of each nutrition literacy item via Email. The judgment basis and familiarity of experts towards the items, active coefficient, authority coefficient and harmony coefficient were evaluated and analyzed to generate the final list of nutrition literacy items. Results: In the first round of E-Delphi consultation, the active coefficient and authority coefficient were 88.9%(8/9) and(0.88±0.07).The harmony coefficient was 0.350 (χ²=36.432, P=0.001). In the second round, the active coefficient and authority coefficient were 100% (9/9) and (0.89±0.11).The harmony coefficient was 0.347 (χ²=34.330, P<0.001). After qualitative and quantitative analyses, we identified the final list of nutrition literacy items consisting of two scales (basic knowledge, lifestyles and dietary behaviors), six subscales (food knowledge, food characteristic, food choice, dietary behavior, dietary safety, and physical activity)with 14 items in total. Conclusion: The framework system and core items of nutrition literacy are established for Chinese preschool children, which could provide a reference basis for the implementation of nutrition education project and the establishment of standardized evaluation tools.

Multiyear in-situ L-band microwave radiometry of land surface processes on the Tibetan Plateau

We report a unique multiyear L-band microwave radiometry dataset collected at the Maqu site on the eastern Tibetan Plateau and demonstrate its utilities in advancing our understandings of microwave observations of land surface processes. The presented dataset contains measurements of L-band brightness temperature by an ELBARA-III microwave radiometer in horizontal and vertical polarization, profile soil moisture and soil temperature, turbulent heat fluxes, and meteorological data from the beginning of 2016 till August 2019, while the experiment is still continuing. Auxiliary vegetation and soil texture information collected in dedicated campaigns are also reported. This dataset can be used to validate the Soil Moisture and Ocean Salinity (SMOS) and Soil Moisture Active Passive (SMAP) satellite based observations and retrievals, verify radiative transfer model assumptions and validate land surface model and reanalysis outputs, retrieve soil properties, as well as to quantify land-atmosphere exchanges of energy, water and carbon and help to reduce discrepancies and uncertainties in current Earth System Models (ESM) parameterizations. Measurement cases in winter, pre-monsoon, monsoon and post-monsoon periods are presented.

Computational modelling for the spiral flow in umbilical arteries with different systole/diastole flow velocity ratios

The systole/diastole (S/D) flow velocity ratios in umbilical arteries (UAs) have been used to assess the health status of the feto-placental circulation, yet its connection to the morphology of UAs, specifically its coiling pattern remains unclear. Spiral flow induces unbalanced wall shear stress (WSS) distribution in UAs, and may contribute to the uneven arterial wall thickness, and the chirality. In this paper, we use a 3D computational fluid dynamics (CFD) technique to quantify the wall shear stress (WSS) in UA models of two configurations, i.e. at 0.17 and 0.50 spirals per centimeter, to represent normo- and hyper-coiling, respectively. For CFD simulations we use two different S/D ratios (3.02 and 5.70) revealed from the ultrasonography waveforms of a normal and an intrauterine growth restriction (IUGR) case. We found that more coils in the UA model enhanced WSS throughout a cardiac cycle (up to 24%) with the same inflow condition. In addition, time-averaged WSS are generally increased and more uneven in the hyper-coiling model. We suggest that the large WSS difference between the peak systole and end diastole (62% higher in the IURG case than the normal case) may induce uneven stenosis distribution at UAs, and contribute to UA chirality.

Association of CNVs with methylation variation

Germline copy number variants (CNVs) and single-nucleotide polymorphisms (SNPs) form the basis of inter-individual genetic variation. Although the phenotypic effects of SNPs have been extensively investigated, the effects of CNVs is relatively less understood. To better characterize mechanisms by which CNVs affect cellular phenotype, we tested their association with variable CpG methylation in a genome-wide manner. Using paired CNV and methylation data from the 1000 genomes and HapMap projects, we identified genome-wide associations by methylation quantitative trait locus (mQTL) analysis. We found individual CNVs being associated with methylation of multiple CpGs and vice versa. CNV-associated methylation changes were correlated with gene expression. CNV-mQTLs were enriched for regulatory regions, transcription factor-binding sites (TFBSs), and were involved in long-range physical interactions with associated CpGs. Some CNV-mQTLs were associated with methylation of imprinted genes. Several CNV-mQTLs and/or associated genes were among those previously reported by genome-wide association studies (GWASs). We demonstrate that germline CNVs in the genome are associated with CpG methylation. Our findings suggest that structural variation together with methylation may affect cellular phenotype.

Targeted antimicrobial peptide delivery in vivo to tumor with near infrared photoactivated mesoporous silica nanoparticles

Antimicrobial peptide PA-C1b (chensinin-1b conjugated with palmitic acid) showed potent anticancer activity with no obvious hemolytic activity, which made it a potential agent for treating cancers. However, after in vivo administration, peptides can be degraded by proteases because there is no effective protection. In this study, a tumor-targeting photoresponsive antimicrobial peptide delivery system was developed, and the peptide PA-C1b labeled with the dye sulfo-cyanine7 (Cy7) was loaded into mesoporous silica nanoparticles (MSNs). The final MSN@Cy7-PA-C1b nanoparticles were wrapped by graphene oxide (GO), and then folic acid was conjugated to the surface of the MSNs for targeting purposes. The final MSN@Cy7-PA-C1b@FA-GO nanoparticles were constructed to allow light-mediated peptide release and folate receptor-targeted cancer therapy. The Cy7 dye serves as a real-time indicator, and GO acts as a gatekeeper to prevent leakage of the loaded peptides in the absence of near-infrared light irradiation. Upon light irradiation, the GO wrapping detaches, and the photoresponsive peptide delivery system works well both in in vitro cell experiments and during in vivo administration in mouse tumor experiments. The construction of the MSN@Cy7-PA-C1b@FA-GO platform provides a novel approach to deliver antimicrobial peptides in vivo for the treatment of infections by pathogenic microorganisms and cancers.

Ancient Genomes Reveal the Evolutionary History and Origin of Cashmere-Producing Goats in China

Goats are one of the most widespread farmed animals across the world; however, their migration route to East Asia and local evolutionary history remain poorly understood. Here, we sequenced 27 ancient Chinese goat genomes dating from the Late Neolithic period to the Iron Age. We found close genetic affinities between ancient and modern Chinese goats, demonstrating their genetic continuity. We found that Chinese goats originated from the eastern regions around the Fertile Crescent, and we estimated that the ancestors of Chinese goats diverged from this population in the Chalcolithic period. Modern Chinese goats were divided into a northern and a southern group, coinciding with the most prominent climatic division in China, and two genes related to hair follicle development, FGF5 and EDA2R, were highly divergent between these populations. We identified a likely causal de novo deletion near FGF5 in northern Chinese goats that increased to high frequency over time, whereas EDA2R harbored standing variation dating to the Neolithic. Our findings add to our understanding of the genetic composition and local evolutionary process of Chinese goats.

LepR-Expressing Stem Cells Are Essential for Alveolar Bone Regeneration

Stem cells play a critical role in bone regeneration. Multiple populations of skeletal stem cells have been identified in long bone, while their identity and functions in alveolar bone remain unclear. Here, we identified a quiescent leptin receptor–expressing (LepR+) cell population that contributed to intramembranous bone formation. Interestingly, these LepR+ cells became activated in response to tooth extraction and generated the majority of the newly formed bone in extraction sockets. In addition, genetic ablation of LepR+ cells attenuated extraction socket healing. The parabiosis experiments revealed that the LepR+ cells in the healing sockets were derived from resident tissue rather than peripheral blood circulation. Further studies on the mechanism suggested that these LepR+ cells were responsive to parathyroid hormone/parathyroid hormone 1 receptor (PTH/PTH1R) signaling. Collectively, we demonstrate that LepR+ cells, a postnatal skeletal stem cell population, are essential for alveolar bone regeneration of extraction sockets.

A parallelized strategy for epistasis analysis based on Empirical Bayesian Elastic Net models

MOTIVATION

Epistasis reflects the distortion on a particular trait or phenotype resulting from the combinatorial effect of two or more genes or genetic variants. Epistasis is an important genetic foundation underlying quantitative traits in many organisms as well as in complex human diseases. However, there are two major barriers in identifying epistasis using large genomic datasets. One is that epistasis analysis will induce over-fitting of an over-saturated model with the high-dimensionality of a genomic dataset. Therefore, the problem of identifying epistasis demands efficient statistical methods. The second barrier comes from the intensive computing time for epistasis analysis, even when the appropriate model and data are specified.

RESULTS

In this study, we combine statistical techniques and computational techniques to scale up epistasis analysis using Empirical Bayesian Elastic Net (EBEN) models. Specifically, we first apply a matrix manipulation strategy for pre-computing the correlation matrix and pre-filter to narrow down the search space for epistasis analysis. We then develop a parallelized approach to further accelerate the modeling process. Our experiments on synthetic and empirical genomic data demonstrate that our parallelized methods offer tens of fold speed up in comparison with the classical EBEN method which runs in a sequential manner. We applied our parallelized approach to a yeast dataset, and we were able to identify both main and epistatic effects of genetic variants associated with traits such as fitness.

AVAILABILITY AND IMPLEMENTATION

The software is available at github.com/shilab/parEBEN.

Identification of single nucleotide pleomorphisms associated with periodontal disease in head and neck cancer irradiation patients by exome sequencing

OBJECTIVE

Periodontal disease (PD) is a common oral complication in patients with head and neck cancer (HNC) undergoing radiation therapy (RT). Our objective was to identify candidate single nucleotide polymorphisms (SNPs) associated with PD in radiation-treated patients with HNC.

STUDY DESIGN

DNA was extracted from the saliva of patients with HNC (n = 69) before RT. Clinical attachment loss (CAL) increment greater than 0.2 mm over 24 months after RT was used to define PD progression. After exome sequencing, SNPs associated with post-RT PD progression were identified by using logistic regression and homozygosity analyses. The web tools STRING, the Database for Annotation, Visualization and Integrated Discovery (DAVID), GeneCodis, and Ensembl Variant Effect Predictor were used for functional analysis.

RESULTS

Of the 48 patients with HNC with post-RT PD progression, 24 had no tooth with 5 mm or greater pocket depth before RT, whereas of the 21 patients with HNC without progression, 11 had PD initially. A total of 330 SNPs (249 genes) with over-represented homozygous genotype (98.5% variant allele) were found to be associated with post-RT PD. Sixty of these corresponded to PD-related pathways, including previously identified genes. In patients with HNC with post-RT PD progression, SNPs were found in genes (n = 10) in contrast to those without progression (n = 7).

CONCLUSIONS

The SNPs of collagen genes were identified, potentially defining susceptibility to PD in patients with HNC, and this could be further investigated to characterize PD drug targets.

Enhancing Cr(VI) reduction and immobilization by magnetic core-shell structured NZVI@MOF derivative hybrids

Hexavalent chromium (Cr(VI)) has significantly threatened the environmental health because of its distinct toxicity. A novel magnetic core-shell structured NZVI@ZD composite was designed for simultaneous adsorption and reduction of Cr(VI). NZVI@ZD was synthesized by carbonization of the as-prepared core-shell structure NZVI@zeolitic imidazole framework-67 (ZIF-67). After carbonization, the original ZIF-67 shell shape was preserved well with marginal parts developing to graphitized carbon. Both cobalt (Co) and NZVI nanoparticles were finely dispersed in the porous ZIF-67 derivative (ZD). NZVI@ZD exhibited excellent removal performance for Cr(VI), owing to its high specific surface area and large pore size favorable for Cr(VI) adsorption and diffusion. The maximum adsorption capacity of NZVI@ZD for Cr(VI) was surprisingly as high as 226.5 mg g^-1, surpassing the pristine ZIF-67 (29.35 mg g^-1) and NZVI@ZIF-67 (36.53 mg g^-1). Zeta potential and X-ray photoelectron spectroscopy (XPS) spectra revealed that electrostatic attraction, reduction and precipitation might be involved in the Cr(VI) removal process by NZVI@ZD, resulting in the conversion of the adsorbed Cr(VI) to Cr(III) of lower toxicity and an eventual immobilization on the NZVI@ZD. The magnetic core-shell structured NZVI@ZD possessed superior adsorptive reactivity for Cr(VI) to most other traditional or newly reported materials, thus should be deemed highly efficient for Cr(VI)-contaminated wastewater treatment.

Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia

Despite considerable progress in schizophrenia genetics, most findings have been for large rare structural variants and common variants in well-imputed regions with few genes implicated from exome sequencing. Whole genome sequencing (WGS) can potentially provide a more complete enumeration of etiological genetic variation apart from the exome and regions of high linkage disequilibrium. We analyze high-coverage WGS data from 1162 Swedish schizophrenia cases and 936 ancestry-matched population controls. Our main objective is to evaluate the contribution to schizophrenia etiology from a variety of genetic variants accessible to WGS but not by previous technologies. Our results suggest that ultra-rare structural variants that affect the boundaries of topologically associated domains (TADs) increase risk for schizophrenia. Alterations in TAD boundaries may lead to dysregulation of gene expression. Future mechanistic studies will be needed to determine the precise functional effects of these variants on biology.

Common variants identified by large-scale genomewide association studies cannot account fully account for the heritability of schizophrenia (SCZ). Here, the authors report high-coverage whole-genome sequencing of 1162 SCZ cases and 936 controls and explore the contribution of different types of variants to SCZ.

Effect of high concentrations of dietary vitamin D3 on pullet and laying hen performance, skeleton health, eggshell quality, and yolk vitamin D3 content when fed to W36 laying hens from day of hatch until 68 wk of age

The objective of this experiment was to investigate the effects of various dietary concentrations of vitamin D₃ (D₃) on pullet and laying hen performance, eggshell quality, bone health, and yolk D₃ content from day of hatch until 68 wk of age. Initially, 440 Hy-line W36-day-old chicks were randomly assigned to 5 dietary treatments: 1,681 (control); 8,348; 18,348; 35,014; 68,348 IU D₃/kg. At 17 wk of age, pullets were assigned to experimental diets with 12 replicate groups of 6 birds. At 17 wk of age, pullets fed diets containing 8,348 and 35,014 IU D₃/kg had an increased bone mineral density in comparison to the control fed birds (P ≤ 0.01). Body weights of pullets fed the diet with 68,348 IU D₃/kg were lower than other treatments (P ≤ 0.01). Hen-housed egg production (HHEP) of hens fed the 35,014 IU D₃/kg diet was increased in comparison to control-fed hens (P ≤ 0.01), whereas HHEP of those fed 68,348 IU D₃/kg diet was reduced in comparison to all other treatments (P ≤ 0.01). Shell breaking strength of eggs from hens fed 8,348, 35,014 and 68,348 IU D₃/kg was increased in comparison to eggs from control-fed birds (P ≤ 0.01). Fat-free tibia ash content of hens fed any of the diets supplemented with D₃ (8,348 to 68,348 IU D₃/kg) was increased in comparison to control-fed hens (P ≤ 0.05). Yolk D₃ content increased linearly with dietary D₃ and the D₃ transfer efficiency for the control, 8,348 IU, 18,348 IU, 35,014 IU, and 68,348 IU D₃ treatments were 8.24, 10.29, 11.27, 12.42, and 12.06%, respectively. These data suggest that supplementation of dietary D₃ up to 35,014 IU D₃/kg feed maintained if not increased laying hen performance and enhanced pullet and laying hen skeletal quality as well as yolk D₃ content and eggshell quality. Feeding pullets at a higher level 68,348 IU of D₃ resulted in reduced growth and ultimately decreased performance of laying hens.

Employment status and the association of sociocultural stress with sleep in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

STUDY OBJECTIVES

We examined the association of sociocultural stress severity (i.e. acculturation stress, ethnic discrimination) and chronic stress burden with multiple dimensions of sleep in a population-based sample of US Hispanics/Latinos. We also explored whether employment status modified stress-sleep associations.

METHODS

We conducted survey linear regressions to test the cross-sectional association of sociocultural stress severity and stress burden with sleep dimensions using data collected between 2010 and 2013 from individuals who participated in both the Hispanic Community Health Study/Study of Latinos Sueño and Sociocultural Ancillary studies (N = 1192).

RESULTS

Greater acculturation stress (B = 0.75, standard error [SE] = 0.26, p < .01) and chronic psychosocial stress burden (B = 1.04, SE = 0.18, p < .001) were associated with greater insomnia symptoms but were not associated with actigraphic measures of sleep. Ethnic discrimination was not associated with any of the sleep dimensions. The association of acculturation stress with insomnia severity was greater in unemployed (B = 2.06, SE = 0.34) compared to employed (B = 1.01, SE = 0.31) participants (p-interaction = .08).

CONCLUSIONS

Acculturation stress severity and chronic stress burden are important and consistent correlates of insomnia, but not actigraphically measured sleep dimensions. If replicated, future research should test whether interventions targeting the resolution of sociocultural stress improve sleep quality in Hispanics/Latinos.

Feeling the Burn: Intestinal Epithelial Cells Modify Their Lipid Metabolism in Response to Bacterial Fermentation Products

Intestinal epithelial absorption of dietary lipids is a major determinant of animal energy balance and metabolic health. Recent studies uncovered significant roles for intestinal microbiota in this process, but underlying mechanisms remain unresolved. Araújo et al. (2020) identify two end-products of bacterial fermentation that regulate intestinal lipid absorption and metabolism.

LSD1 contributes to programmed oocyte death by regulating the transcription of autophagy adaptor SQSTM1/p62

In female mammals, the size of the initially established primordial follicle (PF) pool within the ovaries determines the reproductive lifespan of females. Interestingly, the establishment of the PF pool is accompanied by a remarkable programmed oocyte loss for unclear reasons. Although apoptosis and autophagy are involved in the process of oocyte loss, the underlying mechanisms require substantial study. Here, we identify a new role of lysine-specific demethylase 1 (LSD1) in controlling the fate of oocytes in perinatal mice through regulating the level of autophagy. Our results show that the relatively higher level of LSD1 in fetal ovaries sharply reduces from 18.5 postcoitus (dpc). Meanwhile, the level of autophagy increases while oocytes are initiating programmed death. Specific disruption of LSD1 resulted in significantly increased autophagy and obviously decreased oocyte number compared with the control. Conversely, the oocyte number is remarkably increased by the overexpression of Lsd1 in ovaries. We further demonstrated that LSD1 exerts its role by regulating the transcription of p62 and affecting autophagy level through its H3K4me2 demethylase activity. Finally, in physiological conditions, a decrease in LSD1 level leads to an increased level of autophagy in the oocyte when a large number of oocytes are being lost. Collectively, LSD1 may be one of indispensible epigenetic molecules who protects oocytes against preterm death through repressing the autophagy level in a time-specific manner. And epigenetic modulation contributes to programmed oocyte death by regulating autophagy in mice.

Meta-Analysis of Hematological Biomarkers as Reliable Indicators of Soft Tissue Sarcoma Prognosis

Background: Several recent studies have reported the reliable prognostic effect of hematological biomarkers in various tumors. Yet, the prognostic value of these hematological markers in soft tissue sarcoma (STS) remains inconclusive. Thus, the aim of this meta-analysis was to check the effect of hematological markers on the prognosis of STS. Methods: We systematically searched for relevant papers published before October 2019 in the PubMed and EMBASE databases. Overall survival (OS) and disease-specific survival (DSS) were the primary outcome, whereas disease-free survival was the secondary outcome. A thorough study of hazard ratios (HR) and 95% of confidence intervals (CIs) was done for determining the prognostic significance. Results: We performed 23 studies that comprised of 4,480 patients with STS. The results revealed that higher neutrophil-to-lymphocyte ratio (NLR), C-reactive protein (CRP), and platelet-to-lymphocyte ratio (PLR) were associated with poor OS/DFS (HR = 2.08/1.72, for NLR; HR = 1.92/1.75, for CRP, and HR = 1.86/1.61, for PLR). In contrast, a low lymphocyte-to-monocyte ratio (LMR) was relate to worse OS/DFS (HR = 2.01/1.90, for LMR). Moreover, pooled analysis illustrated that elevated NLR and CRP represents poor DSS, with HRs of 1.46 and 2.06, respectively. In addition, combined analysis revealed that higher Glasgow prognostic score (GPS) was linked to an adverse OS/DSS (HR = 2.35/2.77). Conclusion: Our meta-analysis suggested that hematological markers (NLR, CRP, PLR, LMR, and GPS) are one of the important prognostic indicators for patients affected by high-grade STS and patients with the STS being located in the extremity.

QTL Analysis Beyond eQTLs

Expression quantitative trait locus (eQTL) analysis is a powerful method to understand the association between genetic variant and gene expression; it also has potential impact for the study of transcription medicine for human complex disease. In the past two decades, the researchers focus on studying the eQTL, while more and more evidence shows that the regulatory genetic variants locating noncoding region have strong effect for the gene expression. More and more researchers working on eQTL analysis realize the importance of other types of QTLs beyond eQTL. In this chapter, we will explore some QTLs beyond eQTLs that show the regulatory association with eQTLs and explain the underlying link among these types of QTLs.

MnO2-Based nanosystems for cancer therapy

Recent achievements of MnO₂-based nanosystems for various cancer therapies are comprehensively reviewed.

Independent association between the visceral adiposity index and microalbuminuria in patients with newly diagnosed type 2 diabetes

AIMS

Visceral adiposity and albuminuria are commonly observed in patients with type 2 diabetes mellitus (T2DM). Recently, the visceral adipose index (VAI) was found to be an indicator of visceral fat accumulation. However, the relationship between the VAI and urinary albumin has not been investigated in T2DM patients, and whether the predictive value of the VAI is superior to that of the triglyceride/high-density lipoprotein cholesterol (TG/HDL-c) ratio remains unknown.

MATERIALS AND METHODS

Three hundred and forty one newly diagnosed T2DM patients were enrolled. The anthropometric parameters, blood pressure, glucose, lipid profiles, urinary albumin, and other biochemical indices were examined. Linear and logistic regression models were developed to assess the association between the VAI and urinary albumin.

RESULTS

The prevalence of microalbuminuria was 41.3% (n = 141) and increased with increasing levels of VAI. An age-adjusted partial correlation analysis showed that the VAI and TG/HDL-c ratio were significantly associated with the waist-to-hip ratio, heart rate, total cholesterol, low-density lipoprotein cholesterol, and uric acid. In the stepwise linear regression analysis, the VAI (β = .21, .009) and TG/HDL-c (β = .25, .002) were significant determinants of urinary albumin. Moreover, in the multiple logistic regression model, the odds ratio (OR) of microalbuminuria per one SD increase in the VAI was 1.94 (95% CI, 1.11-3.38), and a similar result was observed with a higher TG/HDL-c ratio (OR = 2.03, 95% CI, 1.13-3.65).

CONCLUSION

We are the first to show a clear association between the VAI and urinary albumin in Chinese type 2 diabetic patients. Additionally, the VAI and TG/HDL-c ratio had similar predictive power regarding albuminuria risk. The VAI could be a rapid and reliable tool for assessing early-stage renal damage in newly diagnosed T2DM patients.

A network view of microRNA and gene interactions in different pathological stages of colon cancer

BACKGROUND

Colon cancer is one of the common cancers in human. Although the number of annual cases has decreased drastically, prognostic screening and translational methods can be improved. Hence, it is critical to understand the molecular mechanisms of disease progression and prognosis.

RESULTS

In this study, we develop a new strategy for integrating microRNA and gene expression profiles together with clinical information toward understanding the regulation of colon cancer. Particularly, we use this approach to identify microRNA and gene expression networks that are specific to certain pathological stages. To demonstrate the application of our method, we apply this approach to identify microRNA and gene interactions that are specific to pathological stages of colon cancer in The Cancer Genome Atlas (TCGA) datasets.

CONCLUSIONS

Our results show that there are significant differences in network connections between miRNAs and genes in different pathological stages of colon cancer. These findings point to a hypothesis that these networks signify different roles of microRNA and gene regulation in the pathogenesis and tumorigenesis of colon cancer.

[Artificial intelligence evaluation of simulated phantom lung nodules with different pre-adaptive iteration techniques]

Objective: To investigate the detection rate of pulmonary nodules and the accuracy of automated measurement in chest simulation phantom by artificial intelligent computer-aided detection of pulmonary nodules with different pre-adaptive iterative techniques (ASIR-V) in wide-spectrum CT scanning. Methods: Sixteen pulmonary nodules with different diameters, densities and shapes were placed in the chest simulation phantom from December 2017 to March 2018. The weight of ASIR-V was set at 0%, 20%, 30%, 40% and 50% respectively by using Revolution CT broadband energy spectrum scanning protocol. Spearman correlation analysis was used to analyze the dose volume CT dose index (CTDIvol) and dose length product (DLP) of each group. Scanning data were imported into Tuma Shenwei artificial pulmonary nodule analysis software to evaluate the nature of the detected nodules, and ICC was used to detect the differences among groups. Results: With the increase of ASIR-V weight, the effective dose of patients decreased gradually. CTDIvol of five groups of radiation dose volume CT dose index was 7.93, 7.24, 5.85, 5.15, 3.76 mGy,dose-length product DLP was 379, 346, 280, 246, 179 mGy·cm.There was a linear negative correlation between ASIR-V weights and CTDIvol as well as DLP, r value was-0.969, P<0.01.There was no significant difference in the detection rate of pulmonary nodules between AI and physicians (P>0.05). There was high intraclass correlation coefficients for the diameter, volume, CT value and malignant percentage of pulmonary nodules (ICCs:0.981-1.000). Conclusions: Radiation dose of unenhanced chest CT scan using wide detector spectral imaging decreased with the increasing of preset ASIR-V. Lung nodule detection rate and evaluation performance can be maintained well by using ASIR-V reconstructions at lower radiation dosage.

Ptprj-as1 mediates inflammatory injury after intracerebral hemorrhage by activating NF-κB pathway

OBJECTIVE

We aimed at investigating the expression of long non-coding RNA (lncRNA) Ptprj-as1 and the role of lncRNAPtprj-as1 in inflammatory cells after intracerebral hemorrhage and its potential mechanism.

MATERIALS AND METHODS

The rat model of intracerebral hemorrhage was established. Expressions of Ptprj-as1 and inflammatory cytokines in inflammatory cells were detected by quantitative Real-time PCR (qRT-PCR). After BV2 cells were transfected with lentivirus, cell proliferation, migrative ability and apoptosis were detected by cell counting kit-8 (CCK-8) assay, transwell chamber and flow cytometry, respectively. Immunofluorescence was used to explore the ratio of M1 and M2 glial cells. The detection of tumor necrosis factor alpha (TNF-α) expression was performed using enzyme-linked immunosorbent assay (ELISA). Moreover, the expressions of key genes in NF-κB pathway were evaluated using Western blot.

RESULTS

Ptprj-as1 was highly expressed in inflammatory tissues caused by intracerebral hemorrhage (ICH). Overexpressed Ptprj-as1 promoted the migration of BV2 cells and expression levels of inflammatory cytokines such as TNF-α, interleukin-1β (IL-1β), interleukin-6 (IL-6), iNOS and NO. Meanwhile, Ptprj-as1 enhanced the proportion of M1 glial cells, the mechanism of which might be related to the activation of NF-κB pathway.

CONCLUSIONS

Ptprj-as1 activates NF-κB pathway in microglia and promotes the secretion of inflammatory cytokines, which is involved in inflammatory injury caused by intracerebral hemorrhage.

Crocin Protects Human Umbilical Vein Endothelial Cells from High Glucose-Induced Injury Via Inhibiting the Endoplasmic Reticulum Stress Response

BACKGROUND

Endothelial dysfunction plays a key role in diabetic atherosclerosis. High glucose (HG) is considered a stimulator in the development of diabetic atherosclerosis. The endoplasmic reticulum (ER) stress response is involved in HG-induced vascular injury. Crocin has antioxidative and antiapoptotic properties.

OBJECTIVE

The current study was to evaluate whether crocin can protect human umbilical vein endothelial cells (HUVECs) from HG-induced injury and explored the associated mechanism.

METHODS

HUVECs were treated with 33 mmol/L glucose as the HG condition. The endothelial protective effects of crocin were evaluated by comparison with the control groups.

RESULTS

The exposure of HUVECs to HG for 24 h remarkably induced the ER stress response and a sequence of injuries, as demonstrated an increase in the apoptotic cell number, the reactive oxygen species level and inflammatory cytokine generation, as well as a decline in vascular endothelial growth factor A expression. These changes were markedly alleviated by pretreating the HUVECs with either crocin or 4-phenylbutyrate (ER stress inhibitor) before exposure to HG.

CONCLUSION

Crocin exerted antioxidative, antiapoptotic, anti-inflammatory and proangiogenic effects in the HG-induced HUVEC injury model, which were probably mediated by a favorable modification of ER stress that requires further investigation.