Host-induced gene silencing in wild apple germplasm Malus hupehensis confers resistance to the fungal pathogen Botryosphaeria dothidea.

Host-induced gene silencing (HIGS) is an inherent mechanism of plant resistance to fungal pathogens, resulting from cross-kingdom RNA interference (RNAi) mediated by small RNAs (sRNAs) delivered from plants into invading fungi. Introducing artificial sRNA precursors into crops can trigger HIGS of selected fungal genes, and thus has potential applications in agricultural disease control. To investigate the HIGS of apple (Malus sp.) during the interaction with Botryosphaeria dothidea, the pathogenic fungus causing apple ring rot disease, we evaluated whether apple miRNAs can be transported into and target genes in B. dothidea. Indeed, miR159a from Malus hupehensis, a wild apple germplasm with B. dothidea resistance, silenced the fungal sugar transporter gene BdSTP. The accumulation of miR159a in extracellular vesicles (EVs) of both infected M. hupehensis and invading B. dothidea suggests that this miRNA of the host is transported into the fungus via the EV pathway. Knockout of BdSTP caused defects in fungal growth and proliferation, whereas knockin of a miR159a-insensitive version of BdSTP resulted in increased pathogenicity. Inhibition of miR159a in M. hupehensis substantially enhanced plant sensitivity to B. dothidea, indicating miR159a-mediated HIGS against BdSTP being integral to apple immunity. Introducing artificial sRNA precursors targeting BdSTP and BdALS, an acetolactate synthase gene, into M. hupehensis revealed that double-stranded RNAs were more potent than engineered MIRNAs in triggering HIGS alternative to those natural of apple and inhibiting infection. These results provide preliminary evidence for cross-kingdom RNAi in the apple-B. dothidea interaction and establish HIGS as a potential disease control strategy in apple.

Leveraging the local genetic structure for trans-ancestry association mapping.

Over the past two decades, genome-wide association studies (GWASs) have successfully advanced our understanding of the genetic basis of complex traits. Despite the fruitful discovery of GWASs, most GWAS samples are collected from European populations, and these GWASs are often criticized for their lack of ancestry diversity. Trans-ancestry association mapping (TRAM) offers an exciting opportunity to fill the gap of disparities in genetic studies between non-Europeans and Europeans. Here, we propose a statistical method, LOG-TRAM, to leverage the local genetic architecture for TRAM. By using biobank-scale datasets, we showed that LOG-TRAM can greatly improve the statistical power of identifying risk variants in under-represented populations while producing well-calibrated p values. We applied LOG-TRAM to the GWAS summary statistics of various complex traits/diseases from BioBank Japan, UK Biobank, and African populations. We obtained substantial gains in power and achieved effective correction of confounding biases in TRAM. Finally, we showed that LOG-TRAM can be successfully applied to identify ancestry-specific loci and the LOG-TRAM output can be further used for construction of more accurate polygenic risk scores in under-represented populations.

An indel introduced by Neanderthal introgression, rs3835124:ATTTATT > ATT, might contribute to prostate cancer risk by regulating PDK1 expression.

INTRODUCTION: Prostate cancer is one of the most common cancer types in males and rs12621278:A > G has been suggested to be associated with this disease by previous genome-wide association studies. One thousand genomes project data analysis indicated that rs12621278:A > G is within two long-core haplotypes. However, the origin, causal variant(s), and molecular function of these haplotypes were remaining unclear. MATERIALS AND METHODS: Population genetics analysis and functional genomics work was performed for this locus. RESULTS: Phylogeny analysis verified that the rare haplotype is derived from Neanderthal introgression. Genome annotation suggested that three genetic variants in the core haplotypes, rs116108611:G > A, rs139972066:AAAAAAAA > AAAAAAAAA, and rs3835124:ATTTATT > ATT, are located in functional regions. Luciferase assay indicated that rs139972066:AAAAAAAA > AAAAAAAAA and rs116108611:G > A are not able to alter ITGA6 (integrin alpha 6) and ITGA6 antisense RNA 1 expression, respectively. In contrast, rs3835124:ATTTATT > ATT can significantly influence PDK1 (pyruvate dehydrogenase kinase 1) expression, which was verified by expression quantitative trait locus analysis. This genetic variant can alter transcription factor cut like homeobox 1 interaction efficiency. The introgressed haplotype was observed to be subject to positive selection in East Asian populations. The molecular function of the haplotype suggested that Neanderthal should be with lower PDK1 expression and further different energy homeostasis from modern human. CONCLUSION: This study provided new insight into the contribution of Neanderthal introgression to human phenotypes.

PALM: a powerful and adaptive latent model for prioritizing risk variants with functional annotations.

MOTIVATION: The findings from genome-wide association studies (GWASs) have greatly helped us to understand the genetic basis of human complex traits and diseases. Despite the tremendous progress, much effects are still needed to address several major challenges arising in GWAS. First, most GWAS hits are located in the non-coding region of human genome, and thus their biological functions largely remain unknown. Second, due to the polygenicity of human complex traits and diseases, many genetic risk variants with weak or moderate effects have not been identified yet. RESULTS: To address the above challenges, we propose a powerful and adaptive latent model (PALM) to integrate cell-type/tissue-specific functional annotations with GWAS summary statistics. Unlike existing methods, which are mainly based on linear models, PALM leverages a tree ensemble to adaptively characterize non-linear relationship between functional annotations and the association status of genetic variants. To make PALM scalable to millions of variants and hundreds of functional annotations, we develop a functional gradient-based expectation-maximization algorithm, to fit the tree-based non-linear model in a stable manner. Through comprehensive simulation studies, we show that PALM not only controls false discovery rate well, but also improves statistical power of identifying risk variants. We also apply PALM to integrate summary statistics of 30 GWASs with 127 cell type/tissue-specific functional annotations. The results indicate that PALM can identify more risk variants as well as rank the importance of functional annotations, yielding better interpretation of GWAS results. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/YangLabHKUST/PALM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Interaction between ferroptosis and TNF-α: Impact in obesity-related osteoporosis.

The relationship of obesity and osteoporosis has been widely studied over the past years. However, the implications of obesity for bone health remain controversial, and the underlying molecular mechanism is not yet fully understood. This study demonstrated that high-fat diet-induced obesity leads to significantly decreased bone volume/tissue volume (BV/TV), trabecular number (Tb.N), and cortical thickness (Ct.Th) of male rat femur after mechanical loading effects of body weight were controlled. HFD-induced obese rats exhibited attenuated expression of ferroptosis inhibitory protein SLC7A11 and GPX4 in bone tissues, which was correlated with elevated serum TNF-α concentration. Ferroptosis inhibitor administration could effectively rescue decreased osteogenesis-associated type H vessels and osteoprogenitors, and downregulate serum levels of TNF-α to ameliorate bone loss in obese rats. Since ferroptosis and TNF-α both affect bone and vessel formation, we further investigated the interaction between ferroptosis and TNF-α, and its impact in osteogenesis and angiogenesis in vitro. In human osteoblast-like MG63 and umbilical vein endothelial cells (HUVEC), TNF-α/TNFR2 signaling promoted cystine uptake and GSH biosynthesis to provide protection against low-dose ferroptosis inducer erastin. While, TNF-α/TNFR1 facilitated ferroptosis in the presence of high-dose erastin through ROS accumulation. Moreover, TNF-α regulated ferroptosis-induced osteogenic and angiogenic dysfunctions based on its ferroptosis regulatory role. Meanwhile, ferroptosis inhibitors could reduce intracellular ROS overproduction and enhance osteogenesis and angiogenesis in TNF-α-treated MG63 and HUVECs. This study revealed the interaction between ferroptosis and TNF-α and its impact in osteogenesis and angiogenesis, which provides new insights into the pathogenesis and regenerative therapy of obesity-related osteoporosis.

Meroterpenoids from Marine Sponge Hyrtios sp. and Their Anticancer Activity against Human Colorectal Cancer Cells.

Two new meroterpenoids, hyrtamide A (1) and hyrfarnediol A (2), along with two known ones, 3-farnesyl-4-hydroxybenzoic acid methyl ester (3) and dictyoceratin C (4), were isolated from a South China Sea sponge Hyrtios sp. Their structures were elucidated by NMR and MS data. Compounds 2-4 exhibited weak cytotoxicity against human colorectal cancer cells (HCT-116), showing IC50 values of 41.6, 45.0, and 37.3 µM, respectively. Furthermore, compounds 3 and 4 significantly suppressed the invasion of HCT-116 cells while also downregulating the expression of vascular endothelial growth factor receptor 1 (VEGFR-1) and vimentin proteins, which are key markers associated with angiogenesis and epithelial-mesenchymal transition (EMT). Our findings suggest that compounds 3 and 4 may exert their anti-invasive effects on tumor cells by inhibiting the expression of VEGFR-1 and impeding the process of EMT.

MicroRNA candidate miRcand137 in apple is induced by Botryosphaeria dothidea for impairing host defense.

MicroRNA (miRNA)-mediated gene silencing is a master gene regulatory pathway in plant-pathogen interactions. The differential accumulation of miRNAs among plant varieties alters the expression of target genes, affecting plant defense responses and causing resistance differences among varieties. Botryosphaeria dothidea is an important phytopathogenic fungus of apple (Malus domestica). Malus hupehensis (Pamp.) Rehder, a wild apple species, is highly resistant, whereas the apple cultivar "Fuji" is highly susceptible. Here, we identified a 22-nt miRNA candidate named miRcand137 that compromises host resistance to B. dothidea infection and whose processing was affected by precursor sequence variation between M. hupehensis and "Fuji." miRcand137 guides the direct cleavage of and produced target-derived secondary siRNA against Ethylene response factor 14 (ERF14), a transcriptional activator of pathogenesis-related homologs that confers disease resistance to apple. We showed that miRcand137 acts as an inhibitor of apple immunity by compromising ERF14-mediated anti-fungal defense and revealed a negative association between miRcand137 expression and B. dothidea sensitivity in both resistant and susceptible apples. Furthermore, MIRCAND137 was transcriptionally activated by the invading fungi but not by the fungal elicitor, implying B. dothidea induced host miRcand137 as an infection strategy. We propose that the inefficient miRcand137 processing in M. hupehensis decreased pathogen-initiated miRcand137 accumulation, leading to higher resistance against B. dothidea.

A Review of New-Onset Ventricular Arrhythmia after Left Ventricular Assist Device Implantation.

INTRODUCTION: Heart failure (HF) is a severe and terminal stage of various heart diseases. Left ventricular assist devices (LVADs) are relatively mature and have contributed to the treatment of end-stage HF. Ventricular arrhythmia (VA) is a common complication after LVAD implantation, including ventricular tachycardia and ventricular fibrillation, both of which may cause abnormal circulation. METHODS: A literature search was conducted in the PubMed database, "Ventricular Arrhythmia" OR "VA" OR "Arrhythmia" OR "Ventricular Tachycardia," OR "Ventricular Fibrillation" AND "LVAD" OR "Left Ventricular Assist Device" OR "Heart Assist Device" as either keywords or MeSH terms, the authors screened the titles and abstracts of the articles. Eventually, 12 original research articles were retrieved. RESULTS: The 0.83 [95% CI: 0.77, 0.89] of patients were male. A whole of 53% [95% CI: 0.25, 0.81] of VA patients had a history of atrial fibrillation and 61% [95% CI: 0.52, 0.69] had a history of VA. 39% [95% CI: 0.29, 0.49] of the participants had no prior history of VA and experienced new VA following CF-LVAD implantation. Following CF-LVAD implantation, 59% [95% CI: 0.51, 0.67] of patients developed early VA (VA ≤30 days). The 30-day mortality rate of patients was 4% [95% CI: 0.01, 0.07]. And overall mortality was 28% [95% CI: 0.15, 0.41]. The reported incidence of VA after LVAD implantation is not identical in different medical centers and ranges from 20% to 60%. The mechanism of VA after LVAD implantation is summarized as primary cardiomyopathy-related, device mechanical stimulation, myocardial scarring, ventricular displacement, electrolyte regulation, and other processes. CONCLUSIONS: A preoperative VA history is considered a predictor of VA following LVAD implantation in most studies. Multiple mechanisms and factors, such as prevention of "suction events," ablation, and implantable cardioverter defibrillator, should be considered for the prevention and treatment of postoperative VA in patients requiring long-term VAD treatment. This study provides a reference for the clinical application of LAVD and the prevention of postoperative VA after LVAD implantation. Future multicenter prospective studies with uniform patient follow-up are needed to screen for additional potential risk factors and predictors. These studies will help to define the incidence rate of VA after LAVD implantation. As a result, we provide guidance for the selection of preventive intervention.

Effect of CPB glucose levels on inflammatory response after pediatric cardiac surgery.

BACKGROUND: Systemic inflammatory response syndrome (SIRS) is a common complication after cardiac surgery. There are no definite optimal glycemic threshold for pediatric patients receiving open-heart surgery with CPB. The study aimed to investigate the optimal cardiopulmonary bypass (CPB) glucose in patients undergoing cardiac surgery. METHODS: We enrolled children with congenital heart disease who underwent surgical repair between June 2012 and December 2020. We included only patients who underwent cardiac surgery with CPB. The primary outcome was severe SIRS. A two-piece-wise regression model was applied to examine threshold effect of CPB glucose on severe SIRS. RESULTS: A total of 7350 patients were enrolled in the present study, of whom 3895 (52.99%) are female. After potential confounders were adjusted, non-linear relationship was detected between CPB glucose and severe SIRS, whose turning point was 8.1. With CPB glucose < 8.1 mmol/L, the estimated dose-response curve was consistent with a horizontal line. However, the prevalence of severe SIRS increased with increasing glucose up to the turning point (Glucose > 8.1 mmol/L); the odds ratio (OR) of the Glucose was 1.35 (95% CI 1.21, 1.50). CONCLUSIONS: The present study indicates the association of CPB glucose with inflammatory response after pediatric cardiac surgery. The patients might have the best outcomes with the optimal CPB glucose no more than 8.1 mmol/L.

Association of LDL to HDL ratio with new-onset atrial fibrillation after on-pump coronary artery bypass graft surgery.

OBJECTIVE: This study aims to analyze the association between preoperative LDL/HDL ratio and new-onset atrial fibrillation (AF) after on-pump coronary artery bypass grafting (on-pump CABG), evaluate the clinic value of preoperative LDL/HDL ratio to identify postoperative rhythm. METHODS: A retrospective study of consecutive patients (n = 2052) who underwent on-pump CABG at TEDA International Cardiovascular Hospital (Tianjin, China), from June 1, 2020, to December 30, 2021, was conducted. The association between preoperative LDL/HDL and new-onset POAF was analyzed by Lowess curve and univariate logistic regression. The receiver operating characteristic curve (ROC) and area under the curve (AUC) were used to evaluate the identification capacity of preoperative LDL/HDL level for new-onset POAF. RESULTS: In studied populations, the incidence of new-onset POAF was about 29.24%. The lowess curve showed that the association between preoperative LDL/HDL ratio and POAF after on-pump CABG was similar to a linear relationship. With the increasement of preoperative LDL/HDL ratio, the incidence of POAF increased simultaneously. ROC analysis showed that preoperative LDL/HDL ratio could identify postoperative arrhythmia after on-pump CABG (AUC = 0.569,95% CI = 0.529-0.608, P = 0.006) among female patients, the best preoperative LDL/HDL ratio cutoff of 2.11, which was considered a predictive factor of incident POAF, showed a sensitivity of 83.60% (95% CI = 0.775-0.886) and a specificity of 30.02% (95% CI = 0.257-0.346). CONCLUSION: Preoperative LDL/HDL ratio is associated with new-onset POAF, but there is a difference in different sex. Preoperative LDL/HDL level can help to identify postoperative rhythm in females.