Hepatic progenitor cell-originated ductular reaction facilitates liver fibrosis through activation of hedgehog signaling.

Background: It is poorly understood what cellular types participate in ductular reaction (DR) and whether DR facilitates recovery from injury or accelerates hepatic fibrosis. The aim of this study is to gain insights into the role of hepatic progenitor cell (HPC)-originated DR during fibrotic progression. Methods: DR in liver specimens of PBC, chronic HBV infection (CHB) or NAFLD, and four rodent fibrotic models by different pathogenic processes was evaluated. Gli1 expression was inhibited in rodent models or cell culture and organoid models by AAV-shGli1 or treating with GANT61. Results: Severity of liver fibrosis was positively correlated with DR extent in patients with PBC, CHB or NAFLD. HPCs were activated, expanded, differentiated into reactive cholangiocytes and constituted "HPC-originated DR", accompanying with exacerbated fibrosis in rodent models of HPC activation & proliferation (CCl4/2-AAF-treated), Μdr2-/- spontaneous PSC, BDL-cholestatic fibrosis or WD-fed/CCl4-treated NASH-fibrosis. Gli1 expression was significantly increased in enriched pathways in vivo and in vitro. Enhanced Gli1 expression was identified in KRT19+-reactive cholangiocytes. Suppressing Gli1 expression by administration of AAV-shGli1 or GANT61 ameliorated HPC-originated DR and fibrotic extent. KRT19 expression was reduced after GANT61 treatment in sodium butyrate-stimulated WB-F344 cells or organoids or in cells transduced with Gli1 knockdown lentiviral vectors. In contrast, KRT19 expression was elevated after transducing Gli1 overexpression lentiviral vectors in these cells. Conclusions: During various modes of chronic injury, Gli1 acted as an important mediator of HPC activation, expansion, differentiation into reactive cholangiocytes that formed DR, and subsequently provoked hepatic fibrogenesis.

wMKL: multi-omics data integration enables novel cancer subtype identification via weight-boosted multi-kernel learning.

BACKGROUND: Cancer is a heterogeneous disease driven by complex molecular alterations. Cancer subtypes determined from multi-omics data can provide novel insight into personalised precision treatment. It is recognised that incorporating prior weight knowledge into multi-omics data integration can improve disease subtyping. METHODS: We develop a weighted method, termed weight-boosted Multi-Kernel Learning (wMKL) which incorporates heterogeneous data types as well as flexible weight functions, to boost subtype identification. Given a series of weight functions, we propose an omnibus combination strategy to integrate different weight-related P-values to improve subtyping precision. RESULTS: wMKL models each data type with multiple kernel choices, thus alleviating the sensitivity and robustness issue due to selecting kernel parameters. Furthermore, wMKL integrates different data types by learning weights of different kernels derived from each data type, recognising the heterogeneous contribution of different data types to the final subtyping performance. The proposed wMKL outperforms existing weighted and non-weighted methods. The utility and advantage of wMKL are illustrated through extensive simulations and applications to two TCGA datasets. Novel subtypes are identified followed by extensive downstream bioinformatics analysis to understand the molecular mechanisms differentiating different subtypes. CONCLUSIONS: The proposed wMKL method provides a novel strategy for disease subtyping. The wMKL is freely available at https://github.com/biostatcao/wMKL .

Integrated transcriptome and physiological analysis revealed core transcription factors that promote flavonoid biosynthesis in apricot in response to pathogenic fungal infection.

MAIN CONCLUSION: Integrated transcriptome and physiological analysis of apricot leaves after Fusarium solani treatment. In addition, we identified core transcription factors and flavonoid-related synthase genes which may function in apricot disease resistance. Apricot (Prunus armeniaca) is an important economic fruit species, whose yield and quality of fruit are limited owing to its susceptibility to diseases. However, the molecular mechanisms underlying the response of P. armeniaca to diseases is still unknown. In this study, we used physiology and transcriptome analysis to characterize responses of P. armeniaca subjected to Fusarium solani. The results showed increasing malondialdehyde (MDA) content, enhanced peroxidase (POD) and catalase (CAT) activity during F. solani infestation. A large number of differentially expressed genes (DEGs), which included 4281 upregulated DEGs and 3305 downregulated DEGs, were detected in P. armeniaca leaves exposed to F. solani infestation. Changes in expression of transcription factors (TFs), including bHLH, AP2/ERF, and WRKY indicated their role in triggering pathogen-responsive genes in P. armeniaca. During the P. armeniaca response to F. solani infestation, the content of total flavonoid was changed, and we identified enzyme genes associated with flavonoid biosynthesis. Ectopic overexpression of PabHLH15 and PabHLH102 in Nicotiana benthamiana conferred elevated resistance to Fspa_1. Moreover, PabHLH15 and PabHLH102 positively interact with the promoter of flavonoid biosynthesis-related genes. A regulatory network of TFs regulating enzyme genes related to flavonoid synthesis affecting apricot disease resistance was constructed. These results reveal the potential underlying mechanisms of the F. solani response of P. armeniaca, which would help improve the disease resistance of P. armeniaca and may cultivate high-quality disease-resistant varieties in the future.

Clinicopathological features and expression of regulatory mechanism of the Wnt signaling pathway in colorectal sessile serrated adenomas/polyps with different syndrome types.

BACKGROUND: Colorectal cancer (CRC) is the third most common cancer worldwide, with the fourth highest mortality among all cancers. Reportedly, in addition to adenomas, serrated polyps, which account for 15%-30% of CRCs, can also develop into CRCs through the serrated pathway. Sessile serrated adenomas/polyps (SSAs/Ps), a type of serrated polyps, are easily misdiagnosed during endoscopy. AIM: To observe the difference in the Wnt signaling pathway expression in SSAs/Ps patients with different syndrome types. METHODS: From January 2021 to December 2021, patients with SSAs/Ps were recruited from the Endoscopy Room of Shanghai Traditional Chinese Medicine-Integrated Hospital, affiliated with Shanghai University of Traditional Chinese Medicine. Thirty cases each of large intestine damp-heat (Da-Chang-Shi-Re, DCSR) syndrome and spleen-stomach weakness (Pi-Wei-Xu-Ruo) syndrome were reported. Baseline comparison of the general data, typical tongue coating, colonoscopy findings, and hematoxylin and eosin findings was performed in each group. The expression of the Wnt pathway-related proteins, namely ß-catenin, adenomatous polyposis coli, and mutated in colorectal cancer, were analyzed using immunohistochemistry. RESULTS: Significant differences were observed with respect to the SSAs/Ps size between the two groups of patients with different syndrome types (P = 0.001). The other aspects did not differ between the two groups. The Wnt signaling pathway was activated in patients with SSAs/Ps belonging to both groups, which was manifested as ß-catenin protein translocation into the nucleus. However, SSAs/Ps patients with DCSR syndrome had more nucleation, higher ß-catenin expression, and negative regulatory factor (adenomatous polyposis coli and mutated in colorectal cancer) expression (P < 0.0001) than SSA/P patients with Pi-Wei-Xu-Ruo syndrome. In addition, the SSA/P size was linearly correlated with the related protein expression. CONCLUSION: Patients with DCSR syndrome had a more obvious Wnt signaling pathway activation and a higher risk of carcinogenesis. A high-quality colonoscopic diagnosis was essential. The thorough assessment of clinical diseases can be improved by combining the diseases of Western medicine with the syndromes of traditional Chinese medicine.

[Dachengqi decoction reduces inflammatory response and promotes recovery of gastrointestinal function in patients with mild acute pancreatitis by regulating the intestinal microbiota].

OBJECTIVE: To explore the therapeutic effect and mechanism of Dachengqi decoction on patients with mild acute pancreatitis (MAP). METHODS: A parallel randomized controlled trial was conducted. Sixty-eight patients with acute pancreatitis (AP) admitted to Shanghai Traditional Chinese Medicine (TCM)-Integrated Hospital from March 2018 to February 2021 were enrolled. Referring to the condition on admission of the patients and whether they agreed to receive the Dachengqi decoction or not, they were divided into conventional treatment group and Dachengqi decoction group according to the principle of 1:1 equal randomness. Meanwhile, 20 healthy volunteers were recruited as controls. Both groups of patients were treated with octreotide, fasting, gastrointestinal decompression, antipyretic and analgesic, anti-inflammatory, inhibition of gastric acid and pancreatic juice secretion, maintenance of electrolyte balance and other western conventional medicine. The patients in the Dachengqi decoction group received Dachengqi decoction orally on the basis of routine treatment, 100 mL each time, twice a day, for seven consecutive days. The inflammation parameters [white blood cell count (WBC), C-reactive protein (CRP), procalcitonin (PCT), interleukin-6 (IL-6)] before and after treatment and the recovery time of gastrointestinal function (first exhaust time, time to recover bowel sounds, first defecation time) of patients were recorded. 16S rRNA gene sequencing of stool samples was recorded, and normalized data were obtained after quality control and other related processing. The data were subjected to diversity analysis (Alpha diversity and Beta diversity) and linear discriminant analysis effect size analysis (LEfSe analysis) to observe changes in the gut microbiota of MAP patients. Spearman rank correlation coefficient was used to analyze the correlation between inflammatory indexes and microorganisms at the intestinal genus level. Blood, urine, stool samples, renal function, and electrocardiogram (ECG) during treatment of MAP patients were detected to assess the safety of the treatment. RESULTS: Of the 68 patients with AP, 16 were excluded from moderate-severe AP, 4 were not collected or voluntarily abandoned treatment. Finally, 48 patients with MAP were enrolled, 24 in the conventional treatment group and 24 in the Dachengqi decoction group. The inflammation parameters levels at 7 days of treatment in both groups were significantly lower than those before treatment. CRP, PCT and IL-6 levels in the Dachengqi decoction group were significantly lower than those in the conventional treatment group [CRP (mg/L): 8.50 (3.50, 13.00) vs. 16.00 (9.25, 29.75), PCT (µg/L): 0.06 (0.03, 0.08) vs. 0.09 (0.05, 0.11), IL-6 (ng/L): 6.36 (3.96, 10.79) vs. 13.24 (6.69, 18.87), all P < 0.05]. The first exhaust time, time to recover bowel sounds and first defecation time in the Dachengqi decoction group were significantly shorter than those in the conventional treatment group [first exhaust time (days): 1.62±0.65 vs. 2.80±0.65, time to recover bowel sounds (days): 1.13±0.58 vs. 2.31±0.76, first defecation time (days): 3.12±0.75 vs. 4.39±0.76, all P < 0.05]. The analysis of intestinal microflora diversity showed that both the diversity and abundance of microbial communities were the highest in the healthy control group and the lowest in the conventional treatment group. In addition, the coincidence degree of microbial communities in healthy controls and MAP patients was small, while the coincidence degree of MAP patients among different treatment methods was relatively large. LEfSe analysis showed that Dachengqi decoction reduced the relative abundance of Escherichia coli-Shigella and Clostridium erysipelae, and increased the relative abundance of three beneficial bacteria, namely Lactobacillus, Rombutzia and Brutella. In the intestines of MAP patients, Lactobacillus mucilaginus and Lactobacillus conjunctus were significantly enriched. Correlation analysis showed that positive correlations between Escherichia coli-Shigella and the four inflammatory indicators including WBC, CRP, PCT, IL-6 were statistically significant (r value was 0.31, 0.41, 0.57, 0.43, respectively, all P < 0.05). There was no significant correlation between other bacteria and inflammatory indicators. During the treatment, there was no obvious abnormality in blood, urine and feces, renal function and ECG of MAP patients. CONCLUSIONS: Dachengqi decoction could reduce inflammatory responses and promote recovery of intestinal microecological balance and gastrointestinal function in patients with MAP by regulating the composition of intestinal flora. No significant adverse effects were observed during the treatment period.

Cancer subtyping with heterogeneous multi-omics data via hierarchical multi-kernel learning.

Differentiating cancer subtypes is crucial to guide personalized treatment and improve the prognosis for patients. Integrating multi-omics data can offer a comprehensive landscape of cancer biological process and provide promising ways for cancer diagnosis and treatment. Taking the heterogeneity of different omics data types into account, we propose a hierarchical multi-kernel learning (hMKL) approach, a novel cancer molecular subtyping method to identify cancer subtypes by adopting a two-stage kernel learning strategy. In stage 1, we obtain a composite kernel borrowing the cancer integration via multi-kernel learning (CIMLR) idea by optimizing the kernel parameters for individual omics data type. In stage 2, we obtain a final fused kernel through a weighted linear combination of individual kernels learned from stage 1 using an unsupervised multiple kernel learning method. Based on the final fusion kernel, k-means clustering is applied to identify cancer subtypes. Simulation studies show that hMKL outperforms the one-stage CIMLR method when there is data heterogeneity. hMKL can estimate the number of clusters correctly, which is the key challenge in subtyping. Application to two real data sets shows that hMKL identified meaningful subtypes and key cancer-associated biomarkers. The proposed method provides a novel toolkit for heterogeneous multi-omics data integration and cancer subtypes identification.

Multi-omics data integration for hepatocellular carcinoma subtyping with multi-kernel learning.

Hepatocellular carcinoma (HCC) is a leading malignant liver tumor with high mortality and morbidity. Patients at the same stage can be defined as different molecular subtypes associated with specific genomic disorders and clinical features. Thus, identifying subtypes is essential to realize efficient treatment and improve survival outcomes of HCC patients. Here, we applied a regularized multiple kernel learning with locality preserving projections method to integrate mRNA, miRNA and DNA methylation data of HCC patients to identify subtypes. We identified two HCC subtypes significantly correlated with the overall survival. The patient 3-years mortality rates in the high-risk and low-risk group was 51.0% and 23.5%, respectively. The high-risk group HCC patients were 3.37 times higher in death risk compared to the low-risk group after adjusting for clinically relevant covariates. A total of 196 differentially expressed mRNAs, 2,151 differentially methylated genes and 58 differentially expressed miRNAs were identified between the two subtypes. Additionally, pathway activity analysis showed that the activities of six pathways between the two subtypes were significantly different. Immune cell infiltration analysis revealed that the abundance of nine immune cells differed significantly between the two subtypes. We further applied the weighted gene co-expression network analysis to identify gene modules that may affect patients prognosis. Among the identified modules, the key module genes significantly associated with prognosis were found to be involved in multiple biological processes and pathways, revealing the mechanism underlying the progression of HCC. Hub gene analysis showed that the expression levels of CDK1, CDCA8, TACC3, and NCAPG were significantly associated with HCC prognosis. Our findings may bring novel insights into the subtypes of HCC and promote the realization of precision medicine.

Multi-omics data integration for subtype identification of Chinese lower-grade gliomas: A joint similarity network fusion approach.

Lower-grade gliomas (LGG), characterized by heterogeneity and invasiveness, originate from the central nervous system. Although studies focusing on molecular subtyping and molecular characteristics have provided novel insights into improving the diagnosis and therapy of LGG, there is an urgent need to identify new molecular subtypes and biomarkers that are promising to improve patient survival outcomes. Here, we proposed a joint similarity network fusion (Joint-SNF) method to integrate different omics data types to construct a fused network using the Joint and Individual Variation Explained (JIVE) technique under the SNF framework. Focusing on the joint network structure, a spectral clustering method was employed to obtain subtypes of patients. Simulation studies show that the proposed Joint-SNF method outperforms the original SNF approach under various simulation scenarios. We further applied the method to a Chinese LGG data set including mRNA expression, DNA methylation and microRNA (miRNA). Three molecular subtypes were identified and showed statistically significant differences in patient survival outcomes. The five-year mortality rates of the three subtypes are 80.8%, 32.1%, and 34.4%, respectively. After adjusting for clinically relevant covariates, the death risk of patients in Cluster 1 was 5.06 times higher than patients in other clusters. The fused network attained by the proposed Joint-SNF method enhances strong similarities, thus greatly improves subtyping performance compared to the original SNF method. The findings in the real application may provide important clues for improving patient survival outcomes and for precision treatment for Chinese LGG patients. An R package to implement the method can be accessed in Github at https://github.com/Sameerer/Joint-SNF.

NCP-BiRW: A Hybrid Approach for Predicting Long Noncoding RNA-Disease Associations by Network Consistency Projection and Bi-Random Walk.

Long non-coding RNAs (lncRNAs) play significant roles in the disease process. Understanding the pathological mechanisms of lncRNAs during the course of various diseases will help clinicians prevent and treat diseases. With the emergence of high-throughput techniques, many biological experiments have been developed to study lncRNA-disease associations. Because experimental methods are costly, slow, and laborious, a growing number of computational models have emerged. Here, we present a new approach using network consistency projection and bi-random walk (NCP-BiRW) to infer hidden lncRNA-disease associations. First, integrated similarity networks for lncRNAs and diseases were constructed by merging similarity information. Subsequently, network consistency projection was applied to calculate space projection scores for lncRNAs and diseases, which were then introduced into a bi-random walk method for association prediction. To test model performance, we employed 5- and 10-fold cross-validation, with the area under the receiver operating characteristic curve as the evaluation indicator. The computational results showed that our method outperformed the other five advanced algorithms. In addition, the novel method was applied to another dataset in the Mammalian ncRNA-Disease Repository (MNDR) database and showed excellent performance. Finally, case studies were carried out on atherosclerosis and leukemia to confirm the effectiveness of our method in practice. In conclusion, we could infer lncRNA-disease associations using the NCP-BiRW model, which may benefit biomedical studies in the future.

Effects of Jinkui Shenqi and Wuzi Yanzong pill on sperm motility and sperm DNA fragmentation rate in asthenospermia

This study was designed to compare the effects of Jinkui Shenqi and Wuzi Yanzong pill on sperm motility and sperm DNA fragmentation rate in patients with asthenospermia. 130 cases were randomly divided into an observation and control group (n=65). The control group was treated with the Wuzi Yanzong pill while the observation group with the Jinkui Shenqi pill. The sperm motility parameters rate (PR), semen concentration, sperm motility, DFI and α-glucosidase, fructose, seminal plasma zinc (Zn), acid phosphatase (ACP) in seminal plasma biochemistry and other indexes of were observed. The biochemical indexes of seminal plasma of α-glucosidase, fructose, Zn, ACP in two groups were significantly (p<0.05) improved after treatment. Compared with the control group, the indexes of the observation group improved more obviously after treatment. Pearson correlation analysis of DFI and PR indexes in 130 patients before treatment showed that sperm DFI and PR percentage were negatively correlated in asthenospermia patients (r =-0.572, P<0.05). There was no significant difference in DFI, semen concentration, PR, and sperm motility between the two groups before treatment. The DFI, semen concentration, PR and sperm viability of the two groups showed a tendency to improve after treatment, and the effect of the observation group was less significant than that of the control group (p<0.05). Two groups of patients have completed treatment successfully, no adverse events occurred during treatment. Jinkui Shenqi pill can effectively treat asthenospermia, which can effectively improve the effect of sperm motility in patients. It has less adverse reactions, safe and reliable, and is worthy of promotion.

The effect of acetate Ringer's solution versus lactate Ringer's solution on acid base physiology in infants with biliary atresia.

BACKGROUND: The choice of the perioperative crystalloid is a key component of the fluid management and must take into account the liver function and the appearing metabolic disorders to avoid increase the liver extra metabolism. The aim of this study is to analyze the effect of acetate Ringer's solution or lactate Ringer's solution in biliary atresia patients. METHODS: We included 68 infant patients aged between 21 ~ 65 d, ASA physical status II or III, who underwent elective Kasai hepatoportoenterostomy, received either AR and LR for intravenous fluid resuscitation according to their group allocation. Lactate concentration, serum electrolytes and pH were noteded before skin incision (T1), end of surgery (T2) and postoperative 12 h. We also recorded the time of operation, stay of hospital, loss of blood and urinary, total volume of infusion of crystalloid. RESULTS: Lactate level was significantly higher in Group LR than in Group AR patients at T2 (0.76 ± 0.13 versus 0.57 ± 0.22, P = 0.03). Compared with T3, sodium and chlorine were significantly higher in two groups at T2 (145.2 ± 3.1 versus 143.4 ± 3.4 and 104.6 ± 3.7 versus 105.2 ± 2.1). No significant differences were noted in potassium, HCO3- and calcium. There was no statistically significant difference in pH. No glycopenia was recorded in two groups. No significant difference was noted in administration of vasoactive drug (0.7% versus 1%). CONCLUSIONS: Resuscitation with AR and LR was associated with similar clinical improvement in infants with biliary atresia. Use of AR reduced the level of lactate comparison with LR.

A correlational study of Weifuchun and its clinical effect on intestinal flora in precancerous lesions of gastric cancer.

BACKGROUND: Weifuchun (WFC), a Chinese herbal prescription consisting of Red Ginseng, Isodon amethystoides and Fructus Aurantii, is commonly used in China to treat a variety of chronic stomach disorders. The aim of the paper was to determine the effect of WFC on intestinal microbiota changes in precancerous lesions of gastric cancer (PLGC) patients. METHODS: PLGC patients of H. pylori negative were randomly divided into two groups and received either WFC tablets for a dose of 1.44 g three times a day or vitacoenzyme (Vit) tablets for a dose of 0.8 g three times a day. All patients were treated for 6 months consecutively. Gastroscopy and histopathology were used to assess the histopathological changes in gastric tissues before and after treatment. 16S rRNA gene sequencing was carried out to assess the effects WFC on intestinal microbiota changes in PLGC patients. Receiver Operating Characteristics (ROC) analysis was used to assess the sensitivity and specificity of different intestinal microbiota in distinguishing between PLGC patients and healthy control group. RESULTS: Gastroscopy and histopathological results indicated that WFC could improve the pathological condition of PLGC patients, especially in the case of atrophy or intestinal metaplasia. The results of 16S rRNA gene sequencing indicated that WFC could regulate microbial diversity, microbial composition, and abundance of the intestinal microbiota of PLGC patients. Following WFC treatment, the relative abundance of Parabacteroides decreased in WFC group when compared with the Vit group. ROC analysis found that the Parabacteroides could effectively distinguish PLGC patients from healthy individuals with sensitivity of 0.79 and specificity of 0.8. CONCLUSIONS: WFC could slow down the progression of PLGC by regulating intestinal microbiota abundance. Trial registration NCT03814629. Name of registry: Randomized Clinical Trial: Weifuchun Treatment on Precancerous Lesions of Gastric Cancer. Registered 3 August 2018-Retrospectively registered, https://register.clinicaltrials.gov/ NCT03814629.

Hyperoside promotes pollen tube growth by regulating the depolymerization effect of actin-depolymerizing factor 1 on microfilaments in okra.

Mature pollen germinates rapidly on the stigma, extending its pollen tube to deliver sperm cells to the ovule for fertilization. The success of this process is an important factor that limits output. The flavonoid content increased significantly during pollen germination and pollen tube growth, which suggests it may play an important role in these processes. However, the specific mechanism of this involvement has been little researched. Our previous research found that hyperoside can prolong the flowering period of Abelmoschus esculentus (okra), but its specific mechanism is still unclear. Therefore, in this study, we focused on the effect of hyperoside in regulating the actin-depolymerizing factor (ADF), which further affects the germination and growth of pollen. We found that hyperoside can prolong the effective pollination period of okra by 2-3-fold and promote the growth of pollen tubes in the style. Then, we used Nicotiana benthamiana cells as a research system and found that hyperoside accelerates the depolymerization of intercellular microfilaments. Hyperoside can promote pollen germination and pollen tube elongation in vitro. Moreover, AeADF1 was identified out of all AeADF genes as being highly expressed in pollen tubes in response to hyperoside. In addition, hyperoside promoted AeADF1-mediated microfilament dissipation according to microfilament severing experiments in vitro. In the pollen tube, the gene expression of AeADF1 was reduced to 1/5 by oligonucleotide transfection. The decrease in the expression level of AeADF1 partially reduced the promoting effect of hyperoside on pollen germination and pollen tube growth. This research provides new research directions for flavonoids in reproductive development.

Development of Au NPs-decorated filter paper as a SERS platform for the detection of benzidine.

In this paper, a simple and cost-efficient strategy was used to construct a uniform Au NPs distribution on the surface of flexible filter paper for the detection of benzidine. Taking full advantage of the adsorption properties of filter paper, small gold nanoparticles were adsorbed onto its surface as gold seeds, and subsequently grown by electroless plating to form a highly uniform distribution of Au NPs substrates. By changing the electroless plating time, an optimal substrate was obtained. The as-prepared substrate exhibited satisfactory sensitivity with a low detection limit of 10-13 M for 4-ATP, and good reproducibility and homogeneity. Furthermore, the as-prepared substrates were successfully used for the detection of benzidine in environmental water, with a minimum detection concentration as low as 0.1 ppm and recoveries in the range of 92.4 to ∼108.5%. This study indicated that filter paper-based SERS substrates have great potential value in the detection of environmental organic pollutants.

Gene-based mediation analysis in epigenetic studies.

Mediation analysis has been a useful tool for investigating the effect of mediators that lie in the path from the independent variable to the outcome. With the increasing dimensionality of mediators such as in (epi)genomics studies, high-dimensional mediation model is needed. In this work, we focus on epigenetic studies with the goal to identify important DNA methylations that act as mediators between an exposure disease outcome. Specifically, we focus on gene-based high-dimensional mediation analysis implemented with kernel principal component analysis to capture potential nonlinear mediation effect. We first review the current high-dimensional mediation models and then propose two gene-based analytical approaches: gene-based high-dimensional mediation analysis based on linearity assumption between mediators and outcome (gHMA-L) and gene-based high-dimensional mediation analysis based on nonlinearity assumption (gHMA-NL). Since the underlying true mediation relationship is unknown in practice, we further propose an omnibus test of gene-based high-dimensional mediation analysis (gHMA-O) by combing gHMA-L and gHMA-NL. Extensive simulation studies show that gHMA-L performs better under the model linear assumption and gHMA-NL does better under the model nonlinear assumption, while gHMA-O is a more powerful and robust method by combining the two. We apply the proposed methods to two datasets to investigate genes whose methylation levels act as important mediators in the relationship: (1) between alcohol consumption and epithelial ovarian cancer risk using data from the Mayo Clinic Ovarian Cancer Case-Control Study and (2) between childhood maltreatment and comorbid post-traumatic stress disorder and depression in adulthood using data from the Gray Trauma Project.

Rivaroxaban treatment for young patients with pulmonary embolism (Review).

Pulmonary embolism (PE) is a serious, life-threatening condition that affects young populations (>18 and <50 years old, according to most literature reviews) with improved recognition of its clinical manifestations and the widespread use of sensitive imaging techniques, PE is increasingly diagnosed in younger patients. At present, there is limited understanding of the clinical features and adequate anticoagulant treatment options for this population. Most studies to date have yet to demonstrate significant differences in PE pathophysiology or symptoms between young and elderly patients. Although the overall incidence of PE is lower in young populations compared with elderly patients, important risk factors also apply for young patients. Hereditary thrombophilia is common and is a major cause of PE in younger patients. Immobilization, trauma, obesity, smoking and infection are also becoming increasingly frequent in young patients with PE. Among female patients, oral contraceptive use, pregnancy and postpartum status are predominant risk factors underlying PE. Rivaroxaban is a direct oral anticoagulant with a rapid onset of action that is associated with less drug-drug interactions compared with other therapies. Because the drug is administered at fixed doses with no requirement for routine coagulation monitoring, it is becoming an attractive option for anticoagulation treatment in young patients with PE. Therefore, the present literature review focuses on the clinical characteristics of PE and rivaroxaban therapy in younger patients.

Increasing the Assembly Efficacy of Peptidic ß-Sheets for a Highly-Sensitive HIV Detection.

Our recent publication illustrates the critical role of phenylalanine-mediated aromatic-aromatic interactions in determining the assembly of peptidic ß-sheets. However, the effect of phenylalanine number on regulating the assembly efficacy of peptidic ß-sheets remains poorly understood. We herein evaluate the assembly efficacy of ß-sheets of a series of oligopeptides which contain 0, 1, 2, or 3 phenylalanine in their molecular backbones. In our assembly system, two phenylalanine (2F) is the minimum number for driving the assembly of ß-sheets of oligopeptides. Oligopeptides with three phenylalanine (3F) show significantly increased assembly efficacy of ß-sheets compared to that with 2F. These results suggest a positive correlation between the phenylalanine number and assembly efficacy of ß-sheets. By improving the assembly efficacy of ß-sheets, we further develop a highly sensitive HIV analytical system in which the specific binding of ß-sheets with Congo Red induces enhanced fluorescence. For HIV p24 detection, the 3F-based analytical system (0.61 pg/mL) shows a significantly lower limit of detection (LOD) than the 2F-based analytical system (2.44 pg/mL), both of which are more sensitive than commercial ELISA (5 pg/mL) used in the clinic. This work not only illustrates the effect of phenylalanine number on regulating the assembly efficacy of ß-sheets but also provides a guideline for the construction of a highly sensitive analytical system of disease diagnosis.

Time Series RNA-seq in Pigeonpea Revealed the Core Genes in Metabolic Pathways under Aluminum Stress.

Pigeonpea is an important economic crop in the world and is mainly distributed in tropical and subtropical regions. In order to further expand the scope of planting, one of the problems that must be solved is the impact of soil acidity on plants in these areas. Based on our previous work, we constructed a time series RNA sequencing (RNA-seq) analysis under aluminum (Al) stress in pigeonpea. Through a comparison analysis, 11,425 genes were found to be differentially expressed among all the time points. After clustering these genes by their expression patterns, 12 clusters were generated. Many important functional pathways were identified by gene ontology (GO) analysis, such as biological regulation, localization, response to stimulus, metabolic process, detoxification, and so on. Further analysis showed that metabolic pathways played an important role in the response of Al stress. Thirteen out of the 23 selected genes related to flavonoids and phenols were downregulated in response to Al stress. In addition, we verified these key genes of flavonoid- and phenol-related metabolism pathways by qRT-PCR. Collectively, our findings not only revealed the regulation mechanism of pigeonpea under Al stress but also provided methodological support for further exploration of plant stress regulation mechanisms.

Long non­coding RNA BCYRN1 promotes glycolysis and tumor progression by regulating the miR­149/PKM2 axis in non­small­cell lung cancer.

Cancer cells use aerobic glycolysis to sustain their proliferation. Long non­coding RNA brain cytoplasmic RNA 1 (BCYRN1) has been reported to act as an oncogene in non­small­cell lung cancer (NSCLC). The present study investigated the role of BCYRN1 in NSCLC glycolysis. BCYRN1 expression was detected in NSCLC cells and tissues using reverse transcription­quantitative PCR. The effect of BCYRN1 on aerobic glycolysis was examined by measuring NSCLC cell glucose catabolism and lactate synthesis. The relationships between BCYRN1 and microRNA (miR)­149, and between miR­149 and pyruvate kinase M1/2 (PKM2) were measured using a dual­luciferase reporter assay. Cell proliferation and invasion were analyzed by the Cell Counting kit­8 assay and the Matrigel invasion assay, respectively. High BCYRN1 expression was observed in NSCLC tissues and cells compared with the corresponding controls. BCYRN1 induced glycolysis and upregulated the expression levels of PKM2 in NSCLC cells. In addition, BCYRN1 regulated miR­149 expression levels, and miR­149 inhibitor rescued the effects of si­BCYRN1 on glucose consumption and lactate production. miR­149 knockdown significantly enhanced the expression of PKM2. Furthermore, PKM2 inhibition significantly reversed the effects of miR­149 inhibitor on glucose catabolism and lactate synthesis. Furthermore, PKM2 was involved in NSCLC cell proliferation and invasion, and BCYRN1 knockdown and miR­149 overexpression inhibited both processes. The present study suggested that BCYRN1 was involved in cell glycolysis, proliferation and invasion during NSCLC via regulating miR­149 and PKM2.

Rosuvastatin protects against oxidized low­density lipoprotein­induced endothelial cell injury of atherosclerosis in vitro.

Atherosclerosis­induced cardiovascular diseases (CVDs) are accompanied by substantial morbidity and mortality. The loss and injury of endothelial cells is the primary cause of atherosclerosis. Rosuvastatin is an alternative agent used to reduce the risk of cardiovascular disease. Subsequently, the present study aimed to investigate the protective effects of rosuvastatin on oxidized­low­density lipoprotein (ox­LDL)­induced human umbilical vein endothelial cell (HUVEC) injury. The viability of ox­LDL­cultured HUVECs with or without rosuvastatin (0.01, 0.1 and 1 µmol/l) pretreatment, and pretreatment at different time points (3, 6, 12 and 24 h) was determined using an MTT assay. Morphological changes and the extent of apoptosis were detected; the anti­oxidase activity, including superoxide dismutase (SOD) and catalase (CAT), was examined, and the contents of malondiahdehyde (MDA) and nitric oxide (NO) were measured. The phosphorylation levels of endothelial nitric oxide synthase (eNOS), protein kinase B (Akt) and phosphoinositide 3 kinase (PI3K) were detected using western blot analysis. The results demonstrated that pretreatment with 0.01­1 µmol/l rosuvastatin decreased cell apoptosis caused by ox­LDL. Notably, pretreatment with 1 µmol/l rosuvastatin for >12 h increased cell viability. Additionally, DAPI staining revealed that rosuvastatin inhibited HUVEC apoptosis. Rosuvastatin treatment also resulted in increased SOD and CAT activities and decreased MDA content in ox­LDL­stimulated HUVECs. Furthermore, pretreatment with 0.01­1 µmol/l rosuvastatin significantly increased` the NO content compared with HUVECs treated with ox­LDL alone. Western blot analyses demonstrated that rosuvastatin upregulated the phosphorylation of eNOS, Akt and PI3K. These findings indicated that rosuvastatin could protect HUVECs against ox­LDL­induced injury through its anti­oxidant effect and its ability to upregulate the expression of vascular endotheliocyte­protecting factors.