Co-exposure to polystyrene nanoplastics and triclosan induces synergistic cytotoxicity in human KGN granulosa cells by promoting reactive oxygen species accumulation.

In recent years, nanoplastics (NPs) and triclosan (TCS, a pharmaceutical and personal care product) have emerged as environmental pollution issues, and their combined presence has raised widespread concern regarding potential risks to organisms. However, the combined toxicity and mechanisms of NPs and TCS remain unclear. In this study, we investigated the toxic effects of polystyrene NPs and TCS and their mechanisms on KGN cells, a human ovarian granulosa cell line. We exposed KGN cells to NPs (150 µg/mL) and TCS (15 µM) alone or together for 24 hours. Co-exposure significantly reduced cell viability. Compared with exposure to NPs or TCS alone, co-exposure increased reactive oxygen species (ROS) production. Interestingly, co-exposure to NPs and TCS produced synergistic effects. We examined the activity of superoxide dismutase (SOD) and catalase (CAT), two antioxidant enzymes; it was significantly decreased after co-exposure. We also noted an increase in the lipid oxidation product malondialdehyde (MDA) after co-exposure. Furthermore, co-exposure to NPs and TCS had a more detrimental effect on mitochondrial function than the individual treatments. Co-exposure activated the NRF2-KEAP1-HO-1 antioxidant stress pathway. Surprisingly, the expression of SESTRIN2, an antioxidant protein, was inhibited by co-exposure treatments. Co-exposure to NPs and TCS significantly increased the autophagy-related proteins LC3B-II and LC3B-Ⅰ and decreased P62. Moreover, co-exposure enhanced CASPASE-3 expression and inhibited the BCL-2/BAX ratio. In summary, our study revealed the synergistic toxic effects of NPs and TCS in vitro exposure. Our findings provide insight into the toxic mechanisms associated with co-exposure to NPs and TCS to KGN cells by inducing oxidative stress, activations of the NRF2-KEAP1-HO-1 pathway, autophagy, and apoptosis.

Effects of propofol versus sevoflurane on surgical field visibility during arthroscopic rotator cuff repair: a randomized trial.

BACKGROUND: During arthroscopic rotator cuff repair (ARCR), clear surgical field visibility (SFV) is the basis of successful surgery, but the choice of anesthesia maintenance drugs may have different effects on SFV. In this study, we aimed to compare the effects of propofol- and sevoflurane-based general anesthesia on SFV in patients undergoing ARCR. METHODS: Patients (n = 130) undergoing elective ARCR in the lateral decubitus position were randomized into either the propofol group or sevoflurane group (65 per group). The duration of surgery and increased pressure irrigation (IPI), Boezaart score, rocuronium consumption and usage of remifentanil were recorded. The time of both spontaneous respiration recovery and extubation and the incidences of postoperative nausea and vomiting and agitation were also recorded. RESULTS: The Boezaart score, duration of IPI and ratio of the duration of IPI to the duration of surgery (IPI/S ratio) were similar between the groups (P > 0.05). Rocuronium consumption, number of patients requiring remifentanil infusion and total remifentanil consumption were significantly lower in the sevoflurane group (P < 0.05). The spontaneous respiration recovery time was significantly longer in the propofol group (P < 0.05), but there were no differences in the extubation time between the groups(P > 0.05). CONCLUSIONS: Compared with propofol, sevoflurane provides equally clear SFV while improving the convenience of anesthesia maintenance in ARCR patients with interscalene plexus (ISB) combined with general anesthesia. TRIAL REGISTRATION: This single-center, prospective, RCT was retrospective registered at Chinese Clinical Trial Registry with the registration number ChiCTR2300072110 (02/06/2023).

Deciphering essential druggable genes reveals potential immune-inflammatory axis in hepatocellular carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) is a malignant tumor with a high mortality rate and poor prognosis in patients. Its pathogenesis is a complex process of multi-factors and multi-steps. However, the etiology and exact molecular mechanism are not completely clear. METHODS: Here, we constructed a specific-expressed network based on RNA sequencing data. Gene and miRNA expression profiles and clinical evidence were integrated to detect hepatocellular carcinoma survival modules. Finally, we attempted to identify potential key biomarkers and drug targets by integrating drug sensitivity analysis and immune infiltration analysis. RESULTS: A total of 42 prognostic modules for hepatocellular carcinoma were detected. The prognostic modules were significantly enriched with known cancer-related molecules and 12.93 % molecules of prognostic modules had been found were the targets of small molecule drug. In addition, we found that 38 of 42 (90.48 %) essential genes were associated with the proportions of at least one of the 7 immune cell types. CONCLUSION: We integrated clinical prognosis information, RNA sequencing data, and drug activity data to explore risk modules of hepatocellular carcinoma. Through drug sensitivity analysis and immune infiltration analysis, we assessed the value of hub genes in the modules as potential biomarkers and drug targets for hepatocellular carcinoma. The protocol provides new insight into parsing the molecular mechanism and theoretical basis of hepatocellular carcinoma.

In-depth mining of single-cell transcriptome reveals the key immune-regulated loops in age-related macular degeneration.

Introduction: Age-related macular degeneration (AMD), an ever-increasing ocular disease, has become one of the leading causes of irreversible blindness. Recent advances in single-cell genomics are improving our understanding of the molecular mechanisms of AMD. However, the pathophysiology of this multifactorial disease is complicated and still an ongoing challenge. To better understand disease pathogenesis and identify effective targets, we conducted an in-depth analysis of the single-cell transcriptome of AMD. Methods: The cell expression specificity of the gene (CESG) was selected as an index to identify the novel cell markers. A computational framework was designed to explore the cell-specific TF regulatory loops, containing the interaction of gene pattern signatures, transcription factors regulons, and differentially expressed genes. Results: Three potential novel cell markers were DNASE1L3 for endothelial cells, ABCB5 for melanocytes, and SLC39A12 for RPE cells detected. We observed a notable change in the cell abundance and crosstalk of fibroblasts cells, melanocytes, schwann cells, and T/NK cells between AMD and controls, representing a complex cellular ecosystem in disease status. Finally, we identified six cell type related and three disease-associated ternary loops and elaborated on the robust association between key immune-pathway and AMD. Discussion: In conclusion, this study facilitates the optimization of screening for AMD-related receptor ligand pathways and proposes to further improve the interpretability of disease associations from single-cell data. It illuminated that immune-related regulation paths could be used as potential diagnostic markers for AMD, and in the future, also as therapeutic targets, providing insights into AMD diagnosis and potential interventions.

Transcriptomic and Metabolomic Changes Reveal the Immunomodulatory Function of Casein Phosphopeptide-Selenium Chelate in Beagle Dogs.

Casein phosphopeptide-selenium chelate (CPP-Se) is an organic compound produced by the chelation of casein phosphopeptide with selenium. This compound showed the ability to modulate canine immune response in our previous study; but its effect on the peripheral blood transcriptome and serum metabolome was unknown. This study aims to reveal the potential mechanism behind the immunomodulatory function of CPP-Se. We have identified 341 differentially expressed genes (DEGs) in CPP-Se groups as compared to the control group which comprised 110 up-regulated and 231 down-regulated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis found that DEGs were mainly involved in immune-related signaling pathways. Moreover, the immune-related DEGs and hub genes were identified. Similarly, metabolomics identified 53 differentially expressed metabolites (DEMs) in the CPP-Se group, of which 17 were up-regulated and 36 were down-regulated. The pathways mainly enriched by DEMs were primary bile acid biosynthesis, tryptophan metabolism, and other amino acids metabolic pathways. Combined analysis of transcriptomic and metabolomic data showed that the DEGs and DEMs were commonly enriched in fatty acid biosynthesis, pyrimidine metabolism, glutathione metabolism, and glycerolipid metabolic pathways. Taken together, our findings provided a theoretical basis for further understanding of the immunomodulatory function of CPP-Se as well as a scientific reference for the future use of CPP-Se in pet foods as a dietary supplement to modulate the immunity.

The ovarian-related effects of polystyrene nanoplastics on human ovarian granulosa cells and female mice.

Nanoplastics (NPs) have recently emerged in the context of global plastic pollution. They may be more toxic than macroplastics litter and microplastic fragments due to its abundances, tiny sizes, and cellular accessibility. The female reproductive toxicity of NPs has been widely documented for aquatic animals, but their effects and underlying mechanisms remain poorly understood in mammals. This study aimed to explore the effects of NPs on female reproduction using human ovarian granulosa cells (GCs) and female mice. The accumulation of polystyrene NPs (PS-NPs) in human granulosa-like tumor cells (KGN cells) and the ovaries of female Balb/c mice were evaluated by exposure to fluorescent PS-NPs. Proliferation and apoptosis, reactive oxygen species (ROS), and Hippo signaling pathway-related factors were analyzed in KGN cells. In addition, fertility rate, litter size, ovarian weight and microstructure, follicle development, serum level of anti-Mullerian hormone, and apoptosis in ovaries were examined in female mice. Here, the PS-NPs can penetrate the KGN cells and accumulate in the ovaries. In vitro, 100 µg/ml PS-NPs inhibited proliferation, induced apoptosis, accumulated ROS, activated three key regulators of the Hippo signaling pathway (MST1, LATS1, and YAP1), and downregulated the mRNA levels of CTGF and Cyr61 in KGN cells. Furthermore, salidroside, an antioxidative compound extracted from Rhodiola rosea, alleviated the damage of PS-NPs to KGN and inhibited the activation of the Hippo signal pathway. In vivo, exposure to 1 mg/day PS-NPs resulted in decreased fertility, abnormal ovarian function, and increased ovarian apoptosis in female mice. Overall, our data suggest that PS-NPs cause granulosa cell apoptosis and affect ovarian functions, leading to reduced fertility in female mice, by inducing oxidative stress and dysregulating the Hippo pathway.

Improved Dual-Polarity Response via Pyro-phototronic Effect for Filterless Visible Light Communication.

Dual-polarity response photodetectors (PDs) take full advantage of the directivity of the photocurrent to identify optical information. The dual-polarity signal ratio, a key parameter that represents the equilibrium degree of responses to different lights, is proposed for the first time. The synchronous enhancement of dual-polarity photocurrents and the amelioration of the dual-polarity signal ratio are beneficial to the practical applications. Herein, based on the selective light absorption and energy band structure design, a self-powered CdS/PEDOT:PSS/Au heterojunction PD consisting of a p-n junction and a Schottky junction exhibits unique wavelength-dependent dual-polarity response, where the photocurrent is negative and positive in the short and long wavelength regions, respectively. More importantly, the pyro-phototronic effect inside the CdS layer significantly improves the dual-polarity photocurrents with the maximum enhancement factors of 120%, 343%, 1167%, 1577%, and 1896% at 405, 450, 532, 650, and 808 nm, respectively. Furthermore, the dual-polarity signal ratio tends to 1:1 due to different degrees of the enhancement. This work provides a novel design strategy for dual-polarity response PDs with a simple working principle and improved performance, which can supply a substitution for two traditional PDs in the filterless visible light communication (VLC) system.

RNAsmc: A integrated tool for comparing RNA secondary structure and evaluating allosteric effects.

RNA structure plays a crucial role in gene regulation, in RNA stability and the essential biological processes. RNA secondary structure (RSS) motifs are the basic building blocks for investigating the biological mechanisms of structure. Here, we present a strategy for structural motif-based dynamic alignment, namely, RNA secondary-structural motif-comparing (RNAsmc), to identify structural motifs and quantitatively evaluate their underlying molecular functions. RNAsmc also has strong robustness to sequence length, folding protocol and RNA structural profile by chemical probing. Notably, it is also applicable to quantify structural variation in special RNA editing events (SNVs or SNPs, fragment insertion or deletion, etc.). The findings indicate that RNAsmc can uncover the heterogeneity of RNA secondary structure and score for similarities among components, which provides an impetus to cluster RNA families and evaluate allosteric effects. We find that RNAsmc exhibits remarkable detection efficiency for experimentally-derived RiboSNitches. Finally, the pipeline was assembled into an R software package to serve as an automated toolkit to explore, align, and cluster RSS. It is freely available for download at https://CRAN.R-project.org/package=RNAsmc.

Novel Pectic Polysaccharides Isolated from Immature Honey Pomelo Fruit with High Immunomodulatory Activity.

A novel pectic polysaccharide (HPP-1) with high immunomodulatory activity was extracted and isolated from the immature honey pomelo fruit (Citrus grandis). Characterization of its chemical structure indicated that HPP-1 had a molecular weight of 59,024 D. In addition, HPP-1 was primarily composed of rhamnose, arabinose, fucose, mannose, and galactose at a molar ratio of 1.00:11.12:2.26:0.56:6.40. Fourier-transform infrared spectroscopy, periodic acid oxidation, and Smith degradation results showed that HPP-1 had α- and ß-glycosidic linkages and 1 → 2, 1 → 4, 1 → 6, and 1 → 3 glycosidic bonds. 13C NMR and 1H NMR analyses revealed that the main glycogroups included 1,4-D-GalA, 1,6-ß-D-Gal, 1,6-ß-D-Man, 1,3-α-L-Ara, and 1,2-α-L-Rha. Immunomodulatory bioactivity analysis using a macrophage RAW264.7 model in vitro revealed that NO, TNF-α, and IL-6 secretions were all considerably increased by HPP-1. Moreover, RT-PCR results showed that HPP-1-induced iNOS, TNF-α, and IL-6 expression was significantly increased in macrophages. HPP-1-mediated activation in macrophages was due to the stimulation of the NF-κB and MAPK signaling pathways based on western blot analyses. HPP-1 extracted from immature honey pomelo fruit has potential applications as an immunomodulatory supplement.

Effects of Casein Phosphopeptide-Selenium Complex on the Immune Functions in Beagle Dogs.

The health of pets is becoming a growing concern for the pet industry and its owners. Immunity is one of the foundational supports for health, thus developing a functional bioactive substance that can boost pets' immunity is essential. Many studies have shown that casein phosphopeptide (CPP) and selenium (Se) can individually regulate immunity in many species, but there has been no reported research on the immunomodulatory function of casein phosphopeptide-selenium complex (CPP-Se). The objective of this study was to investigate the function of CPP-Se on immunomodulation in dogs. Twenty Beagle dogs were equally divided into two groups and fed either a control snack or a test snack supplemented with 0.03% CPP-Se for 30 days. Anticoagulated blood, serum and peripheral blood lymphocytes (PBL) were collected from dogs at 0 d, 10 d, 20 d and 30 d to detect the change in the number of immune cells and the expression of cytokine-related mRNAs and proteins. PBL isolated from blood were exposed to CPP-Se in vitro to measure the proliferative responses and cytokine-related mRNAs expression. During the time the test snack was fed, the number of lymphocytes increased significantly, whereas neutrophils and monocytes remained unaltered. The expression of interleukin-4 (IL-4), interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), interferon-γ (IFN-γ), CD4 molecule (CD4) and CD8α molecule (CD8α) was up-regulated, while interleukin-1ß (IL-1ß) was down-regulated, and interleukin-10 (IL-10) declined initially and subsequently increased. ELISA detection revealed a significant increment in serum IL-4, IL-6, Immunoglobulin M (IgM) and IFN-γ, except for IgG. Furthermore, CPP-Se treatment increased the proliferation and the expression of cytokine-related mRNAs in PBL cultured in vitro. This is the first study to demonstrate that CPP-Se can improve immunity in the dog.

Simulations to Assess the Performance of Multifactor Risk Scores for Predicting Myopia Prevalence in Children and Adolescents in China.

Background: Myopia is the most common visual impairment among Chinese children and adolescents. The purpose of this study is to explore key interventions for myopia prevalence, especially for early-onset myopia and high myopia. Methods: Univariate and multivariate analyses were conducted to evaluate potential associations between risk factor exposure and myopia. LASSO was performed to prioritize the risk features, and the selected leading factors were used to establish the assembled simulation model. Finally, two forecasting models were constructed to predict the risk of myopia and high myopia. Results: Children and adolescents with persistently incorrect posture had a high risk of myopia (OR 7.205, 95% CI 5.999-8.652), which was 2.8 times higher than that in students who always maintained correct posture. In the cohort with high myopia, sleep time of less than 7 h per day (OR 9.789, 95% CI 6.865-13.958), incorrect sitting posture (OR 8.975, 95% CI 5.339-15.086), and siblings with spherical equivalent <-6.00 D (OR 8.439, 95% CI 5.420-13.142) were the top three risk factors. The AUCs of integrated simulation models for myopia and high myopia were 0.8716 and 0.8191, respectively. Conclusion: The findings illustrate that keeping incorrect posture is the leading risk factor for myopia onset, while the onset age of myopia is the primary factor affecting high myopia progression. The age between 8 and 12 years is the crucial stage for clinical intervention, especially for children with parental myopia.

Design, methodology, and baseline of whole city-million scale children and adolescents myopia survey (CAMS) in Wenzhou, China.

BACKGROUND: Myopia is the most common visual impairment in children and adolescents worldwide. This study described an economical and effective population-based screening pipeline and performed the project of a million scale children and adolescents myopia survey (CAMS), which will shed light on the further study of myopia from the level of epidemiology and precision medicine. METHODS: We developed a novel population-based screening pattern, an intelligent screening process and internet-based information transmission and analysis system to carry out the survey consisting of school children in Wenzhou, China. The examination items include unaided distance visual acuity, presenting distance visual acuity, and non-cycloplegic autorefraction. Myopia and high myopia were defined as spherical equivalent (SE) ≤ - 1.00 diopters (D) and SE ≤ - 6.00 D, respectively. Next, the reports of the vision checking were automatically sent to parents and the related departments. The CAMS project will be done two to four times annually with the support of the government. An online eyesight status information management system (OESIMS) was developed to construct comprehensive and efficient electronic vision health records (EVHRs) for myopia information inquiry, risk pre-warning, and further study. RESULTS: The CAMS completed the first-round of screening within 30 days for 99.41% of Wenzhou students from districts and counties, in June 2019. A total of 1,060,925 participants were eligible for CAMS and 1,054,251 (99.37% participation rate) were selected through data quality control, which comprised 1305 schools, and 580,609, 251,050 and 170,967 elementary, middle, and high school students. The mean age of participants was 12.21 ± 3.32 years (6-20 years), the female-to-male ratio was 0.82. The prevalence of myopia in elementary, middle, and high school students was 38.16%, 77.52%, and 84.00%, respectively, and the high myopia incidence was 0.95%, 6.90%, and 12.98%. CONCLUSIONS: The CAMS standardized myopia screening model involves automating large-scale information collection, data transmission, data analysis and early warning, thereby supporting myopia prevention and control. The entire survey reduced 90% of staff, cost, and time consumption compared with previous surveys. This will provide new insights for decision support for public health intervention.

Transcriptome-wide m6A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation.

BACKGROUND: Cryopreservation induces transcriptomic and epigenetic modifications that strongly impairs sperm quality and function, and thus decrease reproductive performance. N6-methyladenosine (m6A) RNA methylation varies in response to stress and has been implicated in multiple important biological processes, including post-transcriptional fate of mRNA, metabolism, and apoptosis. This study aimed to explore whether cryopreservation induces m6A modification of mRNAs associated with sperm energy metabolism, cryoinjuries, and freezability. RESULTS: The mRNA and protein expression of m6A modification enzymes were significantly dysregulated in sperm after cryopreservation. Furthermore, m6A peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. The mRNAs containing highly methylated m6A peaks (fts vs. fs) were significantly associated with metabolism and gene expression, while the genes with less methylated m6A peaks were primarily involved in processes regulating RNA metabolism and transcription. Furthermore, the joint analysis of DMMGs and differentially expressed genes indicated that both of these play a vital role in sperm energy metabolism and apoptosis. CONCLUSIONS: Our study is the first to reveal the dynamic m6A modification of mRNAs in boar sperm during cryopreservation. These epigenetic modifications may affect mRNA expression and are closely related to sperm motility, apoptosis, and metabolism, which will provide novel insights into understanding of the cryoinjuries or freezability of boar sperm during cryopreservation.

Comparative Analysis of piRNA Profiles Helps to Elucidate Cryoinjury Between Giant Panda and Boar Sperm During Cryopreservation.

Cryopreservation induces sperm cryoinjuries, including physiological and functional changes. However, the molecular mechanisms of sperm cryoinjury and cryoresistance are still unknown. Cryoresistance or the freeze tolerance of sperm varies across species, and boar sperm is more susceptible to cold stress. Contrary to boar sperm, giant panda sperm appears to be strongly freeze-tolerant and is capable of surviving repeated cycles of freeze-thawing. In this study, differentially expressed (DE) PIWI-interacting RNAs (piRNAs) of fresh and frozen-thawed sperm with different freeze tolerance capacity from giant panda and boar were evaluated. The results showed that 1,160 (22 downregulated and 1,138 upregulated) and 384 (110 upregulated and 274 downregulated) DE piRNAs were identified in giant panda and boar sperm, respectively. Gene ontology (GO) enrichment analysis revealed that the target DE messenger RNAs (mRNAs) of DE piRNAs were mainly enriched in biological regulation, cellular, and metabolic processes in giant panda and boar sperm. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the target DE mRNAs of DE piRNAs were only distributed in DNA replication and the cyclic adenosine monophosphate (cAMP) signaling pathway in giant panda, but the cAMP, cyclic guanosine monophosphate (cGMP), and mitogen-activated protein kinase (MAPK) signaling pathways in boar sperm were considered as part of the olfactory transduction pathway. In conclusion, we speculated that the difference in the piRNA profiles and the DE piRNAs involved in the cAMP signaling pathway in boar and giant panda may have contributed to the different freeze tolerance capacities between giant panda and boar sperm, which helps to elucidate the molecular mechanism behind sperm cryoinjury and cryoresistance.

A Comparison for Dimensionality Reduction Methods of Single-Cell RNA-seq Data.

Single-cell RNA sequencing (scRNA-seq) is a high-throughput sequencing technology performed at the level of an individual cell, which can have a potential to understand cellular heterogeneity. However, scRNA-seq data are high-dimensional, noisy, and sparse data. Dimension reduction is an important step in downstream analysis of scRNA-seq. Therefore, several dimension reduction methods have been developed. We developed a strategy to evaluate the stability, accuracy, and computing cost of 10 dimensionality reduction methods using 30 simulation datasets and five real datasets. Additionally, we investigated the sensitivity of all the methods to hyperparameter tuning and gave users appropriate suggestions. We found that t-distributed stochastic neighbor embedding (t-SNE) yielded the best overall performance with the highest accuracy and computing cost. Meanwhile, uniform manifold approximation and projection (UMAP) exhibited the highest stability, as well as moderate accuracy and the second highest computing cost. UMAP well preserves the original cohesion and separation of cell populations. In addition, it is worth noting that users need to set the hyperparameters according to the specific situation before using the dimensionality reduction methods based on non-linear model and neural network.

Contribution of structural accessibility to the cooperative relationship of TF-lncRNA in myopia.

Transcriptional regulation is associated with complicated mechanisms including multiple molecular interactions and collaborative drive. Long noncoding RNAs (lncRNAs) have highly structured characteristics and play vital roles in the regulation of transcription in organisms. However, the specific contributions of conformation feature and underlying molecular mechanisms are still unclear. In the present paper, a hypothesis regarding molecular structure effect is presented, which proposes that lncRNAs fold into a complex spatial architecture and act as a skeleton to recruit transcription factors (TF) targeted binding, and which is involved in cooperative regulation. A candidate set of TF-lncRNA coregulation was constructed, and it was found that structural accessibility affected molecular binding force. In addition, transcription factor binding site (TFBS) regions of myopia-related lncRNA transcripts were disturbed, and it was discovered that base mutations affected the occurrence of significant molecular allosteric changes in important elements and variable splicing regions, mediating the onset and development of myopia. The results originated from structureomics and interactionomics and created conditions for systematic research on the mechanisms of structure-mediated TF-lncRNA coregulation in transcriptional regulation. Finally, these findings will help further the understanding of key regulatory roles of molecular allostery in cell physiological and pathological processes.

Context-Specific Coordinately Regulatory Network Prioritize Breast Cancer Genetic Risk Factors.

Breast cancer (BC) is one of the most common tumors, leading the causes of cancer death in women. However, the pathogenesis of BC still remains unclear, and the atlas of BC-associated risk factors is far from complete. In this study, we constructed a BC-specific coordinately regulatory network (CRN) to prioritize potential BC-associated protein-coding genes (PCGs) and non-coding RNAs (ncRNAs). We integrated 813 BC sample transcriptome data from The Cancer Genome Atlas (TCGA) and eight types of regulatory relationships to construct BC-specific CRN, including 387 transcription factors (TFs), 174 microRNAs (miRNAs), 407 long non-coding RNAs (lncRNAs), and 905 PCGs. After that, the random walk with restart (RWR) method was performed on the CRN by using the known BC-associated factors as seeds, and potential BC-associated risk factors were prioritized. The leave-one-out cross-validation (LOOCV) was utilized on the BC-specific CRN and achieved an area under the curve (AUC) of 0.92. The performances of common CRN, common protein-protein interaction (PPI) network, and BC-specific PPI network were also evaluated, demonstrating that the context-specific CRN prioritizes BC risk factors. Functional analysis for the top 100-ranked risk factors in the candidate list revealed that these factors were significantly enriched in cancer-related functions and had significant semantic similarity with BC-related gene ontology (GO) terms. Differential expression analysis and survival analysis proved that the prioritized risk factors significantly associated with BC progression and prognosis. In total, we provided a computational method to predict reliable BC-associated risk factors, which would help improve the understanding of the pathology of BC and benefit disease diagnosis and prognosis.

miR-26a is Involved in Glycometabolism and Affects Boar Sperm Viability by Targeting PDHX.

miR-26a is associated with sperm metabolism and can affect sperm motility and apoptosis. However, how miR-26a affects sperm motility remains largely unknown. Our previous study indicated that the PDHX gene is predicted to be a potential target of miR-26a, which is responsible for pyruvate oxidative decarboxylation which is considered as a key step for connecting glycolysis with oxidative phosphorylation. In this study, we first reported a potential relationship between miR-26a and PDHX and their expressions in fresh, frozen-thawed, and epididymal boar sperm. Then, sperm viability and survival were determined after transfection of miR-26a. mRNA and protein expression level of PDHX in the liquid-preserved boar sperm after transfection were also determined by RT-qPCR and Western Blot (WB). Our results showed that expression level of PDHX was significantly increased during sperm transit from epididymal caput to corpus and cauda. Similarly, expression of PDHX was significantly higher (P < 0.05) in fresh sperm as compared to epididymal cauda and frozen-thawed sperm. However, the expression of miR-26a in epididymal corpus sperm was significantly higher (P < 0.05) than that of caput and cauda sperm. Furthermore, after transfection of boar sperm with miR-26a mimic and inhibitor under liquid storage, the lowest and highest sperm viability was observed in miR-26a mimic and inhibitor treatment (P < 0.05), respectively. The protein levels of PDHX, after 24 and 48 h of transfection of miR-26a mimics and inhibitor, were notably decreased and increased (P < 0.05), respectively, as compared to negative control (NC) group. In conclusion, the novel and enticing findings of our study provide a reasonable evidence that miR-26a via PDHX, a link between glycolysis and oxidative phosphorylation, could regulate the glycometabolic pathway which eventually affect boar sperm viability and survival.

Comparative Analysis of MicroRNA and mRNA Profiles of Sperm with Different Freeze Tolerance Capacities in Boar (Susscrofa) and Giant Panda (Ailuropodamelanoleuca).

Post-thawed sperm quality parameters vary across different species after cryopreservation. To date, the molecular mechanism of sperm cryoinjury, freeze-tolerance and other influential factors are largely unknown. In this study, significantly dysregulated microRNAs (miRNAs) and mRNAs in boar and giant panda sperm with different cryo-resistance capacity were evaluated. From the result of miRNA profile of fresh and frozen-thawed giant panda sperm, a total of 899 mature, novel miRNAs were identified, and 284 miRNAs were found to be significantly dysregulated (195 up-regulated and 89 down-regulated). Combined analysis of miRNA profiling of giant panda sperm and our previously published data on boar sperm, 46, 21 and 4 differentially expressed (DE) mRNAs in boar sperm were believed to be related to apoptosis, glycolysis and oxidative phosphorylation, respectively. Meanwhile, 87, 17 and 7 DE mRNAs in giant panda were associated with apoptosis, glycolysis and oxidative phosphorylation, respectively. Gene ontology (GO) analysis of the targets of DE miRNAs showed that they were mainly distributed on membrane related pathway in giant panda sperm, while cell components and cell processes were tied to the targets of DE miRNAs in boar sperm. Finally, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DE mRNAs indicated that most of these DE mRNAs were distributed in membrane signal transduction-related pathways in giant panda sperm, while those in boar sperm were mainly distributed in the cytokine-cytokine receptor interaction pathway and inflammatory related pathways. In conclusion, although the different freezing extenders and programs were used, the DE miRNAs and mRNAs involved in apoptosis, energy metabolism, olfactory transduction pathway, inflammatory response and cytokine-cytokine interactions, could be the possible molecular mechanism of sperm cryoinjury and freeze tolerance.

Inferring Novel Autophagy Regulators Based on Transcription Factors and Non-Coding RNAs Coordinated Regulatory Network.

Autophagy is a complex cellular digestion process involving multiple regulators. Compared to post-translational autophagy regulators, limited information is now available about transcriptional and post-transcriptional regulators such as transcription factors (TFs) and non-coding RNAs (ncRNAs). In this study, we proposed a computational method to infer novel autophagy-associated TFs, micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs) based on TFs and ncRNAs coordinated regulatory (TNCR) network. First, we constructed a comprehensive TNCR network, including 155 TFs, 681 miRNAs and 1332 lncRNAs. Next, we gathered the known autophagy-associated factors, including TFs, miRNAs and lncRNAs, from public data resources. Then, the random walk with restart (RWR) algorithm was conducted on the TNCR network by using the known autophagy-associated factors as seeds and novel autophagy regulators were finally prioritized. Leave-one-out cross-validation (LOOCV) produced an area under the curve (AUC) of 0.889. In addition, functional analysis of the top 100 ranked regulators, including 55 TFs, 26 miRNAs and 19 lncRNAs, demonstrated that these regulators were significantly enriched in cell death related functions and had significant semantic similarity with autophagy-related Gene Ontology (GO) terms. Finally, extensive literature surveys demonstrated the credibility of the predicted autophagy regulators. In total, we presented a computational method to infer credible autophagy regulators of transcriptional factors and non-coding RNAs, which would improve the understanding of processes of autophagy and cell death and provide potential pharmacological targets to autophagy-related diseases.