Unsupervised and supervised discovery of tissue cellular neighborhoods from cell phenotypes.

It is poorly understood how different cells in a tissue organize themselves to support tissue functions. We describe the CytoCommunity algorithm for the identification of tissue cellular neighborhoods (TCNs) based on cell phenotypes and their spatial distributions. CytoCommunity learns a mapping directly from the cell phenotype space to the TCN space using a graph neural network model without intermediate clustering of cell embeddings. By leveraging graph pooling, CytoCommunity enables de novo identification of condition-specific and predictive TCNs under the supervision of sample labels. Using several types of spatial omics data, we demonstrate that CytoCommunity can identify TCNs of variable sizes with substantial improvement over existing methods. By analyzing risk-stratified colorectal and breast cancer data, CytoCommunity revealed new granulocyte-enriched and cancer-associated fibroblast-enriched TCNs specific to high-risk tumors and altered interactions between neoplastic and immune or stromal cells within and between TCNs. CytoCommunity can perform unsupervised and supervised analyses of spatial omics maps and enable the discovery of condition-specific cell-cell communication patterns across spatial scales.

Capsaicin enhances cisplatin-induced anti-metastasis of nasopharyngeal carcinoma by inhibiting EMT and ERK signaling via SERPINB2.

Cisplatin (DDP)-based combined chemotherapy or concurrent chemoradiotherapy is the mainstay treatment for advanced-stage nasopharyngeal carcinoma (NPC), but needs improvement due to its severe side effects. Capsaicin (CAP) can enhance the anti-tumor activity of cytotoxic drugs. The aim of this study was to investigate the anti-metastasis activity of CAP in combination with DDP in NPC. Herein, CAP and DDP showed synergistic cytotoxic effects on NPC cells. CAP alone and DDP alone inhibited NPC migration and invasion in vitro and in vivo, and the combination of CAP and DDP had the greatest effect. Moreover, CAP upregulated the mRNA and protein expressions of SERPINB2. Further results showed that both SERPINB2 mRNA and protein expressions were downregulated in NPC cell lines and tissues and SERPINB2 overexpression inhibited NPC migration and invasion in vitro and in vivo, while silencing SERPINB2 acted oppositely. In addition, SERPINB2 was abnormally expressed in head and neck squamous cell carcinoma (HNSC) and other multiple cancers and downregulation of SERPINB2 predicted poor prognosis in HNSC according to the Cancer Genome Atlas (TCGA) database. We further found that SERPINB2 overexpression inhibited epithelial-mesenchymal transition (EMT) and the phosphorylated ERK (p-ERK), and the inhibitory effect was enhanced by CAP and DDP. Altogether, our results suggest that the combined inhibition of CAP and DDP on NPC metastasis may be related to the inhibition of EMT and ERK signals mediated by SERPINB2, and CAP may help to improve the efficacy of DDP in the treatment of NPC and develop new therapeutic approaches.

Insights into the multi-chromosomal mitochondrial genome structure of the xero-halophytic plant Haloxylon Ammodendron (C.A.Mey.) Bunge ex Fenzl.

BACKGROUND: Haloxylon ammodendron holds significance as an ecological plant, showcasing remarkable adaptability to desert conditions, halophytic environments, and sand fixation. With its potential for carbon sequestration, it emerges as a promising candidate for environmental sustainability. Furthermore, it serves as a valuable C4 plant model, offering insights into the genetic foundations of extreme drought tolerance. Despite the availability of plastid and nuclear genomes, the absence of a mitochondrial genome (mitogenome or mtDNA) hinders a comprehensive understanding of its its mtDNA structure, organization, and phylogenetic implications. RESULTS: In the present study, the mitochondrial genome of H. ammodendron was assembled and annotated, resulting in a multi-chromosomal configuration with two circular chromosomes. The mtDNA measured 210,149 bp in length and contained 31 protein-coding genes, 18 tRNA and three rRNA. Our analysis identified a total of 66 simple sequence repeats along with 27 tandem repeats, 312 forward repeats, and 303 palindromic repeats were found. Notably, 17 sequence fragments displayed homology between the mtDNA and chloroplast genome (cpDNA), spanning 5233 bp, accounting for 2.49% of the total mitogenome size. Additionally, we predicted 337 RNA editing sites, all of the C-to-U conversion type. Phylogenetic inference confidently placed H. ammodendron in the Amaranthacea family and its close relative, Suaeda glacum. CONCLUSIONS: H. ammodendron mtDNA showed a multi-chromosomal structure with two fully circularized molecules. This newly characterized mtDNA represents a valuable resource for gaining insights into the basis of mtDNA structure variation within Caryophyllales and the evolution of land plants, contributing to their identification, and classification.

pH and ROS Dual-Sensitive Nanocarriers for the Targeted Co-Delivery and On-Demand Sequential Release of Tofacitinib and Glucosamine for Synergistic Rheumatoid Arthritis Treatment.

Rheumatoid arthritis (RA) progression involves multiple cell types, and sequential drug action on target cells is necessary for RA treatment. Nanocarriers are widely used for RA treatment; however, the targeted delivery and on-demand release of multiple drugs remains challenging. Therefore, in this study, a dual-sensitive polymer is developed using chondroitin sulfate (CS) for the co-delivery of the cartilage repair agent, glucosamine (GlcN), and anti-inflammatory drug, tofacitinib (Tof). In the joint cavity, acidic pH facilitates the cleavage of GlcN from CS polymer to repair the cartilage damage. Subsequently, macrophage uptake via CS-CD44 binding and intracellular reactive oxygen species (ROS) mediate conversion of (methylsulfanyl)propylamine to a hydrophilic segment jointly triggered rapid Tof/GlcN release via micelle disassembly. The combined effects of Tof, GlcN, and ROS depletion promote the M1-to-M2 polarization shift to attenuate inflammation. The synergistic effects of these agents against RA are confirmed in vitro and in vivo. Overall, the dual pH/ROS-sensitive CS nanoplatform simultaneously delivers GlcN and Tof, providing a multifunctional approach for RA treatment with synergistic drug effects.

Large-scale preparation of CsPbBr3perovskite quantum dot/EVA composite adhesive film by melting for crystal silicon solar cell.

Silicon solar cell is the most mature photovoltaic conversion device, and in order to further improve the performance of the device, application of downshifting films has become a research hotspot. In this paper, CsPbBr3perovskite quantum dot/EVA composite adhesive film was prepared by melting method with CsPbBr3perovskite quantum dot film under solution processing as masterbatch and EVA particles as excipient. The effect of synthesis conditions on the luminescence properties of the composite films were thoroughly studied. The optimized CsPbBr3perovskite quantum dot/EVA composite adhesive film has excellent performance, and its light transmission reaches 85%. The CsPbBr3perovskite quantum dot/EVA composite adhesive film absolutely improves the efficiency of silicon solar cells by 1.08%, which is much higher than that of pure EVA adhesive film (0.63%). In addition, the device efficiencies have almost no change after 30 d in the air, maintaining the working stability of the device and contributing to industrial applications. This study provides a novel, industrial and low-cost synthesis route for the synthesis of CsPbBr3perovskite quantum dot/EVA composite adhesive film, which is expected to have broad application.

The Comparison of Biomolecular Changes of Epstein-Barr Virus Infection in Nasopharyngeal Epithelial Cells Using Confocal Raman Microspectroscopy.

BACKGROUND: Due to its unique fingerprinting properties, Confocal Raman microscopy (CRM) can be used to examine the biomolecular changes of viruses invading and manipulating host cells. Recently, the biochemical changes due to the invasion and infection of B lymphocyte cells, nerve cells, and epithelial cells by Epstein-Barr virus (EBV) have been reported. However, biomolecular changes in nasopharyngeal epithelial cells that result from EBV infection are still poorly understood. METHODS: In continuation of our prior investigation of EBV infection in nasopharyngeal epithelial cells, we tried to expound on biomolecular changes in EBV-infected nasopharyngeal epithelial cells using Raman microspectroscopy. EBV has two life cycles, latent infection and lytic replication. We have established latent and lytic infection models at the cellular level. In order to understand the characteristics of the two patterns of EBV infection, we used Raman spectroscopy to identify the changes in biomolecules of EBV latent cells (CNE2, CNE2-EBV) and lytic cells (NPEC1-BMI1-CN, NPEC1-BMI1-EBV). RESULTS: During latent infection, levels of glycogen, protein, and lipid molecules in the cell increased while levels of nucleic acid and collagen molecules decreased. Molecular levels of glycogen, proteins, and nucleic acids are reduced during lytic infection. We found that molecular levels of nucleic acid decreased during two different periods of infection, whereas levels of other biomolecules showed the opposite trend. Glycogen, proteins, lipids, nucleic acids, and other molecules are associated with alterations in cellular biochemical homeostasis. These changes correspond to unique Raman spectra in infected and uninfected cells associated with specific biomolecules that have been proven. These molecules are mainly responsible for cellular processes such as cell proliferation and apoptosis. The Raman signatures of these biomolecular changes depend on the different phases of viral infection. CONCLUSIONS: Therefore, by using CRM, it is possible to discern details in the progression of EBV infection in nasopharyngeal epithelial cells at the molecular level.

The effectiveness of esketamine and propofol versus dezocine and propofol sedation during gastroscopy: A randomized controlled study.

WHAT IS KNOWN AND OBJECTIVE: Propofol is widely used in painless gastroscopy. However, sedation with propofol alone might increase the risk of respiratory and circulatory complications. This randomized clinical study compares the efficacy and safety of esketamine or dezocine combined with intravenous (IV) propofol in patients undergoing gastroscopy. METHODS: A total of 102 patients were enrolled in this study and randomized into two groups. All patients were adults aged 18-64 years who underwent upper gastrointestinal gastroscopy. Patients were randomly assigned to two groups to receive esketamine (0.3 mg/kg) combined with propofol (group E) or dezocine (0.05 mg/kg) combined with propofol (group D). In both groups, the drugs were administered intravenously. The primary outcome was the dose of propofol which provided a satisfactory sedative effect, both to the endoscopist and the patients. Secondary outcomes included recovery time, side effects (such as hypotension, nausea and vomiting and agitation), and the number of adverse circulatory and respiratory events. RESULTS: Data of 83 patients were analysed in the present study. Dosage of propofol required in group E (1.44 mg/kg ± 0.67 mg/kg) was significantly lower compared with that in group D (2.12 mg/kg ± 0.37 mg/kg) (p < 0.0001). There was no statistically significant difference in recovery time, side effects, and the frequency of sedation-related adverse events between the two groups. WHAT IS NEW AND CONCLUSION: The study indicates that intravenous injection of propofol and esmketamine is more effective for gastroscopy. Use of esketamine reduces the total amount of propofol required in ASA I-II patients undergoing gastroscopy compared with single use of dezocine. It also provides more stable hemodynamics, without affecting the recovery time and side effects such as respiratory and circulatory adverse events. TRIAL REGISTRATION: The study was registered at the Chinese Clinical Trial Registry (www.chictr.org.cn; registration number: ChiCTR2100051814) on 05/10/2021.

Vertebral endplate defects are associated with bone mineral density in lumbar degenerative disc disease.

PURPOSE: Evidence has shown that lumbar vertebral endplate defects are clinically relevant and closely related to disc degeneration, but the relationship between endplate defects and bone mineral density (BMD) remains unclear. This study aimed to explore the association between endplate defects and BMD-related values in patients with lumbar degenerative disc disease (LDD). METHODS: Three hundred and twenty-five Chinese adult subjects diagnosed with LDD underwent dual energy X-ray absorptiometry. Endplate defects were classified using lumbar MRI. Groups were subdivided based on the occurrence rates of defect endplates. BMD at the lumbar vertebral and bilateral femur necks was compared between groups, and the association between endplate defects and lumbar BMD-related values was analyzed and adjusted for confounders including age, sex, serum levels of 25-hydroxy vitamin D (25(OH)D), calcium (Ca) and phosphorus (P). RESULTS: Of 325 patients and 3250 endplates, 59.72% had defects, and 188 patients were divided into the higher defect rate group (occurrence rate > 50%). The higher defect rate group was associated with older age, more common postmenopausal females, higher osteoporosis rates and lower serum Ca and P levels. Lumbar BMD was greater than that at bilateral femur necks and was not equal to osteoporosis diagnosis. Endplate defects were more prevalent in lower segments. The occurrence of endplate defects was positively associated with lumbar BMD-related values in the partial correlation analysis. The association between endplate defects and lumbar BMD varies for subtypes and segments, with a trend of positive association in rim and erosive subtypes after adjusting for confounders. CONCLUSIONS: The present study demonstrated that the occurrence of endplate defects was associated with greater lumbar BMD values in patients with LDD. This association varies for different defect subtypes and segments. The results indicated that endplate defects should be taken into consideration in osteoporosis treatment to alleviate disc degeneration.

Predictors and tactics for revision surgery in lateral lumbar interbody fusion.

BACKGROUND: The purpose of this study is to analyze the factors affecting the revision of lateral lumbar interbody fusion (LLIF), and to summarize the complications and decision-making strategies for revision surgery after LLIF. METHODS: We retrospectively reviewed 21 cases suffered from a revision surgery after LLIF in our department from May 2017 to June 2020, with a mean follow-up of 14 months (12-25months). We collected X-ray plain films, CT (computed tomography), MRI (magnetic resonance imaging) and medical records of all patients undergoing LLIF surgery, then analyzed the reasons for revision and summarized the revision strategies in different situations. We analysed correlations between revision surgery and several factors, including age, body mass index (BMI), sex, bone quality, mode of internal fixation, spinal stenosis, postperative foraminal stenosis, disc height. Then we brought the different indicators into logistic regression to find out the risk factors of revision after LLIF. All these patients were evaluated by Quality-of-life outcomes. Univariate statistical analysis was performed using T-tests, Mann-Whitney U tests and Chi square tests. RESULTS: Of the 209 cases of LLIF, 21 patients underwent postoperative revision. All revision surgeries were successfully completed. The reasons for revision included vascular injury, unsatistactory implant placement, internal spinal instrumentation failure, cage migration, indirect decompression failure and infection. Indirect decompression failure was the most common indications for revision. Clinical status was apparently improved in ODI scores and VAS scores. Revision surgery did not impact long-term effect and satisfaction. Postoperative foraminal stenosis is a positive predictor for a revision surgical procedure. CONCLUSION: Patients with postoperative foraminal stenosis are at higher risk of undergoing revision surgery after lateral lumbar interbody fusion. The correct choice of revision surgery can achieve satisfactory clinical results.

Effect of scratching and friction on human skin in vivo.

OBJECTIVE: To investigate effect of scratching and friction on human skin function and functional differences between scratching and friction. METHOD: Forty healthy volunteers were enrolled. Scratching and friction behavior was modeled by scalpel and sandpaper simulation to forearm for 80 times, respectively. Noninvasive bioengineering devices were used to measure basic skin physiological parameters and exfoliated stratum corneum collected and protein quantified. Parameters were recorded at baseline (BL) and after every 20 times interventions (20, 40, 60, and 80 times). RESULTS: Compared to BL, transepidermal water loss (TEWL) value increased significantly at both scratched and friction sites (P < .001) with a significant higher value for friction (P < .001). There was no significant difference in stratum corneum hydration (SCH) value postscratching (P > .05), while it decreased first and then increased significantly at friction site (P < .001). Roughness values (contract (CONT), variety (VAR), and scaliness (SEsc)) were raised significantly at both sites (P < .001). Net change in CONT and SEsc values of friction was higher than scratched sites (P > .05). There was no significant difference in blood flow after both scratching and friction (P > .05). Quantity of keratinocyte protein from friction sites was statistically higher than scratching after 80 times interventions (P < .05). CONCLUSION: Both noninvasive detections and protein quantification indicated more damage from friction, which may have significance for behavior guidance of patients with pruritus and implication for further investigation.

The innovation and practice of "Hand as Foot teaching method" in the teaching of motion system injury course.

BACKGROUND: In view of the teaching characteristics of the motion system injury course and the actual clinical teaching. The orthopedic teaching team of the Affiliated Hospital of Inner Mongolia Medical University took the lead in proposing the "Hand as Foot teaching method" and applied it in clinical teaching. Through this teaching method, students' understanding and memorization of key and difficult issues in motion system injuries are strengthened, teacher-student interaction is increased, and teaching effect is improved.  METHODS: The "Hand as Foot teaching method" was used to teach the key and difficult problems to the clinical undergraduate medical students of Inner Mongolia Medical University, and the teaching process was complemented by PPT + model teaching aids. RESULTS: The "Hand as Foot teaching method" is generally welcomed by medical students and has achieved good teacher-student interaction, and is effective in understanding and remembering difficult knowledge points. CONCLUSION: The "Hand as Foot teaching method" is a novel teaching method that can be applied in clinical teaching. This image teaching method improves the teaching effect, enlivens the classroom atmosphere, and enhances the interaction between teachers and students, which makes students' learning process from abstract to intuitive, from simple rote memorization to comprehension and memory, and achieves satisfactory results. It can complement each other with the traditional teaching method of pure PPT + teaching aids model, and to some extent it is worth promoting in the motion system injury courses.

Variation in spatial distance between the lumbar interlaminar window and intervertebral disc space during flexion-extension.

PURPOSE: Knowledge of interlaminar space is important for undertaking percutaneous endoscopic discectomy via an interlaminar approach (PED-IL). However, dynamic changes in the lumbar interlaminar space and the spatial relationship between the interlaminar space and intervertebral disc space (IDS) are not clear. The aim of this study was to anatomically clarify the changes in interlaminar space height (ILH) and variation in distance between the two spaces during flexion-extension of the lumbar spine in vitro. METHODS: First, we used a validated custom-made loading equipment to obtain neutral, flexion, and extension 3D models of eight lumbar specimens through 3D reconstruction software. Changes in ILH (ILH, IL-yH, IL-zH) and distances between the horizontal plane passing through the lowest edge of the lamina of the superior lumbar vertebrae and the horizontal plane passing through the lowest position of the trailing edge of the same-level IDS (DpLID) at L3/4, L4/5 and L5/S1 were examined on 3D lumbar models. RESULTS: We found that ILH was greater at L4/5 than at L3/4 and L5/S1 in the neutral position, but the difference was not significant. In the flexion position, ILH was significantly more than that in neutral and extension positions at L3/4, L4/5, and L5/S1. There were significantly more DpLID changes from neutral to flexion than that from neutral to extension at all levels (L3/4, L4/5, L5/S1). CONCLUSION: These findings demonstrated level-specific changes in ILH and DpLID during flexion-extension. The data may provide a better understanding of the spatial relationship between lumbar interlaminar space and IDS, and aid the development of segment-specific treatment for PED-IL.

FNDC3B 3'-UTR shortening escapes from microRNA-mediated gene repression and promotes nasopharyngeal carcinoma progression.

Alternative polyadenylation (APA), which induces shortening of the 3'-UTR, is emerging as an important feature in cancer development and progression. Nevertheless, the effects and mechanisms of APA-induced 3'-UTR shortening in nasopharyngeal carcinoma (NPC) remain largely unclear. Fibronectin type III domain containing 3B (FNDC3B) tended to use proximal polyadenylation site and produce shorter 3'-UTR according to our previous sequencing study. Herein, we found that FNDC3B with shorter 3'-UTR could escape from miRNA-mediated gene repression, and caused its increased expression in NPC. Knocking down of FNDC3B inhibited NPC cell proliferation, migration, invasion, and metastasis in vitro and in vivo. Overexpression of FNDC3B, especially those with shorter 3'-UTR, promoted NPC progression. Furthermore, the mechanism study revealed that FNDC3B could bind to and stabilize myosin heavy chain 9 (MYH9) to activate the Wnt/ß-catenin signaling pathway. In addition, MYH9 could reverse the inhibitory effects of FNDC3B knockdown in NPC. Altogether, our results suggested that the 3'-UTR shortening of FNDC3B mRNA mediated its overexpression in NPC and promoted NPC progression by targeting MYH9. This newly identified FNDC3B-MYH9-Wnt/ß-catenin axis could represent potential targets for individualized treatment in NPC.

Cutaneous vessel features of sensitive skin and its underlying functions.

BACKGROUND: Following the sufficient studies of the effects of skin barrier impairment and heightened neural reaction on sensitive skin (SS), many scholars have paid great attention to the roles of superficial microvasculature in SS. METHODS: By questionnaire survey, lactic acid sting test, and capsaicin test, eligible subjects were classified as normal skin, only lactic acid sting test positive (LASTP), only capsaicin test positive (CATP), and both positive (both LASTP and CATP). D-OCT was used to photograph images for evaluating the cutaneous vessels features each group. RESULTS: Totally 137 subjects completed the study. Compared with LASTN group, the vascular vessels were closer to epidermis in LASTP group. Mesh and branching vessels were more popular in SS than normal skin. High blood vessel density was more prevalent in SS, while low density frequently presented in normal skin. The vascular depth had a closely negative correlation with face flushing and SSS, and vascular shapes had a good positive correlation with face flushing and SSB. CONCLUSIONS: Our study indicates that there is a significant difference in vascular depth, shape, and density between SS and normal skin which is valuable to explore SS pathologic mechanism and to further investigate cutaneous microvasculature functions in SS.

Application of capsaicin as a potential new therapeutic drug in human cancers.

WHAT IS KNOWN AND OBJECTIVE: Capsaicin, the major active ingredient of chili pepper, may play a "dual role" in tumourigenesis, acting as a carcinogen or as a cancer preventive agent. The aim of this study was to investigate the anticancer mechanisms of capsaicin and the effects of capsaicin on traditional chemotherapeutic drugs and radiotherapy in various cancer types and the potential for clinical application in cancer therapy. METHODS: We conducted extensive literature searches through PubMed to collect representative studies of capsaicin in different cancer types. These studies investigated the anticancer molecular mechanisms of capsaicin. We then searched for the effects of capsaicin on traditional chemotherapeutic drugs or radiotherapy. Finally, in terms of clinical application, we searched for the advances of capsaicin-loaded nanoparticles in malignant tumours. RESULTS AND DISCUSSION: In most studies, capsaicin is a potential anti-tumour compound and the anti-cancer mechanisms are mainly related to anti-proliferation, induction of apoptosis and autophagy, anti-angiogenesis and anti-metastasis. It is worth noting that the biological functions of capsaicin are greatly affected by its concentration and the effective concentration in different malignant tumours varies considerably. Furthermore, capsaicin can affect the anti-cancer activity of conventional chemotherapeutic drugs or radiation therapy and more and more capsaicin-loaded nanoparticles have been developed to prolong the drug retention of capsaicin in the blood circulation and allow active targeting of specific cancer cells to enhance its accurate delivery and targeting specificity, suggesting that capsaicin may be used as a potential chemopreventive or a new auxiliary therapeutic drug for cancer. However, there is still a need for well-controlled studies to assess the safety and efficacy of capsaicin, and further preclinical and clinical trials are needed to elucidate its anti-tumour effects when combined with other standard drugs or radiotherapy. WHAT IS NEW AND CONCLUSION: Capsaicin exhibits strong anti-cancer properties in various cancer types. The combination of capsaicin with conventional chemotherapy drugs or radiotherapy can improve the sensitivity, reduce the side effects and enhance the tolerance of patients to cancer treatment. The development of capsaicin-loaded nanoparticles may provide a very promising approach to chemotherapy for malignant tumours.

Association Between Environmental Factors and Oral Epstein-Barr Virus DNA Loads: A Multicenter Cross-sectional Study in China.

Background: Oral Epstein-Barr virus (EBV) status reflects host EBV activity and potentially links to EBV-associated diseases, however, factors influencing oral EBV loads or reactivation, such as environmental exposures or host factors, are not fully understood. Methods: A 2-stage, multicenter, cross-sectional study of 6558 subjects from 21 administrative cities of southern China and 3 populations from representative geographical areas in China (referred to as the south, north, and northeastern populations) was performed. The relationships between demographical factors and environmental exposures to EBV loads were analyzed by logistic regression models. Results: Current smoking, with a dose-response effect, was found to be strongly associated with higher oral EBV loads in the pooled data, with an odds ratio of 1.58 (95% confidence interval, 1.39-1.79), as well as in each of the separate populations. The odds ratio increased to 3.06 when current smokers in southern China were compared to never smokers in northern China. Additionally, higher oral EBV loads tended to be detected in older participants, male participants, and participants in southern China. Conclusions: This study provided evidence linking the effect of host-environmental factors, particularly smoking, to oral EBV activity. It could strengthen our understanding of the possible causal roles of EBV-related diseases, which may help to prevent or mitigate EBV-associated diseases.

LUADpp: an effective prediction model on prognosis of lung adenocarcinomas based on somatic mutational features.

BACKGROUND: Lung adenocarcinoma is the most common type of lung cancers. Whole-genome sequencing studies disclosed the genomic landscape of lung adenocarcinomas. however, it remains unclear if the genetic alternations could guide prognosis prediction. Effective genetic markers and their based prediction models are also at a lack for prognosis evaluation. METHODS: We obtained the somatic mutation data and clinical data for 371 lung adenocarcinoma cases from The Cancer Genome Atlas. The cases were classified into two prognostic groups (3-year survival), and a comparison was performed between the groups for the somatic mutation frequencies of genes, followed by development of computational models to discrete the different prognosis. RESULTS: Genes were found with higher mutation rates in good (≥ 3-year survival) than in poor (< 3-year survival) prognosis group of lung adenocarcinoma patients. Genes participating in cell-cell adhesion and motility were significantly enriched in the top gene list with mutation rate difference between the good and poor prognosis group. Support Vector Machine models with the gene somatic mutation features could well predict prognosis, and the performance improved as feature size increased. An 85-gene model reached an average cross-validated accuracy of 81% and an Area Under the Curve (AUC) of 0.896 for the Receiver Operating Characteristic (ROC) curves. The model also exhibited good inter-stage prognosis prediction performance, with an average AUC of 0.846 for the ROC curves. CONCLUSION: The prognosis of lung adenocarcinomas is related with somatic gene mutations. The genetic markers could be used for prognosis prediction and furthermore provide guidance for personal medicine.

Increased 27-hydroxycholesterol production during luteolysis may mediate the progressive decline in progesterone secretion.

STUDY QUESTION: Does 27-hydroxycholesterol (27OH) actively facilitate the progression of luteolysis? SUMMARY ANSWER: There is increased mRNA expression of the enzyme that produces 27OH during luteolysis in vivo in rhesus macaques and sheep, and 27OH reduces progesterone secretion from human luteinized granulosa cells. WHAT IS KNOWN ALREADY: There is an increase in mRNA expression of liver x receptor (LXR) and a decrease in sterol regulatory element binding protein 2 (SREBP2) target genes during spontaneous luteolysis in primates, which could result in reduced cholesterol availability for steroidogenesis. Concentrations of 27OH are also increased in primate corpora lutea (CL) during luteolysis, and 27OH is a dual LXR agonist and SREBP2 inhibitor. STUDY DESIGN SIZE, DURATION: This was an in vitro study using primary human luteinized granulosa cells in a control versus treatment(s) design. Analyses of CL from sheep undergoing induced or spontaneous luteolysis were also performed, along with database mining of microarray data from rhesus macaque CL. PARTICIPANTS/MATERIALS, SETTING, METHODS: Primary luteinizing granulosa cells were obtained from 37 women aged 24-44 who were undergoing oocyte donation or IVF for male factor or idiopathic infertility, and cells were further luteinized in vitro using human chorionic gonadotropin. Three approaches to test the effect of 27OH produced via CYP27A1 (cytochrome p450, family 27, subfamily A, polypeptide 1) on luteinized granulosa cells were used: (i) direct 27OH supplementation, (ii) induction of endogenous CYP27A1 activity via pharmacologic inhibition of steroidogenesis, and (iii) siRNA-mediated knockdown to directly inhibit CYP27A1 as well as cholesterol transport into the mitochondria via the steroidogenic acute regulatory protein (STAR). Endpoints included: progesterone (P4) secretion into culture media determined by enzyme immunoassay, cholesterol efflux and uptake assays using fluorescent lipid analogs, and mRNA expression determined via semi-quantitative real-time PCR (QPCR). An additional experiment involved QPCR analysis of 40 CL collected from ewes undergoing induced or spontaneous luteolysis, as well as database mining of microarray data generated from 16 rhesus macaque CL collected during spontaneous luteolysis and 13 macaque CL collected during a luteinizing hormone ablation and replacement protocol. MAIN RESULTS AND THE ROLE OF CHANCE: The mRNA expression of CYP27A1 was significantly increased during luteolysis in rhesus macaques and sheep in vivo, and CYP27A1 transcription was suppressed by luteinizing hormone and hCG. There was a significant decrease in hCG-stimulated P4 secretion from human luteinized granulosa cells caused by 27OH treatment, and a significant increase in basal and hCG-stimulated P4 synthesis when endogenous 27OH production was inhibited via CYP27A1 knockdown, indicating that 27OH inhibits steroidogenesis. Pharmacologic inhibition of steroidogenesis by aminoglutethimide significantly induced LXR and inhibited SREBP2 target gene mRNA expression, indicating that increased oxysterol production occurs when steroidogenesis is suppressed. Inhibiting cholesterol delivery into the mitochondria via knockdown of STAR resulted in reduced SREBP2 target gene mRNA expression, indicating that STAR function is necessary to maintain SREBP2-mediated transcription. The effects of 27OH treatment on markers of LXR and SREBP2 activity were moderate, and knockdown of CYP27A1 did not prevent aminoglutethimide-induced changes in LXR and SREBP2 target gene mRNA expression. These observations indicate that 27OH inhibits P4 secretion partially via mechanisms separate from its role as an LXR agonist and SREBP2 inhibitor, and also demonstrate that other oxysterols are involved in modulating LXR and SREBP2-mediated transcription when steroidogenesis is suppressed. LARGE SCALE DATA: None. LIMITATIONS REASONS FOR CAUTION: Luteinized granulosa cells may differ from luteal cells, and the effect on luteal function in vivo was not directly tested. The mechanisms that cause the initial rise in CYP27A1 mRNA expression during luteolysis are also not clear. WIDER IMPLICATIONS OF THE FINDINGS: The factors causing luteolysis in primates have not yet been determined. This study provides functional evidence of a novel mechanism via increased 27OH synthesis during luteolysis, which subsequently represses progesterone secretion. Increased 27OH may also facilitate the progression of luteolysis in domestic animal species. STUDY FUNDING AND COMPETING INTEREST(S): The authors have nothing to disclose. Support was provided by the Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD) of the National Institutes of Health (NIH), award number R00HD067678 to R.L.B.

Fluorescent copper nanoclusters as a nano-dye for DNA methyltransferase activity analysis and inhibitor screening.

Fluorescent copper nanoslusters (CuNCs) as a new class of fluorophores have attracted more and more attention due to their ease of synthesis, excellent optical properties, and low cost. In this study, a novel label-free fluorescent method was developed for the detection of DNA methyltransferases based on template length-dependent of dsDNA-CuNCs. In the absence of DNA adenine methylation methyltransferase (Dam MTase), the dsDNA containing the methylation-responsive sequence could effectively template the formation of fluorescent CuNCs with bright fluorescence. When the dsDNA substrate is methylated by Dam MTase, the methylation-sensitive restriction endonuclease Dpn I cleaves the methylated dsDNA and produces shorter dsDNA product, which fails to template fluorescent CuNCs. So, the Dam MTase activity could be identified by the changes of CuNCs' fluorescence. Based on this method, a linear range of 0.5-10 U/mL was achieved with high sensitivity and selectivity. Moreover, we also demonstrate the proposed method can be applied to evaluation and screening of inhibitors for Dam MTase.

Differential genome-wide profiling of alternative polyadenylation sites in nasopharyngeal carcinoma by high-throughput sequencing.

BACKGROUND: Alternative polyadenylation (APA) is a widespread phenomenon in the posttranscriptional regulation of gene expression that generates mRNAs with alternative 3'-untranslated regions (3'UTRs). APA contributes to the pathogenesis of various diseases, including cancer. However, the potential role of APA in the development of nasopharyngeal carcinoma (NPC) remains largely unknown. METHODS: A strategy of sequencing APA sites (SAPAS) based on second-generation sequencing technology was carried out to explore the global patterns of APA sites and identify genes with tandem 3'UTRs in samples from 6 NPC and 6 normal nasopharyngeal epithelial tissue (NNET). Sequencing results were then validated using quantitative RT-PCR in a larger cohort of 16 NPC and 16 NNET samples. RESULTS: The sequencing data showed that the use of tandem APA sites was prevalent in NPC, and numerous genes with APA-switching events were discovered. In total, we identified 195 genes with significant differences in the tandem 3'UTR length between NPC and NNET; including 119 genes switching to distal poly (A) sites and 76 genes switching to proximal poly (A) sites. Several gene ontology (GO) terms were enriched in the list of genes with switched APA sites, including regulation of cell migration, macromolecule catabolic process, protein catabolic process, proteolysis, small conjugating protein ligase activity, and ubiquitin-protein ligase activity. CONCLUSIONS: APA site-switching events are prevalent in NPC. APA-mediated regulation of gene expression may play an important role in the development of NPC, and more detailed studies targeting genes with APA-switching events may contribute to the development of novel future therapeutic strategies for NPC.