Ependymal polarity defects coupled with disorganized ciliary beating drive abnormal cerebrospinal fluid flow and spine curvature in zebrafish.

Idiopathic scoliosis (IS) is the most common spinal deformity diagnosed in childhood or early adolescence, while the underlying pathogenesis of this serious condition remains largely unknown. Here, we report zebrafish ccdc57 mutants exhibiting scoliosis during late development, similar to that observed in human adolescent idiopathic scoliosis (AIS). Zebrafish ccdc57 mutants developed hydrocephalus due to cerebrospinal fluid (CSF) flow defects caused by uncoordinated cilia beating in ependymal cells. Mechanistically, Ccdc57 localizes to ciliary basal bodies and controls the planar polarity of ependymal cells through regulating the organization of microtubule networks and proper positioning of basal bodies. Interestingly, ependymal cell polarity defects were first observed in ccdc57 mutants at approximately 17 days postfertilization, the same time when scoliosis became apparent and prior to multiciliated ependymal cell maturation. We further showed that mutant spinal cord exhibited altered expression pattern of the Urotensin neuropeptides, in consistent with the curvature of the spine. Strikingly, human IS patients also displayed abnormal Urotensin signaling in paraspinal muscles. Altogether, our data suggest that ependymal polarity defects are one of the earliest sign of scoliosis in zebrafish and disclose the essential and conserved roles of Urotensin signaling during scoliosis progression.

Rassf7a promotes spinal cord regeneration and controls spindle orientation in neural progenitor cells.

Spinal cord injury (SCI) can cause long-lasting disability in mammals due to the lack of axonal regrowth together with the inability to reinitiate spinal neurogenesis at the injury site. Deciphering the mechanisms that regulate the proliferation and differentiation of neural progenitor cells is critical for understanding spinal neurogenesis after injury. Compared with mammals, zebrafish show a remarkable capability of spinal cord regeneration. Here, we show that Rassf7a, a member of the Ras-association domain family, promotes spinal cord regeneration after injury. Zebrafish larvae harboring a rassf7a mutation show spinal cord regeneration and spinal neurogenesis defects. Live imaging shows abnormal asymmetric neurogenic divisions and spindle orientation defects in mutant neural progenitor cells. In line with this, the expression of rassf7a is enriched in neural progenitor cells. Subcellular analysis shows that Rassf7a localizes to the centrosome and is essential for cell cycle progression. Our data indicate a role for Rassf7a in modulating spindle orientation and the proliferation of neural progenitor cells after spinal cord injury.

Deacylative transformations of ketones via aromatization-promoted C-C bond activation.

Carbon-hydrogen (C-H) and carbon-carbon (C-C) bonds are the main constituents of organic matter. Recent advances in C-H functionalization technology have vastly expanded our toolbox for organic synthesis1. By contrast, C-C activation methods that enable editing of the molecular skeleton remain limited2-7. Several methods have been proposed for catalytic C-C activation, particularly with ketone substrates, that are typically promoted by using either ring-strain release as a thermodynamic driving force4,6 or directing groups5,7 to control the reaction outcome. Although effective, these strategies require substrates that contain highly strained ketones or a preinstalled directing group, or are limited to more specialist substrate classes5. Here we report a general C-C activation mode driven by aromatization of a pre-aromatic intermediate formed in situ. This reaction is suitable for various ketone substrates, is catalysed by an iridium/phosphine combination and is promoted by a hydrazine reagent and 1,3-dienes. Specifically, the acyl group is removed from the ketone and transformed to a pyrazole, and the resulting alkyl fragment undergoes various transformations. These include the deacetylation of methyl ketones, carbenoid-free formal homologation of aliphatic linear ketones and deconstructive pyrazole synthesis from cyclic ketones. Given that ketones are prevalent in feedstock chemicals, natural products and pharmaceuticals, these transformations could offer strategic bond disconnections in the synthesis of complex bioactive molecules.

DeepAEG: a model for predicting cancer drug response based on data enhancement and edge-collaborative update strategies.

MOTIVATION: The prediction of cancer drug response is a challenging subject in modern personalized cancer therapy due to the uncertainty of drug efficacy and the heterogeneity of patients. It has been shown that the characteristics of the drug itself and the genomic characteristics of the patient can greatly influence the results of cancer drug response. Therefore, accurate, efficient, and comprehensive methods for drug feature extraction and genomics integration are crucial to improve the prediction accuracy. RESULTS: Accurate prediction of cancer drug response is vital for guiding the design of anticancer drugs. In this study, we propose an end-to-end deep learning model named DeepAEG which is based on a complete-graph update mode to predict IC50. Specifically, we integrate an edge update mechanism on the basis of a hybrid graph convolutional network to comprehensively learn the potential high-dimensional representation of topological structures in drugs, including atomic characteristics and chemical bond information. Additionally, we present a novel approach for enhancing simplified molecular input line entry specification data by employing sequence recombination to eliminate the defect of single sequence representation of drug molecules. Our extensive experiments show that DeepAEG outperforms other existing methods across multiple evaluation parameters in multiple test sets. Furthermore, we identify several potential anticancer agents, including bortezomib, which has proven to be an effective clinical treatment option. Our results highlight the potential value of DeepAEG in guiding the design of specific cancer treatment regimens.

Crystal Structure and Optical Properties Characterization in Quasi-0D Lead-Free Bromide Crystals (C6H14N)3Bi2Br9·H2O and (C6H14N)3Sb3Br12.

Low dimensional organic inorganic metal halide materials have shown broadband emission and large Stokes shift, making them widely used in various fields and a promising candidate material. Here, the zero-dimensional lead-free bromide single crystals (C6H14N)3Bi2Br9·H2O (1) and (C6H14N)3Sb3Br12 (2) were synthesized. They crystallized in the monoclinic crystal system with the space group of P21 and P21/n, respectively. Through ultraviolet-visible-near-infrared (UV-vis-NIR) absorption analysis, the band gaps of (C6H14N)3Bi2Br9·H2O and (C6H14N)3Sb3Br12 are found to be 2.75 and 2.83 eV, respectively. Upon photoexcitation, (C6H14N)3Bi2Br9·H2O exhibit broad-band red emission peaking at 640 nm with a large Stokes shift of 180 nm and a lifetime of 2.94 ns, and the emission spectrum of (C6H14N)3Sb3Br12 are similar to those of (C6H14N)3Bi2Br9·H2O. This exclusive red emission is ascribed to the self-trapping exciton transition caused by lattice distortion, which is confirmed through both experiments and first-principles calculations. In addition, due to the polar space group structure and the large spin-orbit coupling (SOC) associated with the heavy elements of Bi and Br of crystal 1, an obvious Rashba effect was observed. The discovery of organic inorganic metal bromide material provides a critical foundation for uncovering the connection between 0D metal halide materials' structures and properties.

Modular preparation of biphenyl triazoles via click chemistry as non-competitive hyaluronidase inhibitors.

Hyaluronidase is a promising target in drug discovery, given its overexpression in a range of physiological and pathological processes, including tumor migration, skin aging, sagging, and wrinkling, as well as inflammation and bacterial infections. In this study, to identify novel hyaluronidase inhibitors, we applied click chemistry for the modular synthesis of 370 triazoles in 96-well plates, starting with biphenyl azide. Utilizing an optimized turbidimetric screening assay in microplates, we identified Fmoc-containing triazoles 5 and 6, as well as quinoline-containing triazoles 15 and 16, as highly effective hyaluronidase inhibitors. Subsequent research indicated that these triazoles potentially interact with a novel binding site of hyaluronidase. Notably, these inhibitors displayed minimal cytotoxicity and showed promising anti-inflammatory effects in LPS-stimulated macrophages. Remarkably, compound 6 significantly reduced NO release by 74 % at a concentration of 20 µM.

Development and validation of a nomogram for predicting the prognosis in children with spinal cord injuries.

AIMS: This research aims to construct and verify an accurate nomogram for forecasting the 3-, 5-, and 7-year outcomes in pediatric patients afflicted with spinal cord injury (SCI). METHODS: Pediatric patients with SCI from multiple hospitals in China, diagnosed between Jan 2005 and Jan 2020, were incorporated into this research. Half of these patients were arbitrarily chosen for training sets, and the other half were designated for external validation sets. The Cox hazard model was employed to pinpoint potential prognosis determinants related to the American Spinal Injury Association (ASIA) and Functional Independence Assessment (FIM) index. These determinants were then employed to formulate the prognostic nomogram. Subsequently, the bootstrap technique was applied to validate the derived model internally. RESULTS: In total, 224 children with SCI were considered for the final evaluation, having a median monitoring duration of 68.0 months. The predictive nomogram showcased superior differentiation capabilities, yielding a refined C-index of 0.924 (95% CI: 0.883-0.965) for the training cohort and a C-index of 0.863 (95% CI: 0.735-0.933) for the external verification group. Additionally, when applying the aforementioned model to prognostic predictions as classified by the FIM, it demonstrated a high predictive value with a C-index of 0.908 (95% CI: 0.863-0.953). Moreover, the calibration diagrams indicated a consistent match between the projected and genuine ASIA outcomes across both sets. CONCLUSION: The crafted and verified prognostic nomogram emerges as a dependable instrument to foresee the 3-, 5-, and 7-year ASIA and FIM outcomes for children suffering from SCI.

A nomogram for predicting the hospital-acquired infections in children with spinal cord injuries: a retrospective, multicenter, observational study.

STUDY DESIGN: Retrospective cohort study. OBJECTIVES: Hospital-acquired infections (HAIs) pose a significant risk for pediatric patients with spinal cord injuries (SCIs), potentially leading to extended hospital stays and increased morbidity. This study aims to identify patients at higher risk for HAIs. SETTING: Hospitals from multiple areas in China. METHODS: This retrospective study included 220 pediatric SCI patients from Jan 2005 to Dec 2023, divided into a training set (n = 154) and a validation set (n = 66). We conducted a multivariate logistic regression analysis to identify risk factors associated with HAIs and constructed a predictive nomogram. The model's performance was assessed using receiver operating characteristic (ROC) curves, area under the ROC curve (AUC) and calibration plots, while decision curve analysis was utilized to determine clinical utility. RESULTS: The nomogram incorporated age, time from injury to the hospital, history of urinary and pulmonary infections, urobilinogen positivity, damaged segments, and admission American Spinal Injury Association (ASIA) scores. The model demonstrated excellent discrimination in the training set (AUC = 0.957) and good discrimination in the validation set (AUC = 0.919). Calibration plots indicated an acceptable fit between predicted probabilities and observed outcomes. Decision curve analysis confirmed the model's net benefit over clinical decision thresholds in both sets. CONCLUSION: We developed and validated a predictive nomogram for HAIs in pediatric SCI patients that shows promise for clinical application. The model can assist healthcare providers in identifying patients at higher risk for HAIs, potentially facilitating early interventions and improved patient care strategies.

Application of AI-assisted MRI for the identification of surgical target areas in pediatric hip and periarticular infections.

OBJECTIVE: To develop an AI-assisted MRI model to identify surgical target areas in pediatric hip and periarticular infections. METHODS: A retrospective study was conducted on the pediatric patients with hip and periarticular infections who underwent Magnetic Resonance Imaging(MRI)examinations from January 2010 to January 2023 in three hospitals in China. A total of 7970 axial Short Tau Inversion Recovery (STIR) images were selected, and the corresponding regions of osteomyelitis (label 1) and abscess (label 2) were labeled using the Labelme software. The images were randomly divided into training group, validation group, and test group at a ratio of 7:2:1. A Mask R-CNN model was constructed and optimized, and the performance of identifying label 1 and label 2 was evaluated using receiver operating characteristic (ROC) curves. Calculation of the average time it took for the model and specialists to process an image in the test group. Comparison of the accuracy of the model in the interpretation of MRI images with four orthopaedic surgeons, with statistical significance set at P < 0.05. RESULTS: A total of 275 patients were enrolled, comprising 197 males and 78 females, with an average age of 7.10 ± 3.59 years, ranging from 0.00 to 14.00 years. The area under curve (AUC), accuracy, sensitivity, specificity, precision, and F1 score for the model to identify label 1 were 0.810, 0.976, 0.995, 0.969, 0.922, and 0.957, respectively. The AUC, accuracy, sensitivity, specificity, precision, and F1 score for the model to identify label 2 were 0.890, 0.957, 0.969, 0.915, 0.976, and 0.972, respectively. The model demonstrated a significant speed advantage, taking only 0.2 s to process an image compared to average 10 s required by the specialists. The model identified osteomyelitis with an accuracy of 0.976 and abscess with an accuracy of 0.957, both statistically better than the four orthopaedic surgeons, P < 0.05. CONCLUSION: The Mask R-CNN model is reliable for identifying surgical target areas in pediatric hip and periarticular infections, offering a more convenient and rapid option. It can assist unexperienced physicians in pre-treatment assessments, reducing the risk of missed and misdiagnosis.

Analysis of risk factors for failed closed reduction in pediatric Gartland Type III supracondylar humerus fracture.

PURPOSE: Gartland Type III supracondylar humerus fractures are commonly treated using closed reduction followed by percutaneous pin fixation. However, conversion to open reduction may be necessary if closed reduction fails. This study aimed to identify risk factors associated with failed closed reduction and provide a theoretical basis for clinical decision-making in the treatment of Gartland Type III fractures. METHODS: A retrospective analysis was conducted on children with Gartland Type III supracondylar humerus fracture who underwent surgical treatment between April 2017 and June 2018. Based on whether or not the closed reduction was successful, patients were split into the open reduction group and the closed reduction group. Within the closed reduction group, subgroup analysis based on surgery duration was carried out. Data were collected from medical records and X-ray images. Univariate and multivariate regression analyses were utilized to evaluate the relationship between variables and failed closed reduction. RESULTS: The study included 36 patients in the open reduction group and 135 patients in the closed reduction group. Multivariate analysis revealed that the presence of angle (P=0.024, OR=3.199), rotation (P=0.000, OR=6.359), skin creases (P=0.013, OR=4.077), anterior-posterior displacement ratio (P=0.011, OR=4.337), fracture angle in the anteroposterior view (P=0.014, OR=0.939), and fracture distal displacement direction (P=0.002, OR=5.384) were independent risk factors for failed closed reduction. Subgroup analysis showed that fracture distal displacement direction (P=0.013), skin folds (P=0.013), lateral displacement ratio (P=0.016), and anterior-posterior displacement value (P=0.005) significantly influenced the duration of closed reduction surgery. CONCLUSION: The presence of sharp angle or rotation at the fracture ends, skin folds on the anterior elbow, minor anterior-posterior displacement of the fracture, higher medial inclination of the fracture plane, and distal fracture displacement towards the radial side are independent risk factors for failed closed reduction in pediatric Gartland Type III supracondylar humerus fracture.

The pear genomics database (PGDB): a comprehensive multi-omics research platform for Pyrus spp.

BACKGROUND: Pears are among the most important temperate fruit trees in the world, with significant research efforts increasing over the last years. However, available omics data for pear cannot be easily and quickly retrieved to enable further studies using these biological data. DESCRIPTION: Here, we present a publicly accessible multi-omics pear resource platform, the Pear Genomics Database (PGDB). We collected and collated data on genomic sequences, genome structure, functional annotation, transcription factor predictions, comparative genomics, and transcriptomics. We provide user-friendly functional modules to facilitate querying, browsing and usage of these data. The platform also includes basic and useful tools, including JBrowse, BLAST, phylogenetic tree building, and additional resources providing the possibility for bulk data download and quick usage guide services. CONCLUSIONS: The Pear Genomics Database (PGDB, http://pyrusgdb.sdau.edu.cn ) is an online data analysis and query resource that integrates comprehensive multi-omics data for pear. This database is equipped with user-friendly interactive functional modules and data visualization tools, and constitutes a convenient platform for integrated research on pear.

Phytochrome interacting factor MdPIF7 modulates anthocyanin biosynthesis and hypocotyl growth in apple.

Light affects many physiological and developmental processes of plants by regulating the expression and activity of light-responsive proteins. Among them, phytochrome interacting factors (PIFs) play pivotal roles in the regulation of anthocyanin accumulation and hypocotyl growth. However, the molecular mechanism is not well understood, especially in woody plants, such as apple (Malus × domestica). In this study, we identified a light-responsive PIF protein, MdPIF7, in apple and investigated the molecular mechanism of its regulation of anthocyanin biosynthesis and hypocotyl growth. We found that overexpression of MdPIF7 decreased anthocyanin accumulation in transgenic apple materials and promoted hypocotyl elongation in ectopically expressed Arabidopsis (Arabidopsis thaliana). Further investigation showed that MdPIF7 functioned by interacting with B-box 23 (MdBBX23), a positive regulator of anthocyanin biosynthesis in apple and hypocotyl growth inhibition in ectopically expressed Arabidopsis, and attenuating the transcriptional activation of MdBBX23 on LONG HYPOCOTYL 5 (MdHY5). In addition, MdPIF7 interacted with basic region leucine zipper 44 (MdbZIP44) and ethylene response factor 38 (MdERF38), two positive regulators of anthocyanin biosynthesis, and it negatively regulated MdbZIP44- and MdERF38-promoted anthocyanin accumulation by interfering with the interaction between MdbZIP44/MdERF38 and MdMYB1. Taken together, our results reveal that MdPIF7 regulates anthocyanin biosynthesis in apple and hypocotyl growth in ectopically expressed Arabidopsis through MdPIF7-MdBBX23-MdHY5 and MdPIF7-MdbZIP44/MdERF38-MdMYB1 modules. Our findings enrich the functional studies of PIF proteins and provide insights into the molecular mechanism of PIF-mediated anthocyanin biosynthesis and hypocotyl growth.

Functional characterization of MdERF113 in apple.

The AP2/ERF family is an important class of transcription factors involved in plant growth and various biological processes. One of the AP2/ERF transcription factors, RAP2.6L, participates in various stresses responses. However, the function of RAP2.6L is largely unknown in apples (Malus domestica). In this study, an apple gene homologous to Arabidopsis AtRAP2.6L, MdERF113, was analyzed by bioinformatic characterization, gene expression analysis and subcellular localization assessment. MdERF113 was highly expressed in the sarcocarp and was responsive to hormonal signals and abiotic stresses. MdERF113-overexpression apple calli were less sensitive to low temperature, drought, salinity, and abscisic acid than wild-type. Subcellular localization revealed that MdERF113 was a nuclear-localized transcription factor, and yeast experiments confirmed that MdERF113 has no autonomous activation activity. Overall, this study indicated that MdERF113 plays a role in regulating plant growth under abiotic conditions.

A Novel Method for Treating Distal Radius Diaphyseal Metaphyseal Junction Fracture in Children.

BACKGROUND The treatment of distal radius diaphyseal metaphyseal junction (DMJ) fracture in children is a clinical problem; several treatments are available, but none are very effective. Therefore, this study aimed to report a novel method for treating this fracture using limited open reduction and transepiphyseal intramedullary fixation with Kirschner wire. MATERIAL AND METHODS From January 2018 to December 2019, a total of 15 children (13 boys and 2 girls) with distal radius DMJ fractures with a mean age of 10 years (range: 6-14 years) were included in the study. The operation time, incision length, and X-ray radiation exposure were precisely recorded. All children were followed up regularly. At the final follow-up, clinical outcomes were evaluated according to Price criteria, and complications were recorded. RESULTS The mean operation time of the 15 children was 21.4 min, and the mean incision length was 1.9 cm. The intraoperative X-ray was performed 3.7 times on average. The mean radiographic union of fracture was 4.7 weeks, and the mean time to remove the Kirschner wire was 4.8 weeks for radial instrumentation and 4.7 months for ulnar instrumentation. According to the Price grading evaluation system, clinical outcome was excellent in 14 cases and good in 1 case. Moreover, there were no major complications related to loss of reduction, malunion, nonunion, and physeal arrest of the distal radius. CONCLUSIONS Limited open reduction and transepiphyseal intramedullary fixation with Kirschner wire are effective for treating distal radius DMJ fracture in children, which has the advantages of simple surgical procedures, short operation time, small incision, and less radiation exposure, making it an excellent choice for treating this fracture.

E2f5 is a versatile transcriptional activator required for spermatogenesis and multiciliated cell differentiation in zebrafish.

E2f5 is a member of the E2f family of transcription factors that play essential roles during many cellular processes. E2f5 was initially characterized as a transcriptional repressor in cell proliferation studies through its interaction with the Retinoblastoma (Rb) protein for inhibition of target gene transcription. However, the precise roles of E2f5 during embryonic and post-embryonic development remain incompletely investigated. Here, we report that zebrafish E2f5 plays critical roles during spermatogenesis and multiciliated cell (MCC) differentiation. Zebrafish e2f5 mutants develop exclusively as infertile males. In the mutants, spermatogenesis is arrested at the zygotene stage due to homologous recombination (HR) defects, which finally leads to germ cell apoptosis. Inhibition of cell apoptosis in e2f5;tp53 double mutants rescued ovarian development, although oocytes generated from the double mutants were still abnormal, characterized by aberrant distribution of nucleoli. Using transcriptome analysis, we identified dmc1, which encodes an essential meiotic recombination protein, as the major target gene of E2f5 during spermatogenesis. E2f5 can bind to the promoter of dmc1 to promote HR, and overexpression of dmc1 significantly increased the fertilization rate of e2f5 mutant males. Besides gametogenesis defects, e2f5 mutants failed to develop MCCs in the nose and pronephric ducts during early embryonic stages, but these cells recovered later due to redundancy with E2f4. Moreover, we demonstrate that ion transporting principal cells in the pronephric ducts, which remain intercalated with the MCCs, do not contain motile cilia in wild-type embryos, while they generate single motile cilia in the absence of E2f5 activity. In line with this, we further show that E2f5 activates the Notch pathway gene jagged2b (jag2b) to inhibit the acquisition of MCC fate as well as motile cilia differentiation by the neighboring principal cells. Taken together, our data suggest that E2f5 can function as a versatile transcriptional activator and identify novel roles of the protein in spermatogenesis as well as MCC differentiation during zebrafish development.

Comparison of Surgical Treatment Outcomes of Pediatric Medial Epicondyle Fractures With and Without Elbow Dislocation.

PURPOSE: The aim of this study was to compare surgical treatment outcomes of pediatric medial epicondyle fractures with and without elbow dislocation. METHODS: A total of 139 patients (75 boys and 64 girls; mean ± SD age, 9.6 ± 3.3 years) who received surgical treatment for medial epicondyle fractures at the Children's Hospital of Nanjing Medical University from January 2012 to December 2018 were included in our study. There were 99 cases that had a medial epicondyle fracture alone (group A) and 40 cases had a concomitant elbow dislocation (group B). Pain, ulnar nerve palsy, and stability of the elbow joint were recorded. Robert's criteria was used to assess elbow function. RESULTS: The prevalence of ulnar nerve palsy was lower in group A compared to group B, both before and after surgery. More patients underwent ulnar nerve transposition in group B than in group A. The incidence of elbow valgus instability was higher in group B than in group A. At the final follow-up, all patients had achieved good radiographic restoration of the elbow joint. Clinical outcomes in group A, according to Robert's criteria, were better than those in group B. CONCLUSIONS: Elbow dislocation was associated with poorer functional outcomes following surgical treatment of medial epicondyle fractures in children. TYPE OF STUDY/LEVEL OF EVIDENCE: Therapeutic IV.

Risk factor analysis for tibial tubercle avulsion fractures in children.

PURPOSE: Tibial tubercle avulsion fractures (TTAFs) are rare in children, particularly bilateral TTAFs. This study aimed to elucidate the associating factors of TTAF, and compare the risk factor profiles of unilateral and bilateral injuries, thus provide clinical theoretical basis for reducing the occurrence of TTAFs. METHODS: TTAF paediatric patients who were hospitalized between April 2017 and November 2022 were retrospectively analysed. Children who presented for physical examination during the same period were randomly selected, and were age- and sex-matched as controls. A subgroup analysis based on endocrine function was also performed. A risk factor analysis for bilateral TTAF was performed as well. Data were collected via medical records and a questionnaire. All variables were assessed for association with TTAF using univariate and multiple logistic regression analyses. RESULTS: A total of 64 TTAF patients and controls were respectively included. Multivariate analysis demonstrated BMI (P = 0.000，OR = 3.172), glucose (P = 0.016，OR = 20.878), and calcium (P = 0.034，OR = 0.000) as independent associating factors of TTAF. Subgroup analysis showed significant differences in oestradiol (P = 0.014), progesterone (P = 0.006) and insulin levels (P = 0.005) between the TTAF and control groups. Bilateral TTAF was found to significantly associate with a history of knee joint pain (P = 0.026). CONCLUSION: High BMI, hyperglycaemia, and low calcium levels were found as independent risk factors for TTAF in children. In addition, decreased oestradiol, elevated progesterone, and insulin resistance were identified as potential risk factors for TTAF. A history of knee pain may be suggestive of bilateral TTAF.

Clinical Prognostic Factors and Integrated Multi-Omics Studies Identify Potential Novel Therapeutic Targets for Pediatric Desmoid Tumor.

BACKGROUND: Desmoid tumor (DT), also known as desmoid-type fibromatosis (DTF) or aggressive fibromatosis (AF) is a rare mesenchymal tumor affecting both children and adults. It is non-metastasis but infiltrative, growing with a high recurrence rate to even cause serious health problems. This study investigates the biology of desmoid tumors through integrated multi-omics studies. METHODS: We systematically investigated the clinical data of 98 extra-abdominal cases in our pediatric institute and identified some critical clinical prognostic factors. Moreover, our integrated multi-omics studies (Whole Exome Sequencing, RNA sequencing, and untargeted metabolomics profiling) in the paired PDT tumor/matched normal tissues identified more novel mutations, and potential prognostic markers and therapeutic targets for PDTs. RESULTS: The top mutation genes, such as CTNNB1 (p.T41A and p.S45F) and MUC4 (p.T3775T, p.S3450S, etc.), were observed with a mutation in more than 40% of PDT patients. We also identified a panel of genes that are classed as the FDA-approved drug targets or Wnt/ß-catenin signaling pathway-related genes. The integrated analysis identified pathways and key genes/metabolites that may be important for developing potential treatment of PDTs. We also successfully established six primary PDT cell lines for future studies. CONCLUSIONS: These studies may promote the development of novel drugs and therapeutic strategies for PDTs.

Identification of immune-related key genes in the peripheral blood of ischaemic stroke patients using a weighted gene coexpression network analysis and machine learning.

BACKGROUND: The immune system plays a vital role in the pathological process of ischaemic stroke. However, the exact immune-related mechanism remains unclear. The current research aimed to identify immune-related key genes associated with ischaemic stroke. METHODS: CIBERSORT was utilized to reveal the immune cell infiltration pattern in ischaemic stroke patients. Meanwhile, a weighted gene coexpression network analysis (WGCNA) was utilized to identify meaningful modules significantly correlated with ischaemic stroke. The characteristic genes correlated with ischaemic stroke were identified by the following two machine learning methods: the support vector machine-recursive feature elimination (SVM-RFE) algorithm and least absolute shrinkage and selection operator (LASSO) logistic regression. RESULTS: The CIBERSORT results suggested that there was a decreased infiltration of naive CD4 T cells, CD8 T cells, resting mast cells and eosinophils and an increased infiltration of neutrophils, M0 macrophages and activated memory CD4 T cells in ischaemic stroke patients. Then, three significant modules (pink, brown and cyan) were identified to be significantly associated with ischaemic stroke. The gene enrichment analysis indicated that 519 genes in the above three modules were mainly involved in several inflammatory or immune-related signalling pathways and biological processes. Eight hub genes (ADM, ANXA3, CARD6, CPQ, SLC22A4, UBE2S, VIM and ZFP36) were revealed to be significantly correlated with ischaemic stroke by the LASSO logistic regression and SVM-RFE algorithm. The external validation combined with a RT‒qPCR analysis revealed that the expression levels of ADM, ANXA3, SLC22A4 and VIM were significantly increased in ischaemic stroke patients and that these key genes were positively associated with neutrophils and M0 macrophages and negatively correlated with CD8 T cells. The mean AUC value of ADM, ANXA3, SLC22A4 and VIM was 0.80, 0.87, 0.91 and 0.88 in the training set, 0.85, 0.77, 0.86 and 0.72 in the testing set and 0.87, 0.83, 0.88 and 0.91 in the validation samples, respectively. CONCLUSIONS: These results suggest that the ADM, ANXA3, SLC22A4 and VIM genes are reliable serum markers for the diagnosis of ischaemic stroke and that immune cell infiltration plays a crucial role in the occurrence and development of ischaemic stroke.

Identifying patterns of immune related cells and genes in the peripheral blood of acute myocardial infarction patients using a small cohort.

BACKGROUND: The immune system plays a vital role in the pathophysiology of acute myocardial infarction (AMI). However, the exact immune related mechanism is still unclear. This research study aimed to identify key immune-related genes involved in AMI. METHODS: CIBERSORT, a deconvolution algorithm, was used to determine the proportions of 22 subsets of immune cells in blood samples. The weighted gene co-expression network analysis (WGCNA) was used to identify key modules that are significantly associated with AMI. Then, CIBERSORT combined with WGCNA were used to identify key immune-modules. The protein-protein interaction (PPI) network was constructed and Molecular Complex Detection (MCODE) combined with cytoHubba plugins were used to identify key immune-related genes that may play an important role in the occurrence and progression of AMI. RESULTS: The CIBERSORT results suggested that there was a decrease in the infiltration of CD8 + T cells, gamma delta (γδ) T cells, and resting mast cells, along with an increase in the infiltration of neutrophils and M0 macrophages in AMI patients. Then, two modules (midnightblue and lightyellow) that were significantly correlated with AMI were identified, and the salmon module was found to be significantly associated with memory B cells. Gene enrichment analysis indicated that the 1,171 genes included in the salmon module are mainly involved in immune-related biological processes. MCODE analysis was used to identify four different MCODE complexes in the salmon module, while four hub genes (EEF1B2, RAC2, SPI1, and ITGAM) were found to be significantly correlated with AMI. The correlation analysis between the key genes and infiltrating immune cells showed that SPI1 and ITGAM were positively associated with neutrophils and M0 macrophages, while they were negatively associated with CD8 + T cells, γδ T cells, regulatory T cells (Tregs), and resting mast cells. The RT-qPCR validation results found that the expression of the ITGAM and SPI1 genes were significantly elevated in the AMI samples compared with the samples from healthy individuals, and the ROC curve analysis showed that ITGAM and SPI1 had a high diagnostic efficiency for the recognition of AMI. CONCLUSIONS: Immune cell infiltration plays a crucial role in the occurrence and development of AMI. ITGAM and SPI1 are key immune-related genes that are potential novel targets for the prevention and treatment of AMI.