Gene regulation relies on the precise binding of transcription factors (TFs) at regulatory elements, but simultaneously detecting hundreds of TFs on chromatin is challenging. We developed cFOOT-seq, a cytosine deaminase-based TF footprinting assay, for high-resolution, quantitative genome-wide assessment of TF binding in both open and closed chromatin regions, even with small cell numbers. By utilizing the dsDNA deaminase SsdAtox, cFOOT-seq converts accessible cytosines to uracil while preserving genomic integrity, making it compatible with techniques like ATAC-seq for sensitive and cost-effective detection of TF occupancy at the single-molecule and single-cell level. Our approach enables the delineation of TF footprints, quantification of occupancy, and examination of chromatin influences on TF binding. Notably, cFOOT-seq, combined with FootTrack analysis, enables de novo prediction of TF binding sites and tracking of TF occupancy dynamics. We demonstrate its application in capturing cell type-specific TFs, analyzing TF dynamics during reprogramming, and revealing TF dependencies on chromatin remodelers. Overall, cFOOT-seq represents a robust approach for investigating the genome-wide dynamics of TF occupancy and elucidating the cis-regulatory architecture underlying gene regulation.
Transcription Factors/genetics* ; Humans ; Chromatin/genetics* ; Animals ; Binding Sites ; Mice ; DNA Footprinting/methods*

Objective To compare the efficacy of mediastinoscope-assisted transhiatal esophagectomy (MATHE) and functional minimally invasive esophagectomy (FMIE) for esophageal cancer. Methods Patients who underwent minimally invasive esophagectomy at Jining No.1 Hospital from March 2018 to September 2022 were retrospectively included. The patients were divided into a MATHE group and a FMIE group according to the procedures. The patients were matched via propensity score matching (PSM) with a ratio of 1 : 1 and a caliper value of 0.2. The clinical data of the patients were compared after the matching. Results A total of 73 patients were include in the study, including 54 males and 19 females, with an average age of (65.12±7.87) years. There were 37 patients in the MATHE group and 36 patients in the FMIE group. Thirty pairs were successfully matched. Compared with the FMIE group, MATHE group had shorter operation time (P=0.022), lower postoperative 24 h pain score (P=0.031), and less drainage on postoperative 1-3 days (P<0.001). FMIE group had more lymph node dissection (P<0.001), lower incidence of postoperative hoarseness (P=0.038), lower white blood cell and neutrophil counts on postoperative 1 day (P<0.001). There was no statistically significant difference in the bleeding volume, R0 resection, hospital mortality, postoperative hospital stay, anastomotic leak, chylothorax, or pulmonary infection between the two groups (P>0.05). Conclusion Compared with the FMIE, MATHE has shorter operation time, less postoperative pain and drainage, but removes less lymph nodes, which is deficient in oncology. For some special patients such as those with early cancer or extensive pleural adhesions, MATHE may be a suitable surgical method.

BACKGROUND:Intervertebral disc degeneration is one of the most common underlying factors causing low back pain.Recent studies have shown that melatonin has a positive effect on alleviating intervertebral disc degeneration.However,the underlying mechanism of melatonin remains to be elucidated. OBJECTIVE:To explore the biological effect and potential mechanism of melatonin in inhibiting hydrogen peroxide(H2O2)-induced injury of human nucleus pulposus cells. METHODS:Human nucleus pulposus cells insolated from degenerative intervertebral disc were cultured in vitro.Cell proliferation and the optimal intervention concentration of melatonin and H2O2 were detected by cell counting kit-8.The Human nucleus pulposus cells treated with H2O2 were used as a model group;the cells treated with H2O2 and intervened with melatonin were used as a melatonin group;the cells cultured in simple medium were used as a control group.The reactive oxygen species levels were detected by 2',7'-dichlorofluorescin diacetate(DCFH-DA),the expression levels of BAX and Caspase3 were detected by immunofluorescence,and the mRNA expression levels of BAX,BCL-2,Casepase3,PI3K and AKT were detected using the real-time fluorescent quantitative reverse transcription PCR. RESULTS AND CONCLUSION:The results of cell counting kit-8 experiment showed that the optimal intervention concentration of H2O2 was 400 μmol/L and the optimal intervention concentration of melatonin was 5 μmol/L.The reactive oxygen species level in the melatonin group was significantly lower than that in the model group.The average fluorescence intensity of BAX and Caspase3 in the melatonin group was significantly lower than that in the model group.The mRNA expressions of BAX and Caspase3 in the melatonin group were lower than those in the model group,while the mRNA expression of Bcl-2 was increased.In addition,the mRNA expressions of PI3K and AKT were also higher in the melatonin group compared with the model group.To conclude,melatonin may protect human nucleus pulposus cells from H2O2-induced oxidative damage through the PI3K/AKT signaling pathway.

Objective:To propose a model that could improve image quality of cone-beam computed tomography(CBCT),which based on region-discriminative generative adversarial networks(GAN),in radiotherapy for cervical cancer,so as to meet the requirements of self-adaptive radiotherapy for image quality.Methods:We employed a region-discriminative strategy and a generative adversarial networks idea to construct a model of improving CBCT image quality that could focus on local details of the images of radiotherapy for cervical cancer,which discriminator could improve the quality of generating local details of images.This model of image quality was applied to CBCT images of radiotherapy for cervical cancer.And then,the effects of processing image were evaluated through quantitative indicators and visualization.Results:Both texture clarity and contrast were significantly enhanced after CBCT image quality was improved.The signal to noise ratio of peak value of images was increased by 47.2%,and the indicator of similarity of structure was enhanced to>0.838.Compared with other model,both visualization and indicators can appear better efficiency of model.Compared with Unet network and CycleGAN network,the similarities of structure were respectively increased by 11.88% and 19.54%,and the signal to noise ratios were respectively increased by 19.75% and 25.99%.Conclusion:The GAN bases on region-discrimination can significantly improve the quality of generating integral and detailed CBCT image of radiotherapy for cervical cancer,which can provide new technical pathway for image quality of CBCT with low dose,and can play an important role for improving safety and effectiveness of radiotherapy.It has importantly clinical value for formulating and executing radiotherapy plan.

Objective:To develop a machine learning algorithm based on habitat imaging(HI),which can be used in the grading of gliomas by using multimodal magnetic resonance imaging(MRI),so as to construct the model of support vector machine(SVM)and the visualized heterogeneous regions of gliomas.Methods:A total of 335 glioma patients were collected from the 2019 brain tumor segmentation(BraTS)challenge competition of World Health Organization(WHO),which included 259 cases with high-grade gliomas(HGG)and 76 cases with low-grade gliomas(LGG).Subregions were divided based on HI technology.The PyRadiomics open-source package was used to extract the image features of region of interest(ROI),and to screen the features that stronger correlated with the high and low-grade gliomas.An SVM model was used to classify and predict the screened feature data.The heterogeneity of gliomas in images was analyzed through visualized characterization.The efficacy of glioma grading was assessed by using the area under curve(AUC)of the receiver operating characteristic(ROC)curve.Results:The AUC of test set exceeded 90%.The average accuracy of the performance indicators of test set was(92.74±2.88)%,and the average sensitivity was(93.90±2.10)%,and the average specificity was(90.36±4.59)%,and the average F1 score was(95.24±0.66)%when the tumors were divided into six habitat regions.The SVM model could showed important sub-regions in glioma grading in three-dimensional space.Conclusion:The study method based on HI has significant advantages in glioma grading,which can effectively realize visualized heterogeneity of tumor and construct model of the heterogeneity of tumor.

Objective:In this study,we explored the application prospects and mechanisms of action of co-inhibiting fibroblast growth factor receptor 2(FGFR2)and Src homology region 2-containing protein tyrosine phosphatase 2(SHP2)in gastric cancer with the TACC2-FGFR2 fu-sion gene.Methods:We established human gastric cancer cell lines overexpressing the TACC2-FGFR2 fusion gene(MKN45TACC2-FGFR2 and NUGC4TACC2-FGFR2 cells)or a control lentiviral virus(MKN45NC and NUGC4NC cells).The cells were treated with the FGFR2 inhibitor AZD4547,the SHP2 inhibitor SHP099,or a combination of both.The proliferation and migration of tumor cells were detected using cell counting Kit-8(CCK-8)and scratch assays.After treating MKN45TACC2-FGFR2 and NUGC4TACC2-FGFR2 cells with different formulations for 1 or 48 h,Western blot was used to detect variations in the levels of FGFR2,SHP2,and proteins downstream of the RAS/ERK and PI3K/AKT signaling pathways.Results:Com-pared to monotherapy,the combination of AZD4547 and SHP099 significantly inhibited the proliferation and migration of MKN45TACC2-FGFFR2 and NUGC4TACC2-FGFFR2 cells.After 1 h of treatment,the combination therapy inhibited the RAS/ERK and PI3K/AKT pathways in MKN45TACC2-FGFFR2 cells to a greater extent than the AZD4547 monotherapy.Forty-eight hours of AZD4547 monotherapy resulted in feedback activation of p-FGFR and p-SHP2,but failed to inhibit the RAS/ERK pathway.However,combination therapy continuously suppressed upstream FGFR2 and SHP2 signaling,as well as downstream RAS/ERK and PI3K/AKT pathways.Conclusions:Co-inhibiting FGFR2 and SHP2 further inhibit gastric cancer with the TACC2-FGFR2 fusion gene by suppressing the RAS/ERK and PI3K/AKT pathways.These findings provide a new treatment mode for patients with gastric cancer with the TACC2-FGFR2 fusion gene.

Objective:To investigate the incidence and prothrombotic risk factors of postoperative venous thromboembolism(VTE) in Cushing′s disease and to further develop an assessment model to identify those at high risk of postoperative VTE events.Methods:A retrospective study was performed in 82 patients who were admitted to Huashan Hospital, Fudan University during January 2019 and January 2020 and diagnosed with Cushing′s disease. These patients underwent the evaluation about their clinical, hormonal, and coagulation parameters, as well as ultrasonography and pulmonary angio-CT when necessary. The least absolute shrinkage and selection operator(LASSO) regression analysis was used to screen independent risk factors, and a nomogram model for postsurgical VTE risk assessment in Cushing′s disease was initially established, and Bootstrap method was used for internal verification. Finally, the predictive model was evaluated for calibration and clinical applicability in the study cohort.Results:Nineteen patients(23.17%) developed VTE events, with 14 cases occurring after endoscopic transsphenoidal surgery. Compared to patients without VTE, those in the VTE group were older( P<0.001), had longer postoperative bed rest, higher rates of current infection, higher HbA 1C levels, and more severe glucose tolerance impairment(all P<0.05). Through LASSO regression analysis, two independent risk factors for postoperative VTE were identified: Age and current infection. Then a VTE risk assessment nomogram model was established to predict the patients at high risk of VTE. In the nomogram model for VTE risk assessment, the area under the receiver operating characteristic curve was 0.868(95% CI 0.787-0.949), with the calibration curve closely aligning with the ideal diagonal line and the clinical decision curve exceeding the two extreme curves. Conclusions:Advanced perioperative assessment needs to be taken to screen those with high VTE risks in patients diagnosed with Cushing′s disease. Additionally, during the perioperative period, patients with Cushing′s disease should undergo mandatory physical activity or prophylactic anticoagulant therapy.

Purpose/Significance To apply the 5G ward round robot platform in primary hospitals,so as to effectively improve the treatment capability and management service level of patients with critical and severe diseases.Method/Process Based on technologies such as 5 G,internet of things(IoT)and robotics,the researchers build and deploy a 5 G ward round robot platform and collaborate with domestic experts to provide mobile ward round,remote consultation,intensive care,health education and other services for patients.Re-sult/Conclusion Real time sharing of patient clinical data and efficient collaboration in the diagnosis and treatment process can be a-chieved,multi-mode,accurate and standardized remote ward round and treatment guidance can be carried out according to patients'conditions.

Dura mater, rich in vasculature and immune cells, is the outermost layer of the central nervous system, and thus acts as the first barrier to protect brain. Meningeal lymphatic vessels and immune cells are main components of dural immunity, which respond to a variety of central nervous system diseases. Meanwhile, compared with brain parenchyma, dura mater communicates more with peripheral tissues and is more susceptible to medical interventions. Therefore, dura mater is a promising target to prevent, diagnose and treat intracranial diseases. Here dural immunity is clarified based on meningeal lymphatic vessels and dural immune cells, and current researches inquiring the role of dural immunity in infectious and immune diseases of central nervous system are summarized.

Anaplastic lymphoma kinase (ALK) is the most common fusion gene involved in non-small cell lung cancer (NSCLC), and remarkable response has been achieved with the use of ALK tyrosine kinase inhibitors (ALK-TKIs). However, the clinical efficacy is highly variable. Pre-existing intratumoral heterogeneity (ITH) has been proven to contribute to the poor treatment response and the resistance to targeted therapies. In this work, we investigated whether the variant allele frequencies (VAFs) of ALK fusions can help assess ITH and predict targeted therapy efficacy. Through the application of next-generation sequencing (NGS), 7.2% (326/4548) of patients were detected to be ALK positive. On the basis of the adjusted VAF (adjVAF, VAF normalization for tumor purity) of four different threshold values (adjVAF < 50%, 40%, 30%, or 20%), the association of ALK subclonality with crizotinib efficacy was assessed. Nonetheless, no statistical association was observed between median progression-free survival (PFS) and ALK subclonality assessed by adjVAF, and a poor correlation of adjVAF with PFS was found among the 85 patients who received first-line crizotinib. Results suggest that the ALK VAF determined by hybrid capture-based NGS is probably unreliable for ITH assessment and targeted therapy efficacy prediction in NSCLC.
Humans ; Carcinoma, Non-Small-Cell Lung/pathology* ; Anaplastic Lymphoma Kinase/therapeutic use* ; Crizotinib/therapeutic use* ; Lung Neoplasms/pathology* ; Protein Kinase Inhibitors/pharmacology* ; Gene Frequency