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 investigate the effect of reactive oxygen species(ROS)/silent information regulator 1(SIRT1)on hyperoxia-induced mitochondrial injury in BEAS-2B cells.Methods The experiment was divided into three parts.In the first part,cells were divided into H0,H6,H12,H24,and H48 groups.In the second part,cells were divided into control group,H48 group,H48 hyperoxia+SIRT1 inhibitor group(H48+EX 527 group),and H48 hyperoxia+SIRT1 agonist group(H48+SRT1720 group).In the third part,cells were divided into control group,48-hour hyperoxia+N-acetylcysteine group(H48+NAC group),and H48 group.The ROS kit was used to measure the level of ROS.Western blot and immunofluorescent staining were used to measure the expression levels of SIRT1 and mitochondria-related proteins.Transmission electron microscopy was used to observe the morphology of mitochondria.Results Compared with the H0 group,the H6,H12,H24,and H48 groups had a significantly increased fluorescence intensity of ROS(P<0.05),the H48 group had significant reductions in the expression levels of SIRT1 protein and mitochondria-related proteins(P<0.05),and the H24 and H48 groups had a significant reduction in the fluorescence intensity of mitochondria-related proteins(P<0.05).Compared with the H48 group,the H48+SRT1720 group had significant increases in the expression levels of mitochondria-related proteins and the mitochondrial aspect ratio(P<0.05),and the H48+EX 527 group had a significant reduction in the mitochondrial area(P<0.05).Compared with the H48 group,the H48+NAC group had a significantly decreased fluorescence intensity of ROS(P<0.05)and significantly increased levels of SIRT1 protein,mitochondria-related proteins,mitochondrial area,and mitochondrial aspect ratio(P<0.05).Conclusions The ROS/SIRT1 axis is involved in hyperoxia-induced mitochondrial injury in BEAS-2B cells.

In recent decades,the advent of coronaviruses has engendered multiple large-scale infectious outbreaks,leading to profound human casualties and posing a significant menace to global public health.At the crux of the coronavirus lifecycle,the assembly and release phases emerge as pivotal processes,necessitating meticulous investigation into the underlying mechanisms.This paper systematically expounds upon the intricate assembly and packaging mechanisms intrinsic to coronaviruses,scrutinizes the diverse release pathways employed by these viruses,and delves into the discourse surrounding targeted antiviral drugs.The comprehensive insights encapsulated in this exposition serve as valuable reference points for formulating effective strategies in the prevention and treatment of coronavirus infections.

BACKGROUND:The lower cervical vertebral pedicle is the main stress site of the posterior column of the spine,which is of great significance for the maintenance of the stability of the human center of gravity and the reduction of shock.At present,there are few reports on the characteristics of the internal bone trabeculae,and the characteristics of the joint site of the vertebral pedicle with the articular process and the vertebral body.It is urgent to understand the fine anatomical structure of the vertebral pedicle and the relationship and function of each part. OBJECTIVE:To observe the microanatomical morphology of the vertebral pedicle by Micro-CT scanning of cervical vertebra specimens,and to measure and analyze the microstructure and morphometric parameters of the bone trabecula in the cervical pedicle under normal conditions to evaluate the safety performance of the cervical spine. METHODS:Micro-CT scanning was performed on 31 sets of cervical vertebrae C3-C7.By checking and reconstructing the areas of interest in the bone trabecular within the vertebral pedicle,the morphological characteristics and distribution direction of the bone trabecular within the cervical pedicle were observed,and the bone microstructure parameters were detected,and the differences in the bone microstructure of the C3-C7 vertebral pedicle were analyzed and compared. RESULTS AND CONCLUSION:(1)The Micro-CT images showed that the honeycomb bone trabeculae of the pedicle of the lower cervical spine presented a complex network of microstructures.The trabeculae near the cortical bone were lamellar and relatively compact,extending forward toward the vertebral body and backward toward the articular process lamina.Abatoid bone trabeculae extended into the medullary cavity and transformed into a network structure,and then into rod-shaped bone trabeculae.The rod-shaped bone trabeculae were sparsely distributed in the medullary cavity.(2)Statistical results of morphological parameters of bone trabeculae showed that bone volume fraction values in C4 and C5 were higher than that in C7(P＜0.05).The bone surface/bone volume value in C7 was higher than that in C3,C4 and C6(P＜0.05).The bone surface density of bone trabeculae in C7 was higher than that in C3,C4,C5 and C6(P＜0.05).Trabecular thickness in C7 was higher than that in C3,C4 and C5(P＜0.05).Bone surface/bone volume and bone surface density of the left pedicle bone trabecular were greater than those on the right side(P＜0.05).(3)The microstructural changes of C3-C7 were summarized,in which the load capacity and stress of the C7 pedicle were poor,and the risk of injury was high in this area.

Objective:To compare the effects of unilateral thoracic paravertebal block with lidocaine on hemodynamic and the level of consciousness during double lumen endotracheal intubation.Methods:From June to october 2021,a total of 40 patients American Society of Anesthesiologists(ASA)physical status Ⅰ-Ⅱ,aged 19-65 years,scheduled for elective thoracic sugeries in Peking University Interna-tional Hospital block with under general anesthesia requiring orotracheal intubation were recruited and di-vided into two groups:The double-lumen endobronchial intubation(group C)and double-lumen endo-bronchial intubation after thoracic paravertebal block with lidocaine(group P).After an intravenous an-esthetic induction,the orotracheal double-lumen intubation was performed using a Macintosh direct laryn-goscopy,respectively.Invasive blood pressure(BP)and heart rate(HR)were recorded before and after anesthetic induction,immediately after intubation and 5 min after intubation with 1-minute interval and the intubation time was also noted.Rate-pressure product(RPP)were calculated.Results:After anes-thetic induction,BP and RPP in the two groups decreased significantly compared with their preinduction values.As comparison with their postinduction values,the orotracheal intubation in the two groups caused significant increases in BP,HR and RPP.Diastolic blood pressure(DBP)and mean arterial pressure(MAP)increased significantly and lasted for 1-minute in group C compared with the baseline values.Systolic blood pressure(SBP)was not significant change and DBP increased significantly immediately af-ter intubation in group P.HR of both groups after intubation were significantly higher than their baseline values and lasted for 4 min in group C,HR increased significantly immediately after intubation in group P.SBP,DBP,MAP,HR and RPP after intubation in group P were significantly lower than those of group C during the observation period.The value of BIS was similar between the two groups.Compared with group C,the incidence of SBP greater than 30％and RPP greater than 22 000 was significantly lower in group P in the observation period,and no patient in group P developed RPP greater than 22 000.At the end of the incidence of SBP less than 30％of the basal value and HR less than 30％of the baseline,no severe bradycardia occurred in both groups.Conclusion:During double-lumen endobronchial intubation,unilateral thoracic paravertebal block with lidocaine can provide less hemodynamic response and level of conscionsness.

Tumor aerobic glycolysis is one of the main features of tumor metabolic reprogramming. This abnormal glycolytic metabolism provides bioenergy and biomaterials for tumor growth and proliferation. It is worth noting that aerobic glycolysis will not only provide biological materials and energy for tumor cells, but also help tumor cells to escape immune surveillance through regulation of immune microenvironment, thereby resisting tumor immunotherapy and promoting tumor progression. Based on the pathogenesis of renal cell carcinoma, this paper describes the characteristics of aerobic glycolysis, the effect of glycolytic metabolism on the immune microenvironment of renal cell carcinoma, the effect of glycolysis inhibitors on the immune microenvironment of renal cell carcinoma, and the prospect of glycolysis inhibitors combined with immune checkpoint inhibitors in the treatment of renal cell carcinoma.
Humans ; Carcinoma, Renal Cell/therapy* ; Immunotherapy ; Glycolysis ; Metabolic Reprogramming ; Kidney Neoplasms/therapy* ; Tumor Microenvironment

Aim To investigate the possible mecha-nism of UNC5B-AS1 in regulating the malignant biolog-ical behavior of osteosarcoma cells.Methods RT-qPCR was used to detect the expression of UNC5B-AS1 in osteosarcoma cells MG63,osteosarcoma cells U2OS and osteoblast cells hFOB1.19.After overexpression and knockdown of UNC5B-AS1 in osteosarcoma cells,the proliferation,migration and apoptosis of osteosarco-ma cells were detected by CCK-8 assay,Transwell as-say and flow cytometry,respectively.At the same time,RT-qPCR and Western blot were used to detect the effects of UNC5B-AS1 overexpression and knock-down on the mRNA and protein expression of key fac-tors in the NF-κB signaling pathway.Results Com-pared with normal osteoblast hFOB1.19,UNC5B-AS1 expression was differentially increased in osteosarcoma cells MG63 and U2OS.Overexpression of UNC5B-AS1 significantly promoted the proliferation of osteosarcoma cells and significantly increased the migration ability of osteosarcoma cells,while the apoptosis rate markedly decreased,and NF-κB signaling pathway-related mR-NA and protein expressions apparently increased.Knockdown of UNC5B-AS1 evidently inhibited the pro-liferation of osteosarcoma cells and significantly re-duced the migration ability of osteosarcoma cells,while the apoptosis rate markedly increased,the NF-κB sig-naling pathway related mRNA and protein expression significantly reduced.Conclusions lncRNA UNC5B-AS1 is highly expressed in osteosarcoma cells,which may affect the malignant biological behavior of osteo-sarcoma cells by activating the NF-κB signaling path-way.

Humans ; SARS-CoV-2 ; COVID-19 ; Antibodies ; Antibodies, Viral/therapeutic use* ; Antibodies, Neutralizing/therapeutic use*

Objective:To explore the values of ultrasound, pathology combined with inflammatory indicators in predicting high nodal burden (HNB) in patients with early breast cancer and to construct a nomogram to provide reference for individualized diagnosis and treatment.Methods:The ultrasonographic, pathological features and preoperative inflammatory indicators of 378 female patients diagnosed with early breast cancer confirmed by pathology in the South Hospital of the Sixth People′s Hospital Affiliated to Shanghai Jiaotong University from January 2014 to July 2022 were retrospectively analyzed. They were randomly divided into training set ( n=302) and test set ( n=76) in a ratio of 8∶2, and the baseline data of the two groups were compared. The optimal cutoff values of neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR) and lymphocyte to monocyte ratio (LMR) were obtained by ROC curve. In the training set, with axillary high lymph node load (≥3 metastatic lymph nodes) as the dependent variable, independent influencing factors of HNB were identified by univariate and multivariate Logistic regression analyses, and the nomogram was established. The test set data were used to verify the model. The discrimination, calibration and clinical applicability of the model were assessed by the area under the ROC curve (AUC), C-index, the calibration curve, Brier score and the decision curve analysis, respectively. Results:There were no significant differences in all variables between the training set and the test set (all P>0.05). ROC curve analysis results showed that AUCs of NLR, PLR and LMR were 0.578, 0.547 and 0.516, respectively, and the optimal cut-off values were 2.184, 150 and 3.042, respectively. Univariate Logistic regression analysis showed that age, pathological type, histological grade, Ki-67, lymphovascular invasion, NLR, PLR, ultrasonic characteristics (maximum diameter of primary tumor, shape, long/short diameter of lymph node, cortical thickness, cortical and medullary boundary, lymph node hilum, lymph node blood flow pattern) were correlated with HNB of early breast cancer (all P<0.05). Multivariate Logistic regression analysis showed that ultrasonic characteristics (maximum diameter of primary tumor >2 cm, effacement of lymph node hilum, non-lymphatic portal blood flow), lymphovascular invasion, Ki-67>14% and NLR>2.184 were independent risk factors for HNB in early breast cancer ( OR=7.258, 8.784, 6.120, 8.031, 3.394 and 3.767, respectively; all P<0.05) and were used to construct the nomogram model. The AUC of the training set was 0.914 (95% CI=0.878-0.949), C-index was 0.914; The AUC of the test set was 0.871 (95% CI=0.769-0.973), C-index was 0.871, indicating good discrimination. Calibration curve and Brier score were 0.090, indicating high calibration degree of the model. The clinical decision curve indicated good clinical benefit. Conclusions:The nomogram based on ultrasonic characteristics (maximum diameter of primary tumor, lymph node hilum, lymph node blood flow pattern), lymphovascular invasion, Ki-67 and NLR can effectively predict the risk of HNB in patients with early breast cancer, and provide a reference for precision diagnosis and treatment to avoid excessive or insufficient treatment.

Objective:In the era of precision medicine, there is an urgent need for a preclinical evaluation method with a high cost-benefit ratio to improve the effectiveness and value of clinical trials.Methods:Taking clinical needs and scientific research purposes as the starting point, the platform focused on four aspects of project management, information retrieval, quality control, and practical application, and introduced in detail the management practice of building a patient-derived xenograft model platform system.Results:With the support of the institutional system, quality control system, and information system, the patient-derived xenograft model platform was formed with standardization as the core. With the assistance of this platform and scientific research management, as of December 2021, there are 48 animal models of patient-derived xenograft in the database. In total of 6 SCI scientific and technological articles were published using these animal models, with a total impact factor of 36.77 (the highest single article was 7.333). In total of 6 direct industrial projects, 6 clinical trial-related projects, and 4 NSFC projects were approved with a total research fund of 1.5 million yuan.Conclusions:Continuous construction and improvement of the existing platform will help promote the development of basic research translation and clinical research in the field of oncology, and accelerate the development of new oncological diagnosis and treatment models, thereby benefiting more patients.