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 explore the value of dual-layer spectral detector CT in differentiating the diagnosis of lung cancer and inflammatory nodules.Methods:A total of 92 patients undergoing enhanced chest scan from March 2019 to September 2020 at Renji Hospital, School of Medicine, Shanghai Jiaotong University, were retrospectively enrolled in the study. The conventional CT parameters, spectral CT parameters were measured and the nodules′ morphological characteristics were analyzed. Later the factors with statistical significance were identified as independent variables in a logistic regression model to establish models for predicting malignant nodules. ROC curve was used to assess the diagnostic performance for the conventional CT model, spectral CT parameters and combined model, respectively. Differences in the area under the ROC curve (AUC) were analyzed by the DeLong test.Results:Lobulated sign (42 and 8, respectively, χ2=10.779, P=0.001), short burr sign (41 and 7, respectively, χ2=11.911, P=0.001), pleural indentation sign (45 and 9 respectively, χ2=11.705, P=0.001), vascular convergence sign (35 and 8, respectively, χ2=5.337, P=0.021) and the venous phase iodine concentrations (IC) value [(2.1±0.5) mg/ml, (2.3±0.5) mg/ml, t=-2.464, P=0.016], normalized iodine concentrations (NIC) value (0.40±0.06, 0.45±0.08, t=-6.943, P<0.001), and Z-effective (Z eff) values (8.38±0.21, 8.49±0.19, t=-2.122, P=0.037) were significantly different between the lung cancer group and the inflammatory group, while other CT signs and CT indicators were not significantly different between the lung cancer group and the inflammatory group ( P>0.05). The conventional CT model was established with lobulated sign, short burr sign, pleural indentation sign, vascular convergence sign, and the AUC for differential diagnosis of lung cancer and inflammatory nodules was 0.827. The spectral CT parameter model was established with venous phase IC, venous phase NIC, and venous phase Z eff value, and the AUC for differential diagnosis of lung cancer and inflammatory nodules was 0.899. The conventional CT model combined spectral CT parameter model was established with the significant factors in the univariate analysis, and the AUC for differential diagnosis of lung cancer and inflammatory nodules was 0.925. The AUC of the combined model showed no significant difference from that of the spectral CT parameter model ( Z=1.794, P=0.073). However, AUC of the combined model was significantly higher than that of evaluation based on conventional CT alone ( Z=2.156, P=0.031). Conclusion:Spectral CT parameters combined with conventional CT signs can improve the differential diagnosis efficiency between lung cancer and inflammatory nodules.

Objective To investigate the effect of FBXW7 on the expression and localization of HSF1 in colorectal cancer cells. Methods The expression levels of HSF1 and pHSF1^Ser326 protein in FBXW7 deletion (KO) and wild-type (WT) FBXW7-expressing counterpart colorectal cancer cells were detected by Western blot. The nucleoprotein expression and localization of pHSF1^Ser326 in heat-shocked or recovery stage cells were observed by Western blot and immunofluorescence method. Results The HSF1 expression level in DLD1 cells transfected with FBXW7α was decreased significantly (P < 0.01). The expression levels of HSF1 and pHSF1^Ser326 protein in FBXW7 KO cells were higher than those in WT cells (all P < 0.05). HSF1 and pHSF1^Ser326 in FBXW7 KO cells were mainly expressed in nucleus and weakly expressed in cytoplasm. After warm stimulation, the expression of HSF1 and pHSF1^Ser326 in WT cells recovered to the unstimulated level, while the expression of HSF1 and pHSF1^Ser326 in FBXW7 KO cells were higher in the nucleus (all P < 0.01). Conclusion Loss of FBXW7 could affect the nuclear HSF1 recovery after warm stimulation. It may be associated with FBXW7 deletion inhibiting the degradation of nuclear HSF1.

MLN4924 can inhibit the proliferation,invasion and metastasis of tumor by inducing tumor cells apoptosis,senescence and autophagy,which can inhibit tumor angiogenesis and enhance the sensitivity of radiotherapy and chemotherapy.Therefore,MLN4924 plays a good anti-tumor effect.