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 understand the latent profiles of kinesiophobia in kidney transplant recipients and explore the influencing factors of different profiles.Methods A cross-sectional study was conducted on 230 kidney transplant recipients subjected with convenient sampling from Department of Nephrology,the First Affiliated Hospital of Army Medical University from November 2024 to February 2025.General Information Questionnaire,Tampa Scale of Kinesiophobia-11(TSK-11),Exercise Compliance Questionnaire,Fatigue Scale-14(FS-14),Patient Health Questionnaire-9(PHQ-9)and Chinese Version of the Self-Efficacy to Manage Chronic Disease Scale(C-SEMCD)were used for investigation and latent profile analysis.Univariate analysis and logistic regression analysis were applied to explore the influencing factors of different profiles.Results Kinesiophobia in the participants was classified into 3 latent profiles:fearless movement type-low kinesiophobia group(54 cases,23.48%),cautious movement type-moderate kinesiophobia group(98 cases,42.61%),and resistant movement type-high kinesiophobia group(78 cases,33.91%).Statistical differences were observed among the 3 groups in terms of age,education level,post-operative duration,depression score,fatigue score,and self-efficacy score of chronic disease management(P<0.05).Logistic regression analysis showed that age(OR=8.82,95%CI:1.27～61.10),education level[junior high school or below(OR=0.14,95%CI:0.04～0.50);technical secondary school or senior high school(OR=0.08,95%CI:0.02～0.27)],post-operative duration[<1 year(OR=11.39,95%CI:2.53～51.30);1-5 years(OR=11.05,95%CI:2.48～49.22)],fatigue(OR=1.32,95%CI:1.10～1.59),and depression(OR=1.53,95%CI:1.19～1.98)were influencing factors for resistant movement type-high kinesiophobia in the kidney transplant recipients.Education level(technical secondary school or senior high school:OR=0.32,95%CI:0.12-0.86)and self-efficacy of chronic disease management(OR=0.95,95%CI:0.90-1.00)were influencing factors for cautious movement type-moderate kinesiophobia in the recipients.Conclusion Kinesiophobia in kidney transplant recipients can be classified into 3 latent profiles.Recipients'age,education level,post-operative duration,fatigue,and depression are influencing factors for the resistant movement type-high kinesiophobia,and education level and chronic disease management self-efficacy are important influencing factors for the cautious movement type-moderate kinesiophobia.

ObjectiveTo evaluate the effectiveness and safety of Qiaoqi Formula （翘芪组方） for mild influenza. MethodsA randomized controlled study was designed， recruiting 74 patients with mild influenza， who were randomly divided into trial group and control group. The trial group took Qiaoqi Formula orally， 40ml each time， twice a day； the control group took Lianhua Qingwen Capsules （连花清瘟胶囊） orally， 1.4 g each time， three times a day. Both groups were treated for 3 consecutive days and follow-up for 4 consecutive days after treatment. The time for fever reduction including onset of fever reduction， complete fever reduction time， fever reduction rates at 24， 48 and 72 hours， improvement of influenza symptoms， total traditional Chinese medicine （TCM） symptom score， and safety indicators in two groups after treatment were recorded. ResultsSixty-five patients were ultimately included， including 36 in the trial group and 29 in the control group. Onset time of fever reduction in the trial group was （15.49±23.47） h， the complete fever reduction time （21.37±30.06）h， and the 24 h， 48 h， 72 h， fever reduction rate was 77.14%， 88.57%， 91.42% respectively. The above indicators of the control group showed as （17.58±20.38）h， （24.30±21.87）h， 61.29%， 90.32%， 96.77% respectively， with no statistically significant differences （P＞0.05）. On the 7th day after treatment， the total score of TCM syndromes in trial group and control group decreased compared to those before treatment （P＜0.05）. There was no statistically significant difference in the cure rate， significant effective rate， effective rate， and total effective rate of TCM syndromes between groups （P＞0.05）. On the 4th day， the lymphocyte ratio of patients in the control group was higher than before treatment， while alanine aminotransferase （ALT）， aspartate aminotransferase （AST）， urea， and creatinine of both groups before and after treatment were within the normal range. The main adverse reactions in both groups were mild headache and dizziness， and no serious adverse reactions observed. ConclusionThe therapeutic effect of Qiaoqi Formula in treating mild influenza is equivalent to Lianhua Qingwen Capsules， which can shorten the fever reduction time， improve clinical symptoms， and no adverse events observed during the study.

Objective:To evaluate the immunogenicity, safety, and immune persistence of the sequential booster with the recombinant protein-based COVID-19 vaccine (CHO cell) in healthy people aged 18-84 years.Methods:An open-label, multi-center trial was conducted in October 2021. The eligible healthy individuals, aged 18-84 years who had completed primary immunization with the inactivated COVID-19 vaccine 3 to 9 months before, were recruited from Shangyu district of Shaoxing and Kaihua county of Quzhou, Zhejiang province. All participants were divided into three groups based on the differences in prime-boost intervals: Group A (3-4 months), Group B (5-6 months) and Group C (7-9 months), with 320 persons per group. All participants received the recombinant COVID-19 vaccine (CHO cell). Blood samples were collected before the vaccination and after receiving the booster at 14 days, 30 days, and 180 days for analysis of GMTs, antibody positivity rates, and seroconversion rates. All adverse events were collected within one month and serious adverse events were collected within six months. The incidences of adverse reactions were analyzed after the booster.Results:The age of 960 participants was (52.3±11.5) years old, and 47.4% were males (455). The GMTs of Groups B and C were 65.26 (54.51-78.12) and 60.97 (50.61-73.45) at 14 days after the booster, both higher than Group A′s 44.79 (36.94-54.30) ( P value<0.05). The GMTs of Groups B and C were 23.95 (20.18-28.42) and 27.98 (23.45-33.39) at 30 days after the booster, both higher than Group A′s 15.71 (13.24-18.63) ( P value <0.05). At 14 days after the booster, the antibody positivity rates in Groups A, B, and C were 91.69% (276/301), 94.38% (302/320), and 93.95% (295/314), respectively. The seroconversion rates in the three groups were 90.37% (272/301), 93.75% (300/320), and 93.31% (293/314), respectively. There was no significant difference among these rates in the three groups (all P values >0.05). At 30 days after the booster, antibody positivity rates in Groups A, B, and C were 79.60% (238/299), 87.74% (279/318), and 90.48% (285/315), respectively. The seroconversion rates in the three groups were 76.92% (230/299), 85.85% (273/318), and 88.25% (278/315), respectively. There was a significant difference among these rates in the three groups (all P values <0.001). During the sequential booster immunization, the incidence of adverse events in 960 participants was 15.31% (147/960), with rates of about 14.38% (46/320), 17.50% (56/320), and 14.06% (45/320) in Groups A, B, and C, respectively. The incidence of adverse reactions was 8.02% (77/960), with rates of about 7.50% (24/320), 6.88% (22/320), and 9.69% (31/320) in Groups A, B, and C, respectively. No serious adverse events related to the booster were reported. Conclusion:Healthy individuals aged 18-84 years, who had completed primary immunization with the inactivated COVID-19 vaccine 3 to 9 months before, have good immunogenicity and safety profiles following the sequential booster with the recombinant COVID-19 vaccine (CHO cell).

OBJECTIVE Based on fibroblast activation protein(FAP)gene promoter as the response element,to develop a new dual luciferase reporting system for the screening of drugs related to myocardial fibrosis.METHODS The promoter fragment of mouse FAP gene was synthesized in vitro and cloned into plasmid psiCHECK2 to replace HSV-TK promoter,and then a new recombinant plasmid psiCHECK2-FAP was obtained.After the recombinant plasmid psiCHECK2-FAP was digested by restriction endonucliase Hind Ⅲ,the product digested was identified by agar-gel electrophoresis and sequencing.After psiCHECK2-FAP was transient transfected into mouse cardiac fibroblasts(MCFs),and continued cultured for 24 h,and MCFs were treated with Ransforming growth factor β1(TGF-β1,5 μg·L-1)or angiotensinⅡ(Ang Ⅱ,1 μmol·L-1)or palmitic acid(PA,100 μmol·L-1)for 0,12,24,48 h,respectively,the double luciferase reporter gene assay was used to detect luciferase activity;After psiCHECK2-FAP was transient transfected into MCFs,the cells were pretreated with Dapa(1 μmol·L-1)for 1 h,and supplemented with TGF-β1(5 μg·L-1)or AngⅡ(1 μmol·L-1)or PA(100 μmol·L-1),continued treatment for 24 h,the double luciferase reporter gene assay was used to detect luciferase activity,and the expression of collagenⅠand collagen Ⅲ protein was detected with Western blotting.RESULTS The recombinant plasmid psiCHECK2-FAP was digested into two fragments by Hind Ⅲ with the expected strip size,and the sequencing results were completely consistent with the theoretical sequence;Compared with control group,the collagenⅠand collagen Ⅲ protein expression were significantly increased by TGF-β1 or Ang Ⅱ or PA in MCFs(P<0.05,P<0.01).However,compared with TGF-β1 or Ang Ⅱ or PA group,the intervention of Dapa significantly alleviated the promoter activity of FAP gene and the expression of collagenⅠand collagen Ⅲ protein(P<0.05,P<0.01);Compared with control group,luciferase activity was significantly increased by TGF-β1 or Ang Ⅱ or PA(P<0.05,P<0.01),reaching the peak at 24 h.Compared with TGF-β1 or AngⅡ or PA group,the intervention of Dapa significantly decreased luciferase activity(P<0.05,P<0.01).CONCLUSSION Based on the promoter of FAP gene as the response element,a noval dual luciferase reporter gene system was established and showed a good sensitivity to the promyocardial fibrosis factor in MCFs,which can provide strategies for the development of antimyocar-dial fibrosis drugs.

Trastuzumab has improved survival rates in human epidermal growth factor receptor 2(HER2)-positive breast cancer(BC),but drug resistance leads to treatment failure.Natural killer(NK)cell-mediated antibody-dependent cell cytotoxicity(ADCC)represents an essential antitumor immune mechanism of trastuzumab.Traditional Chinese medicine(TCM)has been used for centuries to treat diseases because of its capacity to improve immune responses.Xianling Lianxia formula(XLLXF),based on the principle of"strengthening body and eliminating toxin",exhibits a synergistic effect in the trastuzumab treatment of patients with HER2-positive BC.Notably,this synergistic effect of XLLXF was executed by enhancing NK cells and ADCC,as demonstrated through in vitro co-culture of NK cells and BC cells and in vivo inter-vention experiments.Mechanistically,the augmented impact of XLLXF on NK cells is linked to a decrease in cytokine inducible Src homology 2(SH2)containing protein(CISH)expression,which in turn activates the Janus kinase 1(JAK1)/signal transducer and activator of transcription 5(STAT5)pathway.Collectively,these findings suggested that XLLXF holds promise for enhancing NK cell function and sensitizing pa-tients with HER2-positive BC to trastuzumab.

Objective:To investigate the current implementation status of early essential newborn care (EENC) core interventions in China.Methods:Based on the Safe Neonatal Project jointly launched by the National Health Commission and United Nations International Children's Emergency Fund (UNICEF), a questionnaire survey was conducted on the implementation of eight EENC core interventions in 161 pilot hospitals. The eight interventions were skin-to-skin contact immediately after birth for at least 90 min, delayed cord clamping (until 1 min after birth or after the cord stopped pulsating), initiation of breastfeeding within the first hour after birth, exclusive breastfeeding at discharge, delayed first bath (24 h after birth), kangaroo mother care, eye care (using erythromycin ointment or other eye drops), and intramuscular injection of vitamin K 1. The survey was completed by the pilot units based on actual conditions from January 1 to December 31, 2022. Neonatal disease information was obtained from medical records from birth to discharge, and neonatal mortality rates were obtained from outpatient and inpatient records in obstetric institutions. The main indicators were the implementation rates of EENC core interventions in the eastern, central, and western regions, as well as the neonatal mortality and the incidence of common neonatal diseases in hospitals that implemented EENC or not. Chi-square test was used for data comparison. Results:A total of 156 pilot hospitals completed the survey, with 66 (42.3%) in the eastern region, 45 (28.8%) in the central region, and 45 (28.8%) in the western region. The implementation rates of skin-to-skin contact immediately after birth for at least 90 min, initiation of breastfeeding within the first hour after birth, exclusive breastfeeding at discharge, kangaroo mother care, eye care, and intramuscular injection of vitamin K 1 were higher in the western region than in the eastern and central regions [60.1% (62 491/104 012) vs. 22.4% (104 991/467 982) and 29.4% (31 419/106 812), 76.5% (78 188/102 266) vs. 41.2% (188 740/458 627) and 62.9% (67 200/106 812), 74.0% (60 062/81 141) vs. 39.7% (181 921/458 627) and 70.2% (74 947/106 812), 27.9% (1 407/5 035) vs. 9.4% (1 670/17 807) and 22.9% (2 510/10 968), 46.9% (48 442/103 313) vs. 23.0% (105 917/461 176) and 31.4% (31 731/100 966), 96.2% (51 674/53 729) vs. 56.6% (263 273/465 433) and 92.1% (98 365/106 812), χ 2 values were 58 218.40, 50 113.04, 55 466.24, 1 456.92, 24 686.13, and 72 696.66, respectively, all P<0.001]. The implementation rates of delayed cord clamping and delayed first bath were higher in the central region than in the eastern and western regions [76.9% (82 161/106 812) vs. 37.0% (163 808/443 285) and 59.3% (60 596/102 266), 75.0% (80 159/106 812) vs. 46.6% (216 935/465 433) and 68.4% (71 161/104 012), χ 2 values were 62 516.10 and 37 987.11, respectively, both P<0.001]. Seventy-six hospitals (48.7%) implemented EENC, while 80 hospitals (51.3%) did not. The neonatal mortality and the incidence of neonatal asphyxia, sepsis, pneumonia, diarrhea, eye infection, and umbilical cord infection were higher in the hospitals that did not implement EENC than in those that did [1.3‰ (478/378 519) vs. 1.0‰ (645/679 795), 1.8% (6 849/378 519) vs. 0.9% (5 895/679 795), 1.0% (3 917/378 519) vs. 0.7% (5 029/679 795), 6.2% (23 481/377 890) vs. 3.8% (25 463/679 795), 0.2% (916/378 519) vs. 0.1% (950/656 781), 0.5% (1 837/370 540) vs. 0.2% (1 403/656 949), 1.1‰ (422/375 149) vs. 0.6‰ (405/672 291), χ 2 values were 22.62, 1 766.11, 184.86, 2 832.09, 100.89, 866.59, and 64.94, respectively, all P<0.001]. Conclusions:About half of the pilot hospitals did not carry out EENC and the implementation of specific measures in hospitals carrying out EENC still needs to be improved. The implementation rate of EENC core measures is high in some regions, but there are regional differences.Neonatal health outcomes were better in hospitals with EENC than in hospitals without EENC.

Objective The study aims to find a suitable obesity index for predicting hyperuricemia (HUA)in Chinese adults. Methods The obesity indexes of 8133 subjects in China Health and Nutrition Survey in 2009 were calculated, and the basic situation of them was analyzed descriptively. χ² test and t test were used to test the differences of categorical variables and continuous variables between the HUA group and the non-HUA group. The area under the curve (AUC) and receiver operating characteristic (ROC) curves were used to analyze the predictive value of these indices for HUA. Binary logistic regression was used to analyze the relationship between obesity and HUA. Results Demographic covariates, prevalence and Body Mass Index (BMI) all have impacts on the prevalence of HUA. Obesity indexes have a good predictive effect on HUA, and the Lipid Accumulation Product (LAP) is the best (AUC=0.77 (95% CI [0.75, 0.78]). Obesity indexes all have a significant correlation with HUA. When covariates were not adjusted, LAP had the highest OR value (OR=5.87, 95% CI [5.08, 6.77]). Conclusion LAP index is significantly related to HUA, and it can be used as an emerging index to assess the prevalence of HUA in Chinese adults.

Nerve regeneration in adult mammalian spinal cord is poor because of the lack of intrinsic regeneration of neurons and extrinsic factors - the glial scar is triggered by injury and inhibits or promotes regeneration. Recent technological advances in spatial transcriptomics (ST) provide a unique opportunity to decipher most genes systematically throughout scar formation, which remains poorly understood. Here, we first constructed the tissue-wide gene expression patterns of mouse spinal cords over the course of scar formation using ST after spinal cord injury from 32 samples. Locally, we profiled gene expression gradients from the leading edge to the core of the scar areas to further understand the scar microenvironment, such as neurotransmitter disorders, activation of the pro-inflammatory response, neurotoxic saturated lipids, angiogenesis, obstructed axon extension, and extracellular structure re-organization. In addition, we described 21 cell transcriptional states during scar formation and delineated the origins, functional diversity, and possible trajectories of subpopulations of fibroblasts, glia, and immune cells. Specifically, we found some regulators in special cell types, such as Thbs1 and Col1a2 in macrophages, CD36 and Postn in fibroblasts, Plxnb2 and Nxpe3 in microglia, Clu in astrocytes, and CD74 in oligodendrocytes. Furthermore, salvianolic acid B, a blood-brain barrier permeation and CD36 inhibitor, was administered after surgery and found to remedy fibrosis. Subsequently, we described the extent of the scar boundary and profiled the bidirectional ligand-receptor interactions at the neighboring cluster boundary, contributing to maintain scar architecture during gliosis and fibrosis, and found that GPR37L1_PSAP, and GPR37_PSAP were the most significant gene-pairs among microglia, fibroblasts, and astrocytes. Last, we quantified the fraction of scar-resident cells and proposed four possible phases of scar formation: macrophage infiltration, proliferation and differentiation of scar-resident cells, scar emergence, and scar stationary. Together, these profiles delineated the spatial heterogeneity of the scar, confirmed the previous concepts about scar architecture, provided some new clues for scar formation, and served as a valuable resource for the treatment of central nervous system injury.
Mice ; Animals ; Gliosis/pathology* ; Cicatrix/pathology* ; Spinal Cord Injuries ; Astrocytes/metabolism* ; Spinal Cord/pathology* ; Fibrosis ; Mammals ; Receptors, G-Protein-Coupled

Objective:To investigate the diagnostic value of diffusion kurtosis imaging (DKI) quantitative parameters in lymph node metastasis of rectal cancer.Methods:The clinicopathological data of 79 patients with rectal cancers in Shanxi Province Cancer Hospital from November 2016 to March 2017 were retrospectively analyzed. All patients underwent routine magnetic resonance image (MRI) sequence and DKI sequence examinations before the operation. The tumor region of interest (ROI) was delineated by two radiologists. Matlab software was applied to calculate DKI quantitative parameters including apparent diffusion coefficient (ADC), mean diffusivity (MD) and mean kurtosis (MK) in two groups, respectively; and the consistency analysis was performed by using the interclass correlation coefficients (ICC). According to the results of postoperative pathology, all patients were divided into lymph node metastasis group and lymph node non-metastasis group; ADC, MD, MK of both groups were compared. The pathological diagnosis results were taken as the gold standard, receiver operating characteristic (ROC) curves of DKI quantitative parameters in the diagnosis of lymph node metastasis of rectal cancer were plotted, the area under the curve (AUC) was calculated, the optimal diagnostic threshold was determined based on the Yoden index, and the sensitivity and specificity were calculated.Results:The ICC of ADC, MD and MK calculated by two physicians were 0.934 (0.833-0.975), 0.963 (0.905-0.981) and 0.971 (0.949-0.991), respectively, showing a good inter-observer consistency. Among the 79 patients with rectal adenocarcinoma, 36 cases were in lymph node metastasis group and 43 cases were in lymph node non-metastasis group. MK value in lymph node metastasis group was higher than that in lymph node non-metastasis group, and the difference was statistically significant (0.97±0.08 vs. 0.89±0.09; t = -4.07, P < 0.001), while the ADC and MD values in lymph node metastasis group were lower than those in lymph node non-metastasis group, and the differences were not statistically significant (all P > 0.05). The AUC of MK value in the diagnosis of lymph node metastasis of rectal cancer was 0.735, and the corresponding sensitivity and specificity were 55.56% and 88.37%, respectively. Conclusions:DKI quantitative parameter MK has a certain diagnostic value in predicting lymph node metastasis of rectal cancer.