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: Observational studies have found associations between inflammatory bowel disease (IBD) and the risk of dementia, including Alzheimer's dementia (AD) and vascular dementia (VD); however, these findings are inconsistent. It remains unclear whether these associations are causal. METHODS: We conducted a meta-analysis by systematically searching for observational studies on the association between IBD and dementia. Mendelian randomization (MR) analysis based on summary genome-wide association studies (GWASs) was performed. Genetic correlation and Bayesian co-localization analyses were used to provide robust genetic evidence. RESULTS: Ten observational studies involving 80,565,688 participants were included in this meta-analysis. IBD was significantly associated with dementia (risk ratio [ RR] =1.36, 95% CI = 1.04-1.78; I ² = 84.8%) and VD ( RR = 2.60, 95% CI = 1.18-5.70; only one study), but not with AD ( RR = 2.00, 95% CI = 0.96-4.13; I ² = 99.8%). MR analyses did not supported significant causal associations of IBD with dementia (dementia: odds ratio [ OR] = 1.01, 95% CI = 0.98-1.03; AD: OR = 0.98, 95% CI = 0.95-1.01; VD: OR = 1.02, 95% CI = 0.97-1.07). In addition, genetic correlation and co-localization analyses did not reveal any genetic associations between IBD and dementia. CONCLUSION Our study did not provide genetic evidence for a causal association between IBD and dementia risk. The increased risk of dementia observed in observational studies may be attributed to unobserved confounding factors or detection bias.
Humans ; Mendelian Randomization Analysis ; Inflammatory Bowel Diseases/complications* ; Dementia/etiology* ; Observational Studies as Topic ; Genome-Wide Association Study

ObjectiveTo observe the effects of Xibining （XBN） and adipose stem cell exosome （ADSC-Exos） in the cases of separate or joint application on cartilage degeneration and mitochondrial autophagy and explore its mechanism of action to improve knee osteoarthritis （KOA）. MethodSD rats were divided into a sham operation group （sham group）， a model group， an ADSC-Exos group （Exos group）， an XBN group， and an ADSC-Exos+XBN group （Exos+XBN group）. KOA model was established by using anterior cruciate ligament transection （ACLT）. The pain sensitivity status of rats was evaluated， and the degeneration degree of the knee joint and cartilage tissue was detected by Micro-CT and pathological staining. The expression of p62 and LC3B was observed by immunofluorescence， and the serum levels of TNF-α， IL-1β， IL-6， and IL-15 in rats were detected by ELISA. The Western blot was used to detect the protein expression levels of MMP-3， MMP-13， ADAMTS5， ColⅡ， TIMP， ACAN， PINK1， Parkin， p62， and LC3A/B. ResultCompared with the sham group， rats in the model group showed decreased cold-stimulated foot-shrinkage thresholds and mechanical pain sensitivity thresholds， varying degrees of abrasion and loss of cartilage tissue， degeneration of cartilage tissue， elevated serum IL-1β， IL-6， IL-15， and TNF-α levels （P<0.01）， and increased protein expression of MMP-3， MMP-13， and ADAMTS5 in cartilage tissue. In addition， the protein expression of ColⅡ， TIMP1， and ACAN was decreased （P<0.01）. Compared with the model group， rats in each treatment group showed higher cold-stimulated foot-shrinkage thresholds and mechanical pain sensitivity thresholds， reduced cartilage tissue degeneration， lower serum levels of IL-1β， IL-6， IL-15， and TNF-α （P<0.05，P<0.01）， decreased protein expression of MMP-3， MMP-13， and ADAMTS5， and higher protein expression of Cold， TIMP1， and ACAN in cartilage tissue （P<0.05，P<0.01）. Moreover， the changes were the most obvious in the Exos+XBN group. ConclusionBoth ADSCs-Exos and XBN can increase the level of mitochondrial autophagy in chondrocytes and delay cartilage tissue degeneration by promoting the expression of the PINK1/Parkin signaling pathway， and the combination of the two can enhance the therapeutic effect.

Objective:To compare the imaging quality and metabolic quantitative parameters of pulmonary nodules between Q. Flex whole information five-dimensional (5D) and conventional three-dimensional (3D) PET/CT imaging for clinical evaluation.Methods:Fifty-four patients (30 males, 24 females, age: 60(42, 75) years; 78 solid pulmonary nodules (maximum diameter≤3 cm) with abnormal uptake of 18F-FDG) from Tianjin Cancer Hospital Airport Hospital between June 2022 and August 2022 were enrolled in this retrospective study. All patients underwent 5D scanning and 3D, 5D reconstruction. Image quality scores, signal-to-noise ratio (SNR), SUV max, SUV mean and metabolic tumor volume (MTV) of pulmonary nodules of 5D group and 3D group were evaluated and compared with χ2 test and Wilcoxon signed rank test. Correlation of quantitative parameters between 2 groups were analyzed by using Spearman rank correlation analysis. Results:Thirty-five of 78(45%) pulmonary nodules with image quality score≥4 were found in 5D group, which were more than those in 3D group (22/78(28%); χ2=4.67, P=0.031). Meanwhile, SNR, SUV max, SUV mean, and MTV were significantly positively correlated between the 2 groups ( rs values: 0.86, 0.86, 0.85, and 0.95, all P<0.001). SNR, SUV max and SUV mean of pulmonary nodules in 5D group were significantly higher than those in 3D group, which were 37.46(18.42, 62.00) vs 32.72(16.97, 54.76) ( z=-4.07, P<0.001), 9.71(5.48, 13.82) vs 8.96(4.82, 12.63) ( z=-3.05, P<0.001) and 6.30(3.39, 8.94) vs 5.61(2.99, 7.63)( z=-4.07, P<0.001) respectively. MTV of pulmonary nodules in 5D group was significantly lower than that in 3D group, which was 1.72(0.66, 2.74) cm 3vs 1.98(1.06, 4.63) cm 3 ( z=-7.13, P<0.001). Quantitative parameters of lower lung field and nodules with maximum diameters of >10 mm and ≤20 mm based on 5D scanning changed most significantly compared with those based on 3D scanning ( z values: from -5.23 to -2.48, all P<0.05). Conclusion:Q. Flex 5D PET significantly improves the quantitative accuracy of SUV and MTV of pulmonary nodules, and the improvement of image quality is substantial without increasing the radiation dose, which has clinical practical value.

Objective:To investigate the improvement effect of cognitive psychotherapy on negative emotions and shame in patients with cancer and depression.Methods:A total of 114 patients with cancer and depression who received treatment at Shaoxing 7 th People's Hospital from February 2022 to May 2023 were included in this randomized controlled study. The patients were randomly divided into two groups: group A and group B, with 57 patients in each group. Group A received routine western medicine treatment, while group B received routine western medicine combined with cognitive psychotherapy. Both groups received treatment for 8 weeks. Various measures were evaluated at the end of the treatment period, including negative emotions (Hamilton Depression Scale score, Hamilton Anxiety Scale score), shame (Social Impact Scale score), self-efficacy (Breastfeeding Self-Efficacy Scale score), sleep quality (Pittsburgh Sleep Quality Index score), and clinical efficacy. Results:After treatment, the Hamilton Depression Scale score and Hamilton Anxiety Scale score in group B were (7.83 ± 2.01) points and (9.78 ± 1.94) points, respectively, which were significantly lower than those in group A [(12.15 ± 2.37) points, (13.06 ± 2.32) points, t = 10.50, 8.19, both P < 0.001). The Social Impact Scale score in group B was significantly lower than that in group A [(44.72 ± 4.93) points vs. (51.63 ± 6.10) points, t = 6.65, P < 0.001]. The Breastfeeding Self-Efficacy Scale score in group B was significantly higher than that in group A [(121.65 ± 11.44) points vs. (100.24 ± 10.73) points, t = -10.31, P < 0.001]. The Pittsburgh Sleep Quality Index score in group B was significantly lower than that in group A [(7.00 ± 0.85) points vs. (9.83 ± 1.10) points, t = 15.37, P < 0.001]. The overall response rate in group B was significantly higher than that in group A [94.74% (54/57) vs. 80.70% (46/57), χ2 = 5.21, P = 0.022]. Conclusion:Cognitive psychotherapy has a significant impact on patients with cancer and depression, effectively alleviating negative emotions and shame, enhancing self-efficacy, and improving sleep quality. Therefore, it deserves clinical promotion.

Objective To explore the clinical value of anti-Müllerian hormone(AMH)to optimize endocrine therapy for peri-menopausal early breast cancer.Methods Two hundred and four patients of pre-menopausal breast cancer aged 45-55 years old between 2020 and 2023 were enrolled,and AMH≤0.1 ng/mL was considered as cut-off value for menopause.Switching from selective estrogen receptor modulator(SERM)to aromatase inhibitor aromatase inhibitor(AI)and initial endocrine therapy regimens were based on AMH,follicle-stimulating hormone(FSH)and estradiol(E2).Results Pre-chemotherapy AMH level was significantly negatively correlated with FSH level(P<0.001).Among 100 cases who were amenorrhea for one year during SERM treatment,42 cases did not have AMH testing.Fourteen out of the 42 cases switched to AI within one year,and ovarian function recovery(OFR)occurred in 2 cases after AI switching.Fifteen cases with AMH>0.1 ng/mL did not switch to AI within one year.Forty among 43 cases with AMH≤0.1 ng/mL switched to AI,after a significantly shorter median SERM treatment duration(3.15 months vs.8.14 months,P<0.001)and a significantly lower OFR rate(0 vs.12.5%,P=0.023)compared with those who did not test AMH but switched to AI.AMH≤0.1 ng/mL was an independent risk factor of transition to menopause shortly in peri-menopausal patients(OR=35.857,P<0.001).Among 104 cases with AMH tested before adjuvant chemotherapy,69 cases had AMH>0.1 ng/mL.Thirty-one out of the 69 cases were treated with ovarian function suppression(OFS)initially and 38 with SERM initially.Thirty-five cases with AMH≤0.1 ng/mL were all treated with SERM initially,with a higher rate of switching to AI(71.4%vs.23.7%,P<0.001)and a shorter SERM treatment duration(6.52 months vs.13.56 months,P=0.016)compared with the 38 cases(AMH>0.1 ng/mL)treated initially with SERM.After a median 30-month follow-up,no recurrence was observed in these thirty-five cases treated with SERM initially and AMH≤0.1 ng/mL,just like in OFS group.And they had a tendency of improved survival outcome compared with those treated with SERM initially and AMH>0.1 ng/mL(Log Rank P=0.076).Conclusion AMH could evaluate and predict menopause accurately,resulting in optimizing endocrine therapy for peri-menopausal patients effectively and safely.

ObjectiveAlveolar macrophages (AMs) are critical for maintaining the homeostasis of pulmonary microenvironment. They process surfactants to ensure alveoli patency, and also serve as the first line of immune defense against pathogen invasion. Available studies have shown that monocyte-derived AMs continuously release pro-inflammatory cytokines and chemokines, recruiting other immune cells to the damaged area during pulmonary fibrosis. These monocyte-derived AMs maintains and amplifies inflammation, playing a negative role in pulmonary fibrosis progression. Current researches have predominantly focused on the gene expression levels of AMs in pulmonary fibrosis microenvironment, with less emphasis on the function and regulation of proteins. This study aims to investigate the differentially expressed proteins (DEPs) of AMs under normal physiological conditions and after pulmonary fibrosis, in order to gain a more comprehensive understanding of the role of AMs in the progression of pulmonary fibrosis. MethodsFirstly, the construction of bleomycin-induced pulmonary fibrosis mouse models was evaluated through using measurements such as body mass, lung coefficient, lungwet-to-dry mass ratio, H&E staining and Masson staining. Subsequently, AMs from both the saline controls and the pulmonary fibrosis models (2.5×10⁵ cells per sample) were collected using FACS sorting, and protein expression profiles of these cells were obtained through label-free proteomics approach. The quality of the proteomic data was assessed by comparing our saline control proteomic data with public proteomic data of physiological AMs. Thirdly, DEPs analysis between the saline controls and the bleomycin groups was carried out using R package Prostar. Functional enrichment analyses of significantly upregulated DEPs were performed using R package Clusterprofiler for GO and KEGG pathways. Finally, the STRING database was used to explore the protein-protein interaction networks related to phagocytosis regulation, inflammatory response regulation, andI-κB/NF-κB signaling pathway. The expression levels of Tlr2 and Pycard were detected respectively by FACS and western blotting. ResultsCompared to the saline controls, mice in the bleomycin groups exhibited a lower average body mass, extensive infiltration of inflammatory cells, and deposition of collagen in the lungs. This indicates that bleomycin successfully induced pulmonary fibrosis in mouse models. The proteomic data of AMs obtained from these models was of high quality and fulfilled the research requirements. A comprehensive analysis showed that 778 proteins were upregulated in pulmonary fibrosis groups compared with control groups. Moreover, the signal pathways enriched in up-regulated DEPs were related to the I‑κB/NF‑κB pathway, inflammatory response regulation, phagocytosis regulation, TGF-β signaling, and HIF-1 pathway, indicating that AMs in pulmonary fibrosis microenvironment exerted pro-inflammatory and pro-fibrotic functions. Protein-protein interaction network analysis of the DEPs suggested that the interactions between Tlr2 and Pycard were control nodes for the pro-inflammatory phenotype of AMs, thereby contributing to pulmonary fibrosis progression. Further validation by FACS and Western blotting respectively confirmed that the expression levels of Tlr2 and Pycard in AMs were significantly increased after pulmonary fibrosis. ConclusionThis study investigates the changes in the protein expression profile of AMs in the pulmonary fibrosis microenvironment. The results show that AMs notably enhanced the activity of various pathways associated with inflammation and fibrosis, suggesting that the interaction between Tlr2 and Pycard serves as a key control node for the highly pro-inflammatory behavior of AMs.

Objective:To integrate and systematically evaluate the self-disclosure experience and feelings of cancer patients.Methods:Qualitative studies on self-disclosure of cancer patients in PubMed, Web of Science, Cochrane Library, Embase, EBSCO, SinoMed, China National Knowledge Infrastructure, Wanfang Data, and VIP searched by computer from the establishment of the databases to March 8, 2023. The literature was evaluated using the authenticity evaluation tool of qualitative studies by the Joanna Briggs Institute Evidence-based Health Care, and the results were summarized in an aggregative integration approach.Results:A total of eight literatures were included, 30 main results were extracted, and similar results were summarized into ten new categories. Finally, two integrated results were composed, which were the promoting factors and the hindering factors of self-disclosure.Conclusions:Self-disclosure can enhance the intimate relationship between cancer patients and others, thereby improving the self-acceptance and mental health of cancer patients.

Objective:To investigate the risk factors of cognitive dysfunction and its relationship with poor prognosis in elderly hypertensive patients with frailty.Methods:A total of 150 elderly hypertensive patients with frailty trea-ted in Eighth People's Hospital of Hebei Province from July 2019 to March 2021 were selected.According to pres-ence of cognitive dysfunction,they were divided into normal cognition group(n=92)and cognitive dysfunction group(n=58),and general data and prognosis condition were collected in two groups.Multivariate Logistic regres-sion analysis was used to analyze the risk factors of cognitive dysfunction in elderly hypertensive patients with frail-ty;Spearman correlation analysis was used to analyze the correlation between cognitive dysfunction degree and prog-nosis.Results:Compared with normal cognition group,cognitive dysfunction group was significantly older and pos-sessed significant higher proportions of diabetes,coronary heart disease,stroke,hyponatremia,multiple medication and malnutrition(P＜0.05 or＜0.01).Multivariate Logistic regression analysis indicated that age ≥75 years,stroke,multiple medication and malnutrition were independent risk factors for cognitive dysfunction in elderly hy-pertensive patients with frailty(OR=2.804～6.434,P＜0.05 or＜0.01).Incidence rate of poor prognosis events in cognitive dysfunction group was significantly higher than that of normal cognition group(51.72％vs.11.96％,P＜0.001).Spearman correlation analysis showed that cognitive dysfunction was significant positively correlated with poor prognosis in these patients(r=0.435,P＜0.001).Conclusion:Age,stroke,multiple medication and malnu-trition are independent risk factors for cognitive dysfunction in elderly hypertensive patients with frailty.Cognitive dysfunction is closely related to poor prognosis in these patients.