1.Expert consensus on clinical application of parenteral direct thrombin inhibitors in perioperative period
Mingyu JIANG ; Yuan BIAN ; Lizhu HAN ; Qinan YIN ; Fengjiao KANG ; Anhua WEI ; Danjie ZHAO ; Lin WANG ; Ying SHAO ; Li TANG ; Yi WANG ; Shuhong LIANG ; Huijuan LIU ; Guirong XIAO ; Yue LI
China Pharmacy 2026;37(6):689-699
OBJECTIVE To form an expert consensus on the clinical application of parenteral direct thrombin inhibitors (DTIs) in patients during the perioperative period. METHODS Led by Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital (the Affiliated Hospital of UESTC), a multidisciplinary working group was established. Through literature review and the Delphi method, clinical questions related to the rational perioperative use of parenteral DTIs were identified. A structured design was adopted using the “Population-Intervention-Comparison-Outcome” framework; systematic searches were conducted in CNKI, Medline, Embase and other databases. Relevant evidence from randomized controlled trials and cohort studies was included and synthesized. Evidence quality was assessed using the Grades of Recommendations Assessment,Development and Evaluation (GRADE) approach, and recommendations were formulated through multiple rounds of Delphi surveys and expert consensus meetings. RESULTS &CONCLUSIONS Seven recommendations (each with an expert consensus rate exceeding 90%) on the use of parenteral DTIs in perioperative patients were developed. These recommendations specify drug selection, dosing ranges, key monitoring points, and safety management strategies for parenteral DTIs in various scenarios, including the perioperative period of ventricular assist device implantation, the perioperative period of cardiac surgery, perioperative patients with lower-extremity atherosclerotic disease, the perioperative period of percutaneous coronary intervention in patients with acute coronary syndrome, the perioperative period of carotid artery stenting in patients with carotid stenosis, the perioperative period of patients with right heart thrombosis, and patients who develop related thrombosis and dysfunction after a central venous catheter insertion. In addition, warning and management pathways for perioperative bleeding and thrombotic events were proposed. This expert consensus, which is formulated based on the best available evidence, provides evidence-based guidance for standardized and individualized use of parenteral DTIs in perioperative period.
2.Relationship between Alzheimer's disease and sarcopenia and body mass index:analysis of GWAS datasets for European populations
Qiwang HE ; Bo CHEN ; Fuchao LIANG ; Zewei KANG ; Yuan ZHOU ; Anxu JI ; Xialin TANG
Chinese Journal of Tissue Engineering Research 2026;30(4):1036-1046
BACKGROUND:Alzheimer's disease has been associated with sarcopenia,but a causal relationship has not been established.Exploring the causal relationship between the two most common disability-burdening diseases in the aging population-Alzheimer's disease and sarcopenia-and their potential mediating factors holds certain implications for further alleviating the healthcare costs and socioeconomic burden for older adults in China.OBJECTIVE:To explore the potential causal relationship between Alzheimer's disease and sarcopenia in the general population using a Mendelian randomization study and to explore the role of body mass index in this context.METHODS:Two-sample Mendelian randomization analysis based on published genome-wide association studies(GWAS)were used to infer causality,and univariate Mendelian randomization and mediation analyses were used in the study design.Through the Integrative Epidemiology Unit(IEU)database,ieu-b-2 was selected as the Alzheimer's disease dataset(sample size:63 926),ieu-b-4816 as the body mass index dataset(99 998),ebi-a-GCST90000027 as the appendicular lean mass dataset(244 730),ukb-b-7478 as the left hand grip strength dataset(461 026),ukb-b-10215 as the right hand grip strength dataset(461 089)and ukb-b-4711 as the walking pace dataset(459 915).Inverse-variance weighting was used as the primary analysis method,and the results were validated by pleiotropy and heterogeneity analysis.The Steiger Directionality Test was performed to validate the reasonableness of the causal direction.RESULTS AND CONCLUSION:(1)The Mendelian randomization analyses provided evidence that Alzheimer's disease predicted the risk of appendicular lean mass[odds ratio(OR)=1.009;95%confidence interval(Cl),1.001-1.017;P=0.023),and walking pace(OR=1.010;95%Cl,1.003-1.017;P=0.008).No correlation with hand grip strength was observed.(2)Alzheimer's disease was negatively correlated with body mass index(OR=0.893;95%Cl,0.811-0.984;P=0.022);body mass index was positively correlated with appendicular lean mass(OR=1.084;95%Cl,1.031-1.141;P=0.002)and negatively correlated with walking pace(OR=0.975;95%Cl,0.969-0.980;P<0.001).(3)Mediation analyses showed that the causal relationship between Alzheimer's disease and appendicular lean mass and walking pace was partially mediated by body mass index,with the proportion of mediations being 50.25%and 32.11%,respectively.(4)The results of this study suggest that based on large-scale population studies,genetic prediction of Alzheimer's disease is a potential risk factor for sarcopenia,in which body mass index plays an important mediating role.This suggests that in clinical practice,attention should be paid to the muscle condition of patients with Alzheimer's disease,and weight management should be implemented,as maintaining a body mass index within the normal high range may have a preventive effect on the occurrence of sarcopenia in patients with Alzheimer's disease.However,further research is needed to verify the applicability of this conclusion to other ethnic groups.This study utilized an international public database for analysis,providing a reference for research on the correlation between Alzheimer's disease and sarcopenia in the Chinese population.It also highlights the significant mediating role of body mass index,offering insights for further prevention and treatment of sarcopenia among Chinese individuals.
3.Relationship between Alzheimer's disease and sarcopenia and body mass index:analysis of GWAS datasets for European populations
Qiwang HE ; Bo CHEN ; Fuchao LIANG ; Zewei KANG ; Yuan ZHOU ; Anxu JI ; Xialin TANG
Chinese Journal of Tissue Engineering Research 2026;30(4):1036-1046
BACKGROUND:Alzheimer's disease has been associated with sarcopenia,but a causal relationship has not been established.Exploring the causal relationship between the two most common disability-burdening diseases in the aging population-Alzheimer's disease and sarcopenia-and their potential mediating factors holds certain implications for further alleviating the healthcare costs and socioeconomic burden for older adults in China.OBJECTIVE:To explore the potential causal relationship between Alzheimer's disease and sarcopenia in the general population using a Mendelian randomization study and to explore the role of body mass index in this context.METHODS:Two-sample Mendelian randomization analysis based on published genome-wide association studies(GWAS)were used to infer causality,and univariate Mendelian randomization and mediation analyses were used in the study design.Through the Integrative Epidemiology Unit(IEU)database,ieu-b-2 was selected as the Alzheimer's disease dataset(sample size:63 926),ieu-b-4816 as the body mass index dataset(99 998),ebi-a-GCST90000027 as the appendicular lean mass dataset(244 730),ukb-b-7478 as the left hand grip strength dataset(461 026),ukb-b-10215 as the right hand grip strength dataset(461 089)and ukb-b-4711 as the walking pace dataset(459 915).Inverse-variance weighting was used as the primary analysis method,and the results were validated by pleiotropy and heterogeneity analysis.The Steiger Directionality Test was performed to validate the reasonableness of the causal direction.RESULTS AND CONCLUSION:(1)The Mendelian randomization analyses provided evidence that Alzheimer's disease predicted the risk of appendicular lean mass[odds ratio(OR)=1.009;95%confidence interval(Cl),1.001-1.017;P=0.023),and walking pace(OR=1.010;95%Cl,1.003-1.017;P=0.008).No correlation with hand grip strength was observed.(2)Alzheimer's disease was negatively correlated with body mass index(OR=0.893;95%Cl,0.811-0.984;P=0.022);body mass index was positively correlated with appendicular lean mass(OR=1.084;95%Cl,1.031-1.141;P=0.002)and negatively correlated with walking pace(OR=0.975;95%Cl,0.969-0.980;P<0.001).(3)Mediation analyses showed that the causal relationship between Alzheimer's disease and appendicular lean mass and walking pace was partially mediated by body mass index,with the proportion of mediations being 50.25%and 32.11%,respectively.(4)The results of this study suggest that based on large-scale population studies,genetic prediction of Alzheimer's disease is a potential risk factor for sarcopenia,in which body mass index plays an important mediating role.This suggests that in clinical practice,attention should be paid to the muscle condition of patients with Alzheimer's disease,and weight management should be implemented,as maintaining a body mass index within the normal high range may have a preventive effect on the occurrence of sarcopenia in patients with Alzheimer's disease.However,further research is needed to verify the applicability of this conclusion to other ethnic groups.This study utilized an international public database for analysis,providing a reference for research on the correlation between Alzheimer's disease and sarcopenia in the Chinese population.It also highlights the significant mediating role of body mass index,offering insights for further prevention and treatment of sarcopenia among Chinese individuals.
4.Analysis of lower limb alignment and gait after TKA for varus knees
Jian Zhou ; Xingyi Hua ; Junqin Lu ; Kang Tang ; Wei Fang
Acta Universitatis Medicinalis Anhui 2025;60(10):1932-1936
Objective :
To investigate the relationship between lower limb alignment and knee functional gait after total knee arthroplasty (TKA) for varus knee deformity.
Methods:
A total of 94 patients with knee osteoarthritis and varus deformity underwent mechanically aligned TKA. The knee society score ( KSS) , hip⁃knee⁃ankle angle (HKA) , medial proximal tibial angle ( mMPTA) , and gait parameters ( step length , gait speed , cadence , thigh jerk acceleration , and thigh swing work) were assessed preoperatively and one month postoperatively. The correlation between KSS scores and changes in lower limb alignment was also analyzed.
Results:
The KSS clinical score of the operated knee significantly improved from 39. 19 ± 9. 55 preoperatively to 73. 01 ± 6. 90 postoperatively (P <0. 001) . The KSS functional score increased from 41. 12 ± 10. 66 to 56. 33 ± 7. 41(P < 0. 001) . Postoperative gait analysis revealed significant improvements in step length , gait speed , cadence , and thigh swing work ( P <0. 001) , while thigh jerk acceleration showed no significant change (P = 0. 525) . The HKA angle of the affected limb increased from 170. 61 ± 4. 39 preoperatively to 177. 30 ± 3. 49 postoperatively ( P < 0. 001) . Similarly , the mMPTA angle increased from 83. 95 ± 3. 32 to 89. 15 ± 1. 94 (P < 0. 001) . Correlation analysis indicated that The KSS clinical score was positively correlated with HKA ( P < 0. 001) and mMPTA ( P < 0. 05 ) of the lower limb force line. The KSS functional score was positively correlated with HKA (P < 0. 05) but not with mMPTA (P >
0. 05) .
Conclusion
In patients with severe knee osteoarthritis due to varus deformity , TKA significantly alleviates pain and improves both clinical and functional KSS scores within one month postoperatively. Restoring lower limb
mechanical alignment is positively associated with joint functional recovery and enhances gait performance.
5.Distribution Tendency of Traditional Chinese Medicine Syndromes in Chronic Persistent Immunoglobulin A Nephropathy and Its Relationship with Prognosis
Kang ZHANG ; Long TANG ; Cun SHEN ; Mengdi WANG ; Yuan MENG ; Wenjing ZHAO
Journal of Guangzhou University of Traditional Chinese Medicine 2025;42(5):1052-1059
Objective To investigate the distribution of traditional Chinese medicine(TCM)syndromes in chronic persistent immunoglobulin A nephropathy(IgAN)and to explore the relationship between TCM syndromes and prognosis based on real-world research.Methods From January 2018 to January 2024,a total of 80 patients with chronic persistent IgAN who were admitted to Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University were included.The clinical baseline data and prognosis-related information were collected.The main outcome indicators were defined as renal failure events of glomerular filtration rate(eGFR)decreased by>50%,serum creatinine doubled or end-stage renal disease(ESRD).The distribution of TCM syndromes in chronic persistent IgAN and the relationship between different deficiency syndromes and prognosis were preliminarily discussed.Results(1)Among the 80 patients with chronic persistent IgAN,the syndrome manifestations with an occurrence frequency of more than 30%in descending order were foamy urine(75.00%),fatigue and lassitude(71.25%),waist ache(61.25%),dry mouth(31.25%),lower extremity edema(31.25%),aversion to cold and cold limbs(30.00%),and insomnia(30.00%).(2)The commonly-seen root-deficiency syndrome in patients with chronic persistent IgAN was qi and yin deficiency syndrome,with a total of 28 cases(35.00%).And other root-deficiency syndromes were spleen and kidney yang deficiency syndrome in 22 cases(27.50%),lung and spleen qi deficiency syndrome in 15 cases(18.75%),and liver and kidney yin deficiency syndrome in 15 cases(18.75%).The commonly-seen complicated syndrome was water-damp syndrome,with a total of 17 cases(21.25%).The other complicated syndromes were damp-heat syndrome in 15 cases(18.75%),blood-stasis syndrome in 9 cases(11.25%),phlegm-damp syndrome in 7 cases(8.75%),turbidity-toxin syndrome in 5 cases(6.25%),liver depression syndrome in 3 cases(3.75%),and cold-damp syndrome in 1 case(1.25%).(3)Among the 80 patients with chronic persistent IgAN,21 cases(26.25%)had renal failure events,and their syndrome types were lung and spleen qi deficiency syndrome in 9 cases(60.00%),qi and yin deficiency syndrome in 3 cases(10.71%),liver and kidney yin deficiency syndrome in 3 cases(20.00%),and spleen and kidney yang deficiency syndrome in 6 cases(27.27%).The incidence of renal failure events in patients with lung and spleen qi deficiency syndrome was significantly higher than that in the other three syndrome types,and the chi-square test showed that the difference was statistically significant(P<0.05).(4)Kaplan-Meier survival analysis showed that the cumulative incidence of 2-year and 5-year endpoint events in patients with lung and spleen qi deficiency syndrome was 23.10%and 46.20%,respectively,and the final incidence was 85.00%.The cumulative incidence of 2-year and 5-year endpoint events in patients with other deficiency syndromes was 4.50%and 19.70%,respectively,and the final incidence was 71.60%.The intergroup comparison(tested by Log-rank)showed that the incidence of renal failure events in patients with lung and spleen qi deficiency syndrome was significantly higher than that in patients with other root-deficiency syndromes,and the difference was statistically significant(P<0.05).(5)COX proportional hazard regression analysis showed that lung and spleen qi deficiency syndrome(HR=7.755,95%CI 1.631-36.874,P<0.05)and anemia(HR=8.205,95%CI 1.007-66.857,P<0.05)were the independent risk factors for renal failure events in patients with chronic persistent IgAN.Conclusion Qi and yin deficiency syndrome is the most common syndrome in the patients with chronic persistent IgAN,and lung and spleen qi deficiency syndrome and anemia are the independent risk factors for renal failure events in IgAN.
6.Study on the correlation between inflammatory indicators in the hyperacute phase of acute ischemic stroke and early neurological deterioration, syndrome factors, and prognosis
Ligaoge KANG ; Ying GAO ; Jinyue BAI ; Huan TANG ; Hongbo SHEN ; Lei LIU ; Lingbo KONG
Journal of Beijing University of Traditional Chinese Medicine 2025;48(1):98-107
Objective:
Inflammatory cascade reactions play a crucial role in secondary neuronal injury in acute ischemic stroke (AIS). The aim of this study was to explore the correlations between specific serological indicators, early neurological deterioration (END), disease prognosis, and syndrome factors in AIS based on this injury mechanism.
Methods:
The data for this study were collected from 135 patients with AIS admitted to the emergency department of Fangshan Hospital, Beijing University of Chinese Medicine, within 24 h of onset between November 2019 and May 2021. Among these, 29 patients had complete data and experienced END. Additionally, 9 non-END patients were matched from the remaining 90 patients with complete data, resulting in a total of 38 patients for statistical analysis. Statistical methods, including logistic regression and receiver operating curves, were used to analyze the correlation between serum levels of tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), interleukin-10 (IL-10), vascular endothelial growth factor (VEGF), and intercellular adhesion molecule-1 (ICAM-1) within 24 h of END onset, disease prognosis, and syndrome factors. Grouping criteria included END occurrence, presence of syndrome elements on the first and third day post-onset, and prognosis at 90 days post-onset.
Results:
All 38 cases had onset time of less than 12 h, and there were no significant differences in age, gender, and onset time between the END and non-END groups. The TNF-α serum level within 24 h of onset was not associated with the occurrence of END but was negatively correlated with all-cause mortality at 90 days [0.1
7.Cervical spondylosis: innovative understanding from traditional Chinese medicine and treatment by classic formulas.
Heng CHEN ; Cong-Yang XUE ; Shuang CHEN ; Zi-Ting CHEN ; Tian TANG ; Xin LIU ; Zhi-Peng XI ; Ran KANG ; Lin XIE
China Journal of Chinese Materia Medica 2025;50(9):2596-2604
As one of the chronic diseases with high incidence in contemporary society, cervical spondylosis has increasing patient groups who gradually present a low age, and it seriously affects social and public health. Although modern medicine has made great progress in the pathological research and clinical treatment of cervical spondylosis, patients still face gastrointestinal side effects of nonsteroidal anti-inflammatory drugs(NSAIDs), neck pain, limited mobility, upper limb numbness, and other symptoms after conservative or surgical treatment. In the theory of traditional Chinese medicine(TCM), cervical spondylosis belongs to the categories of "Bi syndrome" "stiff neck" "stiff Bi", etc. With the change of the times, the change of lifestyle, and the application of western medicine treatment, the etiology and pathogenesis of TCM in cervical spondylosis also show new characteristics. In terms of etiology and pathogenesis, it involves the invasion of wind, cold, and dampness, long-term strain, liver and kidney deficiency, Qi and blood stasis, which are associated with factors such as cervical degeneration, muscle tension and spasm, intervertebral disc herniation, and nerve root compression in modern medicine. In terms of the evolution of pathogenesis, in the early stage, wind, cold, and dampness, were more common in Xuanfu, resulting in unfavorable muscles and bones, poor flow of Qi and blood, and cervical spondylosis and radiculopathy. Medium-term phlegm stasis and internal knots, sluggish muscles and veins, and long-term weathering and fire are more likely to occur in the vertebral artery and sympathetic radiculopathy. In the later stage, the positive Qi is depleted; the true Yin is damaged, and the viscera Qi and blood are deficient, which is most common in cervical myelopathy. The strategy of treating cervical spondylosis with TCM classic formulas applies Gegen Decoction, Wutou Decoction, Qianghuo Shengshi Decoction, Mahuang Jiazhu Decoction to patients with wind, cold, and dampness. Patients with phlegm dampness and blood stasis are treated with Huoxue Xiaoling Dan, Jinlingzi Powder, Siwu Decoction, Banxia Baizhu Tianma Decoction, Shuanghe Decoction, etc. For those patients with liver, spleen, and kidney deficiency, Huangqi Guizhi Wuwu Decoction, Tianma Gouteng Decoction, Guishao Dihuang Pills, Shenling Baizhu Powder, and Lizhong Decoction are used to invigorate the spleen, nourish Qi and blood, and tonify liver and kidney. In clinical practice, the authors advocate a safe and effective treatment plan of classic formulas based on deficiency and excess, the integration of formulas and syndromes, and the combination of modern research results, so as to relieve symptoms, reduce recurrence, and reduce medical burden.
Humans
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Spondylosis/drug therapy*
;
Medicine, Chinese Traditional/methods*
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Drugs, Chinese Herbal/therapeutic use*
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Cervical Vertebrae/pathology*
8.Correlation Between the Spinopelvic Parameters and Morphological Characteristics of Pedicle-Facet Joints in Different Lumbar Spondylolisthesis
Baoqiang HE ; Yebo LENG ; Shicai XU ; Yang LI ; Jiajun ZHOU ; Min KANG ; Yehui LIAO ; Minghao TIAN ; Qiang TANG ; Fei MA ; Qing WANG ; Chao TANG ; Dejun ZHONG
Neurospine 2025;22(1):231-242
Objective:
Based on spinopelvic parameters and biomechanical principles, the pedicle-facet joint (PFJ) morphological characteristics of isthmic and degenerative spondylolisthesis were analyzed, and the mechanism of their onset and progression was discussed.
Methods:
This retrospective cross-sectional study included 194 patients with L5 spondylolysis or L5–S1 low-grade isthmic spondylolisthesis (IS group), 172 patients with L4–5 degenerative spondylolisthesis (DS group), and 366 patients with nonlumbar spondylolysis (NL group). The spinopelvic parameters and PFJ morphological parameters of the patients were measured, the differences in these parameters among and within the 3 groups were compared, and the correlations were analyzed.
Results:
Sacral slope (SS) and lumbar lordosis (LL) were the highest in the IS group, the second highest in the DS group, and the lowest in the NL group. Among the 3 groups, the L4 facet joint angle (FJA) was the largest in the IS group, the second largest in the NL group, and the smallest in the DS group. The L4 pedicle-facet joint angle (PFA) was the largest in the DS group, the second largest in the IS group, and the smallest in the NL group. Pearson correlation analysis showed that within each group, SS and LL were negatively correlated with FJA and positively correlated with PFA.
Conclusion
This study found a correlation between the PFJ morphological characteristics of patients with lumbar spondylolisthesis and spinopelvic parameters, suggesting that the morphological characteristics of PFJs may be caused by varying stresses under different spinopelvic morphologies.
9.Endoplasmic reticulum membrane remodeling by targeting reticulon-4 induces pyroptosis to facilitate antitumor immune.
Mei-Mei ZHAO ; Ting-Ting REN ; Jing-Kang WANG ; Lu YAO ; Ting-Ting LIU ; Ji-Chao ZHANG ; Yang LIU ; Lan YUAN ; Dan LIU ; Jiu-Hui XU ; Peng-Fei TU ; Xiao-Dong TANG ; Ke-Wu ZENG
Protein & Cell 2025;16(2):121-135
Pyroptosis is an identified programmed cell death that has been highly linked to endoplasmic reticulum (ER) dynamics. However, the crucial proteins for modulating dynamic ER membrane curvature change that trigger pyroptosis are currently not well understood. In this study, a biotin-labeled chemical probe of potent pyroptosis inducer α-mangostin (α-MG) was synthesized. Through protein microarray analysis, reticulon-4 (RTN4/Nogo), a crucial regulator of ER membrane curvature, was identified as a target of α-MG. We observed that chemically induced proteasome degradation of RTN4 by α-MG through recruiting E3 ligase UBR5 significantly enhances the pyroptosis phenotype in cancer cells. Interestingly, the downregulation of RTN4 expression significantly facilitated a dynamic remodeling of ER membrane curvature through a transition from tubules to sheets, consequently leading to rapid fusion of the ER with the cell plasma membrane. In particular, the ER-to-plasma membrane fusion process is supported by the observed translocation of several crucial ER markers to the "bubble" structures of pyroptotic cells. Furthermore, α-MG-induced RTN4 knockdown leads to pyruvate kinase M2 (PKM2)-dependent conventional caspase-3/gasdermin E (GSDME) cleavages for pyroptosis progression. In vivo, we observed that chemical or genetic RTN4 knockdown significantly inhibited cancer cells growth, which further exhibited an antitumor immune response with anti-programmed death-1 (anti-PD-1). In translational research, RTN4 high expression was closely correlated with the tumor metastasis and death of patients. Taken together, RTN4 plays a fundamental role in inducing pyroptosis through the modulation of ER membrane curvature remodeling, thus representing a prospective druggable target for anticancer immunotherapy.
Pyroptosis/immunology*
;
Humans
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Endoplasmic Reticulum/immunology*
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Animals
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Nogo Proteins/antagonists & inhibitors*
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Mice
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Cell Line, Tumor
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Xanthones/pharmacology*
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Neoplasms/pathology*
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Mice, Nude
10.Genome-wide investigation of transcription factor footprints and dynamics using cFOOT-seq.
Heng WANG ; Ang WU ; Meng-Chen YANG ; Di ZHOU ; Xiyang CHEN ; Zhifei SHI ; Yiqun ZHANG ; Yu-Xin LIU ; Kai CHEN ; Xiaosong WANG ; Xiao-Fang CHENG ; Baodan HE ; Yutao FU ; Lan KANG ; Yujun HOU ; Kun CHEN ; Shan BIAN ; Juan TANG ; Jianhuang XUE ; Chenfei WANG ; Xiaoyu LIU ; Jiejun SHI ; Shaorong GAO ; Jia-Min ZHANG
Protein & Cell 2025;16(11):932-952
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*
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Humans
;
Chromatin/genetics*
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Animals
;
Binding Sites
;
Mice
;
DNA Footprinting/methods*


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