1.Long-term survival outcomes and prognostic factors following radical resection of pancreatic body and tail cancer:a retrospective analysis of 992 patients
Dong XU ; Yang WU ; Kai ZHANG ; Nan LYU ; Qianqian WANG ; Pengfei WU ; Jie YIN ; Baobao CAI ; Guodong SHI ; Jianzhen LIN ; Yazhou WANG ; Lingdi YIN ; Zipeng LU ; Min TU ; Jianmin CHEN ; Feng GUO ; Jishu WEI ; Junli WU ; Wentao GAO ; Cuncai DAI ; Yi MIAO ; Kuirong JIANG
Chinese Journal of Surgery 2026;64(1):46-54
Objective:To investigate the survival outcomes and prognostic factors in patients undergoing radical resection for pancreatic body and tail cancer.Methods:A retrospective case series study was conducted on 992 patients who underwent radical resection for pancreatic body and tail cancer at the Pancreatic Center of the First Affiliated Hospital of Nanjing Medical University from January 2016 to June 2024. In this study, 577 (58.2%) were male and 415 (41.8%) were female,with an age of (65±9) years (range: 26 to 86 years). Follow-up continued until June 2024. Survival rates were estimated using the Kaplan-Meier method,and prognostic factors were identified using univariate and multivariate Cox proportional hazards models.Results:Among 992 patients,open surgery was the predominant approach (89.1%, 884/992), and radical antegrade modular pancreatosplenectomy (RAMPS) was performed in 317 patients (32.0%). Combined organ resection,venous resection,and arterial resection were performed in 23.5%, 9.3%,and 11.2% of patients,respectively. The rates of R0, R1-1 mm, and R1-direct resections were 49.8% (494/992),41.5% (412/992), and 8.7% (86/992),respectively. Stage ⅡB was the most common TNM stage (32.2%,319/992). A total of 801 patients (80.8%) received adjuvant chemotherapy. The median follow-up period was 32.0(8.8) months(range:3.2 to 105.3 months),during which 508 patients (51.2%) died. The overall median survival (OS) was 26.4 months,with 1-,3-, and 5-year survival rates of 79.0%,40.0%, and 29.0%, respectively. In the recent five years (from 2020 to 2024), the median OS improved significantly to 34.1 months compared to 20.0 months from 2016 to 2019 ( P<0.01). Histological subtype analysis showed that the median OS time was 26.7 months for pancreatic ductal adenocarcinoma (PDAC, n=855),58.9 months for invasive intraductal papillary mucinous carcinoma (IPMC, n=32),and 15.7 months for adenosquamous carcinoma of pancreas (ASCP, n=73) ( P=0.001). Among PDAC patients, adjuvant chemotherapy significantly improved survival (29.1 months vs. 14.4 months, P<0.01);in IPMC patients, adjuvant chemotherapy also extended survival (65.7 months vs. 58.9 months, P=0.047). Although ASCP patients receiving chemotherapy had a longer median OS time than those without (18.8 months vs. 8.9 months),the difference was not statistically significant ( P=0.151). Multivariate Cox regression analysis in PDAC patients indicated that adjuvant chemotherapy, R0 resection, T stage,N stage,and tumor differentiation were independent prognostic factors ( P<0.01). The median OS time by TNM stage was:not reached for stage ⅠA, 51.6 months for ⅠB, 25.5 months for ⅡA, 23.7 months for ⅡB, 23.0 months for Ⅲ, and 14.4 months for Ⅳ. The median OS time for R0,R1-1 mm,and R1-direct resections was 34.1,24.7,and 15.7 months,respectively ( P<0.01). Conclusion:Adjuvant chemotherapy,R0 resection,tumor stage,and differentiation are independent prognostic factors for pancreatic body and tail cancer.
2.Long-term survival outcomes and prognostic factors following radical resection of pancreatic body and tail cancer:a retrospective analysis of 992 patients
Dong XU ; Yang WU ; Kai ZHANG ; Nan LYU ; Qianqian WANG ; Pengfei WU ; Jie YIN ; Baobao CAI ; Guodong SHI ; Jianzhen LIN ; Yazhou WANG ; Lingdi YIN ; Zipeng LU ; Min TU ; Jianmin CHEN ; Feng GUO ; Jishu WEI ; Junli WU ; Wentao GAO ; Cuncai DAI ; Yi MIAO ; Kuirong JIANG
Chinese Journal of Surgery 2026;64(1):46-54
Objective:To investigate the survival outcomes and prognostic factors in patients undergoing radical resection for pancreatic body and tail cancer.Methods:A retrospective case series study was conducted on 992 patients who underwent radical resection for pancreatic body and tail cancer at the Pancreatic Center of the First Affiliated Hospital of Nanjing Medical University from January 2016 to June 2024. In this study, 577 (58.2%) were male and 415 (41.8%) were female,with an age of (65±9) years (range: 26 to 86 years). Follow-up continued until June 2024. Survival rates were estimated using the Kaplan-Meier method,and prognostic factors were identified using univariate and multivariate Cox proportional hazards models.Results:Among 992 patients,open surgery was the predominant approach (89.1%, 884/992), and radical antegrade modular pancreatosplenectomy (RAMPS) was performed in 317 patients (32.0%). Combined organ resection,venous resection,and arterial resection were performed in 23.5%, 9.3%,and 11.2% of patients,respectively. The rates of R0, R1-1 mm, and R1-direct resections were 49.8% (494/992),41.5% (412/992), and 8.7% (86/992),respectively. Stage ⅡB was the most common TNM stage (32.2%,319/992). A total of 801 patients (80.8%) received adjuvant chemotherapy. The median follow-up period was 32.0(8.8) months(range:3.2 to 105.3 months),during which 508 patients (51.2%) died. The overall median survival (OS) was 26.4 months,with 1-,3-, and 5-year survival rates of 79.0%,40.0%, and 29.0%, respectively. In the recent five years (from 2020 to 2024), the median OS improved significantly to 34.1 months compared to 20.0 months from 2016 to 2019 ( P<0.01). Histological subtype analysis showed that the median OS time was 26.7 months for pancreatic ductal adenocarcinoma (PDAC, n=855),58.9 months for invasive intraductal papillary mucinous carcinoma (IPMC, n=32),and 15.7 months for adenosquamous carcinoma of pancreas (ASCP, n=73) ( P=0.001). Among PDAC patients, adjuvant chemotherapy significantly improved survival (29.1 months vs. 14.4 months, P<0.01);in IPMC patients, adjuvant chemotherapy also extended survival (65.7 months vs. 58.9 months, P=0.047). Although ASCP patients receiving chemotherapy had a longer median OS time than those without (18.8 months vs. 8.9 months),the difference was not statistically significant ( P=0.151). Multivariate Cox regression analysis in PDAC patients indicated that adjuvant chemotherapy, R0 resection, T stage,N stage,and tumor differentiation were independent prognostic factors ( P<0.01). The median OS time by TNM stage was:not reached for stage ⅠA, 51.6 months for ⅠB, 25.5 months for ⅡA, 23.7 months for ⅡB, 23.0 months for Ⅲ, and 14.4 months for Ⅳ. The median OS time for R0,R1-1 mm,and R1-direct resections was 34.1,24.7,and 15.7 months,respectively ( P<0.01). Conclusion:Adjuvant chemotherapy,R0 resection,tumor stage,and differentiation are independent prognostic factors for pancreatic body and tail cancer.
3.Clinical efficacy and prognosis of different lithotripsy strategies for difficult common bile duct stones
Pengfei ZHANG ; Ming ZHANG ; Donghai ZHUANG ; Li LIANG ; Baochang SHI ; Jinglong GUO ; Rui WU ; Kai ZHANG
Chinese Journal of Hepatobiliary Surgery 2025;31(6):420-425
Objective:To evaluate the clinical efficacy and prognosis of mechanical lithotripsy, laser lithotripsy under direct peroral cholangioscopy, and their combination in the treatment of difficult common bile duct (CBD) stones.Methods:Clinical data of 345 patients with difficult CBD stones treated at the Department of Hepatobiliary Surgery, Shandong Provincial Third Hospital, Shandong University, between January 2020 and December 2024 were retrospectively analyzed, including 176 males and 169 females, aged (71.2±14.2) years. Patients were categorized into three groups based on the lithotripsy technique used: mechanical lithotripsy group ( n=275), laser lithotripsy group under direct peroral cholangioscopy ( n=34), and combined lithotripsy group ( n=35). Operative time, hospitalization costs, stone clearance rate, and postoperative complications were recorded. Follow-ups were conducted through outpatient visits and telephone reviews to monitor stone recurrence. Propensity score matching (PSM) at a 1: 3 nearest-neighbor ratio with a caliper of 0.02 was performed, using lithotripsy method as the dependent variable, and age, sex, stone size, and bile duct diameter as independent variables, resulting in well-balanced mechanical and laser lithotripsy groups. Kaplan-Meier survival analysis was used to assess recurrence-free survival, with comparisons performed using the log-rank test. Results:Before PSM, there were significant differences in age, sex, stone length, and bile duct diameter between the groups (all P<0.05). After PSM, 40 patients were included in the mechanical lithotripsy group, 34 in the laser group, and 35 in the combined group, with no significant differences in baseline or preoperative clinical characteristics (all P>0.05). The combined group had a significantly longer operative time compared to the mechanical group [71.0 (66.0, 92.0) min vs. 50.5 (40.4, 56.5) min, Z=-5.02, P<0.001] and the laser group [71.0 (66.0, 92.0) min vs. 53.0 (26.5, 73.5) min, Z=-2.61, P=0.001]. The laser group also had a longer operative time than the mechanical group [53.0 (26.5, 73.5) min vs. 50.5 (40.4, 56.5) min, Z=-2.27, P=0.023]. Hospitalization costs were significantly higher in the combined group compared to the mechanical group [43 000(33 000, 50 000) yuan vs. 30 000(26 000, 37 000) yuan; Z=-3.43, P<0.001]. The single-session stone clearance rates were 80.0% (32/40) for the mechanical group, 85.3% (29/34) for the laser group, and 62.9% (22/35) for the combined group. Postoperative complication rates were 20.0% (8/40), 11.7% (4/34), and 11.4% (4/35), respectively, with no statistically significant differences among the three groups (all P>0.05). There were also no significant differences in cumulative recurrence-free survival among the groups ( χ2=0.06, P=0.970). Conclusions:For endoscopic management of difficult CBD stones, combined lithotripsy is associated with longer operative time and higher hospitalization costs compared to mechanical and laser lithotripsy alone. Laser lithotripsy also requires more operative time than mechanical lithotripsy. However, the three lithotripsy strategies show no significant differences in postoperative complications or cumulative recurrence-free survival.
4.Study on the mechanism of PPARγ-Targeted intervention in abnormal lipid Metabolism-Induced dysfunction in placental trophoblast cells in preeclampsia and its clinical relevance
Jingrui LI ; Yaoyu SUO ; Tian TIAN ; Ping CAO ; Zhifeng DONG ; Nan JIANG ; Huiping ZHANG ; Kai WU ; Qing SHI ; Guizhong LI
The Journal of Practical Medicine 2025;41(16):2489-2497
Objective To investigate the causal relationship between abnormal placental lipid metabolism and trophoblast dysfunction in patients with preeclampsia(PE),and to explore the regulatory effects of PPARγ on trophoblast function under hypoxic conditions.Methods Placental tissues were collected from 30 patients with PE and 30 individuals with normal pregnancies at the General Hospital of Ningxia Medical University between October 2020 and November 2021 for the analysis of lipid deposition.A rat model of PE was established,comprising a sham-operated(Sham)group and a reduced uterine perfusion pressure(Rupp)group,with six rats in each group(n=12 total).Human trophoblast cells(HTR-8/SVneo)were cultured in vitro and randomly assigned to four experimental groups:normoxic control,hypoxia,hypoxia+PPARγ agonist(Rosiglitazone),and hypoxia+PPARγ antagonist(T0070907).The expression levels of lipid metabolism-related genes and transcription factors(FASN,FABP4,PPARγ,LXRα)were assessed using RT-qPCR.Western blotting was performed to determine the protein expression levels of PPARγ.Cell migration and invasion capacities were evaluated using scratch wound healing and Transwell assays,respectively.Results Placental lipid deposition in the PE group was significantly higher than that in the control group,particularly in the Rupp model mice(P<0.001).Under hypoxic conditions,the expression levels of FASN and FABP4 were upregulated in trophoblast cells(P<0.001),whereas the expression of PPARγ and LXRα was downregulated(P<0.001).Furthermore,treatment with the PPARγ antagonist T0070907 exacerbated the inhibitory effects of hypoxia on cell function(P<0.001),significantly reducing cell invasion and migration capacity(P<0.001).Additional siRNA-mediated knockdown experiments confirmed that PPARγ deficiency further aggravated hypoxia-induced impairments in cell migration and invasion,and this detrimental effect could not be reversed by Rosiglitazone.Conclusions Abnormal placental lipid metabolism in PE is closely linked to PPARγ-mediated enhancement of lipid synthesis and metabolic dysregulation under hypoxic conditions,which may subsequently impair trophoblast invasion and migration.
5.Comparison of the prognostic value of 15 nutritional/inflammatory indicators in postoperative cancer patients
Xiaoqian LIU ; Kai SUN ; Xiaolin WANG ; Qianqian ZHAO ; Xiaoxiao WU ; Fangqi SHEN ; Xi CHEN ; Chenxu TIAN ; Di WU ; Chunhua SONG ; HongXia XU ; Minghua CONG ; Hanping SHI ; Pingping JIA
Journal of Capital Medical University 2025;46(3):410-419
Objective To explore and identify the nutritional/inflammatory indicator with the highest predictive potential for overall survival(OS)in postoperative tumor patients so as to provide guidance for postoperative rehabilitation of tumor patients.Methods Data from 3 191 surgical patients were collected,including 15 nutritional/inflammatory indicators.The maximum selection rank statistic method was used to calculate the optimal cut-off values for continuous indicators.The Kaplan-Meier method was used to assess OS,and Cox proportional hazards models were used to analyze the association between the aforementioned 15 indicators and survival.The predictive value of these 15 indicators was evaluated with receiver operating characteristic(ROC)curves and C-index.Results Multivariate analysis showed that all 15 indicators were significantly associated with poorer OS in surgical patients(P<0.05 for all).Time-dependent area under the curve(AUC)and C-index analysis indicated that 3 indicators with the highest predictive potential in OS in postoperative tumor patients were the nutritional risk index(NRI)(C-index:0.597),C-reactive protein-to-albumin ratio(CAR)(C-index:0.587),and C-reactive protein-to-lymphocyte ratio(CLR)(C-index:0.587).The optimal cut-off value for NRI was determined to be 104.31(i.e.,NRI<104.31 suggests malnutrition)with the maximum selection rank statistic method,the optimal cut-off value for CAR to be 0.05(i.e.,CAR≥0.05 suggests a strong inflammatory response,often accompanied by malnutrition),and the optimal cut-off value for CLR to be 1.18(i.e.,CLR≥1.18 suggests a strong inflammatory response).Subgroup analysis indicated that NRI,CAR,and CLR had good correlation with tumor staging,and there were significant differences between tumor node metastasis(TNM)Ⅲ/Ⅳ stage patients and TNM Ⅰ/Ⅱ stage patients when there was a strong inflammatory response or malnutrition.Conclusion In postoperative tumor patients,NRI,CLR,and CAR have high prognostic value.Combining these with the patient's clinical stage,it enables more precise guidance for clinical diagnosis and treatment strategies.
6.Survival analysis of female breast cancer in Shanghai:a population-based study from 2002 to 2017
Chunxiao WU ; Yi PANG ; Kai GU ; Jiaying YAN ; Chunfang WANG ; Yongmei XIANG ; Yan SHI
China Oncology 2025;35(3):291-297
Background and purpose:The Shanghai Municipal Center for Disease Control and Prevention provides annual updates on cancer statistics in Shanghai.Breast cancer is one of the common malignant tumors among women.In recent years,the incidence of female breast cancer was increasing,while its trend of mortality showed declining.This study aimed to investigate the survival rates of new female breast cancer cases in Shanghai from 2002 to 2017.Methods:Data of new cases and deaths of female breast cancer patients with follow-up information from 2002 to 2017 were obtained from the Population-based Cancer Registry and Vital Statistics System of Shanghai Municipal Center for Disease Control and Prevention.Numbers,proportions,and survival rates were stratified by year of diagnosis,age,histological type and stage at diagnosis for analysis.The 5-year observed survival rates were calculated based on the life table method.The probabilities of surviving from 0 to 99 years were estimated with the Elandt-Johnson model,and then cumulative expected survival rates were calculated using the Ederer Ⅱ method.Finally,the 5-year relative survival rates were calculated.The annual percent change(APC)of survival rates was estimated by Joinpoint Regression Program.Results:A total of 73 600 new female breast cancer cases were diagnosed from 2002 to 2017 in Shanghai.Among them,67 681 cases were morphological verification,accounting for 91.96%.By December 31,2022,23 745(32.26%)cases had died,and 19 466(26.45%)cases had died of cancer.A total of 68 332(92.84%)cases,who were either dead or followed for over 5 years,were considered to have complete follow-up.The remaining 5 268(7.16%)cases were lost to follow-up.73 538(99.92%)cases were included in the observed cohort for survival analysis.The number of observed cases nearly doubled from 3330 in 2002 to 6095 in 2017.The 5-year observed survival rate changed from 78.77%in 2002 to 84.55%in 2017 dynamically,showed a low increasing trend with an average rate of 0.50%per year(APC=0.50%,t=8.75,P<0.001).The 5-year relative survival rate also increased from 83.46%to 89.24%slowly,with an average rate of 0.47%(APC=0.47%,t=9.80,P<0.001).The overall 5-year observation survival rate of female cancer was 83.24%(82.96%-83.52%),and the 5-year relative survival rate was 87.58%(87.29%-87.87%)in Shanghai from 2002 to 2017.It was increasing over time,decreasing with aging and advanced stage at diagnosis continuously.There was no significant difference in the 5-year relative survival rates between the groups aged 15 to 64(P>0.05).The group with an unknown stage had the highest number of cases,followed by the stage Ⅱ group,and then the stage Ⅰ group.The 5-year relative survival rate of cases with stage Ⅰ disease reached 99.10%(98.78%-99.42%),but these cases only accounted for 25.51%of the total.The 5-year relative survival rate of cases with stage Ⅳ disease was 52.54%(50.98%-54.11%),and these cases accounted for 6.13%of the total.The 5-year relative survival rate of cases with s unknown stage was 82.04%(81.42%-82.65%),and these cases accounted for 31.05%of the total.Conclusion:The diagnostic levels and survival rates of female breast cancer in Shanghai were relatively high and continue to improve.However,the proportions of cases with unknown histological type and unknown stage remain relatively high,and the proportion of stage Ⅰ cases is not very large.The survival rates of stage Ⅳ cases are relatively low.This study provides evidence for further research,prevention and control efforts for female breast cancer.
7.Intelligent recognition and automatic measurement of uterine fibroids based on ultrasonic images
Yanhui ZHANG ; Yi XIONG ; Bo SHI ; Xiaobing LIANG ; Meilan CHEN ; Kai WU
Chinese Journal of Ultrasonography 2025;34(7):602-607
Objective:To develop an intelligent recognition and precise segmentation technique using ultrasonic images,and to enhance diagnostic efficiency and accuracy.Methods:A total of 1,430 patients diagnosed with uterine fibroids through transvaginal ultrasonography at the Maternal and Child Health Hospital of Guangming from November 2020 to October 2024 were retrospectively included. Ultrasonic images were manually annotated by two experienced physicians and reviewed by a senior expert. The Mask DINO deep learning model was used for lesion segmentation,and the segmentation results were optimized using ellipse fitting technology. Model performance was evaluated using the Dice coefficient,intraclass correlation coefficient(ICC),mean absolute error(MAE),and measurement accuracy.Results:In the test set of 286 cases,the average Dice coefficient of model prediction was 0.992,indicating extremely high segmentation accuracy. The average accuracy of lesion identification by the model was 0.909,with 241 correctly identified samples,19 basically correct samples,and 26 incorrect samples. In terms of long and short axis measurements,the ICC of the model's direct predictions were 0.871(short axis)and 0.784(long axis),with MAE of 0.436 cm(short axis)and 0.508 cm(long axis). After optimization with ellipse fitting,the ICC increased to 0.893(short axis)and 0.866(long axis),and the MAE decreased to 0.191 cm(short axis)and 0.274 cm(long axis),the measurement accuracy improved significantly.Conclusions:The intelligent recognition and precise segmentation technique for uterine fibroids based on ultrasonic images constructed in this study performed excellently in lesion segmentation and measurement,it can significantly improve the efficiency and accuracy of diagnosis.
8.Incidence and mortality analysis of biliary tract cancer in Shanghai: population-based study from 2002 to 2020
Chunxiao WU ; Yi PANG ; Lei CHEN ; Yan SHI ; Kai GU
Journal of Surgery Concepts & Practice 2025;30(3):214-222
Objective To analyze the epidemiological characteristics and trends of the incidence and mortality of biliary tract cancer in Shanghai from 2002 to 2020. Methods Data on new cases and deaths of malignant tumors of the gallbladder, extrahepatic bile ducts, and other biliary tract organs from 2002 to 2020 were obtained from the Population-based Cancer Registry and Vital Statistics System of Shanghai Municipal Center for Disease Control and Prevention. Cases or deaths, proportion, crude rate, age-specific rate, age-standardized rate (ASR) and others were calculated stratified by year of diagnosis or death, gender and age-group. ASRs were calculated using Segi′s 1960 world standard population. Trends of the annual percent change (APC) of ASRs, age-specific rates and proportions of new cases with selected diagnostic character of biliary tract cancer stratified by different groups were analyzed by Joinpoint analysis software. Results Annual new cases of biliary tract cancer in Shanghai increased from 963 in 2002 to 1 537 in 2020, with ASR of incidence changing from 3.91/10⁵ to 3.59/10⁵. Annual deaths increased from 830 to 1 225, with ASR of mortality decreased from 3.36/10⁵ to 2.69/10⁵. In 2020, the crude rate of incidence of biliary tract cancer was 10.43/10⁵ (9.54/10⁵ in males and 11.30/10⁵ in females) in Shanghai, and the ASR was 3.59/10⁵ (3.54/10⁵ in males and 3.61/10⁵ in females), with no statistically significant gender difference (P=0.731). The crude rate of mortality was 8.31/10⁵ (7.60/10⁵ in males and 9.00/10⁵ in females), and the ASR was 2.69/10⁵ (2.69/10⁵ in males and 2.66/10⁵ in females), also with no significant gender difference (P=0.874). Age-specific nunbers and rates of incidence and mortality generally increased with aging. Stratified by gender, the trend of ASRs of incidence of biliary tract cancer in Shanghai in males showed no significant change (P=0.179) from 2002 to 2020, nor did that of ASRs of mortality (P=0.738). In females, the ASRs of incidence decreased at an average annual rate of 1.58% (P<0.001), while the trend of ASRs of mortality showed no significant change from 2002 to 2011 (P=0.774), but ASRs decreased at an average annual rate of 3.72% from 2011 to 2020 (P<0.001). Among new cases, the proportions of morphological verification increased, while the proportions of imaging verification decreased. The gallbladder was the most common site, but its proportions decreased significantly, whereas the proportions of extrahepatic bile duct increased from 25.75% to 42.88%. Over 60% of cases were unknown stage at diagnosis, while the combined proportions of stages Ⅰ-Ⅲ remained less than that of stage Ⅳ. Conclusions The ASRs for incidence and mortality of biliary tract cancer in Shanghai remain relatively high, with distinct epidemiological characteristics. The improvement in the diagnosis and treatment of biliary diseases maybe have impact on the incidence patterns of biliary tract cancer in Shanghai, but the effect on increasing survival rates and reducing mortality rates is relatively lagging. It needs a big progress to advance the screening, diagnosis, and survival of biliary tract cancer in Shanghai. This study provides a foundation for further research and prevention strategies for biliary tract cancer.
9.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
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Chromatin/genetics*
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Animals
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Binding Sites
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Mice
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DNA Footprinting/methods*
10.Pathogenesis and treatment strategies for infectious keratitis: Exploring antibiotics, antimicrobial peptides, nanotechnology, and emerging therapies.
Man YU ; Ling LI ; Yijun LIU ; Ting WANG ; Huan LI ; Chen SHI ; Xiaoxin GUO ; Weijia WU ; Chengzi GAN ; Mingze LI ; Jiaxu HONG ; Kai DONG ; Bo GONG
Journal of Pharmaceutical Analysis 2025;15(9):101250-101250
Infectious keratitis (IK) is a leading cause of blindness worldwide, primarily resulting from improper contact lens use, trauma, and a compromised immune response. The pathogenic microorganisms responsible for IK include bacteria, fungi, viruses, and Acanthamoeba. This review examines standard therapeutic agents for treating IK, including broad-spectrum empiric antibiotics for bacterial keratitis (BK), antifungals such as voriconazole and natamycin for fungal infections, and antiviral nucleoside analogues for viral keratitis (VK). Additionally, this review discusses therapeutic agents, such as polyhexamethylene biguanide (PHMB), for the treatment of Acanthamoeba keratitis (AK). The review also addresses emerging drugs and the challenges associated with their clinical application, including anti-biofilm agents that combat drug resistance and nuclear factor kappa-B (NF-κB) pathway-targeted therapies to mitigate inflammation. Furthermore, methods of Photodynamic Antimicrobial Therapy (PDAT) are explored. This review underscores the importance of integrating novel and traditional therapies to tackle drug resistance and enhance drug delivery, with the goal of advancing treatment strategies for IK.

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