1.The Refinement and Innovation of The UV Cross-linking and Immunoprecipitation
Jia-Min ZHAO ; Cheng-Jiang LU ; Ming YANG ; Nashun BUHE ; Gang WANG
Progress in Biochemistry and Biophysics 2025;52(4):1036-1052
RNA-binding proteins (RBPs) are ubiquitous components within cells, fulfilling essential functions in a myriad of biological processes. These proteins interact with RNA molecules to regulate gene expression at various levels, including transcription, splicing, transport, localization, translation, and degradation. Understanding the intricate network of RBP-RNA interactions is crucial for deciphering the complex regulatory mechanisms that govern cellular function and organismal development. Ultravidet (UV) cross-linking and immunoprecipitation (CLIP) stands out as a powerful approach designed to map the precise locations where RBPs bind to RNA. By using UV light to create covalent bonds between proteins and RNA, followed by immunoprecipitation to isolate the protein-RNA complexes, researchers can identify the direct targets of specific RBPs. The advent of high-throughput sequencing technologies has revolutionized CLIP, enabling the identification of not only the types but also the exact sequences of RNA bound by RBPs on a genome-wide scale. The evolution of CLIP has led to the development of specialized variants, each with unique features that address specific challenges and expand the scope of what can be studied. High-throughput sequencing CLIP (HITS-CLIP) was one of the first advancements, significantly increasing the throughput and resolution of RNA-protein interaction mapping. Photoactivatable-ribonucleoside-enhanced CLIP (PAR-CLIP) introduced the use of photoactivatable ribonucleosides to enhance cross-linking efficiency and specificity, reducing background noise and improving the detection of low-abundance RNA-protein interactions. Individual-nucleotide resolution CLIP (iCLIP) further refined the technique, achieving unprecedented precision by resolving individual nucleotides involved in RBP binding, which is particularly valuable for studying the fine details of RNA structure and function. Despite the remarkable progress, there remains room for improvement in CLIP technology. Researchers continue to seek methods to increase sensitivity, reduce technical variability, and improve the reproducibility of results. Advances in sample preparation, data analysis algorithms, and computational tools are critical for addressing these challenges. Moreover, the application of CLIP to more diverse biological systems, including non-model organisms and clinical samples, requires the development of tailored protocols and the optimization of existing ones. Looking forward, the field of RNA biology is poised to benefit greatly from ongoing innovations in CLIP technology. The exploration of non-canonical RNA-protein interactions, such as those involving long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), promises to reveal new layers of cellular regulation and may lead to the discovery of novel therapeutic targets. Furthermore, integrating CLIP data with other omics approaches, such as proteomics and metabolomics, will provide a more comprehensive understanding of the dynamic interplay between RNA and its binding partners within the cell. In conclusion, the continuous refinement and expansion of CLIP techniques have not only deepened our knowledge of RNA biology but have also opened up new avenues for investigating the molecular underpinnings of health and disease. As the technology matures, it is expected to play an increasingly pivotal role in both basic and applied research, contributing to the advancement of medical science and biotechnology.
2.Increased CT Attenuation of Pericolic Adipose Tissue as a Noninvasive Marker of Disease Severity in Ulcerative Colitis
Jun LU ; Hui XU ; Jing ZHENG ; Tianxin CHENG ; Xinjun HAN ; Yuxin WANG ; Xuxu MENG ; Xiaoyang LI ; Jiahui JIANG ; Xue DONG ; Xijie ZHANG ; Zhenchang WANG ; Zhenghan YANG ; Lixue XU
Korean Journal of Radiology 2025;26(5):411-421
Objective:
Accurate evaluation of inflammation severity in ulcerative colitis (UC) can guide treatment strategy selection. The potential value of the pericolic fat attenuation index (FAI) on CT as an indicator of disease severity remains unknown.This study aimed to assess the diagnostic accuracy of pericolic FAI in predicting UC severity.
Materials and Methods:
This retrospective study enrolled 148 patients (mean age 48 years; 87 males). The fat attenuation on CT was measured in four different locations: the mesocolic vascular side (MS) and opposite side of MS (OMS) around the most severe bowel lesion, the retroperitoneal space (RS), and the subcutaneous area. The fat attenuation indices (FAI MS, FAI OMS, and FAI RS) were calculated as the fat attenuation measured in MS, OMS, and RS, respectively, minus that of the subcutaneous area, and were obtained in the non-enhanced, arterial, and delayed phases. Correlations between the FAI and UC Endoscopic Index of Severity (UCEIS) were assessed using Spearman’s correlation. Predictors of severe UC (UCEIS ≥7) were selected by univariable analysis. The performance of FAI in predicting severe UC was evaluated using the area under the receiver operating characteristic curve (AUC).
Results:
The FAIMS and FAI OMS scores were significantly higher than FAI RS in three phases (all P < 0.001). The FAIMS and FAI OMS scores moderately correlated with the UCEIS score (r = 0.474–0.649 among the three phases). Additionally, FAI MS and FAI OMS identified severe UC, with AUC varying from 0.77 to 0.85.
Conclusion
Increased CT attenuation of pericolic adipose tissue could serve as a noninvasive marker for evaluating UC severity. FAI MS and FAI OMS of three phases showed similar prediction accuracies for severe UC identification.
3.Increased CT Attenuation of Pericolic Adipose Tissue as a Noninvasive Marker of Disease Severity in Ulcerative Colitis
Jun LU ; Hui XU ; Jing ZHENG ; Tianxin CHENG ; Xinjun HAN ; Yuxin WANG ; Xuxu MENG ; Xiaoyang LI ; Jiahui JIANG ; Xue DONG ; Xijie ZHANG ; Zhenchang WANG ; Zhenghan YANG ; Lixue XU
Korean Journal of Radiology 2025;26(5):411-421
Objective:
Accurate evaluation of inflammation severity in ulcerative colitis (UC) can guide treatment strategy selection. The potential value of the pericolic fat attenuation index (FAI) on CT as an indicator of disease severity remains unknown.This study aimed to assess the diagnostic accuracy of pericolic FAI in predicting UC severity.
Materials and Methods:
This retrospective study enrolled 148 patients (mean age 48 years; 87 males). The fat attenuation on CT was measured in four different locations: the mesocolic vascular side (MS) and opposite side of MS (OMS) around the most severe bowel lesion, the retroperitoneal space (RS), and the subcutaneous area. The fat attenuation indices (FAI MS, FAI OMS, and FAI RS) were calculated as the fat attenuation measured in MS, OMS, and RS, respectively, minus that of the subcutaneous area, and were obtained in the non-enhanced, arterial, and delayed phases. Correlations between the FAI and UC Endoscopic Index of Severity (UCEIS) were assessed using Spearman’s correlation. Predictors of severe UC (UCEIS ≥7) were selected by univariable analysis. The performance of FAI in predicting severe UC was evaluated using the area under the receiver operating characteristic curve (AUC).
Results:
The FAIMS and FAI OMS scores were significantly higher than FAI RS in three phases (all P < 0.001). The FAIMS and FAI OMS scores moderately correlated with the UCEIS score (r = 0.474–0.649 among the three phases). Additionally, FAI MS and FAI OMS identified severe UC, with AUC varying from 0.77 to 0.85.
Conclusion
Increased CT attenuation of pericolic adipose tissue could serve as a noninvasive marker for evaluating UC severity. FAI MS and FAI OMS of three phases showed similar prediction accuracies for severe UC identification.
4.Increased CT Attenuation of Pericolic Adipose Tissue as a Noninvasive Marker of Disease Severity in Ulcerative Colitis
Jun LU ; Hui XU ; Jing ZHENG ; Tianxin CHENG ; Xinjun HAN ; Yuxin WANG ; Xuxu MENG ; Xiaoyang LI ; Jiahui JIANG ; Xue DONG ; Xijie ZHANG ; Zhenchang WANG ; Zhenghan YANG ; Lixue XU
Korean Journal of Radiology 2025;26(5):411-421
Objective:
Accurate evaluation of inflammation severity in ulcerative colitis (UC) can guide treatment strategy selection. The potential value of the pericolic fat attenuation index (FAI) on CT as an indicator of disease severity remains unknown.This study aimed to assess the diagnostic accuracy of pericolic FAI in predicting UC severity.
Materials and Methods:
This retrospective study enrolled 148 patients (mean age 48 years; 87 males). The fat attenuation on CT was measured in four different locations: the mesocolic vascular side (MS) and opposite side of MS (OMS) around the most severe bowel lesion, the retroperitoneal space (RS), and the subcutaneous area. The fat attenuation indices (FAI MS, FAI OMS, and FAI RS) were calculated as the fat attenuation measured in MS, OMS, and RS, respectively, minus that of the subcutaneous area, and were obtained in the non-enhanced, arterial, and delayed phases. Correlations between the FAI and UC Endoscopic Index of Severity (UCEIS) were assessed using Spearman’s correlation. Predictors of severe UC (UCEIS ≥7) were selected by univariable analysis. The performance of FAI in predicting severe UC was evaluated using the area under the receiver operating characteristic curve (AUC).
Results:
The FAIMS and FAI OMS scores were significantly higher than FAI RS in three phases (all P < 0.001). The FAIMS and FAI OMS scores moderately correlated with the UCEIS score (r = 0.474–0.649 among the three phases). Additionally, FAI MS and FAI OMS identified severe UC, with AUC varying from 0.77 to 0.85.
Conclusion
Increased CT attenuation of pericolic adipose tissue could serve as a noninvasive marker for evaluating UC severity. FAI MS and FAI OMS of three phases showed similar prediction accuracies for severe UC identification.
5.Effect of Wulao Qisun Prescription on Proliferation and Osteogenic Differentiation of AS Fibroblasts by Regulating Wnt/β-catenin Signaling Pathway
Juanjuan YANG ; Ping CHEN ; Haidong WANG ; Zhendong WANG ; Haolin LI ; Zhimin ZHANG ; Yuping YANG ; Weigang CHENG ; Jin SU ; Jingjing SONG ; Dongsheng LU
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(2):67-73
ObjectiveTo investigate the effect and underlying mechanism of the Wulao Qisun prescription on pathological new bone formation in ankylosing spondylitis (AS). MethodsSynovial fibroblasts were isolated from the hip joints of AS patients and observed under a microscope to assess cell morphology. The cells were identified using immunofluorescence staining. The isolated AS fibroblasts were divided into blank group, low drug-containing serum group, medium drug-containing serum group, high drug-containing serum group, and positive drug group. After drug intervention, cell proliferation was measured using the cell counting kit-8 (CCK-8) assay to observe fibroblast growth and determine the optimal intervention time. Alkaline phosphatase (ALP) activity was measured using the alkaline phosphatase assay. Protein expression of osteocalcin (OCN), osteopontin (OPN), and runt-related transcription factor 2 (Runx2) was detected by Western blot. The mRNA expression levels of Wnt5a, β-catenin, and Dickkopf-1 (DKK-1) were measured by real-time quantitative polymerase chain reaction (Real-time PCR). ResultsCompared with the blank group, each drug-containing serum group of Wulao Qisun prescription and the positive drug group inhibited the proliferation of AS fibroblasts and reduced ALP expression (P<0.01). Compared with the blank group, the low drug-containing serum group of Wulao Qisun prescription downregulated β-catenin mRNA expression (P<0.05). The medium and high drug-containing serum groups and the positive drug group significantly downregulated Wnt5a and β-catenin mRNA expression (P<0.05, P<0.01), with the positive drug group showing the most pronounced effect (P<0.01). The high drug-containing serum group and the positive drug group significantly upregulated DKK-1 mRNA expression (P<0.01). Compared with the blank group, the low drug-containing serum group of Wulao Qisun prescription inhibited the expression of OPN and Runx2 proteins (P<0.05, P<0.01), while the medium and high drug-containing serum groups and the positive drug group inhibited the expression of OCN, OPN, and Runx2 proteins (P<0.05, P<0.01). ConclusionThe Wulao Qisun prescription can inhibit the proliferation and osteogenic differentiation of AS fibroblasts, thereby delaying the formation of pathological new bone in AS. The possible mechanism involves the regulation of Wnt/β-catenin-related gene expression, further inhibiting the transcription of downstream target genes.
6.Increased CT Attenuation of Pericolic Adipose Tissue as a Noninvasive Marker of Disease Severity in Ulcerative Colitis
Jun LU ; Hui XU ; Jing ZHENG ; Tianxin CHENG ; Xinjun HAN ; Yuxin WANG ; Xuxu MENG ; Xiaoyang LI ; Jiahui JIANG ; Xue DONG ; Xijie ZHANG ; Zhenchang WANG ; Zhenghan YANG ; Lixue XU
Korean Journal of Radiology 2025;26(5):411-421
Objective:
Accurate evaluation of inflammation severity in ulcerative colitis (UC) can guide treatment strategy selection. The potential value of the pericolic fat attenuation index (FAI) on CT as an indicator of disease severity remains unknown.This study aimed to assess the diagnostic accuracy of pericolic FAI in predicting UC severity.
Materials and Methods:
This retrospective study enrolled 148 patients (mean age 48 years; 87 males). The fat attenuation on CT was measured in four different locations: the mesocolic vascular side (MS) and opposite side of MS (OMS) around the most severe bowel lesion, the retroperitoneal space (RS), and the subcutaneous area. The fat attenuation indices (FAI MS, FAI OMS, and FAI RS) were calculated as the fat attenuation measured in MS, OMS, and RS, respectively, minus that of the subcutaneous area, and were obtained in the non-enhanced, arterial, and delayed phases. Correlations between the FAI and UC Endoscopic Index of Severity (UCEIS) were assessed using Spearman’s correlation. Predictors of severe UC (UCEIS ≥7) were selected by univariable analysis. The performance of FAI in predicting severe UC was evaluated using the area under the receiver operating characteristic curve (AUC).
Results:
The FAIMS and FAI OMS scores were significantly higher than FAI RS in three phases (all P < 0.001). The FAIMS and FAI OMS scores moderately correlated with the UCEIS score (r = 0.474–0.649 among the three phases). Additionally, FAI MS and FAI OMS identified severe UC, with AUC varying from 0.77 to 0.85.
Conclusion
Increased CT attenuation of pericolic adipose tissue could serve as a noninvasive marker for evaluating UC severity. FAI MS and FAI OMS of three phases showed similar prediction accuracies for severe UC identification.
7.Increased CT Attenuation of Pericolic Adipose Tissue as a Noninvasive Marker of Disease Severity in Ulcerative Colitis
Jun LU ; Hui XU ; Jing ZHENG ; Tianxin CHENG ; Xinjun HAN ; Yuxin WANG ; Xuxu MENG ; Xiaoyang LI ; Jiahui JIANG ; Xue DONG ; Xijie ZHANG ; Zhenchang WANG ; Zhenghan YANG ; Lixue XU
Korean Journal of Radiology 2025;26(5):411-421
Objective:
Accurate evaluation of inflammation severity in ulcerative colitis (UC) can guide treatment strategy selection. The potential value of the pericolic fat attenuation index (FAI) on CT as an indicator of disease severity remains unknown.This study aimed to assess the diagnostic accuracy of pericolic FAI in predicting UC severity.
Materials and Methods:
This retrospective study enrolled 148 patients (mean age 48 years; 87 males). The fat attenuation on CT was measured in four different locations: the mesocolic vascular side (MS) and opposite side of MS (OMS) around the most severe bowel lesion, the retroperitoneal space (RS), and the subcutaneous area. The fat attenuation indices (FAI MS, FAI OMS, and FAI RS) were calculated as the fat attenuation measured in MS, OMS, and RS, respectively, minus that of the subcutaneous area, and were obtained in the non-enhanced, arterial, and delayed phases. Correlations between the FAI and UC Endoscopic Index of Severity (UCEIS) were assessed using Spearman’s correlation. Predictors of severe UC (UCEIS ≥7) were selected by univariable analysis. The performance of FAI in predicting severe UC was evaluated using the area under the receiver operating characteristic curve (AUC).
Results:
The FAIMS and FAI OMS scores were significantly higher than FAI RS in three phases (all P < 0.001). The FAIMS and FAI OMS scores moderately correlated with the UCEIS score (r = 0.474–0.649 among the three phases). Additionally, FAI MS and FAI OMS identified severe UC, with AUC varying from 0.77 to 0.85.
Conclusion
Increased CT attenuation of pericolic adipose tissue could serve as a noninvasive marker for evaluating UC severity. FAI MS and FAI OMS of three phases showed similar prediction accuracies for severe UC identification.
8.Clinical value of peripheral immune function status in the assessment of ‘Deficiency of Vital Qi’ in lung cancer metastasis
XU Fan1,2 ; TIAN Jianhui1,2 ; LIU Youjun1,2 ; CHENG Zhenyang1,2 ; QUE Zujun2 ; LUO Bin1 ; YANG Yun1 ; YAO Jialiang1 ; YAO Wang1 ; LU Xinyi1,2 ; LIU Yao1,2 ; ZHOU Yiyang1 ; WU Jianchun1 ; LUO Yingbin1 ; LI Minghua1 ; SHI Wenfei1 ; CUI Yajing1 ; SHANGGUAN Wenji3 ; LI Yan1
Chinese Journal of Cancer Biotherapy 2025;32(10):1065-1070
[摘 要] 目的:探索外周免疫功能状态与肺癌转移的关联,筛选可用于肺癌转移“正虚”评估的外周血免疫标志物。方法:回顾性分析2023年3月至2025年4月期间上海中医药大学附属市中医医院收治的肺癌患者治疗前的外周血免疫标志物,根据是否存在远处转移,将患者分为无转移组与转移组,比较两组间免疫细胞和细胞因子的表达差异。将单因素分析P < 0.05的外周血免疫指标纳入多因素二元Logistic回归模型,以识别肺癌转移的独立预测因素。结果:共纳入193例肺癌患者(无转移组101例,转移组92例),两组在性别、年龄、吸烟史、饮酒史、病理类型间的差异均无统计学意义(均P > 0.05)。单因素分析显示,无转移组与转移组间有多项免疫指标存在显著差异(均P < 0.05),包括:淋巴细胞计数,CD3+、CD4+、CD8+ T、CD19+ B细胞及CD3-CD16+56+ NK细胞绝对计数,Treg细胞、CD8+CD28+ Treg细胞、G-MDSC和CD3-CD16+CD56+dim NK细胞百分率,以及细胞因子IL-1β、IL-6和IL-10水平。将差异性指标行二元Logistic回归分析,提示外周血中Treg细胞和CD8+CD28+ Treg细胞百分率是肺癌发生远处转移的独立预测因素[OR = 1.193, 95% CI(1.047, 1.36), P < 0.01; OR = 0.978, 95% CI(0.957, 0.999), P < 0.05]。结论:外周血免疫功能紊乱是肺癌转移“正虚”的生物学基础,本研究以量化指标证实外周免疫功能状态与肺癌转移的相关性,为“正虚伏毒”和“肿瘤转移态”理论提供了实证。
9.Proficiency testing on determination of the content of geniposide in Gardeniae fructus by HPLC
Xiaohan GUO ; Yan CHANG ; Jiating ZHANG ; Kunzi YU ; Jianbo YANG ; Minghua LI ; Siyu MA ; Yiyun LU ; Xinhua XIANG ; Xianlong CHENG ; Feng WEI
Chinese Journal of Pharmacoepidemiology 2024;33(10):1115-1123
Objective To carry out a proficiency testing of content determination of geniposide in Gardeniae fructus,evaluate the content determination ability of index components in traditional Chinese medicine in the laboratory of inspection and detection in drug-related fields,and improve the quality control ability of content determination of related laboratories.Methods The laboratory's capability-verification activities were conducted based on the CNAS-RL02 Rules for Proficiency Testing and ISO/IEC 17043 Conformity Assessment-General Requirements for Proficiency Testing.After preparing the sample,the results of homogeneity and stability tests were analyzed according to CNAS-GL003 Guidance on Evaluating the Homogeneity and Stability of Samples Used for Proficiency Testing.After the test results were qualified,they were used as proficiency testing samples and randomly distributed to participants.The results were collected,and the robust statistical method and the Z scores were used to analyze the results of these laboratories'reports.Results 403 laboratories in this proficiency testing program reported the results,of which 367 results were acceptable,accounting for 91.07%,17(4.22%)laboratories obtained suspicious results,and 19 laboratories gave unsatisfactory results,with the dissatisfaction rate of 4.71%.Conclusion The majority of the 403 participant laboratories have the ability to determine the content of geniposide in Gardeniae fructus by HPLC and the laboratory testing ability and quality management level of the drug monitoring system are high.This proficiency testing provides a basis for understanding the technical reserve capacity and management level of China's pharmaceutical inspection and testing laboratories,and provides technical support for future government supervision.
10.Establish the method of bacterial endotoxins test for human papillomavirus bivalent(types 16,18)vaccine(pichia pastoris)
Li WANG ; Chongyi YANG ; Hongyan WANG ; Jiansheng LU ; Bin CHENG
Chinese Journal of Pharmacoepidemiology 2024;33(11):1239-1246
Objective Establish the method of bacterial endotoxins test for human papillomavirus bivalent(types 16,18)vaccine(pichia pastoris).Methods The method of gel-clot technique and photometric technique(kinetic-turbidimetric assay and kinetic-chromogenic assay)for the determination of bacterial endotoxins was carried out according to the Appendix of China Pharmacopoeia in 2020 Vol Ⅲ 1143"bacterial endotoxins test"and Vol IV 9251"guidelines for bacterial endotoxin test".Results There is no interference after more than forty times dilution for gel-clot technique,the recovery rates of kinetic-turbidimetric assay and kinetic-chromogenic assay can also meet the requirements.Conclusion It is feasible to establish gel-clot technique,kinetic-turbidimetric assay and kinetic-chromogenic assay for bacterial endotoxin test of human papillomavirus bivalent(types 16,18)vaccine(pichia pastoris).

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