1.Analysis of T7 RNA Polymerase: From Structure-function Relationship to dsRNA Challenge and Biotechnological Applications
Wei-Chen NING ; Yu HUA ; Hui-Ling YOU ; Qiu-Shi LI ; Yao WU ; Yun-Long LIU ; Zhen-Xin HU
Progress in Biochemistry and Biophysics 2025;52(9):2280-2294
T7 RNA polymerase (T7 RNAP) is one of the simplest known RNA polymerases. Its unique structural features make it a critical model for studying the mechanisms of RNA synthesis. This review systematically examines the static crystal structure of T7 RNAP, beginning with an in-depth examination of its characteristic “thumb”, “palm”, and “finger” domains, which form the classic “right-hand-like” architecture. By detailing these structural elements, this review establishes a foundation for understanding the overall organization of T7 RNAP. This review systematically maps the functional roles of secondary structural elements and their subdomains in transcriptional catalysis, progressively elucidating the fundamental relationships between structure and function. Further, the intrinsic flexibility of T7 RNAP and its applications in research are also discussed. Additionally, the review presents the structural diagrams of the enzyme at different stages of the transcription process, and through these diagrams, it provides a detailed description of the complete transcription process of T7 RNAP. By integrating structural dynamics and kinetics analyses, the review constructs a comprehensive framework that bridges static structure to dynamic processes. Despite its advantages, T7 RNAP has a notable limitation: it generates double-stranded RNA (dsRNA) as a byproduct. The presence of dsRNA not only compromises the purity of mRNA products but also elicits nonspecific immune responses, which pose significant challenges for biotechnological and therapeutic applications. The review provides a detailed exploration of the mechanisms underlying dsRNA formation during T7 RNAP catalysis, reviews current strategies to mitigate this issue, and highlights recent progress in the field. A key focus is the semi-rational design of T7 RNAP mutants engineered to minimize dsRNA generation and enhance catalytic performance. Beyond its role in transcription, T7 RNAP exhibits rapid development and extensive application in fields, including gene editing, biosensing, and mRNA vaccines. This review systematically examines the structure-function relationships of T7 RNAP, elucidates the mechanisms of dsRNA formation, and discusses engineering strategies to optimize its performance. It further explores the engineering optimization and functional expansion of T7 RNAP. Furthermore, this review also addresses the pressing issues that currently need resolution, discusses the major challenges in the practical application of T7 RNAP, and provides an outlook on potential future research directions. In summary, this review provides a comprehensive analysis of T7 RNAP, ranging from its structural architecture to cutting-edge applications. We systematically examine: (1) the characteristic right-hand domains (thumb, palm, fingers) that define its minimalistic structure; (2) the structure-function relationships underlying transcriptional catalysis; and (3) the dynamic transitions during the complete transcription cycle. While highlighting T7 RNAP’s versatility in gene editing, biosensing, and mRNA vaccine production, we critically address its major limitation—dsRNA byproduct formation—and evaluate engineering solutions including semi-rationally designed mutants. By synthesizing current knowledge and identifying key challenges, this work aims to provide novel insights for the development and application of T7 RNAP and to foster further thought and progress in related fields.
2.Electroacupuncture Promotes Functional Recovery after Facial Nerve Injury in Rats by Regulating Autophagy via GDNF and PI3K/mTOR Signaling Pathway.
Jun-Peng YAO ; Xiu-Mei FENG ; Lu WANG ; Yan-Qiu LI ; Zi-Yue ZHU ; Xiang-Yun YAN ; Yu-Qing YANG ; Ying LI ; Wei ZHANG
Chinese journal of integrative medicine 2024;30(3):251-259
OBJECTIVE:
To explore the mechanism of electroacupuncture (EA) in promoting recovery of the facial function with the involvement of autophagy, glial cell line-derived neurotrophic factor (GDNF), and phosphatidylinositol-3-kinase (PI3K)/mammalian target of rapamycin (mTOR) signaling pathway.
METHODS:
Seventy-two male Sprague-Dawley rats were randomly allocated into the control, sham-operated, facial nerve injury (FNI), EA, EA+3-methyladenine (3-MA), and EA+GDNF antagonist groups using a random number table, with 12 rats in each group. An FNI rat model was established with facial nerve crushing method. EA intervention was conducted at Dicang (ST 4), Jiache (ST 6), Yifeng (SJ 17), and Hegu (LI 4) acupoints for 2 weeks. The Simone's 10-Point Scale was utilized to monitor the recovery of facial function. The histopathological evaluation of facial nerves was performed using hematoxylin-eosin (HE) staining. The levels of Beclin-1, light chain 3 (LC3), and P62 were detected by immunohistochemistry (IHC), immunofluorescence, and reverse transcription-polymerase chain reaction, respectively. Additionally, IHC was also used to detect the levels of GDNF, Rai, PI3K, and mTOR.
RESULTS:
The facial functional scores were significantly increased in the EA group than the FNI group (P<0.05 or P<0.01). HE staining showed nerve axons and myelin sheaths, which were destroyed immediately after the injury, were recovered with EA treatment. The expressions of Beclin-1 and LC3 were significantly elevated and the expression of P62 was markedly reduced in FNI rats (P<0.01); however, EA treatment reversed these abnormal changes (P<0.01). Meanwhile, EA stimulation significantly increased the levels of GDNF, Rai, PI3K, and mTOR (P<0.01). After exogenous administration with autophagy inhibitor 3-MA or GDNF antagonist, the repair effect of EA on facial function was attenuated (P<0.05 or P<0.01).
CONCLUSIONS
EA could promote the recovery of facial function and repair the facial nerve damages in a rat model of FNI. EA may exert this neuroreparative effect through mediating the release of GDNF, activating the PI3K/mTOR signaling pathway, and further regulating the autophagy of facial nerves.
Rats
;
Male
;
Animals
;
Rats, Sprague-Dawley
;
Electroacupuncture
;
Phosphatidylinositol 3-Kinase/metabolism*
;
Facial Nerve Injuries/therapy*
;
Phosphatidylinositol 3-Kinases/metabolism*
;
Beclin-1
;
Glial Cell Line-Derived Neurotrophic Factor
;
Signal Transduction
;
TOR Serine-Threonine Kinases/metabolism*
;
Autophagy
;
Mammals/metabolism*
3.Bioinformatics-based screening for ferroptosis-related DEGs of EGFR-TKIs resistance in non-small cell lung cancer
Ying FENG ; Yao ZHENG ; Chengfeng QIU ; Liming TAN
International Journal of Laboratory Medicine 2024;45(6):744-750
Objective To screen for ferroptosis-related differentially expressed genes(DEGs)of epidermal growth factor receptor(EGFR)-tyrosine kinase inhibitors(TKIs)resistance in non-small cell lung cancer(NSCLC).Methods The gene sequencing dataset GSE117846 of NSCLC EGFR-TKIs resistant cells was se-lected from the Gene Expression Omnibus data base(GEO)and screened for DEGs with P<0.05 and | log2 FC |1.Ferroptosis-related genes were collected using the FerrDb database and jvenn was used to intersected the DEGs screened from GSE117846 dataset with the ferroptosis-related genes obtained from FerrDb database.GO function and KEGG pathway enrichment analysis of intersection genes were performed,and protein-pro-tein interaction(PPI)network was drawn.The score of intersection genes was calculated by using Cytohubba plug-in in Cytoscape software,and the top 10 genes were used for Hub genes screening.ULCAN and GEPIA2 databases were used to analyze the expression of Hub genes in NSCLC and its effect on the survival prognosis of patients.Real-time fluorescence quantitative PCR(qPCR)was used to detect the relative expression levels of Hub gene mRNA in NSCLC patients'cancer tissues,adjacent tissues and in vitro cells to verify the results of bioinformatics analysis.Results A total of 60 ferroptosis-related DEGs of EGFR-TKIs resistance in NSCLC were screened out,including 30 up-regulated genes and 30 down-regulated genes.The 60 genes were mainly enriched in P53 signaling pathway,ferroptosis pathway and FoxO signaling pathway.There were 57 nodes and 99 edges in the PPI network,with an average clustering coefficient of 0.377 and PPI enrichment P<0.01.The Hub gene screened out by Cytohubba plug-in was tumor protein P63(TP63).ULCAN and GE-PIA2 database analysis showed that the expression of TP63 in lung adenocarcinoma tissue was significantly lower than that in normal tissue,while the expression of TP63 in lung squamous cell carcinoma tissue was sig-nificantly higher than that in normal tissue,and the differences were statistically significant(P<0.05).In pa-tients with lung adenocarcinoma,there was no significant difference in the survival prognosis between TP63 high and low expression groups(P>0.05),while in patients with lung squamous cell carcinoma,the survival prognosis of TP63 low expression group was better,and the difference was statistically significant(P<0.05).QPCR showed that TP63 mRNA highly expressed in lung squamous cell carcinoma tissue and lowly expressed in lung adenocarcinoma tissue compared with adjacent tissues(P<0.05).The expression of TP63 mRNA was down-regulated in gefitinib-resistant PC9/GR cells(P<0.05),which was consistent with the re-sults of bioinformatics analysis.Conclusion TP63 may be an important gene linking NSCLC EGFR-TKIs re-sistance to ferroptosis.
4.A clinical prediction model based on 68Ga-PSMA-11 PET/CT and mpMRI parameters to determine the diagnostic accuracy of targeted biopsy alone in prostate cancer population
Chaoli AN ; Xuefeng QIU ; Feng WANG ; Yao FU ; Xiaozhi ZHAO ; Hongqian GUO
Journal of Modern Urology 2024;29(3):212-218
【Objective】 To develop a clinical prediction model based on 68Ga-prostate-specific membrane antigen-11 (68Ga-PSMA-11), positron emission tomography/computed tomography (PET/CT) and multiparametric magnetic resonance imaging (mpMRI) parameters to stratify prostate cancer patients undergoing targeted biopsy, so as to avoid unnecessary systematic biopsy. 【Methods】 A total of 96 clinically significant prostate cancer (csPCa) patients who underwent 68Ga-PSMA-11 PET/CT and mpMRI prior to prostate targeted biopsy with systematic biopsy during Jan.2020 and Feb.2023 in Nanjing Drum Tower Hospital were retrospectively analyzed.By univariate and multivariate logistic regression analyses, maximum standard uptake value (SUVmax) in 68Ga-PSMA-11 PET/CT and minimum apparent diffusion coefficien (ADCmin) in mpMRI, as well as clinical parameters were evaluated to identify the independent predictors correlative with the effective diagnosis of targeted biopsy, and a clinical prediction model was constructed. 【Results】 Multivariate logistic regression analysis showed that SUVmax (OR=0.878, 95%CI: 0.804-0.959, P=0.004) and ADCmin (OR=1.005, 95%CI:1.001-1.010, P=0.027) were independent predictors of the effective diagnosis of targeted biopsy alone.The sensitivity, specificity, accuracy and area under the receiver operator characteristic curve (AUC) of the model were 0.80, 0.80, 0.83 and 0.84, respectively. 【Conclusion】 The clinical prediction model based on 68Ga-PSMA-11 PET/CT and mpMRI parameters is helpful to improve the effective diagnosis of targeted biopsy alone, and has practical value to stratify patients with csPCa so as to safely avoid systematic biopsy and effectively balance the benefits and risks.
5.Trends in age-, period- and cohort-specific incidence of hepatitis C in Chifeng City from 2008 to 2022
LI Wenjun ; LI Hui ; YANG Jingyuan ; YANG Hong ; GAO Ya ; GAO Baicheng ; LI Yao ; ZHANG Qiyue ; QIU Yafei
Journal of Preventive Medicine 2024;36(6):514-517,522
Objective:
To explore incidence trend of hepatitis C in Chifeng City, Inner Mongolia Autonomous Region from 2008 to 2022, so as to provide the basis for formulating prevention and control measures for hepatitis C.
Methods:
Data of reported hepatitis C cases in Chifeng City from 2008 to 2022 was collected through the Infectious Disease Information Reporting Management System. Trends in incidence of hepatitis C were analyzed using annual percent change (APC) and average annual percent change (AAPC). Impact of age, period and birth cohort on the risk of developing hepatitis C were analyzed by an age-period-cohort model.
Results:
The annual average reported incidence rate of hepatitis C in Chifeng City was 59.13/105 from 2008 to 2022. The incidence showed an upward trend from 2008 to 2018 (APC=9.405%, P<0.05) and a downward trend from 2018 to 2022 (APC=-17.475%, P<0.05), but the overall trend was not statistically significant (AAPC=0.937%, P>0.05). The age-period-cohort model analysis showed that the incidence risks of hepatitis C in the residents aged 0 to 4 years and 45 to 84 years were higher than those in the residents aged 40 to 44 years (the control group). The incidence risk of hepatitis C increased with age from 40 to 79 years. Compared with 2008-2012, the incidence risk of hepatitis C showed an increasing trend followed by a decline in 2008-2022. The incidence risk was higher in 2013-2017 and lower in 2018-2022 than in 2008-2012. The incidence risk of hepatitis C showed an increasing trend followed by a decreasing trend by using the birth cohort from 1968 to 1972 as the control. The birth cohort from 1953 to 1977 had a higher incidence risk of hepatitis C than other birth cohorts.
Conclusions
The overall incidence of hepatitis C in Chifeng City from 2008 to 2022 appeared a tendency towards a decline, and the incidence risk increased with age. Screening and health education for the elderly and high-risk birth cohorts should be strengthened.
6.Expert consensus on digital intraoral scanning technology
Jie YOU ; Wenjuan YAN ; Liting LIN ; Wen-Zhen GU ; Yarong HOU ; Wei XIAO ; Hui YAO ; Yaner LI ; Lihui MA ; Ruini ZHAO ; Junqi QIU ; Jianzhang LIU ; Yi ZHOU
Journal of Prevention and Treatment for Stomatological Diseases 2024;32(8):569-577
Digital intraoral scanning is a hot topic in the field of oral digital technology.In recent years,digital intra-oral scanning has gradually become the mainstream technology in orthodontics,prosthodontics,and implant dentistry.The precision of digital intraoral scanning and the accuracy and stitching of data collection are the keys to the success of the impression.However,the operators are less familiar with the intraoral scanning characteristics,imaging process-ing,operator scanning method,oral tissue specificity of the scanned object,and restoration design.Thus far,no unified standard and consensus on digital intraoral scanning technology has been achieved at home or abroad.To deal with the problems encountered in oral scanning and improve the quality of digital scanning,we collected common expert opin-ions and sought to expound the causes of scanning errors and countermeasures by summarizing the existing evidence.We also describe the scanning strategies under different oral impression requirements.The expert consensus is that due to various factors affecting the accuracy of digital intraoral scanning and the reproducibility of scanned images,adopting the correct scanning trajectory can shorten clinical operation time and improve scanning accuracy.The scanning trajec-tories mainly include the E-shaped,segmented,and S-shaped methods.When performing fixed denture restoration,it is recommended to first scan the abutment and adjacent teeth.When performing fixed denture restoration,it is recommend-ed to scan the abutment and adjacent teeth first.Then the cavity in the abutment area is excavated.Lastly,the cavity gap was scanned after completing the abutment preparation.This method not only meets clinical needs but also achieves the most reliable accuracy.When performing full denture restoration in edentulous jaws,setting markers on the mucosal tissue at the bottom of the alveolar ridge,simultaneously capturing images of the vestibular area,using different types of scanning paths such as Z-shaped,S-shaped,buccal-palatal and palatal-buccal pathways,segmented scanning of dental arches,and other strategies can reduce scanning errors and improve image stitching and overlap.For implant restora-tion,when a single crown restoration is supported by implants and a small span upper structure restoration,it is recom-mended to first pre-scan the required dental arch.Then the cavity in the abutment area is excavated.Lastly,scanning the cavity gap after installing the implant scanning rod.When repairing a bone level implant crown,an improved indi-rect scanning method can be used.The scanning process includes three steps:First,the temporary restoration,adjacent teeth,and gingival tissue in the mouth are scanned;second,the entire dental arch is scanned after installing a standard scanning rod on the implant;and third,the temporary restoration outside the mouth is scanned to obtain the three-di-mensional shape of the gingival contour of the implant neck,thereby increasing the stability of soft tissue scanning around the implant and improving scanning restoration.For dental implant fixed bridge repair with missing teeth,the mobility of the mucosa increases the difficulty of scanning,making it difficult for scanners to distinguish scanning rods of the same shape and size,which can easily cause image stacking errors.Higher accuracy of digital implant impres-sions can be achieved by changing the geometric shape of the scanning rods to change the optical curvature radius.The consensus confirms that as the range of scanned dental arches and the number of data concatenations increases,the scanning accuracy decreases accordingly,especially when performing full mouth implant restoration impressions.The difficulty of image stitching processing can easily be increased by the presence of unstable and uneven mucosal mor-phology inside the mouth and the lack of relatively obvious and fixed reference objects,which results in insufficient ac-curacy.When designing restorations of this type,it is advisable to carefully choose digital intraoral scanning methods to obtain model data.It is not recommended to use digital impressions when there are more than five missing teeth.
7.Clinical significance of tumor budding as a marker for predicting distant metastasis after radical gastrectomy in elderly patients
Yu JIE ; Pei WANG ; Lin YAO ; Yimeng SUN ; Wei XU ; Yue QIU ; Dapeng JIANG ; Xiaoyan WANG ; Yu FAN
Chinese Journal of Geriatrics 2024;43(3):311-316
Objective:To investigate the clinical significance of tumor budding as an indicator of postoperative distant organ metastasis after radical gastrectomy in elderly patients diagnosed with gastric cancer.Methods:The clinical and pathological data of 124 elderly patients who experienced metastasis after undergoing radical gastrectomy were retrospectively analyzed.The analysis was conducted from March 2015 to June 2022, focusing on the clinicopathological factors that influenced the occurrence of postoperative distant metastasis in these patients.Tumor budding in gastric cancer tissues was assessed using hematoxylin-eosin staining, and its clinical significance was analyzed.Results:The tumor budding grade of gastric cancer tissues showed a significant correlation with vascular invasion( χ2=6.731, P=0.009), the number of lymph node metastases( rs=0.481, P<0.001), and the time of distant metastasis( rs=-0.450, P<0.001).In the univariate analysis, factors such as tumor budding grade, tumor size, vascular invasion, postoperative chemotherapy, cancerous nodule, preoperative serum carbohydrate antigen 125, and the number of lymph node metastases were found to influence distant metastasis-free survival after radical gastrectomy in elderly patients(all P<0.05).The multifactorial analysis also indicated that tumour outgrowth grade was an important independent prognostic factor for postoperative distant metastasis in elderly gastric cancer patients( HR=3.731, P<0.001). Conclusions:The findings of this study indicate that tumor budding may serve as a potential marker for predicting distant organ metastasis in elderly patients who have undergone radical gastrectomy.This discovery holds significant clinical implications.
8.Pathological characteristics of false-positive lesions of prostate cancer on 68Ga-PSMA-11 PET/CT
Renjie LI ; Yao FU ; Shan PENG ; Fengjiao YANG ; Feng WANG ; Hongqian GUO ; Xuefeng QIU
Journal of Modern Urology 2024;29(11):988-992
[Objective] To investigate the pathological characteristics of false-positive lesions of prostate cancer on 68Ga-PSMA-11 PET/CT based on the pathology of whole mount specimens, in order to more accurately assess the degree of malignancy within the prostate tissue and avoid overdiagnosis and unnecessary treatment. [Methods] A total of 77 patients who underwent 68Ga-PSMA-11 PET/CT before radical prostatectomy in Nanjing Drum Tower Hospital during Jan.2018 and Dec.2022 were retrospectively analyzed.The pathology of whole mount specimens was detected.Two nuclear physicians examined all imaging plates without knowing the pathological results.Two pathological physicians completed all pathological diagnosis without knowing the imaging results.The pathological characteristics of false-positive lesions were determined by matching 68Ga-PSMA-11 PET/CT and pathological specimens.To analyze the pathological features of false-positive lesions, true-negative lesions were randomly delineated and defined.The pathological features of false-positive and true-negative lesions were analyzed and compared using Fisher exact test. [Results] After the imaging and pathological sections were matched, 21(16.3%) false-positive lesions were identified.The pathological characteristics of the 21 false-positive lesions were as follows: 16 (76.2%) simple atrophy with cyst formation, 3(14.3%) prostatic nodular hyperplasia, and 2(9.5%) inflammation.The pathological characteristics of 21 true-negative lesions were: 13(61.9%) normal glands, 5(23.8%) prostatic nodular hyperplasia and 3(14.3%) simple atrophy with cyst formation.Fisher exact test showed that the proportion of simple atrophy with cyst formation in the pathological features of false-positive lesions and true-negative lesions was statistically significant (76.2% vs.14.3%, P<0.001). [Conclusion] Simple atrophy with cyst formation may be a characteristic pathological type of the false-positive lesions of prostate cancer on 68Ga-PSMA-11 PET/CT.
9.Risk factors and prediction model for periprosthetic femoral fracture after total knee arthroplasty in the elderly
Meng ZHU ; Xue-Yu HU ; Ting-Ting ZHAO ; Rong QIU ; Ke LEI ; Yao SONG
Journal of Regional Anatomy and Operative Surgery 2024;33(2):157-161
Objective To investigate the risk factors of periprosthetic femoral fracture(PFF)after total knee arthroplasty(TKA)in the elderly and to construct a predictive model for the prevention of PFF after clinical operation.Methods The clinical data of 537 elderly patients who underwent TKA in the orthopedic department of the First Affiliated Hospital of Air Medical University from October 2016 to October 2021 were retrospectively analyzed.The occurrence of PFF during the follow-up period was statistically analyzed and the clinical data were collected.Binary Logistic regression was used to analyze the risk factors of PFF after TKA in the elderly,and a predictive model of PFF after TKA in the elderly was constructed based on the risk factors.Receiver operating characteristic(ROC)curve and Hosmer-Lemeshow(H-L)were used to test the discrimination and calibration of prediction model.Results The patients were followed up for 12 to 72 months after discharge,with a median time of 47 months.During the follow-up period,31 patients(5.77%)developed PFF.Age,osteoporosis,Parkinson's disease and anterior femoral notch(AFN)were the risk factors for PFF after TKA in the elderly(P<0.05),and cross fixation of prosthesis and bone cement fixation were the protective factors(P<0.05).The results of H-L test showed that the risk prediction model of PFF after TKA in the elderly had good calibration(P>0.05).ROC curve analysis showed that the risk prediction model of PFF after TKA in the elderly has high discrimination(area under the curve was 0.858,95%CI:0.826 to 0.887),the sensitivity was 83.87%,the specificity was 88.34%.Conclusion The risk of PFF after TKA in the elderly is high,and prevention should be carried out according to the high risk factors.The prediction model constructed based on the high risk factors has good prediction efficiency.
10.Curative effect and prognosis of Zheng′s 4C suspension transumbilical laparoendoscopic single-site surgery for cervical cancer
Qiu-Min HE ; Chong-Yuan ZHANG ; Si-Si ZHANG ; Yao HU
Journal of Regional Anatomy and Operative Surgery 2024;33(2):162-165
Objective To investigate the effect of Zheng's 4C suspension transumbilical laparoendoscopic single-site surgery(TU-LSSS)in the treatment of cervical cancer,and analyze its prognosis.Methods A total of 92 patients with cervical cancer admitted to our hospital were selected and randomly divided into the control group(traditional laparoscopic surgery)and the observation group(Zheng's 4C suspension TU-LSSS),with 46 cases in each group.The perioperative related indicators of patients between the two groups were compared.The patients were followed up for 3 years,the progression-free survival(PFS)and overall survival(OS)were recorded,and the influencing factors of prognosis were analyzed.Results Compared with the control group,patients in the observation group had longer surgical time(P<0.05),less intraoperative bleeding(P<0.05),shorter recovery time for postoperative bowel sounds and hospital stay(P<0.05),higher postoperative 3-year PFS rate and 3-year OS rate(P<0.05).During 3-year follow-up,there were 11 cases of disease progression or death.The univariate analysis results showed that there were statistically significant differences in tumor diameter,clinical stage,lymph node metastasis,vascular infiltration,and treatment methods of patients between the good prognosis group and the poor prognosis group(P<0.05).The binary Logistic regression results showed that tumor diameter(≥4 cm),clinical stage(≥stage ⅠB2),lymph node metastasis,and vascular infiltration were the risk factors for the prognosis of patietns with cervical cancer(P<0.05),while Zheng's 4C suspension TU-LSSS was the protective factors(P<0.05).Conclusion Zheng's 4C suspension TU-LSSS can effectively promote the recovery of patients with cervical cancer,and improve 3-year PFS rate and 3-year OS rate.The prognosis is related to many factors,and targeted treatment should be performed according to different risk factors.


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