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.Preparation and evaluation of long-acting light-protective nanogel based on fullerenol-cerium oxide composite system
Tianlong ZHANG ; Jia LIU ; Qing ZHAO ; Yue ZHOU ; Ming YANG ; Qianyu LUO
China Pharmacy 2025;36(17):2106-2112
OBJECTIVE To develop a long-acting light-protective nanogel with both physical barrier and chemical clearance functions, and evaluate its performance. METHODS The photoprotective nanogel composed of mussel mucin and sodium hyaluronate was constructed based on a fullerenol-cerium oxide composite nano system, namely fullerenol-cerium oxide nanogel (FCN), and was characterized. The antioxidant capacity of FCN was evaluated using in vitro free radical scavenging experiments; its UV shielding ability was assessed by using an SPF value detector; its biosafety was assessed according to the requirements of the Guidelines for Drug Safety Evaluation; skin adhesion was assessed using small animal 3D live imaging technology; its sun protection ability was assessed through skin sunscreen detection and histopathological observation. RESULTS The average particle sizes of cerium oxide and fullerenol nanoparticles in FCN were about 20 and 10 nm, respectively, and FCN exhibited good UV absorption and free radical scavenging abilities. SPF value of FCN was 58.95±0.82, and the ultraviolet A protection level value was 6.21±0.15. No pathogenic colonies such as Staphylococcus aureus, were detected in the nanogel, and the contents of lead, arsenic, mercury and cadmium all met the standards for pharmaceutical excipients; FCN group did not show any irritating reactions such as erythema, edema, or desquamation; blood biochemical indicators of the FCN group were within the normal reference range. The material clearance rate of mice in the artificial sweat flushing group was less than 30%, while the material clearance rate of mice in the dry cleaning group reached about 92%. The mice in the protective group did not show obvious erythema or ulcer formation throughout the experiment. Histopathology showed that the fibers were arranged in an orderly manner, and the number of collagen fibers was close to that of the control group. CONCLUSIONS The FCN formulation constructed in this study meets the relevant requirements of the Chinese Pharmacopoeia, has good safety and skin compatibility, and achieves dual synergistic protection of UV shielding and free radical scavenging.
3.No Incidence of Liver Cancer Was Observed in A Retrospective Study of Patients with Aristolochic Acid Nephropathy.
Tao SU ; Zhi-E FANG ; Yu-Ming GUO ; Chun-Yu WANG ; Jia-Bo WANG ; Dong JI ; Zhao-Fang BAI ; Li YANG ; Xiao-He XIAO
Chinese journal of integrative medicine 2024;30(2):99-106
OBJECTIVE:
To assess the risk of aristolochic acid (AA)-associated cancer in patients with AA nephropathy (AAN).
METHODS:
A retrospective study was conducted on patients diagnosed with AAN at Peking University First Hospital from January 1997 to December 2014. Long-term surveillance and follow-up data were analyzed to investigate the influence of different factors on the prevalence of cancer. The primary endpoint was the incidence of liver cancer, and the secondary endpoint was the incidence of urinary cancer during 1 year after taking AA-containing medication to 2014.
RESULTS:
A total of 337 patients diagnosed with AAN were included in this study. From the initiation of taking AA to the termination of follow-up, 39 patients were diagnosed with cancer. No cases of liver cancer were observed throughout the entire follow-up period, with urinary cancer being the predominant type (34/39, 87.17%). Logistic regression analysis showed that age, follow-up period, and diabetes were potential risk factors, however, the dosage of the drug was not significantly associated with urinary cancer.
CONCLUSIONS
No cases of liver cancer were observed at the end of follow-up. However, a high prevalence of urinary cancer was observed in AAN patients. Establishing a direct causality between AA and HCC is challenging.
Humans
;
Retrospective Studies
;
Incidence
;
Carcinoma, Hepatocellular
;
Liver Neoplasms/epidemiology*
;
Kidney Diseases/chemically induced*
;
Aristolochic Acids/adverse effects*
4.Influencing factors for medication compliance in patients with comorbidities of chronic diseases: a meta-analysis
LIU Yudan ; ZHANG Caiyun ; GUO Mingmei ; ZHENG Yujuan ; JIA Ming ; YANG Jiale ; HOU Jianing ; ZHAO Hua
Journal of Preventive Medicine 2024;36(9):790-795,800
Objective:
To systematically evaluate the influencing factors for medication compliance in patients with comorbidities of chronic diseases, so as to provide the evidence for improving medication compliance.
Methods:
Literature on influencing factors for medication compliance in patients with comorbidities of chronic diseases were retrived from CNKI, Wanfang Data, VIP, SinoMed, PubMed, Web of Science, Cochrane Library and Embase from inception to January 20, 2024. After independent literature screening, data extraction, and quality assessment by two researchers, a meta-analysis was performed using RevMan 5.4 and Stata 16.0 softwares. Literature were excluded one by one for sensitivity analysis. Publication bias was assessed using Egger's test.
Results:
Initially, 7 365 relevant articles were retrieved, and 35 of them were finally included, with a total sample size of about 150 000 individuals. There were 30 cross-sectional studies and 5 cohort studies; and 11 high-quality studies and 24 medium-quality studies. The meta-analysis showed that the demographic factors of lower level of education (OR=2.148, 95%CI: 1.711-2.696), lower economic income (OR=1.897, 95%CI: 1.589-2.264), male (OR=0.877, 95%CI: 0.782-0.985), living alone (OR=2.833, 95%CI: 1.756-4.569) and unmarried (OR=2.784, 95%CI: 1.251-6.196); the medication treatment factors of polypharmacy (OR=1.794, 95%CI: 1.190-2.706), potentially inappropriate medication (OR=2.988, 95%CI: 1.527-5.847), low frequency of daily medication (OR=0.533, 95%CI: 0.376-0.754) and adverse drug reactions (OR=3.319, 95%CI: 1.967-5.602); the disease factors of long course of disease (OR=2.118, 95%CI: 1.643-2.730), more comorbidities (OR=1.667, 95%CI: 1.143-2.431) and cognitive impairment (OR=2.007, 95%CI: 1.401-2.874); and the psychosocial factors of poor belief in taking medication (OR=1.251, 95%CI: 1.011-1.547), poor self-rated health (OR=1.990, 95%CI: 1.571-2.522) and being guided by healthcare professionals (OR=0.151, 95%CI: 0.062-0.368) were the influencing factors for medication compliance in patients with chronic comorbidities.
Conclusion
The medication compliance in patients with comorbidities of chronic diseases is associated with demographic factors, pharmacological factors, disease factors and psychosocial factors, mainly including living alone, adverse drug reactions, course of disease, number of comorbidities and medication beliefs.
5.Development of a national health standard:Guideline for pediatric transfusion
Rong HUANG ; Qingnan HE ; Mingyan HEI ; Minghua YANG ; Xiaofan ZHU ; Jun LU ; Xiaojun XU ; Tian-Ming YUAN ; Rong ZHANG ; Xu WANG ; Jinping LIU ; Jing WANG ; Zhili SHAO ; Mingyi ZHAO ; Jia GUO ; Xiny-In WU ; Jiarui CHEN ; Qirong CHEN ; Rong GUI ; Yongjian GUO
Chinese Journal of Blood Transfusion 2024;37(7):839-844
Children and adults differ significantly in physiology,biochemistry and immune function,which leads to sig-nificant differences in blood transfusion strategies between children and adults.To guide the clinical transfusion practice of pediatric patients and improve the prognosis of children,the National Health Commission organized the formulation and re-lease of the health industry standard Guideline for Pediatric Transfusion(WS/T 795-2022).This paper will briefly introduce some concepts that help understand of the Standard and the preparation process of the Standard,and explain and interpret the preparation of the"scope","general provisions"and"factors to consider"of the Standard,hoping to contribute to the understanding and implementation of the Standard.
6.Incidence and influencing factors of depression in family caregivers of Alzheimer's disease patients: a meta-analysis
LIU Xingyu ; YANG Zhilan ; CUI Liping ; JIA Ming ; SHI Hongrui ; ZHAO Huimin ; YAN Zhili
Journal of Preventive Medicine 2024;36(4):322-327
Objective:
To systematically evaluate the incidence and influencing factors of depression in family caregivers of Alzheimer's disease (AD) patients, so as to provide the basis for the prevention and treatment of depression among the family caregivers of AD patients.
Methods:
Publications pertaining to depression in family caregivers of AD patients were retrieved from CNKI, Wanfang Data, PubMed and other databases from the time of their establishment to June 15, 2023. The evaluation criteria recommended by the Agency for Healthcare Research and Quality (AHRQ) and the Newcastle-Ottawa Scale were used to assess the quality of cross-sectional and cohort studies, respectively. Stata 16.0 and Revman 5.4 softwares were used to conduct a meta-analysis on the incidence and influencing factors of depression in family caregivers of AD patients. Sensitivity analysis and publication bias assessment were also performed on the results.
Results:
A total of 2 324 articles were retrieved, and ultimately 14 articles were included, with a total sample size of 8 313 individuals. There were 6 high-quality articles and 8 moderate-quality articles. Meta-analysis showed that the incidence of depression in family caregivers of AD patients was 37.5% (95%CI: 30.2%-45.1%). Factors associated with depression included patients' high degree of dementia (OR=1.718, 95%CI: 1.059-2.789), patients' low scores on Activities of Daily Living Scale (OR=1.344, 95%CI: 1.059-1.706), patients' psychobehavioral abnormalities (OR=1.248, 95%CI: 1.155-1.348), long duration of caregiving (OR=1.998, 95%CI: 1.637-2.437), less involvement of other family members in caregiving (OR=1.597, 95%CI: 1.237-2.061), low educational level (OR=1.191, 95%CI: 1.044-1.359), poor caregiving skills (OR=3.060, 95%CI: 2.257-4.149), poor self-rated health (OR=2.536, 95%CI: 1.114-5.771) and social support (OR=0.424, 95%CI: 0.232-0.774). The results of depression incidence demonstrated good stability with no significant publication bias. However, publication bias was observed in the influencing factors for depression, which were patients' high degree of dementia and patients' low scores on Activities of Daily Living Scale.
Conclusions
The incidence of depression in family caregivers of AD patients ranges from 30.2% to 45.1%. It is primarily influenced by the severity of patients' symptoms and ability to perform daily activities, and caregivers' educational level, caregiving skills, health status, caregiving duration and social support.
7.Prognostic prediction models for patients with comorbidity of chronic diseases: a scoping review
JIA Ming ; ZHAO Hua ; PENG Juyi ; LIU Xingyu ; LIU Yudan ; HOU Jianing ; YANG Jiale
Journal of Preventive Medicine 2024;36(6):491-495
Objective:
To conduct a scoping review on prognostic prediction models for patients with comorbidity of chronic diseases, and understand modeling methods, predictive factors and predictive effect of the models, so as to provide the reference for prognostic evaluation on patients with comorbidity of chronic diseases.
Methods:
Literature on prognostic prediction models for patients with comorbidity of chronic diseases was collected through SinoMed, CNKI, Wanfang Data, VIP, PubMed, Embase, Cochrane Library and Web of Science published from the time of their establishment to November 1, 2023. The quality of literature was assessed using prediction model risk of bias assessment tool (PROBAST), then modeling methods, predictive factors and predictive effects were reviewed.
Results:
Totally 2 130 publications were retrieved, and nine publications were finally enrolled, with an overall high risk of bias. Thirteen models were involved, with three established using machine learning methods and ten established using logistic regression. The prediction results of four models were death, with main predictive factors being age, gender, body mass index (BMI), Barthel index and pressure ulcers; the prediction results of nine models were rehospitalization, with main predictive factors being age, BMI, hospitalization frequency, duration of hospital stay and hospitalization costs. Eleven models reported the area under the receiver operating characteristic curve (AUC), ranging from 0.663 to 0.991 6; two models reported the C-index, ranging from 0.64 to 0.70. Eight models performed internal validation, one model performed external validation, and four models did not reported verification methods.
Conclusions
The prognostic prediction models for patients with comorbidity of chronic diseases are established by logistic regression and machine learning methods with common nursing evaluation indicators, and perform well. Laboratory indicators should be considered to add in the models to further improve the predictive effects.
8.Nanomaterial-based Therapeutics for Biofilm-generated Bacterial Infections
Zhuo-Jun HE ; Yu-Ying CHEN ; Yang ZHOU ; Gui-Qin DAI ; De-Liang LIU ; Meng-De LIU ; Jian-Hui GAO ; Ze CHEN ; Jia-Yu DENG ; Guang-Yan LIANG ; Li WEI ; Peng-Fei ZHAO ; Hong-Zhou LU ; Ming-Bin ZHENG
Progress in Biochemistry and Biophysics 2024;51(7):1604-1617
Bacterial biofilms gave rise to persistent infections and multi-organ failure, thereby posing a serious threat to human health. Biofilms were formed by cross-linking of hydrophobic extracellular polymeric substances (EPS), such as proteins, polysaccharides, and eDNA, which were synthesized by bacteria themselves after adhesion and colonization on biological surfaces. They had the characteristics of dense structure, high adhesiveness and low drug permeability, and had been found in many human organs or tissues, such as the brain, heart, liver, spleen, lungs, kidneys, gastrointestinal tract, and skeleton. By releasing pro-inflammatory bacterial metabolites including endotoxins, exotoxins and interleukin, biofilms stimulated the body’s immune system to secrete inflammatory factors. These factors triggered local inflammation and chronic infections. Those were the key reason for the failure of traditional clinical drug therapy for infectious diseases.In order to cope with the increasingly severe drug-resistant infections, it was urgent to develop new therapeutic strategies for bacterial-biofilm eradication and anti-bacterial infections. Based on the nanoscale structure and biocompatible activity, nanobiomaterials had the advantages of specific targeting, intelligent delivery, high drug loading and low toxicity, which could realize efficient intervention and precise treatment of drug-resistant bacterial biofilms. This paper highlighted multiple strategies of biofilms eradication based on nanobiomaterials. For example, nanobiomaterials combined with EPS degrading enzymes could be used for targeted hydrolysis of bacterial biofilms, and effectively increased the drug enrichment within biofilms. By loading quorum sensing inhibitors, nanotechnology was also an effective strategy for eradicating bacterial biofilms and recovering the infectious symptoms. Nanobiomaterials could intervene the bacterial metabolism and break the bacterial survival homeostasis by blocking the uptake of nutrients. Moreover, energy-driven micro-nano robotics had shown excellent performance in active delivery and biofilm eradication. Micro-nano robots could penetrate physiological barriers by exogenous or endogenous driving modes such as by biological or chemical methods, ultrasound, and magnetic field, and deliver drugs to the infection sites accurately. Achieving this using conventional drugs was difficult. Overall, the paper described the biological properties and drug-resistant molecular mechanisms of bacterial biofilms, and highlighted therapeutic strategies from different perspectives by nanobiomaterials, such as dispersing bacterial mature biofilms, blocking quorum sensing, inhibiting bacterial metabolism, and energy driving penetration. In addition, we presented the key challenges still faced by nanobiomaterials in combating bacterial biofilm infections. Firstly, the dense structure of EPS caused biofilms spatial heterogeneity and metabolic heterogeneity, which created exacting requirements for the design, construction and preparation process of nanobiomaterials. Secondly, biofilm disruption carried the risk of spread and infection the pathogenic bacteria, which might lead to other infections. Finally, we emphasized the role of nanobiomaterials in the development trends and translational prospects in biofilm treatment.
9.Effect of Combined Frequency Stimulation on The Electrophysiology of Granule Neurons in The Hippocampal Dentate Gyrus Area of Hindlimb Unloading Mice
Jun-Qiao ZHAO ; Ming-Qiang ZHU ; Hai-Jun ZHU ; Rui FU ; Ze ZHANG ; Jia-Le WANG ; Chong DING
Progress in Biochemistry and Biophysics 2024;51(7):1670-1686
ObjectiveIn recent years, the negative impact of microgravity on astronauts’ nervous systems has received widespread attention. The repetitive transcranial magnetic stimulation (rTMS) technology has shown significant positive effects in the treatment of neurological and psychiatric disorders. The potential benefits of combined frequency stimulation (CFS) which combines different frequency stimulation patterns in ameliorating neurological dysfunctions induced by the microgravity environment, still require in-depth investigation. Exploring the therapeutic effects and electrophysiological mechanisms of CFS in improving various neurological disorders caused by microgravity holds significant importance for neuroscience and the clinical application of magnetic stimulation. MethodsThis study employed 40 C57BL/6 mice, randomly divided into 5 groups: sham group, hindlimb unloading (HU) group, 10 Hz group, 20 Hz group, and combined frequency stimulation (10 Hz+20 Hz, CFS) group. Mice in all groups except the sham group received 14 d of simulated microgravity conditions along with 14 d of repetitive transcranial magnetic stimulation. The effects of CFS on negative emotions and spatial cognitive abilities were assessed through sucrose preference tests and water maze experiments. Finally, patch-clamp techniques were used to record action potentials, resting membrane potentials, and ion channel dynamics of granule neurons in the hippocampal dentate gyrus (DG) region. ResultsCompared to the single-frequency stimulation group, behavioral results indicated that the combined frequency stimulation (10 Hz+20 Hz) significantly improved cognitive impairments and negative emotions in simulated microgravity mice. Electrophysiological experiments revealed a decrease in excitability of granule neurons in the hippocampal DG region after HU manipulation, whereas the combined frequency stimulation notably enhanced neuronal excitability and improved the dynamic characteristics of voltage-gated Na+ and K+ channels. ConclusionThe repetitive transcranial magnetic stimulation with combined frequencies (10 Hz+20 Hz) effectively ameliorates cognitive impairments and negative emotions in simulated microgravity mice. This improvement is likely attributed to the influence of combined frequency stimulation on neuronal excitability and the dynamic characteristics of Na+ and K+ channels. Consequently, this study holds the promise to provide a theoretical basis for alleviating cognitive and emotional disorders induced by microgravity environments.
10.Small molecule deoxynyboquinone triggers alkylation and ubiquitination of Keap1 at Cys489 on Kelch domain for Nrf2 activation and inflammatory therapy
Linghu KE-GANG ; Zhang TIAN ; Zhang GUANG-TAO ; Lv PENG ; Zhang WEN-JUN ; Zhao GUAN-DING ; Xiong SHI-HANG ; Ma QIU-SHUO ; Zhao MING-MING ; Chen MEIWAN ; Hu YUAN-JIA ; Zhang CHANG-SHENG ; Yu HUA
Journal of Pharmaceutical Analysis 2024;14(3):401-415
Activation of nuclear factor erythroid 2-related factor 2(Nrf2)by Kelch-like ECH-associated protein 1(Keap1)alkylation plays a central role in anti-inflammatory therapy.However,activators of Nrf2 through alkylation of Keap1-Kelch domain have not been identified.Deoxynyboquinone(DNQ)is a natural small molecule discovered from marine actinomycetes.The current study was designed to investigate the anti-inflammatory effects and molecular mechanisms of DNQ via alkylation of Keap1.DNQ exhibited signif-icant anti-inflammatory properties both in vitro and in vivo.The pharmacophore responsible for the anti-inflammatory properties of DNQ was determined to be the α,β-unsaturated amides moieties by a chemical reaction between DNQ and N-acetylcysteine.DNQ exerted anti-inflammatory effects through activation of Nrf2/ARE pathway.Keap1 was demonstrated to be the direct target of DNQ and bound with DNQ through conjugate addition reaction involving alkylation.The specific alkylation site of DNQ on Keap1 for Nrf2 activation was elucidated with a synthesized probe in conjunction with liquid chromatography-tandem mass spectrometry.DNQ triggered the ubiquitination and subsequent degra-dation of Keap1 by alkylation of the cysteine residue 489(Cys489)on Keap1-Kelch domain,ultimately enabling the activation of Nrf2.Our findings revealed that DNQ exhibited potent anti-inflammatory capacity through α,β-unsaturated amides moieties active group which specifically activated Nrf2 signal pathway via alkylation/ubiquitination of Keap1-Kelch domain,suggesting the potential values of targeting Cys489 on Keap1-Kelch domain by DNQ-like small molecules in inflammatory therapies.


Result Analysis
Print
Save
E-mail