1.Molecular Characteristics of Prognosis and Chemotherapy Response in Breast Cancer: Biomarker Identification Based on Gene Mutations and Pathway
Liyan LI ; Hongwei LYU ; Qian CHEN ; Yating BAI ; Jing YU ; Ruigang CAI
Journal of Breast Cancer 2025;28(2):61-71
Purpose:
This study aimed to investigate the molecular characteristics associated with better prognosis in breast cancer.
Methods:
We performed targeted sequencing of 962 genes in 56 samples, categorizing them into long-term and short-term survival groups as well as chemotherapy-sensitive and chemotherapy-resistant groups for further analyses.
Results:
The results indicated that the tumor mutational burden values were significantly higher in the short-term survival and chemotherapy-resistant groups (p = 0.008 and p = 0.003, respectively). Somatic mutation analysis revealed that the mutation frequencies of BCL9L and WHSC1 were significantly lower in the long-term survival group than those in the short-term survival group (p = 0.029 and p = 0.024, respectively). CREB-regulated transcription coactivator 1 (CRTC1) mutations occurred significantly more frequently in the chemotherapy-resistant group (p = 0.027) and were associated with shorter progression-free survival (p = 0.036).Signature weighting analysis showed a significant increase in Signature.3, which is associated with homologous recombination repair deficiency in the chemotherapy-sensitive group (p = 0.045). Conversely, signatures related to effective DNA repair mechanisms, Signature.1 and Signature.15, were significantly reduced (p = 0.002 and p < 0.001, respectively). Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that gene mutations were significantly enriched in the JAK-STAT signaling pathway.
Conclusion
This study, through intergroup comparative analysis, found that immunotherapy (using programmed death 1/programmed death-ligand 1 inhibitors) may improve the prognosis of patients with short survival and chemotherapy resistance. Additionally, the study revealed that mutations in BCL9L and WHSC1 could serve as biomarkers for breast cancer prognosis, while CRTC1 mutations and Signature.3 could predict chemotherapy response. The study also found that the JAK-STAT pathway might be a potential therapeutic target for chemotherapy resistance. Therefore, this study identifies molecular characteristics that influence the prognosis of breast cancer patients, providing important theoretical insights for the development of personalized treatment strategies.
2.Molecular Characteristics of Prognosis and Chemotherapy Response in Breast Cancer: Biomarker Identification Based on Gene Mutations and Pathway
Liyan LI ; Hongwei LYU ; Qian CHEN ; Yating BAI ; Jing YU ; Ruigang CAI
Journal of Breast Cancer 2025;28(2):61-71
Purpose:
This study aimed to investigate the molecular characteristics associated with better prognosis in breast cancer.
Methods:
We performed targeted sequencing of 962 genes in 56 samples, categorizing them into long-term and short-term survival groups as well as chemotherapy-sensitive and chemotherapy-resistant groups for further analyses.
Results:
The results indicated that the tumor mutational burden values were significantly higher in the short-term survival and chemotherapy-resistant groups (p = 0.008 and p = 0.003, respectively). Somatic mutation analysis revealed that the mutation frequencies of BCL9L and WHSC1 were significantly lower in the long-term survival group than those in the short-term survival group (p = 0.029 and p = 0.024, respectively). CREB-regulated transcription coactivator 1 (CRTC1) mutations occurred significantly more frequently in the chemotherapy-resistant group (p = 0.027) and were associated with shorter progression-free survival (p = 0.036).Signature weighting analysis showed a significant increase in Signature.3, which is associated with homologous recombination repair deficiency in the chemotherapy-sensitive group (p = 0.045). Conversely, signatures related to effective DNA repair mechanisms, Signature.1 and Signature.15, were significantly reduced (p = 0.002 and p < 0.001, respectively). Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that gene mutations were significantly enriched in the JAK-STAT signaling pathway.
Conclusion
This study, through intergroup comparative analysis, found that immunotherapy (using programmed death 1/programmed death-ligand 1 inhibitors) may improve the prognosis of patients with short survival and chemotherapy resistance. Additionally, the study revealed that mutations in BCL9L and WHSC1 could serve as biomarkers for breast cancer prognosis, while CRTC1 mutations and Signature.3 could predict chemotherapy response. The study also found that the JAK-STAT pathway might be a potential therapeutic target for chemotherapy resistance. Therefore, this study identifies molecular characteristics that influence the prognosis of breast cancer patients, providing important theoretical insights for the development of personalized treatment strategies.
3.Molecular Characteristics of Prognosis and Chemotherapy Response in Breast Cancer: Biomarker Identification Based on Gene Mutations and Pathway
Liyan LI ; Hongwei LYU ; Qian CHEN ; Yating BAI ; Jing YU ; Ruigang CAI
Journal of Breast Cancer 2025;28(2):61-71
Purpose:
This study aimed to investigate the molecular characteristics associated with better prognosis in breast cancer.
Methods:
We performed targeted sequencing of 962 genes in 56 samples, categorizing them into long-term and short-term survival groups as well as chemotherapy-sensitive and chemotherapy-resistant groups for further analyses.
Results:
The results indicated that the tumor mutational burden values were significantly higher in the short-term survival and chemotherapy-resistant groups (p = 0.008 and p = 0.003, respectively). Somatic mutation analysis revealed that the mutation frequencies of BCL9L and WHSC1 were significantly lower in the long-term survival group than those in the short-term survival group (p = 0.029 and p = 0.024, respectively). CREB-regulated transcription coactivator 1 (CRTC1) mutations occurred significantly more frequently in the chemotherapy-resistant group (p = 0.027) and were associated with shorter progression-free survival (p = 0.036).Signature weighting analysis showed a significant increase in Signature.3, which is associated with homologous recombination repair deficiency in the chemotherapy-sensitive group (p = 0.045). Conversely, signatures related to effective DNA repair mechanisms, Signature.1 and Signature.15, were significantly reduced (p = 0.002 and p < 0.001, respectively). Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that gene mutations were significantly enriched in the JAK-STAT signaling pathway.
Conclusion
This study, through intergroup comparative analysis, found that immunotherapy (using programmed death 1/programmed death-ligand 1 inhibitors) may improve the prognosis of patients with short survival and chemotherapy resistance. Additionally, the study revealed that mutations in BCL9L and WHSC1 could serve as biomarkers for breast cancer prognosis, while CRTC1 mutations and Signature.3 could predict chemotherapy response. The study also found that the JAK-STAT pathway might be a potential therapeutic target for chemotherapy resistance. Therefore, this study identifies molecular characteristics that influence the prognosis of breast cancer patients, providing important theoretical insights for the development of personalized treatment strategies.
4.Exploration and practice of humanistic care in children's fever clinics from the perspective of narrative medicine
Yutao CAI ; Xue CHEN ; Xiulan WEN ; Liyan YE ; Handan HONG ; Canying LI ; Xian CAI ; Qiumei YANG ; Yansong SU
Chinese Medical Ethics 2024;37(5):586-591
To explore the application of humanistic care in children's fever clinics,the children's fever clinics of Guangzhou Women and Children's Medical Center conducted relevant research using narrative medicine as a guiding concept.This paper elaborated on the medical humanistic dilemmas and narrative care needs in children's fever clinics,and focused on exploring the practice paths of narrative medicine in pediatric with Chinese characteristics from five dimensions,including the cultivation of nursing staff's abilities of professional narrative and humanistic care,the establishment of health lectures featuring narrative patient education,the alleviation of medical anxiety for children and their families,related support of narrative nursing,and caring services.The aim was to improve the narrative care ability of nurses in children's fever clinics,develop methods for pediatric patients that can eliminate the fear of seeking medical treatment,and protect children's physical and mental health.A carrier of care,support,and emotional expression can be provided for parents.The foundation for nursing staff to achieve professional growth through narrative reflection can be laid.Thus,it can assist in establishing a life narrative community relationship between doctors and patients,and jointly explore the meaning of life.
5.Virulence gene distribution and molecular epidemiological characteristics of carbapenem-resistant Klebsiella pneumoniae in the ICU
Yaxuan HUANG ; Yihan CAI ; Wanxia HE ; Liyan ZHANG ; Yue ZHAO
Journal of Central South University(Medical Sciences) 2024;49(5):730-736
Objective:The drug-resistant genes carried by carbapenem-resistant Klebsiella pneumoniae(CRKP)limit clinical treatment options,and its virulence genes severely affect patient prognosis.This study aims to investigate the distribution of virulence genes,capsular serotypes,and molecular epidemiological characteristics of CRKP in ICU,to understand the characteristics of CRKP infections in ICU,and to provide a scientific basis for effective monitoring and control of CRKP infections in ICU. Methods:A total of 40 non-duplicate strains of CRKP isolated from the ICU of Guangdong Provincial People's Hospital between January 2021 and December 2022 were collected and analyzed.Whole-genome sequencing was used to analyze the distribution of resistance genes,virulence genes,and capsular serotypes of the strains.The sequences of 7 housekeeping genes of CRKP genome were uploaded to the Klebsiella pneumoniae(KPN)multilocus sequence typing(MLST)database to determine the sequence types(STs)of the strains. Results:The age of the 40 ICU CRKP-infected patients was(69.03±17.82)years old,with various underlying diseases,and there were 20 patients with improved clinical outcome and 20 patients with death.The isolated strains primarily originated from mid-stream urine and bronchoalveolar lavage fluid.Whole-genome sequencing results revealed that the strains predominantly carried blaKPC-1(29 strains,72.5%)and blaNDM-1(6 strains,15.0%),with 5 strains carrying both blaKPC-1 and blaNDM-1.Various virulence genes were detected,among which the carriage rates of genes such as entA,entB,entE,entS,fepA,fepC,fepG,yag/ecp,and ompA reached 100%,while the carriage rates of genes such as entD,fimB,iroB,iroD,fes,and pla were low.The CRKP strains isolated from ICU were predominantly ST11(27 cases,67.5%),with KL64 being the main capsular serotype(29 cases,72.5%).A total of 23 ST11-KL64 CRKP strains were detected,accounting for 57.5%. Conclusion:The main type of ICU CRKP is ST11-KL64,carrying various virulence genes,primarily those related to iron absorption.Furthermore,blaKPC has shifted from blaKPC-2 to blaKPC-1.Therefore,close monitoring of the molecular epidemiological changes of CRKP is necessary,and strict control measures should be implemented to effectively curb the occurrence of CRKP infections.
6.A survey on the needs and modes of continuing education and training in laboratory medicine
Bin WEI ; Xizhe HUANG ; Bei CAI ; Liyan LIN ; Keyi ZHANG ; Junlong ZHANG ; Qian NIU
Chinese Journal of Medical Education Research 2024;23(6):765-771
Objective:To analyze the advantages and disadvantages of online and offline laboratory medicine continuing education and training, and to discuss the future continuing education and training mode under new technology development and new situation.Methods:A questionnaire was administered to the trainees who participated in the 2019 and/or 2020 national continuing medical education project—Clinical Application and Evaluation of New Technologies and Methods of Laboratory Medicine—sponsored by the Department of Laboratory Medicine, West China Hospital, Sichuan University. One hundred and twenty-four questionnaires were completed for the 2019 offline training, and 503 questionnaires were completed for the 2020 online training. The rank sum test, Fisher's exact test, and chi-square test were performed for statistical analysis with the use of SPSS 26.0.Results:The participants in 2020 were significantly younger and the proportion of female participants in 2020 was significantly higher compared with those in 2019. Intermediate titles or above accounted for 66.93% (83/124) in 2019, and intermediate titles or below accounted for 88.67% (446/503) in 2020. The proportion of people from Sichuan Province was significantly higher in 2019. The proportion of trainees from primary institutions was significantly lower in 2019. In 2019, public institutions were mainly tertiary hospitals (74.31%, 81/109), and the majority of participants from private institutions were from third party testing institutions (60.00%, 9/15). In 2020, the percentage of tertiary hospitals in public institutions decreased to 60.99% (258/423), while the percentage of community medical institutions increased to 10.64% (45/423), and 75.00% (60/80) of trainees from private institutions were from tertiary and secondary medical institutions. Trainees with lower educational levels were more likely to appreciate the value of the training course, especially with higher degrees of satisfaction with improvements in theoretical levels and practical skills, and participants from primary institutions believed that the training course could effectively improve their theoretical and practical levels. The number of participants who provided suggestions on laboratory medicine continuing education and training needs in 2019 (83.75%, 67/80) was higher than that in 2020 (48.51%, 244/503). The overall pass rate of post-training assessment in 2020 was 88.52% (424/479).Conclusions:Online and offline training modes have different audience groups and training effects. Online continuing education can provide training opportunities to more primary care personnel and junior and intermediate professionals, which is conducive to improving the basic professional literacy and testing skills of laboratory personnel on the whole. At the same time, the integration of online and offline modes will promote the development of laboratory medicine continuing education.
7.Clinical comprehensive evaluation of recombinant Mycobacterium tuberculosis fusion protein
Xiaofeng NI ; Sha DIAO ; Siyi HE ; Xuefeng JIAO ; Xiao CHENG ; Zhe CHEN ; Zheng LIU ; Linan ZENG ; Deying KANG ; Bin WU ; Chaomin WAN ; Binwu YING ; Hui ZHANG ; Rongsheng ZHAO ; Liyan MIAO ; Zhuo WANG ; Xiaoyu LI ; Maobai LIU ; Benzhi CAI ; Feng QIU ; Feng SUN ; Naihui CHU ; Minggui LIN ; Wei SHA ; Lingli ZHANG
China Pharmacy 2023;34(4):391-396
OBJECTIVE To evaluate the effectiveness, safety, economy, innovation, suitability and accessibility of recombinant Mycobacterium tuberculosis fusion protein (EC), and to provide evidence for selecting skin detection methods for tuberculosis infection diagnosis and auxiliary diagnosis of tuberculosis. METHODS The effectiveness and safety of EC compared with purified protein derivative of tuberculin (TB-PPD) were analyzed by the method of systematic review. Cost minimization analysis, cost-effectiveness analysis and cost-utility analysis were used to evaluate the short-term economy of EC compared with TB-PPD, and cost-utility analysis was used to evaluate the long-term economy. The evaluation dimensions of innovation, suitability and accessibility were determined by systematic review and improved Delphi expert consultation, and the comprehensive score of EC and TB-PPD in each dimension were calculated by the weight of each indicator. RESULTS The scores of effectiveness, safety, economy, innovation and suitability of EC were all higher than those of TB-PPD. The affordability scores of the two drugs were consistent, while the availability score of EC was lower than those of TB-PPD. After considering dimensions and index weight, the scores of effectiveness, safety, economy, innovation, suitability, accessibility and the comprehensive score of EC were all higher than those of TB-PPD. CONCLUSIONS Compared with TB-PPD, EC performs better in all dimensions of effectiveness, safety, economy, innovation, suitability and accessibility. However, it is worth noting that EC should further improve its availability in the dimension of accessibility.
8.Clinical Significance of Serum IgG4 in the Diagnosis and Treatment Response of IgG4-Related Disease in Adults of Southwest China: A Retrospective Study
Bin WEI ; Ying GUO ; Xiaoqi OU ; Liyan LIN ; Zhenzhen SU ; Lixin LI ; XiaoJuan WU ; Bei CAI
Annals of Laboratory Medicine 2023;43(5):461-469
Background:
There is no standard cut-off value of serum IgG4 concentration and serum IgG4/total IgG ratio for the diagnosis of IgG4-related disease (IgG4-RD) or as a marker of treatment responses. We aimed to explore this issue through a retrospective cohort analysis of adults in southwest China.
Methods:
The diagnostic performance of serum IgG4 concentration and IgG4/IgG ratio for IgG4-RD was evaluated in a retrospective analysis of 177 adults newly diagnosed as having IgG4-RD and 877 adults without IgG4-RD. Dynamic analysis was performed to evaluate the significance of serum IgG4 concentration on IgG4-RD treatment responses.
Results:
The serum IgG4 concentration differed according to sex. The optimal cut-off values of serum IgG4 concentration and IgG4/IgG ratio for IgG4-RD diagnosis were 1.92 g/L and 0.12 in males and 1.83 g/L and 0.11 in females, respectively. For patients with serum IgG4 concentration >2.01 g/L, the cut-off values in the total population were >3.00 g/L and 0.19, respectively. The median serum IgG4 concentration decreased over time, and the decrease rate increased over time. The serum IgG4 concentration significantly decreased at >1 week post-treatment (P=0.004), and the median decrease rate was close to 50% at >4 weeks post-treatment.
Conclusions
Serum IgG4 can be a good indicator for IgG4-RD diagnosis; however, different diagnostic cut-off values should be determined according to sex. The decreasing rate is more conducive than the serum IgG4 concentration to monitor treatment efficacy. The IgG4/IgG ratio did not improve the diagnostic efficacy for IgG4-RD.
9.Late-stage cascade of oxidation reactions during the biosynthesis of oxalicine B in Penicillium oxalicum.
Tao ZHANG ; Guowei GU ; Guodong LIU ; Jinhua SU ; Zhilai ZHAN ; Jianyuan ZHAO ; Jinxiu QIAN ; Guowei CAI ; Shan CEN ; Dewu ZHANG ; Liyan YU
Acta Pharmaceutica Sinica B 2023;13(1):256-270
Oxalicine B ( 1) is an α-pyrone meroterpenoid with a unique bispirocyclic ring system derived from Penicillium oxalicum. The biosynthetic pathway of 15-deoxyoxalicine B ( 4) was preliminarily reported in Penicillium canescens, however, the genetic base and biochemical characterization of tailoring reactions for oxalicine B ( 1) has remained enigmatic. In this study, we characterized three oxygenases from the metabolic pathway of oxalicine B ( 1), including a cytochrome P450 hydroxylase OxaL, a hydroxylating Fe(II)/α-KG-dependent dioxygenase OxaK, and a multifunctional cytochrome P450 OxaB. Intriguingly, OxaK can catalyze various multicyclic intermediates or shunt products of oxalicines with impressive substrate promiscuity. OxaB was further proven via biochemical assays to have the ability to convert 15-hydroxdecaturin A ( 3) to 1 with a spiro-lactone core skeleton through oxidative rearrangement. We also solved the mystery of OxaL that controls C-15 hydroxylation. Chemical investigation of the wild-type strain and deletants enabled us to identify 10 metabolites including three new compounds, and the isolated compounds displayed potent anti-influenza A virus bioactivities exhibiting IC50 values in the range of 4.0-19.9 μmol/L. Our studies have allowed us to propose a late-stage biosynthetic pathway for oxalicine B ( 1) and create downstream derivatizations of oxalicines by employing enzymatic strategies.
10.Expression of SF3B1, UBE2V2 and SETD2 and association with osteoporotic vertebral fractures inelderly patients
Chuanbao WANG ; Xiuli GUO ; Liyan YU ; Wenqing QU ; Shuxia CAI
Chinese Journal of Endocrine Surgery 2022;16(4):463-467
Objective:To explore the relationship between the expression of SF3B1, UBE2V2, SETD2 and osteoporotic vertebral fracture (OVF) in elderly patients.Methods:Peripheral blood samples were collected from 31 elderly patients with osteoporotic vertebral fractures (VF group) and 16 elderly patients with osteoporotic non-vertebral fractures (NVF group) in Yantai Mountain Hospital. RNA was extracted for transcriptome sequencing to screen for differentially expressed genes. VF related genes were screened by Gene Ontology (GO) analysis, protein protein interaction (PPI) network analysis and ROC curve analysis. Qrt-pcr was used to detect gene expression levels.Results:Compared with NVF group, 691 genes were up-regulated while 131 genes were down regulatedin VF group. qRT-PCR results revealed that, compared with NVF patients (1.55±0.33) (1.70±0.33) (1.64±0.33) , SF3B1 (1.83±0.23) ( t=2.84, P=0.008) , UBE2V2 (2.24±0.43) ( t=3.91, P<0.001) expression were increased while SETD2 (1.18±0.46) ( t=3.25, P=0.003) expression was decreased in peripheral blood of VF patients. ROC curve analysis showed that the AUCs of SF3B1, UBE2V2 and SETD2 in VF were 0.8034 ( P=0.007) , 0.8145 ( P=0.005) and 0.7863 ( P=0.0014) , respectively. Conclusion:SF3B1, UBE2V2 and SETD2 are highly correlated with OVF in elderly patients, and are of great value in the diagnosis and prediction of OVF.

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