1.Structural and Spatial Analysis of The Recognition Relationship Between Influenza A Virus Neuraminidase Antigenic Epitopes and Antibodies
Zheng ZHU ; Zheng-Shan CHEN ; Guan-Ying ZHANG ; Ting FANG ; Pu FAN ; Lei BI ; Yue CUI ; Ze-Ya LI ; Chun-Yi SU ; Xiang-Yang CHI ; Chang-Ming YU
Progress in Biochemistry and Biophysics 2025;52(4):957-969
ObjectiveThis study leverages structural data from antigen-antibody complexes of the influenza A virus neuraminidase (NA) protein to investigate the spatial recognition relationship between the antigenic epitopes and antibody paratopes. MethodsStructural data on NA protein antigen-antibody complexes were comprehensively collected from the SAbDab database, and processed to obtain the amino acid sequences and spatial distribution information on antigenic epitopes and corresponding antibody paratopes. Statistical analysis was conducted on the antibody sequences, frequency of use of genes, amino acid preferences, and the lengths of complementarity determining regions (CDR). Epitope hotspots for antibody binding were analyzed, and the spatial structural similarity of antibody paratopes was calculated and subjected to clustering, which allowed for a comprehensively exploration of the spatial recognition relationship between antigenic epitopes and antibodies. The specificity of antibodies targeting different antigenic epitope clusters was further validated through bio-layer interferometry (BLI) experiments. ResultsThe collected data revealed that the antigen-antibody complex structure data of influenza A virus NA protein in SAbDab database were mainly from H3N2, H7N9 and H1N1 subtypes. The hotspot regions of antigen epitopes were primarily located around the catalytic active site. The antibodies used for structural analysis were primarily derived from human and murine sources. Among murine antibodies, the most frequently used V-J gene combination was IGHV1-12*01/IGHJ2*01, while for human antibodies, the most common combination was IGHV1-69*01/IGHJ6*01. There were significant differences in the lengths and usage preferences of heavy chain CDR amino acids between antibodies that bind within the catalytic active site and those that bind to regions outside the catalytic active site. The results revealed that structurally similar antibodies could recognize the same epitopes, indicating a specific spatial recognition between antibody and antigen epitopes. Structural overlap in the binding regions was observed for antibodies with similar paratope structures, and the competitive binding of these antibodies to the epitope was confirmed through BLI experiments. ConclusionThe antigen epitopes of NA protein mainly ditributed around the catalytic active site and its surrounding loops. Spatial complementarity and electrostatic interactions play crucial roles in the recognition and binding of antibodies to antigenic epitopes in the catalytic region. There existed a spatial recognition relationship between antigens and antibodies that was independent of the uniqueness of antibody sequences, which means that antibodies with different sequences could potentially form similar local spatial structures and recognize the same epitopes.
2.Zinc Finger Protein 639 Expression Is a Novel Prognostic Determinant in Breast Cancer
Fang LEE ; Shih-Ping CHENG ; Ming-Jen CHEN ; Wen-Chien HUANG ; Yi-Min LIU ; Shao-Chiang CHANG ; Yuan-Ching CHANG
Journal of Breast Cancer 2025;28(2):86-98
Purpose:
Zinc finger protein 639 (ZNF639) is often found within the overlapping amplicon of PIK3CA, and previous studies suggest its involvement in the pathogenesis of esophageal and oral squamous cell carcinomas. However, its expression and significance in breast cancer remain uncharacterized.
Methods:
Immunohistochemical analysis of ZNF639 was performed using tissue microarrays.Functional studies, including colony formation, Transwell cell migration, and in vivo metastasis, were conducted on breast tumor cells with ZNF639 knockdown via small interfering RNA transfection.
Results:
Reduced ZNF639 immunoreactivity was observed in 82% of the breast cancer samples, independent of hormone receptor and human epidermal growth factor receptor 2 status. In multivariate Cox regression analyses, ZNF639 expression was associated with favorable survival outcomes, including recurrence-free survival (hazard ratio, 0.35; 95% confidence interval [CI], 0.14–0.89) and overall survival (hazard ratio, 0.41; 95% CI, 0.16– 1.05). ZNF639 knockdown increased clonogenicity, cell motility, and lung metastasis in NOD/ SCID mice. Following the ZNF639 knockdown, the expression of Snail1, vimentin, and C-C chemokine ligand 20 (CCL20) was upregulated, and the changes in cell phenotype mediated by ZNF639 were reversed by the subsequent knockdown of CCL20.
Conclusion
Low ZNF639 expression is a novel prognostic factor for recurrence-free survival in patients with breast cancer.
3.Zinc Finger Protein 639 Expression Is a Novel Prognostic Determinant in Breast Cancer
Fang LEE ; Shih-Ping CHENG ; Ming-Jen CHEN ; Wen-Chien HUANG ; Yi-Min LIU ; Shao-Chiang CHANG ; Yuan-Ching CHANG
Journal of Breast Cancer 2025;28(2):86-98
Purpose:
Zinc finger protein 639 (ZNF639) is often found within the overlapping amplicon of PIK3CA, and previous studies suggest its involvement in the pathogenesis of esophageal and oral squamous cell carcinomas. However, its expression and significance in breast cancer remain uncharacterized.
Methods:
Immunohistochemical analysis of ZNF639 was performed using tissue microarrays.Functional studies, including colony formation, Transwell cell migration, and in vivo metastasis, were conducted on breast tumor cells with ZNF639 knockdown via small interfering RNA transfection.
Results:
Reduced ZNF639 immunoreactivity was observed in 82% of the breast cancer samples, independent of hormone receptor and human epidermal growth factor receptor 2 status. In multivariate Cox regression analyses, ZNF639 expression was associated with favorable survival outcomes, including recurrence-free survival (hazard ratio, 0.35; 95% confidence interval [CI], 0.14–0.89) and overall survival (hazard ratio, 0.41; 95% CI, 0.16– 1.05). ZNF639 knockdown increased clonogenicity, cell motility, and lung metastasis in NOD/ SCID mice. Following the ZNF639 knockdown, the expression of Snail1, vimentin, and C-C chemokine ligand 20 (CCL20) was upregulated, and the changes in cell phenotype mediated by ZNF639 were reversed by the subsequent knockdown of CCL20.
Conclusion
Low ZNF639 expression is a novel prognostic factor for recurrence-free survival in patients with breast cancer.
4.Zinc Finger Protein 639 Expression Is a Novel Prognostic Determinant in Breast Cancer
Fang LEE ; Shih-Ping CHENG ; Ming-Jen CHEN ; Wen-Chien HUANG ; Yi-Min LIU ; Shao-Chiang CHANG ; Yuan-Ching CHANG
Journal of Breast Cancer 2025;28(2):86-98
Purpose:
Zinc finger protein 639 (ZNF639) is often found within the overlapping amplicon of PIK3CA, and previous studies suggest its involvement in the pathogenesis of esophageal and oral squamous cell carcinomas. However, its expression and significance in breast cancer remain uncharacterized.
Methods:
Immunohistochemical analysis of ZNF639 was performed using tissue microarrays.Functional studies, including colony formation, Transwell cell migration, and in vivo metastasis, were conducted on breast tumor cells with ZNF639 knockdown via small interfering RNA transfection.
Results:
Reduced ZNF639 immunoreactivity was observed in 82% of the breast cancer samples, independent of hormone receptor and human epidermal growth factor receptor 2 status. In multivariate Cox regression analyses, ZNF639 expression was associated with favorable survival outcomes, including recurrence-free survival (hazard ratio, 0.35; 95% confidence interval [CI], 0.14–0.89) and overall survival (hazard ratio, 0.41; 95% CI, 0.16– 1.05). ZNF639 knockdown increased clonogenicity, cell motility, and lung metastasis in NOD/ SCID mice. Following the ZNF639 knockdown, the expression of Snail1, vimentin, and C-C chemokine ligand 20 (CCL20) was upregulated, and the changes in cell phenotype mediated by ZNF639 were reversed by the subsequent knockdown of CCL20.
Conclusion
Low ZNF639 expression is a novel prognostic factor for recurrence-free survival in patients with breast cancer.
5.Expression and functional study of FKBP10 in oral squamous cell carcinoma
FANG Zhikai ; JIN Hui ; YANG Shan ; JIANG Nan ; ZHANG Mingyu ; ZHOU Shuang ; LI Chang ; LI Lili
Journal of Prevention and Treatment for Stomatological Diseases 2025;33(7):529-541
Objective:
To investigate the expression and functional role of FK506 binding protein 10 (FKBP10) in oral squamous cell carcinoma (OSCC), and to provide a research basis for the estimated prognosis and targeted therapy of OSCC.
Methods:
A total of 284 OSCC samples and 19 normal samples were selected from the Cancer Genome Atlas (TCGA) database, and diagnostic analysis was performed to determine mRNA expression. Survival analysis for FKBP10 and OSCC was conducted on a gene expression profile interaction analysis website. Real-time fluorescence quantitative PCR and Western Blot were used to detect the mRNA and protein expression of FKBP10 in four OSCC cell lines and SAS and SCC9 cells transfected with siRNA. The cell proliferation ability of FKBP10-silenced cells was detected using the CCK8 method, and the cell cycle distribution and apoptosis were detected by flow cytometry. Cell migration and invasion ability were detected through wound healing and invasion experiments. The expression changes of total protein and phosphatidylinositol 3-kinase (PI3K)-serine/threonine kinase (AKT) after FKBP10 silencing were analyzed by proteomics and Western Blot.
Results:
According to the analysis of gene expression levels, the mRNA expression level of FKBP10 in OSCC was significantly higher than that in normal tissues (P < 0.001). In terms of diagnosis, the expression level of FKBP10 has unique diagnostic value for OSCC (P < 0.05). The survival analysis of FKBP10 and OSCC showed that a high expression of FKBP10 led to a decrease in patient survival and poor prognosis (P < 0.05). The expression of FKBP10 mRNA and protein in OSCC cell lines was higher than that in normal oral keratinocytes (P < 0.001). Silencing FKBP10 can reduce the proliferation, invasion, and migration ability of SAS and SCC9 (P < 0.001), and also block their cell cycle in the G0/G1 phase (P < 0.001), with a significant increase in apoptosis (P < 0.05). Protein mass spectrometry and Western blot analysis revealed that FKBP10 silencing significantly downregulated the expression of multiple proteins in the RAP1 signaling pathway, mainly RAP guanine nucleotide exchange factor 1 (RAPGEF1) (P < 0.05) and the phosphorylation of PI3K-AKT proteins (P < 0.05).
Conclusion
FKBP10 is highly expressed in OSCC, leading to poor prognosis for patients. Downregulated FKBP10 expression can inhibit the proliferation, migration, and invasion ability of OSCC cells, hinder cell cycle progression, and promote apoptosis via the RAP1-PI3K-AKT axis. FKBP10 is a potential therapeutic target and prognostic biomarker for OSCC.
6.PES1 Repression Triggers Ribosomal Biogenesis Impairment and Cellular Senescence Through p53 Pathway Activation
Chang-Jian ZHANG ; Yu-Fang LI ; Feng-Yun WU ; Rui JIN ; Chang NIU ; Qi-Nong YE ; Long CHENG
Progress in Biochemistry and Biophysics 2025;52(7):1853-1865
ObjectiveThe nucleolar protein PES1 (Pescadillo homolog 1) plays critical roles in ribosome biogenesis and cell cycle regulation, yet its involvement in cellular senescence remains poorly understood. This study aimed to comprehensively investigate the functional consequences of PES1 suppression in cellular senescence and elucidate the molecular mechanisms underlying its regulatory role. MethodsInitially, we assessed PES1 expression patterns in two distinct senescence models: replicative senescent mouse embryonic fibroblasts (MEFs) and doxorubicin-induced senescent human hepatocellular carcinoma HepG2 cells. Subsequently, PES1 expression was specifically downregulated using siRNA-mediated knockdown in these cell lines as well as additional relevant cell types. Cellular proliferation and senescence were assessed by EdU incorporation and SA-β-gal staining assays, respectively. The expression of senescence-associated proteins (p53, p21, and Rb) and SASP factors (IL-6, IL-1β, and IL-8) were analyzed by Western blot or qPCR. Furthermore, Northern blot and immunofluorescence were employed to evaluate pre-rRNA processing and nucleolar morphology. ResultsPES1 expression was significantly downregulated in senescent MEFs and HepG2 cells. PES1 knockdown resulted in decreased EdU-positive cells and increased SA‑β‑gal-positive cells, indicating proliferation inhibition and senescence induction. Mechanistically, PES1 suppression activated the p53-p21 pathway without affecting Rb expression, while upregulating IL-6, IL-1β, and IL-8 production. Notably, PES1 depletion impaired pre-rRNA maturation and induced nucleolar stress, as evidenced by aberrant nucleolar morphology. ConclusionOur findings demonstrate that PES1 deficiency triggers nucleolar stress and promotes p53-dependent (but Rb-independent) cellular senescence, highlighting its crucial role in maintaining nucleolar homeostasis and regulating senescence-associated pathways.
7.Preliminary application of foldable pedicled latissimus dorsi myocutaneous flap for repairing soft tissue defects in shoulder and back.
Jian ZHOU ; Yucen ZHENG ; Shune XIAO ; Zairong WEI ; Kaiyu NIE ; Zhiyuan LIU ; Shusen CHANG ; Wenhu JIN ; Wei CHEN ; Fang ZHANG
Chinese Journal of Reparative and Reconstructive Surgery 2024;38(1):69-73
OBJECTIVE:
To explore the feasibility and effectiveness of a foldable pedicled latissimus dorsi myocutaneous flap to repair soft tissue defects in the shoulder and back.
METHODS:
Between August 2018 and January 2023, the foldable pedicled latissimus dorsi myocutaneous flaps were used to repair soft tissue defects in the shoulder and back of 8 patients. There were 5 males and 3 females with the age ranged from 21 to 56 years (mean, 35.4 years). Wounds were located in the shoulder in 2 cases and in the shoulder and back in 6 cases. The causes of injury were chronic infection of skin and bone exposure in 2 cases, secondary wound after extensive resection of skin and soft tissue tumor in 4 cases, and wound formation caused by traffic accident in 2 cases. Skin defect areas ranged from 14 cm×13 cm to 20 cm×16 cm. The disease duration ranged from 12 days to 1 year (median, 6.6 months). A pedicled latissimus dorsi myocutaneous flap was designed and harvested. The flap was divided into A/B flap and then were folded to repair the wound, with the donor area of the flap being pulled and sutured in one stage.
RESULTS:
All 7 flaps survived, with primary wound healing. One patient suffered from distal flap necrosis and delayed healing was achieved after dressing change. The incisions of all donor sites healed by first intention. All patients were followed up 6 months to 4 years (mean, 24.7 months). The skin flap has a good appearance with no swelling in the pedicle. At last follow-up, 6 patients had no significant difference in bilateral shoulder joint motion, and 2 patients had a slight decrease in abduction range of motion compared with the healthy side. The patients' daily life were not affected, and linear scar was left in the donor site.
CONCLUSION
The foldable pedicled latissimus dorsi myocutaneous flap is an ideal method to repair the soft tissue defect of shoulder and back with simple operation, less damage to the donor site, and quick recovery after operation.
Male
;
Female
;
Humans
;
Young Adult
;
Adult
;
Middle Aged
;
Plastic Surgery Procedures
;
Myocutaneous Flap/surgery*
;
Shoulder/surgery*
;
Skin Transplantation
;
Superficial Back Muscles/transplantation*
;
Soft Tissue Injuries/surgery*
;
Wound Healing
;
Treatment Outcome
;
Perforator Flap
8.Echo-guiding percutaneous aortic stent implantation for coarctation of the aortic: A case report
Junke CHANG ; Peijian WEI ; Yaoxing LU ; Fengwen ZHANG ; Fang FANG ; Chuangshi WANG ; Shouzheng WANG ; Wenbin OUYANG ; Junyi WAN ; Xiangbin PAN
Chinese Journal of Clinical Thoracic and Cardiovascular Surgery 2024;31(02):325-328
Currently, transcatheter intervention has emerged as a first-line treatment for coarctation of the aortic. Due to the radiation exposure associated with catheter interventional therapy, there are numerous restrictions, which harms both patients and medical personnel and is dependent on sizable radiation apparatus. Here, we report for the first time a case of echo-guiding percutaneous aortic stent implantation for a 27 years female patient of reproductive age. After discharge, the patient's aortic coarctation pressure decreased to 18 mm Hg, and the surgical results were satisfactory.
9.The value of HPV DNA and HPV E6/E7 mRNA detection in screening for cervical lesions
Hantao SONG ; Xiaojuan LIU ; Fang LIU ; Li CHANG ; Jie TENG
International Journal of Laboratory Medicine 2024;45(4):467-470
Objective To investigate the value of human papillomavirus(HPV)DNA and HPV E6/E7 mRNA detection in screening for cervical lesions.Methods A total of 619 patients who were screened for cer-vical lesions in West China Second University Hospital from September 2021 to August 2022 were selected as the study objects.The value of HPV DNA and HPV E6/E7 mRNA detection in cervical lesion screening was evaluated based on their pathological results.Results The positive rate of HPV DNA detection was 64.78%(401/619)and that of HPV E6/E7 mRNA detection was 60.74%(376/619)in 619 patients.Cervical lesion screening was mainly conducted in sexually active people aged 30-<40 years and 40-<50 years.The posi-tive rates of HPV DNA and HPV E6/E7 mRNA increased with the increase of cervical lesion grade.The sen-sitivity,positive predictive value and negative predictive value of the two methods were higher than those of HPV DNA or HPV E6/E7 mRNA detection.Conclusion The combined detection of the two methods can be used for screening cervical lesions at various pathological stages,which can provide greater guidance value in clinical diagnosis and treatment.
10.Factors influencing number of lymph nodes obtained by prophylactic central lymph node dissection for pap-illary thyroid cancer
Keyi LIU ; Guangpeng LIANG ; Fang CHAI ; Chang LIU
The Journal of Practical Medicine 2024;40(4):508-514
Objective To investigate the factors affecting the number of lymph nodes obtained by unilateral lobectomy and isthmus combined with prophylactic ipsilateral central lymph node dissection for papillary thyroid cancer,and to analyze the pattern of change so as to provide an important basis for clinical treatment of papillary thyroid cancer.Methods Retrospective analysis was performed on the clinical and pathological data of 193 patients admitted to the department of Thyroid Surgery of the First Affiliated Hospital of Jinzhou Medical University from January 2019 to January 2022 for papillary thyroid cancer who underwent unilateral glandular lobe and isthmus resec-tion combined with prophylactic ipsilateral central lymph node dissection.The number of obtained lymph nodes was divided into a group with high number of obtained lymph nodes(n>6)and a group with low number of obtained lymph nodes(n≤6).Univariate analysis and multivariate analysis were used to explore the factors affecting the num-ber of obtained lymph nodes.The influence of the number of lymph nodes on the central lymph node metastasis was evaluated by correlation analysis,and the influence of the number of lymph nodes on the quality of life of patients by postoperative complications analysis.Results The number of lymph nodes obtained was positively correlated with the number of lymph node metastases in the central region(r = 0.240,P<0.05)and the rate of lymph node metastasis(r = 0.161,P<0.05),respectively.The number of lymph node metastases controlled remained unchanged,and the rate of lymph node metastasis decreased with the increase of the number of obtained lymph nodes(r =-0.444,P<0.05).Univariate analysis of the number of lymph nodes between the two groups showed no significant differences in terms of sex,age,operation duration,BMI,maximum tumor diameter,multifocality,Hashimoto's thyroiditis,focal location,capsular invasion,contralateral thyroid nodule,parathyroid transplantation and BRAF gene V600E mutation(P>0.05).There was statistical significance in the application of nano carbon between the two groups(P<0.05).Logistic binary regression analysis showed that the combination of Hashimoto's thyroiditis and the application of carbon nanoparticles were independent influencing factors for the high number of lymph nodes obtained(P<0.05).ROC curve analysis suggested that the area under the curve occupied by carbon nanoscale was 0.658(95%CI:0.580~0.735,P<0.05),and the area under the curve occupied by Hashimoto's thyroiditis was 0.584(95%CI:0.504~0.665,P<0.05).In addition,there was no significant difference in the incidence of vocal cord paralysis and lymphatic leakage between the two groups(P>0.05).Conclusions When the number of lymph nodes in the cen-tral region remained unchanged,the higher the number of lymph nodes obtained,the lower the rate of lymph node metastasis.The application of nano-carbon and patients with Hashimoto's thyroiditis could increase the number of lymph nodes obtained,and there is no significant difference in the incidence of postoperative complications between high and low number of lymph nodes obtained.


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