Yuyang Zeng

All Publications

• <i>SDE</i>: Early Screening for Dry Eye Disease with Wireless Signals PROCEEDINGS OF THE ACM ON INTERACTIVE MOBILE WEARABLE AND UBIQUITOUS TECHNOLOGIES-IMWUT Xue, M., Zeng, Y., Gu, S., Zhang, Q., Tian, B., Chen, C. 2023; 7 (4)

  View details for DOI 10.1145/3631438

  View details for Web of Science ID 001168287200049

• Identification of Diagnostic Biomarkers and Their Correlation with Immune Infiltration in Age-Related Macular Degeneration. Diagnostics (Basel, Switzerland) Zeng, Y., Yin, X., Chen, C., Xing, Y. 2021; 11 (6)

  Abstract

  Age-related macular degeneration (AMD) is a progressive neurodegenerative disease of the central retina, with no suitable biomarkers for early diagnosis and treatment. This study aimed to find potential diagnostic biomarker candidates for AMD and investigate their immune-related roles in this pathology. Weight gene correlation analysis was first performed based on data from the Gene Expression Omnibus database and 20 hub genes were identified. The functional enrichment analyses showed that the innate immune response, inflammatory response, and complement activation were key pathways associated with AMD. Complement C1s (C1S), adrenomedullin (ADM), and immediate early response 5 like (IER5L) were identified as the crucial genes with favorable diagnostic values for AMD by using LASSO analysis and multiple logistic regression. Furthermore, a 3-gene model was constructed and proved to be of good diagnostic and predictive performance for AMD (AUC = 0.785, 0.840, and 0.810 in training, test, and validation set, respectively). Finally, CIBERSORT was used to evaluate the infiltration of immune cells in AMD tissues. The results showed that the NK cells, CD4 memory T cell activation, and macrophage polarization may be involved in the AMD process. C1S, ADM, and IER5L were correlated with the infiltration of the above immune cells. In conclusion, our study suggests that C1S, ADM, and IER5L are promising diagnostic biomarker candidates for AMD and may regulate the infiltration of immune cells in the occurrence and progression of AMD.

  View details for DOI 10.3390/diagnostics11061079

  View details for PubMedID 34204836

  View details for PubMedCentralID PMC8231534

• Positive Rate of Serology and RT-PCR for COVID-19 among healthcare workers during different periods in Wuhan, China. The Journal of infection He, L., Zeng, Y., Zeng, C., Zhou, Y., Li, Y., Xie, X., Xu, W., Luo, W., Hu, J., Yi, Z., Wang, X., Tang, S., Xu, L., Chen, C. 2021; 82 (2): e27-e28

  View details for DOI 10.1016/j.jinf.2020.08.027

  View details for PubMedID 32853598

  View details for PubMedCentralID PMC7444622

• Bioinformatics analysis of multi-omics data identifying molecular biomarker candidates and epigenetically regulatory targets associated with retinoblastoma. Medicine Zeng, Y., He, T., Liu, J., Li, Z., Xie, F., Chen, C., Xing, Y. 2020; 99 (47): e23314

  Abstract

  Retinoblastoma (RB) is the commonest malignant tumor of the infant retina. Besides genetic changes, epigenetic events are also considered to implicate the occurrence of RB. This study aimed to identify significantly altered protein-coding genes, DNA methylation, microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and their molecular functions and pathways associated with RB, and investigate the epigenetically regulatory mechanism of DNA methylation modification and non-coding RNAs on key genes of RB via bioinformatics method.We obtained multi-omics data on protein-coding genes, DNA methylation, miRNAs, and lncRNAs from the Gene Expression Omnibus database. We identified differentially expressed genes (DEGs) using the Limma package in R, discerned their biological functions and pathways using enrichment analysis, and conducted the modular analysis based on protein-protein interaction network to identify hub genes of RB. Survival analyses based on The Cancer Genome Atlas clinical database were performed to analyze prognostic values of key genes of RB. Subsequently, we identified the differentially methylated genes, differentially expressed miRNAs (DEMs) and lncRNAs (DELs), and intersected them with key genes to analyze possible targets of the underlying epigenetic regulatory mechanisms. Finally, the ceRNA network of lncRNAs-miRNAs-mRNAs was constructed using Cytoscape.A total of 193 DEGs, 74 differentially methylated-DEGs (DM-DEGs), 45 DEMs, 5 DELs were identified. The molecular pathways of DEGs were enriched in cell cycle, p53 signaling pathway, and DNA replication. A total of 10 key genes were identified and found significantly associated with poor survival outcome based on survival analyses, including CDK1, BUB1, CCNB2, TOP2A, CCNB1, RRM2, KIF11, KIF20A, NDC80, and TTK. We further found that hub genes MCM6 and KIF14 were differentially methylated, key gene RRM2 was targeted by DEMs, and key genes TTK, RRM2, and CDK1 were indirectly regulated by DELs. Additionally, the ceRNA network with 222 regulatory associations was constructed to visualize the correlations between lncRNAs-miRNAs-mRNAs.This study presents an integrated bioinformatics analysis of genetic and epigenetic changes that may be associated with the development of RB. Findings may yield many new insights into the molecular biomarker candidates and epigenetically regulatory targets of RB.

  View details for DOI 10.1097/MD.0000000000023314

  View details for PubMedID 33217867

  View details for PubMedCentralID PMC7676602

• Presence of SARS-CoV-2 RNA in isolation ward environment 28 days after exposure. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases Zhou, Y., Zeng, Y., Chen, C. 2020; 97: 258-259

  Abstract

  Recent studies have reported that surfaces and objects in the rooms of infected patients that are frequently touched by both medical staff and patients could be contaminated with SARS-CoV-2. In December 2019, Wuhan China suffered the earliest from this COVID-19 pandemic, and we took that opportunity to investigate whether the SARS-CoV-2 RNA exists in the ward environment after a long time from exposure. We found that on the 28th day following the discharge of COVID-19 patients, SARS-CoV-2 RNA could still be detected on the surfaces of pagers and in drawers in the isolation wards. Thorough disinfection of the ward environment was subsequently performed, after which these surfaces in the isolation wards tested negative for the presence of SARS-CoV-2 RNA. The findings remind us that the contaminated environment in the wards may become potential infectious resources and that despite a long time from exposure, the thorough disinfection in the COVID-10 units after is still necessary.

  View details for DOI 10.1016/j.ijid.2020.06.015

  View details for PubMedID 32534140

  View details for PubMedCentralID PMC7286264

• Ocular Findings and Proportion with Conjunctival SARS-COV-2 in COVID-19 Patients. Ophthalmology Zhou, Y., Duan, C., Zeng, Y., Tong, Y., Nie, Y., Yang, Y., Chen, Z., Chen, C. 2020; 127 (7): 982-983

  View details for DOI 10.1016/j.ophtha.2020.04.028

  View details for PubMedID 32359840

  View details for PubMedCentralID PMC7194804

• Clinicopathological and prognostic significance of caveolin-1 and ATG4C expression in the epithelial ovarian cancer. PloS one Zeng, Y., Chen, M., Ganesh, S., Hu, S., Chen, H. 2020; 15 (5): e0232235

  Abstract

  Altered expression of caveolin-1 (CAV1) and autophagy marker ATG4C is observed in various types of human cancers. However, the clinical significance of CAV1 and ATG4C expression in epithelial ovarian cancer (EOC) remains largely unknown. The present study aims to explore the clinicopathological value and prognostic significance of CAV1 and ATG4C expression in EOC.The expression pattern and prognostic value of CAV1 and ATG4C mRNA in EOC were analyzed using data from the Cancer Genome Atlas (TCGA) database (N = 373). In addition, immunohistochemistry analysis was performed to detect and assay the expression of CAV1 and ATG4C proteins in tissue microarray of EOC.Based on TCGA data, Kaplan-Meier analysis indicated that patients with low CAV1 mRNA (p = 0.021) and high ATG4C mRNA (p = 0.018) expression had a significantly shorter overall survival (OS). Cox regression analysis demonstrated that the expression levels of CAV1 (p = 0.023) and ATG4C mRNA (p = 0.040) were independent prognostic factors for OS in EOC. In addition, the Concordance Index of the nomogram for OS prediction was 0.660. Immunohistochemical analysis showed the expression levels of stromal CAV1 and cancerous ATG4C proteins, and high expression of both CAV1 and ATG4C protein in the stroma were found to significantly correlate with the histologic subtypes of EOC, especially with serous subtype.Decreased expression of CAV1 mRNA and increased expression of ATG4C mRNA in EOC can predict poor overall survival. The expression levels of CAV1 protein in stromal cells and ATG4C protein in cancer cells are significantly associated with histologic subtypes of EOC. These findings suggest that CAV1 and ATG4C serve as useful prognostic biomarkers and candidate therapeutic targets in EOC.

  View details for DOI 10.1371/journal.pone.0232235

  View details for PubMedID 32401768

  View details for PubMedCentralID PMC7219755

• A Novel Glycolysis-Related Signature for Predicting the Prognosis and Immune Infiltration of Uveal Melanoma. Ophthalmic research Guo, X., Yu, X., Zhang, Y., Luo, H., Huang, R., Zeng, Y., Duan, C., Chen, C. 2023; 66 (1): 692-705

  Abstract

  As the most common aggressive intraocular cancer in adults, uveal melanoma (UVM) threatens the survival and vision of many people. Glycolysis is a novel hallmark of cancer, but the role of glycolysis-related genes in UVM prognosis remains unknown. The purpose of the study was to establish a glycolysis-related gene signature (GRGS) to predict UVM prognosis.Raw data were obtained from TCGA-UVM and GSE22138 datasets. The GRGS was established by univariate, LASSO, and multivariate Cox regression analyses. Kaplan-Meier survival and time-dependent receiver operating characteristic curves were used to evaluate the predictive ability of the GRGS. The relationships of the GRGS with infiltrating immune cell levels and mutations were analyzed with CIBERSORT and maftools.A novel GRGS (risk score = 0.690861*ISG20 + 0.070991*MET - 0.227520*SDC2 + 0.690223*FBP1 + 0.048008*CLN6 - 0.128520*SDC3) was developed for predicting UVM prognosis. The GRGS had robust predictive stability in UVM. Enrichment annotation suggested that the high-risk group had stronger adaptive immune responses and that the low-risk group had more innate immune cell infiltration. Moreover, BAP1 mutation was related to high risk, and SF3B1 mutation was related to low risk.This study developed and validated a novel GRGS to predict UVM prognosis and immune infiltration. The signature revealed an association between glycolysis-related genes and the tumor microenvironment, providing new insights into the role of glycolysis in UVM.

  View details for DOI 10.1159/000529818

  View details for PubMedID 36858025

• Antibody responses of the first wave of survivors infected with SARS-CoV-2 1 year ago. Journal of medical virology He, L., Zeng, C., Zeng, Y., Xu, W., Li, Y., Xie, X., Xu, W., Xia, H., Tang, F., Tang, S., Xu, L., Chen, C. 2022; 94 (5): 1770-1772

  View details for DOI 10.1002/jmv.27551

  View details for PubMedID 34952979

  View details for PubMedCentralID PMC9015559

• Positive Rate of Serology and RT-PCR for COVID-19 among Community Residents and Healthcare Workers in Wuhan, China. Japanese journal of infectious diseases He, L., Zeng, Y., Zeng, C., Zhou, Y., Li, Y., Xie, X., Xu, W., Luo, W., Hu, J., Yi, Z., Wang, X., Tang, S., Xu, L., Chen, C. 2021; 74 (4): 333-336

  Abstract

  This study aimed to evaluate the infection rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among different populations in Wuhan, China. This cross-sectional survey-based study examined the results of SARS-CoV-2-specific serological tests and RT-PCR tests for 4,454 community residents and 4,614 healthcare workers performed from May 15 to May 29, 2020. The healthcare workers were classified as administrative and logistical staff (n = 1,378), non-first-line healthcare workers (n = 2,630), or first-line healthcare workers (n = 606) according to their frequency of contact with coronavirus disease (COVID-19) patients. The positive rates of SARS-CoV-2-specific IgG, IgM, and RNA were 2.9%, 0.4%, and 0.1% for the community residents and 3.3%, 0.6%, and 0.2% for the healthcare workers, respectively. There were no statistically significant differences between the rates of the two groups. Spearman's correlation analysis showed that the frequency of contact with COVID-19 patients negatively correlated with the positive rates of RT-PCR (rs = -0.036, P = 0.016), but did not significantly correlate with the positive rates of IgM (rs = -0.006, P = 0.698) or IgG (rs = 0.017, P = 0.239). There was no statistically significant difference between the SARS-CoV-2-specific IgG, IgM, or RNA positive rates of the community residents and those of the healthcare workers. The positive rate of SARS-CoV-2 RNA was lower for the first-line healthcare workers than for the non-first-line healthcare workers and the administrative and logistical staff.

  View details for DOI 10.7883/yoken.JJID.2020.691

  View details for PubMedID 33390427

• The promising immune checkpoint LAG-3: from tumor microenvironment to cancer immunotherapy. Genes & cancer Long, L., Zhang, X., Chen, F., Pan, Q., Phiphatwatchara, P., Zeng, Y., Chen, H. 2018; 9 (5-6): 176-189

  Abstract

  Cancer immunotherapy and tumor microenvironment have been at the forefront of research over the past decades. Targeting immune checkpoints especially programmed death 1 (PD-1)/programmed death ligand 1 (PD-L1) has made a breakthrough in treating advanced malignancies. However, the low response rate brings a daunting challenge, changing the focus to dig deeply into the tumor microenvironment for alternative therapeutic targets. Strikingly, the inhibitory immune checkpoint lymphocyte activation gene-3 (LAG-3) holds considerable potential. LAG-3 suppresses T cells activation and cytokines secretion, thereby ensuring immune homeostasis. It exerts differential inhibitory impacts on various types of lymphocytes and shows a remarkable synergy with PD-1 to inhibit immune responses. Targeting LAG-3 immunotherapy is moving forward in active clinical trials, and combination immunotherapy of anti-LAG-3 and anti-PD-1 has shown exciting efficacy in fighting PD-1 resistance. Herein, we shed light on the significance of LAG-3 in the tumor microenvironment, highlight its role to regulate different lymphocytes, interplay with other immune checkpoints especially PD-1, and emphasize new advances in LAG-3-targeted immunotherapy.

  View details for DOI 10.18632/genesandcancer.180

  View details for PubMedID 30603054

  View details for PubMedCentralID PMC6305110