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He Q, Su Q, Wei C, Zhang P, Liu W, Chen J, Su X, Zhuang W. Extrachromosomal circular DNAs in prostate adenocarcinoma: global characterizations and a novel prediction model. Front Pharmacol 2024; 15:1464145. [PMID: 39355773 PMCID: PMC11442297 DOI: 10.3389/fphar.2024.1464145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Accepted: 08/19/2024] [Indexed: 10/03/2024] Open
Abstract
Background The role of focal amplifications and extrachromosomal circular DNA (eccDNA) is still uncertain in prostate adenocarcinoma (PRAD). Here, we first mapped the global characterizations of eccDNA and then investigate the characterization of eccDNA-amplified key differentially expressed encoded genes (eKDEGs) in the progression, immune response and immunotherapy of PRAD. Methods Circular_seq was used in conjunction with the TCGA-PRAD transcriptome dataset to sequence, annotate, and filter for eccDNA-amplified differentially expressed coding genes (eDEGs) in PRAD and para-cancerous normal prostate tissues. Afterwards, risk models were created and eKDEGs linked to the PRAD prognosis were identified using Cox and Lasso regression analysis. The immune microenvironment of the risk model was quantified using a variety of immunological algorithms, which also identified its characteristics with regard to immunotherapy, immune response, and immune infiltration. Results In this research, there was no significant difference in the size, type, and chromosomal distribution of eccDNA in PRAD and para-cancerous normal prostate tissues. However, 4,290 differentially expressed eccDNAs were identified and 1,981 coding genes were amplified. Following that, 499 eDEGs were tested in conjunction with the transcriptome dataset from TCGA-PRAD. By using Cox and Lasso regression techniques, ZNF330 and PITPNM3 were identified as eKDEGs of PRAD, and a new PRAD risk model was conducted based on this. Survival analysis showed that the high-risk group of this model was associated with poor prognosis and validated in external data. Immune infiltration analysis showed that the model risks affected immune cell infiltration in PRAD, not only mediating changes in immune cell function, but also correlating with immunophenotyping. Furthermore, the high-risk group was negatively associated with anti-CTLA-4/anti-PD-1 response and mutational burden. In addition, Tumor Immune Dysfunction and Exclusion analyses showed that high-risk group was more prone to immune escape. Drug sensitivity analyses identified 10 drugs, which were instructive for PRAD treatment. Conclusion ZNF330 and PITPNM are the eKDEGs for PRAD, which can be used as potential new prognostic markers. The two-factor combined risk model can effectively assess the survival and prognosis of PRAD patients, but also can predict the different responses of immunotherapy to PRAD patients, which may provide new ideas for PRAD immunotherapy.
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Affiliation(s)
- Qingliu He
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Qingfu Su
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Chengcheng Wei
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Pu Zhang
- Department of Urology, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Weihui Liu
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Junyi Chen
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Xiaoping Su
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Department of Nursing, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Wei Zhuang
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
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Zhang S, Jiang Z, Zeng P. Incorporating genetic similarity of auxiliary samples into eGene identification under the transfer learning framework. J Transl Med 2024; 22:258. [PMID: 38461317 PMCID: PMC10924384 DOI: 10.1186/s12967-024-05053-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/01/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND The term eGene has been applied to define a gene whose expression level is affected by at least one independent expression quantitative trait locus (eQTL). It is both theoretically and empirically important to identify eQTLs and eGenes in genomic studies. However, standard eGene detection methods generally focus on individual cis-variants and cannot efficiently leverage useful knowledge acquired from auxiliary samples into target studies. METHODS We propose a multilocus-based eGene identification method called TLegene by integrating shared genetic similarity information available from auxiliary studies under the statistical framework of transfer learning. We apply TLegene to eGene identification in ten TCGA cancers which have an explicit relevant tissue in the GTEx project, and learn genetic effect of variant in TCGA from GTEx. We also adopt TLegene to the Geuvadis project to evaluate its usefulness in non-cancer studies. RESULTS We observed substantial genetic effect correlation of cis-variants between TCGA and GTEx for a larger number of genes. Furthermore, consistent with the results of our simulations, we found that TLegene was more powerful than existing methods and thus identified 169 distinct candidate eGenes, which was much larger than the approach that did not consider knowledge transfer across target and auxiliary studies. Previous studies and functional enrichment analyses provided empirical evidence supporting the associations of discovered eGenes, and it also showed evidence of allelic heterogeneity of gene expression. Furthermore, TLegene identified more eGenes in Geuvadis and revealed that these eGenes were mainly enriched in cells EBV transformed lymphocytes tissue. CONCLUSION Overall, TLegene represents a flexible and powerful statistical method for eGene identification through transfer learning of genetic similarity shared across auxiliary and target studies.
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Affiliation(s)
- Shuo Zhang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Zhou Jiang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Ping Zeng
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Center for Medical Statistics and Data Analysis, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Key Laboratory of Environment and Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Xuzhou Engineering Research Innovation Center of Biological Data Mining and Healthcare Transformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Jiangsu Engineering Research Center of Biological Data Mining and Healthcare Transformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
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Qi J, Shi L, Zhu L, Chen Y, Zhu H, Cheng W, Chen AF, Fu C. Functions, Mechanisms, and therapeutic applications of the inositol pyrophosphates 5PP-InsP 5 and InsP 8 in mammalian cells. J Cardiovasc Transl Res 2024; 17:197-215. [PMID: 37615888 DOI: 10.1007/s12265-023-10427-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023]
Abstract
Water-soluble myo-inositol phosphates have long been characterized as second messengers. The signaling properties of these compounds are determined by the number and arrangement of phosphate groups on the myo-inositol backbone. Recently, higher inositol phosphates with pyrophosphate groups were recognized as signaling molecules. 5-Diphosphoinositol 1,2,3,4,6-pentakisphosphate (5PP-InsP5) is the most abundant isoform, constituting more than 90% of intracellular inositol pyrophosphates. 5PP-InsP5 can be further phosphorylated to 1,5-bisdiphosphoinositol 2,3,4,6-tetrakisphosphate (InsP8). These two molecules, 5PP-InsP5 and InsP8, are present in various subcellular compartments, where they participate in regulating diverse cellular processes such as cell death, energy homeostasis, and cytoskeletal dynamics. The synthesis and metabolism of inositol pyrophosphates are subjected to tight regulation, allowing for their highly specific functions. Blocking the 5PP-InsP5/InsP8 signaling pathway by inhibiting the biosynthesis of 5PP-InsP5 demonstrates therapeutic benefits in preclinical studies, and thus holds promise as a therapeutic approach for certain diseases treatment, such as metabolic disorders.
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Affiliation(s)
- Ji Qi
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Linhui Shi
- Department of Critical Care Unit, Ningbo Medical Center Li Huili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Limei Zhu
- Department of Trauma Orthopedics, Ningbo No.6 Hospital, Ningbo, 315040, China
| | - Yuanyuan Chen
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Hong Zhu
- Department of Obstetrics and Gynecology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Weiwei Cheng
- Department of Nuclear Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Alex F Chen
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
| | - Chenglai Fu
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
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Peng J, Gao Y, Shi X, Yang C, Xie G, Tang T, Wang D, Zheng L, Liu Y, Zhang D. Zinc finger protein 330 regulates Ramie mosaic virus infection in the whitefly Bemisia tabaci MED. PEST MANAGEMENT SCIENCE 2023; 79:1750-1759. [PMID: 36617695 DOI: 10.1002/ps.7350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 12/07/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND The whitefly, Bemisia tabaci (Gennadius) is one of the most economically important pests that cause serious damage to agricultural production by transmitting plant pathogenic viruses. Approximately 90% of the virus species transmitted by the whitefly are members of the genus begomovirus. Ramie mosaic virus (RaMoV) is a new bipartite begomovirus that causes severe damage to ramie and several other economic crops in China. In previous studies, we have demonstrated that RaMoV had no obvious direct or indirect effects on B. tabaci. However, whether B. tabaci affects RaMoV infection and the molecular mechanisms of their interaction remain unclear. RESULTS Here, we identified a zinc finger protein 330 (ZNF330) in B. tabaci MED interacted with the coat protein (CP) of RaMoV by the yeast two-hybrid assay. Then the interaction between ZNF330 and RaMoV CP was further verified by glutathione S-transferase (GST) pull-down assay. The expression of ZNF330 gene was continuously induced after RaMoV infection. ZNF330 negatively regulated RaMoV replication in the B. tabaci MED. Furthermore, the longevity and fecundity of RaMoV-infected female adults were significantly decreased after silencing of ZNF330. CONCLUSIONS Our results indicated that the ZNF330 protein was involved in the negative regulation of RaMoV replication in the B. tabaci MED. High viral accumulation caused by ZNF330 silencing is detrimental to fecundity and longevity of the B. tabaci MED. These findings provided a new insight into identifying the binding partners in whitefly with viral CP and fully understanding the complex interactions between begomoviruses and their whitefly vector. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Jing Peng
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yang Gao
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xiaobin Shi
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Chunxiao Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
| | - Gang Xie
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Tao Tang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Dongwei Wang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Limin Zheng
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yong Liu
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Deyong Zhang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
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Wang N, Bai X, Wang X, Wang D, Ma G, Zhang F, Ye J, Lu F, Ji C. A Novel Fatty Acid Metabolism-Associated Risk Model for Prognosis Prediction in Acute Myeloid Leukaemia. Curr Oncol 2023; 30:2524-2542. [PMID: 36826154 PMCID: PMC9955245 DOI: 10.3390/curroncol30020193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Acute myeloid leukaemia (AML) is the most common acute leukaemia in adults, with an unfavourable outcome and a high rate of recurrence due to its heterogeneity. Dysregulation of fatty acid metabolism plays a crucial role in the development of several tumours. However, the value of fatty acid metabolism (FAM) in the progression of AML remains unclear. In this study, we obtained RNA sequencing and corresponding clinicopathological information from the TCGA and GEO databases. Univariate Cox regression analysis and subsequent LASSO Cox regression analysis were utilized to identify prognostic FAM-related genes and develop a potential prognostic risk model. Kaplan-Meier analysis was used for prognostic significances. We also performed ROC curve to illustrate that the risk model in prognostic prediction has good performance. Moreover, significant differences in immune infiltration landscape were found between high-risk and low-risk groups using ESTIMATE and CIBERSOT algorithms. In the end, differential expressed genes (DEGs) were analyzed by gene set enrichment analysis (GSEA) to preliminarily explore the possible signaling pathways related to the prognosis of FAM and AML. The results of our study may provide potential prognostic biomarkers and therapeutic targets for AML patients, which is conducive to individualized precision therapy.
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Affiliation(s)
- Nana Wang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Xiaoran Bai
- Department of Hematology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Xinlu Wang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Dongmei Wang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Guangxin Ma
- Hematology and Oncology Unit, Department of Geriatrics, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Fan Zhang
- Department of Critical Care Medicine, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Jingjing Ye
- Department of Hematology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Fei Lu
- Department of Hematology, Qilu Hospital of Shandong University, Jinan 250012, China
- Correspondence: (F.L.); (C.J.)
| | - Chunyan Ji
- Department of Hematology, Qilu Hospital of Shandong University, Jinan 250012, China
- Correspondence: (F.L.); (C.J.)
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Wang T, Qiao J, Zhang S, Wei Y, Zeng P. Simultaneous test and estimation of total genetic effect in eQTL integrative analysis through mixed models. Brief Bioinform 2022; 23:6535679. [PMID: 35212359 DOI: 10.1093/bib/bbac038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/22/2022] [Accepted: 02/07/2021] [Indexed: 11/14/2022] Open
Abstract
Integration of expression quantitative trait loci (eQTL) into genome-wide association studies (GWASs) is a promising manner to reveal functional roles of associated single-nucleotide polymorphisms (SNPs) in complex phenotypes and has become an active research field in post-GWAS era. However, how to efficiently incorporate eQTL mapping study into GWAS for prioritization of causal genes remains elusive. We herein proposed a novel method termed as Mixed transcriptome-wide association studies (TWAS) and mediated Variance estimation (MTV) by modeling the effects of cis-SNPs of a gene as a function of eQTL. MTV formulates the integrative method and TWAS within a unified framework via mixed models and therefore includes many prior methods/tests as special cases. We further justified MTV from another two statistical perspectives of mediation analysis and two-stage Mendelian randomization. Relative to existing methods, MTV is superior for pronounced features including the processing of direct effects of cis-SNPs on phenotypes, the powerful likelihood ratio test for assessment of joint effects of cis-SNPs and genetically regulated gene expression (GReX), two useful quantities to measure relative genetic contributions of GReX and cis-SNPs to phenotypic variance, and the computationally efferent parameter expansion expectation maximum algorithm. With extensive simulations, we identified that MTV correctly controlled the type I error in joint evaluation of the total genetic effect and proved more powerful to discover true association signals across various scenarios compared to existing methods. We finally applied MTV to 41 complex traits/diseases available from three GWASs and discovered many new associated genes that had otherwise been missed by existing methods. We also revealed that a small but substantial fraction of phenotypic variation was mediated by GReX. Overall, MTV constructs a robust and realistic modeling foundation for integrative omics analysis and has the advantage of offering more attractive biological interpretations of GWAS results.
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Affiliation(s)
- Ting Wang
- Department of Biostatistics at Xuzhou Medical University, China
| | - Jiahao Qiao
- Department of Biostatistics at Xuzhou Medical University, China
| | - Shuo Zhang
- Department of Biostatistics at Xuzhou Medical University, China
| | - Yongyue Wei
- Department of Biostatistics at Nanjing Medical University, China
| | - Ping Zeng
- Department of Biostatistics, Center for Medical Statistics and Data Analysis and Key Laboratory of Human Genetics and Environmental Medicine at Xuzhou Medical University, China
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Han Z, Zhuang X, Yang B, Jin L, Hong P, Xue J, Chen S, Tian Z. SYDE1 Acts as an Oncogene in Glioma and has Diagnostic and Prognostic Values. Front Mol Biosci 2021; 8:714203. [PMID: 34722629 PMCID: PMC8552071 DOI: 10.3389/fmolb.2021.714203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/28/2021] [Indexed: 12/21/2022] Open
Abstract
Objectives: Gliomas remain one of serious public health problems worldwide which demand further and deeper investigation. The aim of this study was to explore the association between synapse defective protein 1 homolog 1 (SYDE1) and gliomas via public database analysis and in vitro validation to determine the potential diagnostic and prognostic values. Methods and Results: Compared with healthy brain tissues, there was a significant increase in SYDE1 expression in glioma tissues. Additionally, SYDE1 exhibited higher expression levels in glioma patients with unfavorable clinicopathological factors. In vitro knockdown of SYDE1 in glioma cell lines A172 inhibited their migrative and invasive ability but not the proliferative ability. GO and KEGG pathway analysis of the top 100 genes coexpressed with SYDE1 showed enrichments of tumor-associated terms. Further bioinformatic analysis revealed that the SNHG16/hsa-miR-520e/SYDE1 axis might be involved in glioma development. Conclusions: SYDE1 is expressed at higher levels in gliomas than in healthy brains, and can promote metastasis and invasion but not proliferation of gliomas. Furthermore, SYDE1 has values in the diagnosis and prognosis prediction of gliomas.
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Affiliation(s)
- Zhenyuan Han
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China.,Department of Oral Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China
| | - Xiaodong Zhuang
- Department of Stomatology, Affiliated Fuzhou First Hospital of Fujian Medical University, Fuzhou, China
| | - Biao Yang
- Department of Neurosurgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Lihui Jin
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pengjie Hong
- Department of Neurosurgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Junqing Xue
- Department of Oral Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shunjie Chen
- Department of Nephrology, Shanghai Fourth People's Hospital Affiliated to Tongji Universtiy, Shanghai, China
| | - Zhen Tian
- Department of Oral Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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