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Wang Q, Cao SH, Li YY, Zhang JB, Yang XH, Zhang B. Advances in precision therapy of low-grade serous ovarian cancer: A review. Medicine (Baltimore) 2024; 103:e34306. [PMID: 38669365 PMCID: PMC11049748 DOI: 10.1097/md.0000000000034306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/19/2023] [Indexed: 04/28/2024] Open
Abstract
Low-grade serous ovarian carcinoma (LGSOC) is a rare subtype of ovarian cancer that accounts for approximately 6% to 10% of serous ovarian cancers. The clinical treatment of LGSOC is similar to that of high-grade serous ovarian carcinoma, however, its clinical and molecular characteristics are different from those of high-grade serous ovarian carcinoma. This article reviews the research on gene diagnosis, surgical treatment, chemotherapy, and biological therapy of LGSOC, providing reference for clinical diagnosis and treatment of LGSOC. Surgery is the cornerstone of LGSOC treatment and maximum effort must be made to achieve R0 removal. Although LGSOC is not sensitive to chemotherapy, postoperative platinum-based combination chemotherapy remains the first-line treatment option for LGSOC. Additional clinical trials are needed to confirm the clinical benefits of chemotherapy and explore new chemotherapy protocols. Hormone and targeted therapies may also play important roles. Some patients, particularly those with residual lesions after treatment, may benefit from hormone maintenance therapy after chemotherapy. Targeted therapies, such as MEKi, show good application prospects and are expected to change the treatment pattern of LGSOC. Continuing to further study the genomics of LGSOC, identify its specific gene changes, and combine traditional treatment methods with precision targeted therapy based on second-generation sequencing may be the direction for LGSOC to overcome the treatment bottleneck. In future clinical work, comprehensive genetic testing should be carried out for LGSOC patients to accumulate data for future scientific research, in order to find more effective methods and drugs for the treatment of LGSOC.
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Affiliation(s)
- Qing Wang
- Department of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Sheng-Han Cao
- Graduate School of Bengbu Medical University, Bengbu, Anhui, China
| | - Yan-Yu Li
- Department of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Jing-Bo Zhang
- Department of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Xin-Hui Yang
- Department of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
| | - Bei Zhang
- Department of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou, Jiangsu, China
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Zheng L, Wang Y, Liu Z, Wang Z, Tao C, Wu A, Li H, Xiao T, Li Z, Rong W. Identification of molecular characteristics of hepatocellular carcinoma with microvascular invasion based on deep targeted sequencing. Cancer Med 2024; 13:e7043. [PMID: 38572921 PMCID: PMC10993708 DOI: 10.1002/cam4.7043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/29/2024] [Accepted: 02/13/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND As an indicator of tumor invasiveness, microvascular invasion (MVI) is a crucial risk factor for postoperative relapse, metastasis, and unfavorable prognosis in hepatocellular carcinoma (HCC). Nevertheless, the genetic mechanisms underlying MVI, particularly for Chinese patients, remain mostly uncharted. METHODS We applied deep targeted sequencing on 66 Chinese HCC samples. Focusing on the telomerase reverse transcriptase (TERT) promoter (TERTp) and TP53 co-mutation (TERTp+/TP53+) group, gene set enrichment analysis (GSEA) was used to explore the potential molecular mechanisms of the TERTp+/TP53+ group on tumor progression and metastasis. Additionally, we evaluated the tumor immune microenvironment of the TERTp+/TP53+ group in HCC using multiplex immunofluorescence (mIF) staining. RESULTS Among the 66 HCC samples, the mutated genes that mostly appeared were TERT, TP53, and CTNNB1. Of note, we found 10 cases with TERTp+/TP53+, of which nine were MVI-positive and one was MVI-negative, and there was a co-occurrence of TERTp and TP53 (p < 0.05). Survival analysis demonstrated that patients with the TERTp+/TP53+ group had lower the disease-free survival (DFS) (p = 0.028). GSEA results indicated that telomere organization, telomere maintenance, DNA replication, positive regulation of cell cycle, and negative regulation of immune response were significantly enriched in the TERTp+/TP53+ group (all adjusted p-values (p.adj) < 0.05). mIF revealed that the TERTp+/TP53+ group decreased CD8+ T cells infiltration (p = 0.25) and enhanced PDL1 expression (p = 0.55). CONCLUSIONS TERTp+/TP53+ was significantly enriched in MVI-positive patients, leading to poor prognosis for HCC patients by promoting proliferation of HCC cell and inhibiting infiltration of immune cell surrounding HCC. TERTp+/TP53+ can be utilized as a potential indicator for predicting MVI-positive patients and poor prognosis, laying a preliminary foundation for further exploration of co-mutation in HCC with MVI and clinical treatment.
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Affiliation(s)
- Linlin Zheng
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yaru Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhenrong Liu
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhihao Wang
- Department of Hepatobiliary Hernia SurgeryLiaocheng Dongcangfu People's HospitalLiaochengChina
| | - Changcheng Tao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Anke Wu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Haiyang Li
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhuo Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Weiqi Rong
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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Zhu Y, Zhou M, Li C, Kong W, Hu Y. Gastric cancer with brain metastasis: from molecular characteristics and treatment. Front Oncol 2024; 14:1310325. [PMID: 38577333 PMCID: PMC10991736 DOI: 10.3389/fonc.2024.1310325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/12/2024] [Indexed: 04/06/2024] Open
Abstract
Gastric cancer is one of the cancers with increasing incidence and ranks fourth globally among the most frequent causes of cancer-related mortality. Early gastric cancer is often asymptomatic or presents with atypical symptoms, and the majority of patients present with advanced disease upon diagnosis. Brain metastases are present in approximately 1% of gastric cancer patients at the time of diagnosis, which significantly contributed to the overall mortality of the disease worldwide. Conventional therapies for patients with brain metastases remain limited and the median overall survival of patients is only 8 months in advanced cases. Recent studies have improved our understanding of the molecular mechanisms underlying gastric cancer brain metastases, and immunotherapy has become an important treatment option in combination with radiotherapy, chemotherapy, targeted therapy and surgery. This review aims to provide insight into the cellular processes involved in gastric cancer brain metastases, discuss diagnostic approaches, evaluate the integration of immune checkpoint inhibitors into treatment and prognosis, and explore the predictive value of biomarkers in immunotherapy.
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Affiliation(s)
- Yingze Zhu
- Department of Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Miao Zhou
- Department of Oncology, Tang Shan Central Hospital, Tangshan, China
| | - Congling Li
- School of Clinical Medicine, Affiliated Hospital, North China University of Science and Technology, Tangshan, China
| | - Wenyue Kong
- School of Clinical Medicine, Affiliated Hospital, North China University of Science and Technology, Tangshan, China
| | - Yuning Hu
- School of Clinical Medicine, Affiliated Hospital, North China University of Science and Technology, Tangshan, China
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Du M, Gong M, Wu G, Jin J, Wang X, Jin Q. Conjugated Linolenic Acid (CLnA) vs Conjugated Linoleic Acid (CLA): A Comprehensive Review of Potential Advantages in Molecular Characteristics, Health Benefits, and Production Techniques. J Agric Food Chem 2024; 72:5503-5525. [PMID: 38442367 DOI: 10.1021/acs.jafc.3c08771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Conjugated linoleic acid (CLA) has been extensively characterized due to its many biological activities and health benefits, but conjugated linolenic acid (CLnA) is still not well understood. However, CLnA has shown to be more effective than CLA as a potential functional food ingredient. Current research has not thoroughly investigated the differences and advantages between CLnA and CLA. This article compares CLnA and CLA based on molecular characteristics, including structural, chemical, and metabolic characteristics. Then, the in vivo research evidence of CLnA on various health benefits is comprehensively reviewed and compared with CLA in terms of effectiveness and mechanism. Furthermore, the potential of CLnA in production technology and product protection is analyzed. In general, CLnA and CLA have similar physicochemical properties of conjugated molecules and share many similarities in regulation effects and pathways of various health benefits as well as in the production methods. However, their specific properties, regulatory capabilities, and unique mechanisms are different. The superior potential of CLnA must be specified according to the practical application patterns of isomers. Future research should focus more on the advantageous characteristics of different isomers, especially the effectiveness and safety in clinical applications in order to truly exert the potential value of CLnA.
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Affiliation(s)
- Meijun Du
- State Key Laboratory of Food Science and Resources, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, International Joint Research Laboratory for Lipid Nutrition and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Mengyue Gong
- State Key Laboratory of Food Science and Resources, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, International Joint Research Laboratory for Lipid Nutrition and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Gangcheng Wu
- State Key Laboratory of Food Science and Resources, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, International Joint Research Laboratory for Lipid Nutrition and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Jun Jin
- State Key Laboratory of Food Science and Resources, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, International Joint Research Laboratory for Lipid Nutrition and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Xingguo Wang
- State Key Laboratory of Food Science and Resources, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, International Joint Research Laboratory for Lipid Nutrition and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Qingzhe Jin
- State Key Laboratory of Food Science and Resources, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, International Joint Research Laboratory for Lipid Nutrition and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
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Kang Y, Yu K, Huang Z, Pang B, Liu S, Peng T, Li Y, Wang D. Prevalence and molecular characteristics of Shewanella infection in diarrhea patients in Beijing, China 2017-2019. Front Microbiol 2024; 15:1293577. [PMID: 38357347 PMCID: PMC10866003 DOI: 10.3389/fmicb.2024.1293577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/03/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Shewanella is an important opportunistic pathogen distributed in marine environments that has caused an increasing number of clinical infections. However, there are few reports on the distribution and characteristics of Shewanella in the diarrheal pathogen spectrum. In this study, we have systematically described the prevalence of Shewanella infections in diarrhea patients in Beijing, China 2017-2019, and genome characteristics and antimicrobial susceptibility of Shewanella isolates. Methods Stool samples were collected from diarrhea patients in a surveillance project from 2017 to 2019. Shewanella strains were isolated, and identified using VITEKR 2 COMPACT and MALDI-TOF MS. Average nucleotide identity (ANI) analysis, multi-locus sequence typing (MLST), phylogenetic analysis, virulence-associated genes and antimicrobial resistance genes analysis were used for genome characteristics description. The antibiotic susceptibility test was performed with microbroth dilution method. Results 1104 fecal samples were collected, and the Shewanella detection rate was 2.36% (26/1104). The main manifestations of infection caused by Shewanella spp. were diarrhea (100%, 26/26), abdominal pain (65.38%, 17/26), and vomiting (38.46%, 10/26). The 26 isolates were classified into 3 species (S. algae (n = 18), S. indica (n = 5), and S. chilikensis (n = 3)) and 22 sequence types. Core genome single nucleotide polymorphism-based evolutionary tree identified three clone groups corresponding to three infection events in the same months in 2017 and 2019. The putative virulence-associated gene pool consisted of 56 potential virulence genes, including 19 virulence gene factors. The resistance rates of the 26 isolates to 17 antibiotics from high to low were as follows: polymyxin E (76.92%), cefotaxime (57.69%), ampicillin (50%), ampicillin-sulbactam (34.62%), nalidixic acid (15.38%), ciprofloxacin (11.54%), selectrin (3.846%,1/26), and tetracycline (3.846%, 1/26). The rate of multidrug resistance was 38.46% (10/26). Discussion Monitoring for Shewanella spp. should be added to the routine surveillance of infectious diarrhea during the epidemic season.
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Affiliation(s)
- Ying Kang
- Shunyi District Center for Disease Control and Prevention, Beijing, China
- Workstation for Microbial Infectious Disease, Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Keyi Yu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Zhenzhou Huang
- Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Bo Pang
- Workstation for Microbial Infectious Disease, Shunyi District Center for Disease Control and Prevention, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Shengtian Liu
- Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Tao Peng
- Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Ying Li
- Shunyi District Center for Disease Control and Prevention, Beijing, China
- Workstation for Microbial Infectious Disease, Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Duochun Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
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Li X, Guan H, Ma C, Dai Y, Su J, Chen X, Yuan Q, Wang J. Combination of bulk RNA sequencing and scRNA sequencing uncover the molecular characteristics of MAPK signaling in kidney renal clear cell carcinoma. Aging (Albany NY) 2024; 16:1414-1439. [PMID: 38217548 PMCID: PMC10866414 DOI: 10.18632/aging.205436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/01/2023] [Indexed: 01/15/2024]
Abstract
The MAPK signaling pathway significantly impacts cancer progression and resistance; however, its functions remain incompletely assessed across various cancers, particularly in kidney renal clear cell carcinoma (KIRC). Therefore, there is an urgent need for comprehensive pan-cancer investigations of MAPK signaling, particularly within the context of KIRC. In this research, we obtained TCGA pan-cancer multi-omics data and conducted a comprehensive analysis of the genomic and transcriptomic characteristics of the MAPK signaling pathway. For in-depth investigation in KIRC, status of MAPK pathway was quantitatively estimated by ssGSEA and Ward algorithm was utilized for cluster analysis. Molecular characteristics and clinical prognoses of KIRC patients with distinct MAPK activities were comprehensively explored using a series of bioinformatics algorithms. Subsequently, a combination of LASSO and COX regression analyses were utilized sequentially to construct a MAPK-related signature to help identify the risk level of each sample. Patients in the C1 subtype exhibited relatively higher levels of MAPK signaling activity, which were associated with abundant immune cell infiltration and favorable clinical outcomes. Single-cell RNA sequencing (scRNA-seq) analysis of KIRC samples identified seven distinct cell types, and endothelial cells in tumor tissues had obviously higher MAPK scores than normal tissues. The immunohistochemistry results indicated the reduced expression levels of PAPSS1, MAP3K11, and SPRED1 in KIRC samples. In conclusion, our study represents the first integration of bulk RNA sequencing and single-cell RNA sequencing to elucidate the molecular characteristics of MAPK signaling in KIRC, providing a solid foundation for precision oncology.
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Affiliation(s)
- Xiunan Li
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Hewen Guan
- Department of Dermatology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Chuanyu Ma
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yunfei Dai
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Ji Su
- Department of Urology, Central Hospital of Benxi, Benxi, Liaoning, China
| | - Xu Chen
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Qihang Yuan
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jianbo Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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Zhu S, Xu N, Zeng H. Molecular complexity of intraductal carcinoma of the prostate. Cancer Med 2024; 13:e6939. [PMID: 38379333 PMCID: PMC10879723 DOI: 10.1002/cam4.6939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/21/2023] [Accepted: 12/04/2023] [Indexed: 02/22/2024] Open
Abstract
Intraductal carcinoma of the prostate (IDC-P) is an aggressive subtype of prostate cancer characterized by the growth of tumor cells within the prostate ducts. It is often found alongside invasive carcinoma and is associated with poor prognosis. Understanding the molecular mechanisms driving IDC-P is crucial for improved diagnosis, prognosis, and treatment strategies. This review summarizes the molecular characteristics of IDC-P and their prognostic indications, comparing them to conventional prostate acinar adenocarcinoma, to gain insights into its unique behavior and identify potential therapeutic targets.
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Affiliation(s)
- Sha Zhu
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduChina
| | - Nanwei Xu
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduChina
| | - Hao Zeng
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduChina
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Wang H, Wang W, Wang Z, Li X. Transcriptomic correlates of cell cycle checkpoints with distinct prognosis, molecular characteristics, immunological regulation, and therapeutic response in colorectal adenocarcinoma. Front Immunol 2023; 14:1291859. [PMID: 38143740 PMCID: PMC10749195 DOI: 10.3389/fimmu.2023.1291859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023] Open
Abstract
Backgrounds Colorectal adenocarcinoma (COAD), accounting for the most common subtype of colorectal cancer (CRC), is a kind of malignant digestive tumor. Some cell cycle checkpoints (CCCs) have been found to contribute to CRC progression, whereas the functional roles of a lot of CCCs, especially the integrated role of checkpoint mechanism in the cell cycle, remain unclear. Materials and methods The Genomic Data Commons (GDC) The Cancer Genome Atlas (TCGA) COAD cohort was retrieved as the training dataset, and GSE24551 and GSE29623 were downloaded from Gene Expression Omnibus (GEO) as the validation datasets. A total of 209 CCC-related genes were derived from the Gene Ontology Consortium and were subsequently enrolled in the univariate, multivariate, and least absolute shrinkage and selection operator (LASSO) Cox regression analyses, finally defining a CCC signature. Cell proliferation and Transwell assay analyses were utilized to evaluate the functional roles of signature-related CCCs. The underlying CCC signature, molecular characteristics, immune-related features, and therapeutic response were finally estimated. The Genomics of Drug Sensitivity in Cancer (GDSC) database was employed for the evaluation of chemotherapeutic responses. Results The aberrant gene expression of CCCs greatly contributed to COAD development and progression. Univariate Cox regression analysis identified 27 CCC-related genes significantly affecting the overall survival (OS) of COAD patients; subsequently, LASSO analysis determined a novel CCC signature. Noticeably, CDK5RAP2, MAD1L1, NBN, RGCC, and ZNF207 were first identified to be correlated with the prognosis of COAD, and it was proven that all of them were significantly correlated with the proliferation and invasion of HCT116 and SW480 cells. In TCGA COAD cohort, CCC signature robustly stratified COAD patients into high and low CCC score groups (median OS: 57.24 months vs. unreached, p< 0.0001), simultaneously, with the good AUC values for OS prediction at 1, 2, and 3 years were 0.74, 0.78, and 0.77. Furthermore, the prognostic capacity of the CCC signature was verified in the GSE24551 and GSE29623 datasets, and the CCC signature was independent of clinical features. Moreover, a higher CCC score always indicated worse OS, regardless of clinical features, histological subtypes, or molecular subgroups. Intriguingly, functional enrichment analysis confirmed the CCC score was markedly associated with extracellular, matrix and immune (chemokine)-related signaling, cell cycle-related signaling, and metabolisms. Impressively, a higher CCC score was positively correlated with a majority of chemokines, receptors, immunostimulators, and anticancer immunity, indicating a relatively immune-promoting microenvironment. In addition, GSE173839, GSE25066, GSE41998, and GSE194040 dataset analyses of the underlying CCC signature suggested that durvalumab with olaparib and paclitaxel, taxane-anthracycline chemotherapy, neoadjuvant cyclophosphamide/doxorubicin with ixabepilone or paclitaxel, and immunotherapeutic strategies might be suitable for COAD patients with higher CCC score. Eventually, the GDSC database analysis showed that lower CCC scores were likely to be more sensitive to 5-fluorouracil, bosutinib, gemcitabine, gefitinib, methotrexate, mitomycin C, and temozolomide, while patients with higher CCC score seemed to have a higher level of sensitivity to bortezomib and elesclomol. Conclusion The novel CCC signature exhibited a good ability for prognosis prediction for COAD patients, and the CCC score was found to be highly correlated with molecular features, immune-related characteristics, and therapeutic responses, which would greatly promote clinical management and precision medicine for COAD.
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Affiliation(s)
- Heng Wang
- Department of Colorectal Surgery, Shanghai Yangpu Hospital of Traditional Chinese Medicine, Shanghai, China
| | - Wei Wang
- Department of Colorectal Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Zhen Wang
- Department of Colorectal Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Xu Li
- Department of Colorectal Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, China
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Cai Y, Han Q, Guo H. Identifying clinical features and molecular characteristics of the endometrial clear cell carcinoma. Front Oncol 2023; 13:1286176. [PMID: 38045002 PMCID: PMC10691759 DOI: 10.3389/fonc.2023.1286176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/27/2023] [Indexed: 12/05/2023] Open
Abstract
Objective The aim of this study was to verify TCGA subtypes in endometrial clear cell carcinoma (ECCC) and determine their clinical and molecular characteristics. Methods We summarized and compared the clinical features of 28 clear cell carcinoma and 112 endometrioid carcinoma patients. Of the 28 ECCCs, 19 underwent TCGA classification, and other markers (ER, PR, ARID1A, ARIB1B, TAF1, and HER-2) were also detected by IHC, and outcomes were assessed. Results Compared to endometrioid carcinoma, ECCC had an older age of onset (median age, 64.5 years, range 31-81 years), higher rate of myometrial invasion (42.8% vs. 21.5% in endometrioid carcinoma), LVSI (33% vs. 16%), and more advanced FIGO stage. Among the ECCCs, LVSI was a poor prognostic factor. TCGA classification was performed for 19 ECCCs: two POLEmut cases (10.5%), three MMRd (15.8%), 11 p53wt (57.9%), and three p53abn (15.8%). Of the 19 ECCCs, six (31.6%) showed HER-2 positive expression, and eight (42.1%) had TAF1 expression loss. ECCCs possessed HER-2 and TAF1 expression had worse outcomes. Conclusion Our study summarized the clinical features of ECCC. The outcomes of patients with ECCC with TCGA subtypes differed from those of patients with endometrioid carcinoma. HER-2 and TAF1 may be new prognostic factors.
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Affiliation(s)
| | | | - Hongyan Guo
- Department of Gynecology, Peking University Third Hospital, Beijing, China
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Wu Y, Zhang G, Jiang H, Xin T, Jia L, Zhang Y, Yang Y, Qin T, Xu C, Cao J, Ameni G, Ahmad A, Ding J, Li L, Ma Y, Fan X. Molecular Characteristics of Bovine Viral Diarrhea Virus Strains Isolated from Persistently Infected Cattle. Vet Sci 2023; 10:413. [PMID: 37505819 PMCID: PMC10384089 DOI: 10.3390/vetsci10070413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/08/2023] [Accepted: 06/15/2023] [Indexed: 07/29/2023] Open
Abstract
In this study, we reported the isolation, identification, and molecular characteristics of nine BVDV strains that were isolated from the serum of persistently infected cattle. The new strains were designated as BVDV TJ2101, TJ2102, TJ2103, TJ2104, TJ2105, TJ2106, TJ2107, TJ2108 and TJ2109. The TJ2102 and TJ2104 strains were found to be cytopathic BVDV, and the other strains were non-cytopathic BVDV. An alignment and phylogenetic analysis showed that the new isolates share 92.2-96.3% homology with the CP7 strain and, thus, were classified as the BVDV-1b subgenotype. A recombination analysis of the genome sequences showed that the new strains could be recombined by the major parent BVDV-1a NADL strain and the minor parent BVDV-1m SD-15 strain. Some genome variations or unique amino acid mutations were found in 5'-UTR, E0 and E2 of these new isolates. In addition, a potential linear B cell epitopes prediction showed that the potential linear B cell epitope at positions 56-61 is highly variable in BVDV-1b. In conclusion, the present study has identified nine strains of BVDV from persistently infected cattle in China. Further studies on the virulence and pathogenesis of these new strains are recommended.
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Affiliation(s)
- Yinghao Wu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Guangzhi Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hui Jiang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ting Xin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Li Jia
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Yichen Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yifei Yang
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Tong Qin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chuang Xu
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jie Cao
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Gobena Ameni
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Abu Dhabi P.O. Box 15551, United Arab Emirates
| | - Arfan Ahmad
- University Diagnostic Lab, University of Veterinary & Animal Sciences, Lahore 54000, Pakistan
| | - Jiabo Ding
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Limin Li
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Yuzhong Ma
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Xuezheng Fan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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11
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Yu K, Liu X, Lu Y, Long M, Bai J, Qin Q, Su X, He G, Mi X, Yang C, Wang R, Wang H, Chen Y, Wei Z, Huang W, Ouyang K. Biological Characteristics and Pathogenicity Analysis of a Low Virulence G2a Porcine Epidemic Diarrhea Virus. Microbiol Spectr 2023; 11:e0453522. [PMID: 37199637 PMCID: PMC10269638 DOI: 10.1128/spectrum.04535-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 04/27/2023] [Indexed: 05/19/2023] Open
Abstract
Since the outbreak caused by a porcine epidemic diarrhea virus (PEDV) variant in 2010, the current epidemic of PEDV genotype 2 (G2) has caused huge economic losses to the pig industry in China. In order to better understand the biological characteristics and pathogenicity of the current PEDV field strains, 12 PEDV isolates were collected and plaque purified during 2017 to 2018 in Guangxi, China. The neutralizing epitopes of the spike proteins and the ORF3 proteins were analyzed to evaluate genetic variations, and they were compared with the reported G2a and G2b strains. Phylogenetic analysis of the S protein showed that the 12 isolates were clustered into the G2 subgroup (with 5 and 7 strains in G2a and G2b, respectively) and that they shared 97.4 to 99.9% amino acid identities. Among them, one of the G2a strains, CH/GXNN-1/2018, which had a titer of 106.15 PFU/mL, was selected for pathogenicity analysis. Although piglets infected with the CH/GXNN-1/2018 strain exhibited severe clinical signs and the highest level of virus shedding within 24 h postinfection (hpi), recovery and decreased virus shedding were seen after 48 hpi, and no piglets died during the whole process. Thus, the CH/GXNN-1/2018 strain had low virulence in suckling piglets. Virus neutralizing antibody analysis showed that the CH/GXNN-1/2018 strain induced cross-protection against both homologous G2a and heterologous G2b PEDV strains as early as 72 hpi. These results are of great significance for understanding PEDV in Guangxi, China, and they provide a promising naturally occurring low-virulent vaccine candidate for further study. IMPORTANCE The current epidemic of porcine epidemic diarrhea virus (PEDV) G2 has caused huge economic losses to the pig industry. Evaluation for low virulence of the PEDV strains of subgroup G2a would be useful for the future development of effective vaccines. In this study, 12 field strains of PEDV were obtained successfully, and they were characterized from Guangxi, China. The neutralizing epitopes of the spike proteins and the ORF3 proteins were analyzed to evaluate antigenic variations. One of the G2a strains, CH/GXNN-1/2018, was selected for pathogenicity analysis, and it showed that the CH/GXNN-1/2018 strain had low virulence in suckling piglets. These results provide a promising naturally occurring low-virulent vaccine candidate for further study.
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Affiliation(s)
- Kechen Yu
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Xueting Liu
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Ying Lu
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Meijing Long
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Jiaguo Bai
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Qiuying Qin
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Xueli Su
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Guifu He
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Xue Mi
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Chunjie Yang
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Ruomu Wang
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Hejie Wang
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Ying Chen
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, China
| | - Zuzhang Wei
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, China
| | - Weijian Huang
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, China
| | - Kang Ouyang
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, China
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12
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Song J, Lu H, Ma L, Zhu S, Yan D, Han J, Zhang Y. Molecular Characteristics of Enterovirus B83 Strain Isolated from a Patient with Acute Viral Myocarditis and Global Transmission Dynamics. Viruses 2023; 15:1360. [PMID: 37376658 DOI: 10.3390/v15061360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
This study determined the global genetic diversity and transmission dynamics of enterovirus B83 (EV-B83) and proposed future disease surveillance directions. Blood samples were collected from a patient with viral myocarditis, and viral isolation was performed. The complete genome sequence of the viral isolate was obtained using Sanger sequencing. A dataset of 15 sequences (from three continents) that had sufficient time signals for Bayesian phylogenetic analysis was set up, and the genetic diversity and transmission dynamics of global EV-B83 were analyzed using bioinformatics methods, including evolutionary dynamics, recombination event analysis, and phylogeographic analysis. Here, we report the complete genome sequence of an EV-B83 strain (S17/YN/CHN/2004) isolated from a patient with acute viral myocarditis in Yunnan Province, China. All 15 EV-B83 strains clustered together in a phylogenetic tree, confirming the classification of these isolates as a single EV type, and the predicted time for the most recent common ancestor appeared in 1998. Recombinant signals were detected in the 5'-untranslated region and 2A-3D coding regions of the S17 genome. The phylogeographic analysis revealed multiple intercontinental transmission routes of EV-B83. This study indicates that EV-B83 is globally distributed. Our findings add to the publicly available EV-B83 genomic sequence data and deepen our understanding of EV-B83 epidemiology.
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Affiliation(s)
- Juan Song
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Huanhuan Lu
- National Polio Laboratory and WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Lin Ma
- Yunnan Institute of Endemic Diseases Control and Prevention, No.5, Wenhua Road, Dali 671000, China
| | - Shuangli Zhu
- National Polio Laboratory and WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Dongmei Yan
- National Polio Laboratory and WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jun Han
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yong Zhang
- National Polio Laboratory and WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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13
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Downton TDF, Wing K, Cosentino SB, Karanth NV. The molecular characteristics of non-small cell lung cancer in the Northern Territory's Top End. Asia Pac J Clin Oncol 2023. [PMID: 37278121 DOI: 10.1111/ajco.13967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 01/01/2023] [Accepted: 04/27/2023] [Indexed: 06/07/2023]
Abstract
AIM Indigenous Australians with lung cancer have poorer survival than non-Indigenous Australians. The reasons for the disparity are not fully understood and this study hypothesized that there may be a difference in the molecular profiles of tumors. The aim of this study, therefore, was to describe and compare the characteristics of non-small cell lung cancer (NSCLC) in the Northern Territory's Top End, between Indigenous and non-Indigenous patients, and describe the molecular profile of tumors in the two groups. METHODS A retrospective review was conducted of all adults with a new diagnosis of NSCLC in the Top End from 2017 to 2019. Patient characteristics assessed were Indigenous status, age, sex, smoking status, disease stage, and performance status. Molecular characteristics assessed were epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), v-raf murine sarcoma viral oncogene homolog B (BRAF), ROS proto-oncogene 1 (ROS1), Kirsten rat sarcoma viral oncogene homolog (KRAS), mesenchymal-epithelial transition (MET), human epidermal growth factor receptor 2 (HER2), and programmed death-ligand 1 (PD-L1). Student's t-test and Fisher's Exact Test were used in the statistical analysis. RESULTS There were 152 patients diagnosed with NSCLC in the Top End from 2017-2019. Thirty (19.7%) were Indigenous and 122 (80.3%) were non-Indigenous. Indigenous patients compared to non-Indigenous patients were younger at diagnosis (median age 60.7 years versus 67.1 years, p = 0.00036) but were otherwise similar in demographics. PD-L1 expression was similar between Indigenous and non-Indigenous patients (p = 0.91). The only mutations identified among stage IV non-squamous NSCLC patients were EGFR and KRAS but testing rates and overall numbers were too small to draw conclusions about differences in prevalence between Indigenous and non-Indigenous patients. CONCLUSION This is the first study to investigate the molecular characteristics of NSCLC in the Top End.
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Affiliation(s)
- Teesha Dzu Fun Downton
- Division of Medicine, Royal Darwin Hospital, Tiwi, Australia
- Garvan Institute of Medical Research, Sydney, Australia
| | - Kristof Wing
- Division of Medicine, Royal Darwin Hospital, Tiwi, Australia
| | - Stevie Brooke Cosentino
- Division of Medicine, Royal Darwin Hospital, Tiwi, Australia
- Department of Medicine, Cairns Hospital, Cairns, Australia
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14
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Fang L, Jia H, Hu Y, Wang Y, Cui Z, Qi L, Zhao P. Molecular characterization and pathogenicity study of a highly pathogenic strain of chicken anemia virus that emerged in China. Front Cell Infect Microbiol 2023; 13:1171622. [PMID: 37284496 PMCID: PMC10240067 DOI: 10.3389/fcimb.2023.1171622] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/25/2023] [Indexed: 06/08/2023] Open
Abstract
Chicken infectious anemia (CIA) is caused by chicken anemia virus (CAV). Recently, severe anemia has emerged in layer chickens (8 to 10-week-old) on poultry farms in China. However, the etiological characteristics and pathogenic potential of CAV in chickens at 6 weeks or older are not well understood. In this study, we isolated a CAV strain, termed SD15, from two-month-old chicken with severe anemia and analyzed the genetic evolution relationship. We found that strain SD15 had the highest homology (98.9%) with CAV18 strain. Comparison with 33 reference strains revealed 16 amino acid mutations in strain SD15, two of which were previously unknown (F210S in VP1 and L25S in Vp3). Compared with low pathogenic strains (Cux-1 and C14), highly pathogenic strains (SDLY08 and SD15) had three base mutations in their noncoding region. To further understand its pathogenicity, 10-week-old specific-pathogen-free (SPF) chickens were challenged with the novel strain and SDLY08. No obvious clinical symptoms were observed in the SDLY08 group. However, SD15-infected chickens showed significant growth retardation and immunosuppression. The main manifestations of immunosuppression were the significantly reduced thymus and bursa indices and AIV-H9 vaccine-induced antibody levels (P < 0.05). The lowest number of red blood cells in the SD15 group was just 60% of that in the control group. Taken together, the novel strain SD15 not only showed higher pathogenicity but also exhibited the potential ability to break the age resistance of older chickens to CAV. Our study enhanced the understanding of the epidemiological characteristics of chickens infected with severe anemia and can facilitate the development of improved control strategies of CIA in China.
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Affiliation(s)
- Lichun Fang
- Innovation Team for Major Livestock and Poultry Disease Prevention and Control, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Huiyue Jia
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, Shandong, China
| | - Yuhang Hu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Yixin Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, Shandong, China
| | - Zhizhong Cui
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, Shandong, China
| | - Lihong Qi
- Innovation Team for Major Livestock and Poultry Disease Prevention and Control, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Peng Zhao
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, Shandong, China
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15
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Li N, Jia X, Wang Z, Wang K, Qu Z, Chi D, Sun Z, Jiang J, Cui Y, Wang C. Characterization of anoikis-based molecular heterogeneity in pancreatic cancer and pancreatic neuroendocrine tumor and its association with tumor immune microenvironment and metabolic remodeling. Front Endocrinol (Lausanne) 2023; 14:1153909. [PMID: 37234801 PMCID: PMC10206226 DOI: 10.3389/fendo.2023.1153909] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/21/2023] [Indexed: 05/28/2023] Open
Abstract
Background Accumulating evidence suggests that anoikis plays a crucial role in the onset and progression of pancreatic cancer (PC) and pancreatic neuroendocrine tumors (PNETs); nevertheless, the prognostic value and molecular characteristics of anoikis in cancers are yet to be determined. Materials and methods We gathered and collated the multi-omics data of several human malignancies using the TCGA pan-cancer cohorts. We thoroughly investigated the genomics and transcriptomics features of anoikis in pan-cancer. We then categorized a total of 930 patients with PC and 226 patients with PNETs into distinct clusters based on the anoikis scores computed through single-sample gene set enrichment analysis. We then delved deeper into the variations in drug sensitivity and immunological microenvironment between the various clusters. We constructed and validated a prognostic model founded on anoikis-related genes (ARGs). Finally, we conducted PCR experiments to explore and verify the expression levels of the model genes. Results Initially, we identified 40 differentially expressed anoikis-related genes (DE-ARGs) between pancreatic cancer (PC) and adjacent normal tissues based on the TCGA, GSE28735, and GSE62452 datasets. We systematically explored the pan-cancer landscape of DE-ARGs. Most DE-ARGs also displayed differential expression trends in various tumors, which were strongly linked to favorable or unfavorable prognoses of patients with cancer, especially PC. Cluster analysis successfully identified three anoikis-associated subtypes for PC patients and two anoikis-associated subtypes for PNETs patients. The C1 subtype of PC patients showed a higher anoikis score, poorer prognosis, elevated expression of oncogenes, and lower level of immune cell infiltration, whereas the C2 subtype of PC patients had the exact opposite characteristics. We developed and validated a novel and accurate prognostic model for PC patients based on the expression traits of 13 DE-ARGs. In both training and test cohorts, the low-risk subpopulations had significantly longer overall survival than the high-risk subpopulations. Dysregulation of the tumor immune microenvironment could be responsible for the differences in clinical outcomes between low- and high-risk groups. Conclusions These findings provide fresh insights into the significance of anoikis in PC and PNETs. The identification of subtypes and construction of models have accelerated the progress of precision oncology.
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Affiliation(s)
- Ning Li
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Department of General Surgery, Wafangdian Central Hospital, Dalian, Liaoning, China
- Graduate School of Dalian Medical University, Dalian, Liaoning, China
| | - Xingqing Jia
- Department of Digestive, Jinan City People’s Hospital, Jinan, Shandong, China
| | - Zhong Wang
- Department of General Surgery, Wafangdian Central Hospital, Dalian, Liaoning, China
| | - Kaige Wang
- Graduate School of Dalian Medical University, Dalian, Liaoning, China
| | - Zumin Qu
- Department of Pathology, Wafangdian Central Hospital, Dalian, Liaoning, China
| | - Dong Chi
- Department of General Surgery, Wafangdian Central Hospital, Dalian, Liaoning, China
| | - Zhubo Sun
- Department of General Surgery, Wafangdian Central Hospital, Dalian, Liaoning, China
| | - Jian Jiang
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yougang Cui
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Department of General Surgery, The Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Changmiao Wang
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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16
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Jin Y, Li J, Tang C, He K, Shan D, Yan S, Deng G. A risk signature of necroptosis-related lncRNA to predict prognosis and probe molecular characteristics for male with bladder cancer. Medicine (Baltimore) 2023; 102:e33664. [PMID: 37145007 PMCID: PMC10158872 DOI: 10.1097/md.0000000000033664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 04/10/2023] [Indexed: 05/06/2023] Open
Abstract
Bladder cancer (BC) is a frequently diagnosed cancer with high mortality. Male patients have a higher risk of developing BC than female patients. As a type of caspase-independent cell death, necroptosis plays a significant role in the occurrence and progression of BC. The aberrant function of long non-coding RNAs (lncRNAs) plays an indispensable role in GI. However, the relationship between lncRNA and necroptosis in male patients with BC remains unclear. The clinical information and RNA-sequencing profiles of all BC patients were retrieved from The Cancer Genome Atlas Program. A total of 300 male participants were selected for the study. We conducted to identify the necroptosis-related lncRNAs (NRLs) by Pearson correlation analysis. Subsequently, least absolute shrinkage and selection operator Cox regression were conducted to establish a risk signature with overall survival-related NRLs in the training set and to validate it in the testing set. Finally, we verified the effectiveness of the 15-NRLs signature in prognostic prediction and therapy via survival analysis, receiver operating characteristic curve analysis, and Cox regression. Furthermore, we analyzed the correlation between the signature risk score and pathway enrichment analysis, immune cell infiltration, anticancer drug sensitivity, and somatic gene mutations. We developed 15-NRLs (AC009974.1, AC140118.2, LINC00323, LINC02872, PCAT19, AC017104.1, AC134312.5, AC147067.2, AL139351.1, AL355922.1, LINC00844, AC069503.1, AP003721.1, DUBR, LINC02863) signature, and divided patients into a high-risk group and low-risk group through the median risk score. Kaplan-Meier and receiver operating characteristic curves showed that the prognosis prediction had satisfactory accuracy. Cox regression analysis indicated that the 15-NRLs signature was a risk factor independent of various clinical parameters. Additionally, immune cell infiltration, half-maximal inhibitory concentration, and somatic gene mutations differed significantly among different risk subsets, implying that the signature could assess the clinical efficacy of chemotherapy and immunotherapy. This 15-NRLs risk signature may be helpful in assessing the prognosis and molecular features of male patients with BC and improve treatment modalities, thus can be further applied clinically.
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Affiliation(s)
- Yuzhou Jin
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Jiacheng Li
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Chenhao Tang
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Kangwei He
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Donggang Shan
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Shenze Yan
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Gang Deng
- Hangzhou First People’s Hospital, Hangzhou, China
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17
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Wu H, Xiong X, CUI X, Xiong J, Zhang Y, Xiang L, Xu TAO. Analysis of the influence of pyroptosis-related genes on molecular characteristics in patients with acute myocardial infarction. Medicine (Baltimore) 2023; 102:e33620. [PMID: 37083810 PMCID: PMC10118340 DOI: 10.1097/md.0000000000033620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/04/2023] [Indexed: 04/22/2023] Open
Abstract
Pyroptosis is a newly identified mode of programmed cell death, but the potential role in patients with acute myocardial infarction (AMI) remains unclear. In this study, bioinformatics methods were used to identify differentially expressed genes from peripheral blood transcriptome data between normal subjects and patients with AMI which were downloaded by the Gene Expression Omnibus database. Comparing Random Forest (RF) and Support Vector Machine (SVM) training algorithms were used to identify pyroptosis-related genes, predicting patients with AMI by nomogram based on informative genes. Moreover, clustering was used to amplify the feature of pyroptosis, in order to facilitate analysis distinct biological differences. Diversity analysis indicated that a majority of pyroptosis-related genes are expressed at higher levels in patients with AMI. The receiver operating characteristic curves show that the RF model is more responsive than the SVM machine learning model to the pyroptosis characteristics of these patients in vivo. We obtained a column line graph diagnostic model which was developed based on 19 genes established by the RF model. After the consensus clustering algorithm of single sample Gene Set Enrichment Analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Enrichment Analysis, the results for them found that pyroptosis-related genes mediate the activation of multiple immune cells and many inflammatory pathways in the body. We used RF and SVM algorithms to determine 19 pyroptosis-related genes and evaluate their immunological effects in patients with AMI. We also constructed a series of by nomogram related to pyroptosis-related genes to predict the risk of developing AMI.
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Affiliation(s)
- Huan Wu
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Xiaoman Xiong
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Xueying CUI
- Qingyun County People’s Hospital, Qingyun, Shandong, China
| | - Jianlong Xiong
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Yan Zhang
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Liubo Xiang
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - TAO Xu
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
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18
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Chen Y, Liu X, Zhang L, Zhu F, Yan L, Tang W, Zhang Z, Liu Q, Jiang H, Qiao J. Deciphering the Molecular Characteristics of Human Idiopathic Nonobstructive Azoospermia from the Perspective of Germ Cells. Adv Sci (Weinh) 2023:e2206852. [PMID: 37083227 DOI: 10.1002/advs.202206852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/21/2023] [Indexed: 05/03/2023]
Abstract
Nonobstructive azoospermia (NOA) is one of the most important causes of male infertility, accounting for 10-15% of infertile men worldwide. Among these, more than 70% of cases are idiopathic NOA (iNOA), whose pathogenesis and molecular basis remain unknown. This work profiles 3696 human testicular single-cell transcriptomes from 17 iNOA patients, which are classified into four classes with different arrest periods and variable cell proportions based on the gene expression patterns and pathological features. Genes related to the cell cycle, energy production, and gamete generation show obvious abnormalities in iNOA germ cells. This work identifies several candidate causal genes for iNOA, including CD164, LELP1, and TEX38, which are significantly downregulated in iNOA germ cells. Notably, CD164 knockdown promotes apoptosis in spermatogonia. Cellular communications between spermatogonial stem cells and Sertoli cells are disturbed in iNOA patients. Moreover, BOD1L2, C1orf194, and KRTCAP2 are found to indicate testicular spermatogenic capacity in a variety of testicular diseases, such as Y-chromosome microdeletions and Klinefelter syndrome. In general, this study analyzes the pathogenesis of iNOA from the perspective of germ cell development, transcription factor (TF) regulatory networks, as well as germ cell and somatic cell interactions, which provides new ideas for clinical diagnosis.
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Affiliation(s)
- Yidong Chen
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
| | - Xixi Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
| | - Li Zhang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
| | - Feiyin Zhu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Liying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
| | - Wenhao Tang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
| | - Zhe Zhang
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China
| | - Qiang Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
| | - Hui Jiang
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
- Beijing Advanced Innovation Center for Genomics, Beijing, 100871, China
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Luo C, Yang L, Huang Z, Su Y, Lu Y, Yu D, Zhang M, Wu K. Case report: A case of epidermolysis bullosa complicated with pyloric atresia and a literature review. Front Pediatr 2023; 11:1098273. [PMID: 37033187 PMCID: PMC10076629 DOI: 10.3389/fped.2023.1098273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
Objective This article aims to explore the diagnosis, molecular characteristics, treatment, and prognosis of epidermolysis bullosa with pyloric atresia (EB-PA). Methods The clinical manifestations, diagnosis and treatment, and genetic characteristics of a patient with EB-PA admitted to our hospital were analysed. The disease subtypes, concomitant abnormalities, molecular characteristics, and prognosis of patients with EB-PA were summarized by searching the EB-PA-related literature since 2011. Results We present a very low birth weight female infant with skin blisters and pyloric obstruction. Exome sequencing revealed heterozygous mutations in the ITGB4 gene: c.794dupC (p. S265fs*5) and c.2962G > A (p.A988T). This infant was diagnosed with EB-PA. Coverage of the wounds and Penicillin were used to prevent infection, but the patient eventually developed severe sepsis. A literature review was carried out including 49 cases of EB-PA; among these cases, 34 were preterm infants, weighing between 930 and 3,640 g. Of these EB-PA patients, 28 had accompanying malformations, including urinary system malformations and aplasia cutis congenita (ACC). Thirty-two patients identified the subtype of EB-PA, of whom 25 were diagnosed with junctional epidermolysis bullosa (JEB), 6 with epidermolysis bullosa simplex (EBS), and 1 with dystrophic epidermolysis bullosa (DEB). Genetic testing was conducted on 23 patients, of whom 15 carried Integrin Beta-4 (ITGB4) gene mutations and one JEB patient carried an Integrin Alpha-6 (ITGA6) gene mutation; 4 of the 5 EBS patients had Plectin (PLEC) gene mutations, and the other had an ITGB4 mutation. ITGB4 mutation cases involved 29 mutation sites, primarily concentrated in the region encoding the integrin beta subunit; PLEC mutation cases involved 7 mutation sites. Among all cases, 43 underwent pyloric atresia surgery, of whom 24 died postoperatively, and 6 without surgery therapy died within a short period. Conclusion EB-PA is a rare genetic disorder characterized by increased skin fragility and PA involving mutations in the ITGB4, PLEC, or ITGA6 genes. EB-PA has a high incidence of complications and mortality, surgery and supportive therapy are currently the most common treatment options.
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Affiliation(s)
| | | | | | | | | | | | | | - Kai Wu
- Department of Pediatric Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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Guo Y, Xu L, Wang B, Rao L, Xu Y, Wang X, Zhao H, Yu J, Zhou Y, Yu F. Dissemination of Methicillin-Resistant Staphylococcus aureus Sequence Type 764 Isolates with Mupirocin Resistance in China. Microbiol Spectr 2023; 11:e0379422. [PMID: 36622214 PMCID: PMC9927232 DOI: 10.1128/spectrum.03794-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023] Open
Abstract
Mupirocin, a topical antimicrobial agent, is an important component in the eradication of methicillin-resistant Staphylococcus aureus (MRSA) colonization. The molecular characteristics of 46 mupirocin-resistant MRSA (MR-MRSA) clinical isolates were analyzed by multilocus sequence typing (MLST), staphylococcal cassette chromosome mec element (SCCmec) typing, spa typing, and analysis of virulence genes. All 26 MRSA isolates with low-level mupirocin resistance possessed a V588F mutation in ileS. Among 20 MRSA isolates with high-level resistance to mupirocin, all carried mupA; 2 isolates also possessed the V588F mutation in ileS, and 1 possessed the V631F mutation in ileS (isoleucyl-tRNA synthetase). The majority of MR-MRSA isolates were resistant to erythromycin, clindamycin, tetracycline, ciprofloxacin, and gentamicin, but the rates of resistance to rifampin and fusidic acid were 8.7% and 6.5%, respectively. Eight sequence types (STs) were found among the 46 MR-MRSA isolates, of which ST764 was the most prevalent (76.1%). The most frequent spa type identified was t1084 (52.2%). The SCCmec type most frequently found was type II (80.4%). The most common clone among low-level MR-MRSA isolates was ST764-MRSA-SCCmec type II-t1084 (23 isolates), while ST764-MRSA-SCCmec type II-t002 (9 isolates) was the most common clone among high-level MR-MRSA isolates. Additionally, all toxin genes except the seb gene were not identified among ST764 isolates. Among clonal complex 5 (CC5) isolates, immune evasion cluster (IEC)-associated genes (chp, sak, and scn) and seb were present in ST764 but absent in ST5, while sec, sel1, tsst-1, and hlb genes were identified in ST5 but absent in ST764. In conclusion, the spread of CC5 clones, especially a novel ST764-MRSA-SCCmec type II-t1084 clone with high-level resistance to mupirocin, was responsible for the increase in mupirocin resistance. These findings indicated that the emergence of the ST764 MR-MRSA clone involves a therapeutic challenge for treating serious MRSA infections. IMPORTANCE Mupirocin, a topical antibiotic that is commonly used for the nasal decolonization of MRSA and methicillin-sensitive Staphylococcus aureus in hospital settings and nursing homes, was introduced as a highly effective antibiotic against MRSA. Mupirocin acts by competitively binding isoleucyl-tRNA synthetase, thereby disrupting protein synthesis. This drug shows bacteriostatic and bactericidal activity at low and high concentrations, respectively. However, with the increase in mupirocin use, low-level and high-level resistance during nasal mupirocin treatment has been reported. In a previous study, the proportion of MRSA strains with high-level mupirocin resistance in a Canadian hospital increased from 1.6% in the first 5 years of surveillance (1995 to 1999) to 7.0% (2000 to 2004).
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Affiliation(s)
- Yinjuan Guo
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Linling Xu
- Fenyang Affiliated Hospital of Shanxi Medical University, Fenyang, China
| | - Bingjie Wang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Lulin Rao
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yanlei Xu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Xinyi Wang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Huilin Zhao
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Jingyi Yu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Ying Zhou
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Fangyou Yu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
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21
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Liu C, Liao K, Wang J, Wu B, Hu H, Ren H. Microbial Transformation of Dissolved Organic Sulfur during the Oxic Process in 47 Full-Scale Municipal Wastewater Treatment Plants. Environ Sci Technol 2023; 57:2118-2128. [PMID: 36608328 DOI: 10.1021/acs.est.2c06776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Dissolved organic sulfur (DOS) is a significant part of effluent organic matter of wastewater treatment plants (WWTPs) and poses a potential ecological risk for receiving waters. However, the oxic process is a critical unit of biological wastewater treatment for microorganisms performing organic matter removal, wherein DOS transformation and its mechanism are poorly understood. This study investigated the transformation of DOS during the oxic process in 47 full-scale municipal WWTPs across China from molecular and microbial aspects. Surprisingly, evident differences in DOS variations (ΔDOS) separated sampled WWTPs into two groups: 28 WWTPs with decreased DOS concentrations in effluents (ΔDOS < 0) and 19 WWTPs with increased DOS (ΔDOS > 0). These two groups also presented differences in DOS molecular characteristics: higher nitrogen/carbon (N/C) ratios (0.030) and more peptide-like DOS (8.2%) occurred in WWTPs with ΔDOS > 0, implying that peptide-like DOS generated from microbes contributed to increased DOS in effluents. Specific microbe-DOS correlations (Spearman correlation, p < 0.05) indicated that increased effluent DOS might be explained by peptide-like DOS preferentially being produced during copiotrophic bacterial growth and accumulating due to less active cofactor metabolisms. Considering the potential environmental issues accompanying DOS discharge from WWTPs with ΔDOS > 0, our study highlights the importance of focusing on the transformation and control of DOS in the oxic process.
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Affiliation(s)
- Caifeng Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Kewei Liao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jinfeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
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Zhang LH, Wang TX, Fu PF, Zhao YY, Li HX, Wang DM, Ma SJ, Chen HY, Zheng LL. First Molecular Detection and Genetic Analysis of a Novel Porcine Circovirus (Porcine Circovirus 4) in Dogs in the World. Microbiol Spectr 2023; 11:e0433322. [PMID: 36728419 PMCID: PMC10100769 DOI: 10.1128/spectrum.04333-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/11/2023] [Indexed: 02/03/2023] Open
Abstract
A novel circovirus species was identified in farmed pigs and designated porcine circovirus 4 (PCV4); it has recently been proved to be pathogenic to piglets. However, little is known about its cross-species transmission, and there is no evidence of PCV4 in dogs. A total of 217 fecal samples were collected from diarrheal dogs in Henan Province, China, and tested for the presence of PCV4 using a real-time PCR assay. Among the 217 samples, the total positivity rate for PCV4 was 5.99% (13/217 samples), with rates of 7.44% and 4.17% in 2020 and 2021, respectively. PCV4 was detected in dogs in 6 of 10 cities, demonstrating that PCV4 could be detected in dogs in Henan Province, China. One PCV4 strain (HN-Dog) was sequenced in this study and shared high levels of identity (97.9% to 99.6%) with reference strains at the genome level. Phylogenetic analysis based on complete genome sequences of HN-Dog and 42 reference strains showed that the HN-Dog strain was closely related to 3 PCV4 reference strains (from pig, raccoon dog, and fox) but differed genetically from other viruses in the genus Circovirus. Three genotypes, i.e., PCV4a, PCV4b, and PCV4c, were confirmed by phylogenetic analysis of complete genome sequences of 42 PCV4 strains, and one amino acid variation in Rep protein (V239L) and three amino acid variations in Cap protein (N27S, R28G, and M212L) were considered conserved genotype-specific molecular markers. In conclusion, the present study is the first to report the discovery of the PCV4 genome in dogs, and the association between PCV4 infection and diarrhea warrants further study. IMPORTANCE This study is the first to report the presence of PCV4 in dogs worldwide, and the first complete genome sequence was obtained from a dog affected with diarrhea. Three genotypes of PCV4 strains (PCV4a, PCV4b, and PCV4c) were determined, as supported by specific amino acid markers (V239L for open reading frame 1 [ORF1] and N27S R28G and M212L for ORF2). These findings help us understand the current status of intestinal infections in pet dogs in Henan Province, China, and also prompted us to accelerate research on the pathogenesis, epidemiology, and cross-species transmission of PCV4.
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Affiliation(s)
- Liu-Hui Zhang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, People’s Republic of China
| | - Tong-Xuan Wang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, People’s Republic of China
| | - Peng-Fei Fu
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, Henan Province, People’s Republic of China
| | - You-Yi Zhao
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, People’s Republic of China
| | - Hong-Xuan Li
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, People’s Republic of China
| | - Dong-Mei Wang
- Lushan Dabei Agriculture and Animal Husbandry Food Co., Ltd., Lushan, Henan Province, People’s Republic of China
| | - Shi-Jie Ma
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, People’s Republic of China
| | - Hong-Ying Chen
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, People’s Republic of China
| | - Lan-Lan Zheng
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, People’s Republic of China
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Huang X, Zhang F, Lin J, Lin S, Shen G, Chen X, Chen W. Systematically analyzed molecular characteristics of lung adenocarcinoma using metabolism-related genes classification. Genet Mol Biol 2023; 45:e20220121. [PMID: 36622242 PMCID: PMC9830935 DOI: 10.1590/1678-4685-gmb-2022-0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/06/2022] [Indexed: 01/10/2023] Open
Abstract
High heterogeneity of lung adenocarcinoma (LUAD) is a major clinical challenge. This study aims to characterize the molecular features of LUAD through classification based on metabolism-related genes. A total of 500 LUAD samples from The Cancer Genome Atlas (TCGA) and 612 from Gene Expression Omnibus (GEO) were integrated with 2,753 metabolism-related genes to determine the molecular classification. Systematic bioinformatics analysis was used to conduct correlation analysis between metabolism-related classification and molecular characteristics of LUAD. LUAD patients were divided into three molecular clusters (C1-C3). Survival analysis revealed that C1 and C2 showed good and poor prognoses, respectively. Associational analysis of classification and molecular characteristics revealed that C1 was associated with low pathological stage, metabolic pathways, high metabolic process, active immune process and checkpoint, sensitive drug response, as well as a low genetic mutation. Nevertheless, C2 was associated with high pathological stage, carcinogenic pathways, low metabolic process, inactive immune signatures, resistant drug response, and frequent genetic mutation. Eventually, a classifier with 60 metabolic genes was constructed, confirming the robustness of molecular classification on LUAD. Our findings promote the understanding of LUAD molecular characteristics, and the research data may be used for providing information be helpful for clinical diagnosis and treatment.
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Affiliation(s)
- Xiaoming Huang
- The Affiliated Hospital of Southern Medical University, People’s Hospital of Longhua, Department of respiratory medicine, Shenzhen, China
| | - Feng Zhang
- The First Affiliated Hospital of Jinan University, Department of Intensive Care Unit, Guangzhou, China
| | - Junqi Lin
- The Affiliated Hospital of Southern Medical University, People’s Hospital of Longhua, Department of respiratory medicine, Shenzhen, China
| | - Shaoming Lin
- The Affiliated Hospital of Southern Medical University, People’s Hospital of Longhua, Department of respiratory medicine, Shenzhen, China
| | - Guanle Shen
- The Affiliated Hospital of Southern Medical University, People’s Hospital of Longhua, Department of respiratory medicine, Shenzhen, China
| | - Xiaozhu Chen
- The Affiliated Hospital of Southern Medical University, People’s Hospital of Longhua, Department of Medical Ultrasound Department, Shenzhen, China
| | - Wenbiao Chen
- The Affiliated Hospital of Southern Medical University, People’s Hospital of Longhua, Department of respiratory medicine, Shenzhen, China
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Chang Y, Yue H, Tang C. Prevalence and Molecular Characteristics of Bovine Respiratory Syncytial Virus in Beef Cattle in China. Animals (Basel) 2022; 12. [PMID: 36552433 DOI: 10.3390/ani12243511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/20/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Bovine respiratory syncytial virus (BRSV) is an important pathogen of the bovine respiratory disease complex (BRDC); however, its prevalence and molecular characteristics in China remain largely unknown. In this study, 788 nasal swabs from 51 beef cattle farms with BRDC outbreaks in 16 provinces and one municipality were collected from October 2020 to July 2022, and 18.65% (147/788) of samples from 23 farms across 11 provinces were detected as BRSV-positive by reverse transcription-insulated isothermal PCR (RT-iiPCR) assay. Further, 18 complete G gene sequences were classified into BRSV subgroup III, and 25 complete F gene sequences were obtained from 8 and 10 provinces. Compared to the known BRSV strains in GenBank, the G proteins and F proteins in this study shared several identical amino acid (aa) mutations. Moreover, five nearly complete genome sequences were obtained and clustered into a large branch with two America BRSV subgroup III strains (KU159366 and OM328114) rather than the sole Chinese strain (MT861050) but were located in an independent small branch. In conclusion, this study reveals that BRSV has a wide geographical distribution in China, and subgroup III strains, which have unique evolution characteristics, are the dominant strains. The results contribute to a better understanding of the prevalence and genetic evolution of BRSV.
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Liu Z, Liu B, Feng C, Li C, Wang H, Zhang H, Liu P, Li Z, He S, Tu C. Molecular characterization of immunogenic cell death indicates prognosis and tumor microenvironment infiltration in osteosarcoma. Front Immunol 2022; 13:1071636. [PMID: 36569869 PMCID: PMC9780438 DOI: 10.3389/fimmu.2022.1071636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction Osteosarcoma (OS) is a highly aggressive bone malignancy with a poor prognosis, mainly in children and adolescents. Immunogenic cell death (ICD) is classified as a type of programmed cell death associated with the tumor immune microenvironment, prognosis, and immunotherapy. However, the feature of the ICD molecular subtype and the related tumor microenvironment (TME) and immune cell infiltration has not been carefully investigated in OS. Methods The ICD-related genes were extracted from previous studies, and the RNA expression profiles and corresponding data of OS were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus database. The ICD-related molecular subtypes were classed by the "ConsensusclusterPlus" package and the construction of ICD-related signatures through univariate regression analysis. ROC curves, independent analysis, and internal validation were used to evaluate signature performance. Moreover, a series of bioinformatic analyses were used for Immunotherapy efficacy, tumor immune microenvironments, and chemotherapeutic drug sensitivity between the high- and low-risk groups. Results Herein, we identified two ICD-related subtypes and found significant heterogeneity in clinical prognosis, TME, and immune response signaling among distinct ICD subtypes. Subsequently, a novel ICD-related prognostic signature was developed to determine its predictive performance in OS. Also, a highly accurate nomogram was then constructed to improve the clinical applicability of the novel ICD-related signature. Furthermore, we observed significant correlations between ICD risk score and TME, immunotherapy response, and chemotherapeutic drug sensitivity. Notably, the in vitro experiments further verified that high GALNT14 expression is closely associated with poor prognosis and malignant progress of OS. Discussion Hence, we identified and validated that the novel ICD-related signature could serve as a promising biomarker for the OS's prognosis, chemotherapy, and immunotherapy response prediction, providing guidance for personalized and accurate immunotherapy strategies for OS.
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Affiliation(s)
- Zhongyue Liu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Binfeng Liu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chengyao Feng
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chenbei Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Hua Wang
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Haixia Zhang
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ping Liu
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhihong Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Shasha He
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,*Correspondence: Shasha He, ; Chao Tu,
| | - Chao Tu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,*Correspondence: Shasha He, ; Chao Tu,
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Tarabukina E, Krasova A, Kurlykin M, Tenkovtsev A, Filippov A. Loose Semirigid Aromatic Polyester Bottle Brushes at Poly(2-isopropyl-2-oxazoline) Side Chains of Various Lengths: Behavior in Solutions and Thermoresponsiveness. Polymers (Basel) 2022; 14. [PMID: 36559721 DOI: 10.3390/polym14245354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
A polycondensation aromatic polyester with an oxygen spacer was synthesized and used as a macroinitiator for the grafting of linear poly(2-isopropyl-2-oxazoline) (PiPrOx) by the cationic polymerization method. The length of the thermosensitive side chains was varied by the initiator:monomer ratio. Using methods of molecular hydrodynamics, light scattering and turbidimetry, the copolymers were studied in organic solvents and in water. The molecular characteristics of the main chain and graft copolymers, the polymerization degree of side chains and their grafting density have been determined. The equilibrium rigidity of the macroinitiator and the conformations of grafted macromolecules were evaluated. In selective solvents, they take on a star-like conformation or aggregate depending on the degree of shielding of the main chain by side chains. The thermoresponsiveness of graft copolymers in aqueous solutions was studied, and their LCST were estimated. The results are compared with data for graft copolymers composed of PiPrOx side chains and flexible or rigid chain backbones of aromatic polyester type.
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Yang Y, Abi K, Li Y, Yang C, Yang F. First detection and molecular characteristics of bopivirus from goats in China. Front Vet Sci 2022; 9:1033011. [PMID: 36532341 PMCID: PMC9753977 DOI: 10.3389/fvets.2022.1033011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/14/2022] [Indexed: 10/13/2023] Open
Abstract
A metavirome analysis was performed and detected bopivirus in the diarrhoeal fecal samples of goats in China. A total of 136 fecal samples were collected from yeanlings between the dates of June 2021 and January 2022 in Sichuan province, China. Moreover, "Bopivirus B" strains were detected by a specific RT-PCR targeting the 3D gene of the virus. The results showed that the overall detection rate of "Bopivirus B" was 19.12% (26/136). Additionally, there was a higher detection rate (24.05%, 19/79) in the fecal samples collected from yeanlings with diarrhea compared to those from asymptomatic animals (12.28%, 7/57). In these samples, no other common diarrhea-causing pathogens were detected except for three enteric viruses, namely caprine enterovirus, caprine kobuvirus and caprine hunnivirus (with detection rates of 13.97, 13.97, and 8.82%, respectively). Subsequently, full-length VP4, VP2, VP3, and VP1 genes from "Bopivirus B"-positive samples were amplified, cloned, sequenced, and analyzed. The phylogenetic analysis performed on the VP1 genes revealed that the identified bopivirus belonged to genotype B1 (seven strains) and B2 (three strains) and presented a high genetic diversity. Furthermore, a complete genome sequence of a "Bopivirus B" strain (SWUN/B1/2022) was obtained using PCR from fecal sample of a diarrhoeal yeanling. The complete genome was 7,309 nucleotides in length with a standard picornavirus genome organization, and shares 93.10% and 91.10% nucleotide similarity with bopivirus B1 genotype strain ovine/TB14/2010-HUN and bopivirus B2 genotype strain goat/AGK16/2020-HUN, respectively. According to the species classification criteria put forward by the International Committee on Taxonomy of Viruses and VP1 genotype, the strain SWUN/B1/2022 belongs to the bopivirus B1. This strain has unique amino acid substitutions in the VP4, VP2, VP3, and VP1 genes. Moreover, genomic recombination analysis revealed that this strain may be a minor parental strain of bopivirus B1 ovine/TB14/2010-HUN. Evolutionary analysis based on the 2C and 3CD genes revealed that the new bopivirus B1 strain SWUN/B1/2022 presents a unique evolutionary pattern. This study provided evidence to suggest that "Bopivirus B" is circulating with substantial genetic diversity in goats in China at present, and the mixed infection of "Bopivirus B" with other enteric viruses should be considered to be a composite factor in the occurrence of viral diarrhea in goats.
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Affiliation(s)
- Youwen Yang
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Kehamo Abi
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Yanmin Li
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Chen Yang
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Falong Yang
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
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Li K, Hou M, Zhang L, Tian M, Yang M, Jia L, Liang Y, Zou D, Liu R, Ma Y. Analysis of Antimicrobial Resistance and Genetic Correlations of Escherichia Coli in Dairy Cow Mastitis. J Vet Res 2022; 66:571-9. [PMID: 36846038 DOI: 10.2478/jvetres-2022-0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022] Open
Abstract
Introduction Escherichia coli is a widespread environmental pathogen frequently causing dairy cow mastitis. This bacterium is particularly capable of acquiring antimicrobial resistance, which can have severe impacts on animal food safety and human health. The objective of the study was to investigate antimicrobial resistance and genetic correlations of E. coli from dairy cow mastitis cases in northern China. Material and Methods Forty strains of E. coli from 196 mastitis milk samples were collected, susceptibility to 13 common antibiotics and the prevalence of resistance genes were tested in these strains, and the genetic characteristics were identified by multilocus sequence typing. Results The results showed that most isolates were multidrug resistant (MDR) (75%), and the resistance rates to cefazolin, trimethoprim-sulfamethoxazole and ampicillin were 77.5%, 55.0%, and 52.5%, respectively. The representative genes of the isolates were aadA (62.5%) and tet(B) (60.0%). Multilocus sequence typing showed 19 different sequence types (STs) and 5 clonal complexes (CCs) in the 40 isolates, mainly represented by ST10 and CC10. The strains of the same ST or CC showed a high level of genetic relatedness, but the characteristics of their antimicrobial resistance were markedly different. Conclusion Most E. coli isolates in the study were MDR strains. Some strains of the same ST or CC showed diverse resistance characteristics to common antimicrobials. Therefore, E. coli from dairy cow mastitis in northern China should be investigated to elucidate its antimicrobial resistance and genotypes.
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Zhu H, Luo H, Zhong Q, Cao X, Gu S, Peng S, Xiao Y, Chen Y, Hang Y, Fang X, Zou S, Yu F, Hu L. Comparison of Molecular Characteristics Between Methicillin-Resistant and -Susceptible Staphylococcus aureus Clinical Isolates by Whole-Genome Sequencing. Infect Drug Resist 2022; 15:2949-2958. [PMID: 35706925 PMCID: PMC9190744 DOI: 10.2147/idr.s359654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/12/2022] [Indexed: 11/23/2022] Open
Abstract
Introduction The transmission of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible Staphylococcus aureus (MSSA) are great public health concern worldwide. To better understand S. aureus evolution and dissemination, we compared the molecular features of MSSA and MRSA isolates. Methods In this study, 74 MSSA and 102 MRSA non-duplicate isolates were recovered from clinical samples between 2016 and 2020. Molecular epidemiology, antimicrobial resistance determinants, and virulence gene profiles were carried out by whole-genome sequencing (WGS). Results Twenty distinct sequence types were identified in MRSA isolates, with the most common being ST59, ST630, and ST338. The major genotypes of MSSA were ST188 and ST7. The toxin genes clfA, sek, and seq were significantly associated with MRSA, while splA/B, clfB, map, sdrC/D, and sem-sen-seo-seu were detected more frequently in MSSA isolates than MRSA (P < 0.05). The tst positive isolates were more commonly identified in CC1 and CC72, whereas lukE/D was mainly found in the CC7, CC15, CC88, and completely absent in CC59 clones. Conclusion Our results compared the genetic diversity between MRSA and MSSA strains, suggesting efforts to fight infections caused by MSSA need to be intensified due to MSSA isolates carrying wide range of virulence factors. Comparative epidemiological studies of large populations of MSSA and MRSA will be necessary in the future to understand how MSSA and MRSA populations may co-evolve and interact in the future.
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Affiliation(s)
- Hongying Zhu
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Hong Luo
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Qiaoshi Zhong
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xingwei Cao
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Shumin Gu
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Suqin Peng
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Yanping Xiao
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Yanhui Chen
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Yaping Hang
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xueyao Fang
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Shan Zou
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Fangyou Yu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji UniversitySchool of Medicine, Shanghai, 200082, People's Republic of China
| | - Longhua Hu
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
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Zhang R, Han Y, Xie W, Liu F, Chen S. Advances in Protein-Based Nanocarriers of Bioactive Compounds: From Microscopic Molecular Principles to Macroscopical Structural and Functional Attributes. J Agric Food Chem 2022; 70:6354-6367. [PMID: 35603429 DOI: 10.1021/acs.jafc.2c01936] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Many proteins can be used to fabricate nanocarriers for encapsulation, protection, and controlled release of nutraceuticals. This review examined the protein-based nanocarriers from microscopic molecular characteristics to the macroscopical structural and functional attributes. Structural, physical, and chemical properties of protein-based nanocarriers were introduced in detail. The spatial size, shape, water dispersibility, colloidal stability, etc. of protein-based nanocarriers were largely determined by the molecular physicochemical principles of protein. Different preparative techniques, including antisolvent precipitation, pH-driven, electrospray, and gelation methods, among others, can be used to fabricate different protein-based nanocarriers. Various modifications based on physical, chemical, and enzymatic approaches can be used to improve the functional performance of these nanocarriers. Protein is a natural resource with a wide range of sources, including plant, animal, and microbial, which are usually used to fabricate the nanocarriers. Protein-based nanocarriers have many advantages in aid of the application of bioactive ingredients to the medical, food, and cosmetic industries.
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Affiliation(s)
- Ruyi Zhang
- School of Public Health, Wuhan University, 115 Donghu Road, Wuchang District, Wuhan, Hubei 430071, People's Republic of China
| | - Yahong Han
- Key Laboratory of Aquaculture Facilities Engineering, Ministry of Agriculture and Rural Affairs, College of Engineering, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Weijie Xie
- Shanghai Mental Health Centre, School of Medicine, Shanghai Jiao Tong University, Shanghai 200011, People's Republic of China
| | - Fuguo Liu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Shuai Chen
- School of Public Health, Wuhan University, 115 Donghu Road, Wuchang District, Wuhan, Hubei 430071, People's Republic of China
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Chen Z, Jiang W, Li Z, Zong Y, Deng G. Immune-and Metabolism-Associated Molecular Classification of Ovarian Cancer. Front Oncol 2022; 12:877369. [PMID: 35646692 PMCID: PMC9133421 DOI: 10.3389/fonc.2022.877369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/19/2022] [Indexed: 01/25/2023] Open
Abstract
Ovarian cancer (OV) is a complex gynecological disease, and its molecular characteristics are not clear. In this study, the molecular characteristics of OV subtypes based on metabolic genes were explored through the comprehensive analysis of genomic data. A set of transcriptome data of 2752 known metabolic genes was used as a seed for performing non negative matrix factorization (NMF) clustering. Three subtypes of OV (C1, C2 and C3) were found in analysis. The proportion of various immune cells in C1 was higher than that in C2 and C3 subtypes. The expression level of immune checkpoint genes TNFRSF9 in C1 was higher than that of other subtypes. The activation scores of cell cycle, RTK-RAS, Wnt and angiogenesis pathway and ESTIMATE immune scores in C1 group were higher than those in C2 and C3 groups. In the validation set, grade was significantly correlated with OV subtype C1. Functional analysis showed that the extracellular matrix related items in C1 subtype were significantly different from other subtypes. Drug sensitivity analysis showed that C2 subtype was more sensitive to immunotherapy. Survival analysis of differential genes showed that the expression of PXDN and CXCL11 was significantly correlated with survival. The results of tissue microarray immunohistochemistry showed that the expression of PXDN was significantly correlated with tumor size and pathological grade. Based on the genomics of metabolic genes, a new OV typing method was developed, which improved our understanding of the molecular characteristics of human OV.
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Affiliation(s)
- Zhenyue Chen
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weiyi Jiang
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhen Li
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yun Zong
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Gaopi Deng
- Department Obstetrics and Gynecology, First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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Kang YJ, Shi C, Zhou J, Qian J, Qiu Y, Ge G. Multiple molecular characteristics of circulating enterovirus types among pediatric hand, foot and mouth disease patients after EV71 vaccination campaign in Wuxi, China. Epidemiol Infect 2022; 150:1-19. [PMID: 35473720 PMCID: PMC9128351 DOI: 10.1017/s0950268822000784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/05/2022] [Accepted: 04/16/2022] [Indexed: 11/08/2022] Open
Abstract
The molecular properties of the circulating causative agents of hand, foot and mouth disease (HFMD) in Wuxi remain unclear, posing diagnostic and prevention challenges. Additionally, in several regions of mainland China, the EV71 immunisation drastically reduced related cases and altered the HFMD pathogen spectrum, while the precise situation in Wuxi remained unknown. To address these issues, paediatric HFMD cases diagnosed in the clinic were enrolled and anal swabs were acquired in the spring of 2019. The 5′-UTR and VP1 genes were interpreted using RT-nPCR with degenerate primers to confirm their genotypes. Following that, the entire genome sequences of each viral type were recovered, allowing for the interpretation of several molecular properties. A total of 249 clinically confirmed HFMD cases had their anal swabs taken for viral identification, from which the genome sequences of seven genotypes were recovered. Coxsackievirus A16 is the most prevalent type, followed by Coxsackievirus A6, A10, A2, A4, A5 and Echovirus 11, all of which were genetically determined for the first time in Wuxi. Phylogenetic and recombination analyses were used to evaluate their evolutionary relationships with other strains found in other regions. Noticeably, a CVA16 subtype, responsible for a large proportion of the observed cases, phylogenetically clustered within clade B1a along with some strains from other countries, was the first one to be reported in China. Furthermore, some recombination events were inferred from strains detected in sporadic cases, particularly the recombination between CVA2 and CVA5 strains. Our investigation elucidated the multiple molecular characteristics of the HFMD causal enterovirus strains in Wuxi, underlining the potential hazards associated with these circulating viral types in the population and aiding in future surveillance and prevention of this disease.
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Affiliation(s)
- Yan-Jun Kang
- Department of Pediatric Laboratory, Wuxi Children's Hospital, Wuxi, China
| | - Chao Shi
- Department of Disease Control, Wuxi Center for Disease Control and Prevention, Wuxi, China
| | - Jian Zhou
- Department of Pediatric Laboratory, Wuxi Children's Hospital, Wuxi, China
| | - Jun Qian
- Department of Pediatrics, Wuxi Children's Hospital, Wuxi 214023, China
| | - Yuanwang Qiu
- Department of Infectious Diseases, The Fifth People's Hospital of Wuxi, Wuxi, China
| | - Guizhi Ge
- Department of Infectious Disease, Wuxi Children's Hospital, Wuxi, China
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Luo L, Li L, Liu L, Feng Z, Zeng Q, Shu X, Cao Y, Li Z. A Necroptosis-Related lncRNA-Based Signature to Predict Prognosis and Probe Molecular Characteristics of Stomach Adenocarcinoma. Front Genet 2022; 13:833928. [PMID: 35330731 PMCID: PMC8940523 DOI: 10.3389/fgene.2022.833928] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/11/2022] [Indexed: 12/14/2022] Open
Abstract
Background: As a caspase-independent type of cell death, necroptosis plays a significant role in the initiation, and progression of gastric cancer (GC). Numerous studies have confirmed that long non-coding RNAs (lncRNAs) are closely related to the prognosis of patients with GC. However, the relationship between necroptosis and lncRNAs in GC remains unclear. Methods: The molecular profiling data (RNA-sequencing and somatic mutation data) and clinical information of patients with stomach adenocarcinoma (STAD) were retrieved from The Cancer Genome Atlas (TCGA) database. Pearson correlation analysis was conducted to identify the necroptosis-related lncRNAs (NRLs). Subsequently, univariate Cox regression and LASSO-Cox regression were conducted to establish a 12-NRLs signature in the training set and validate it in the testing set. Finally, the prognostic power of the 12-NRLs signature was appraised via survival analysis, nomogram, Cox regression, clinicopathological characteristics correlation analysis, and the receiver operating characteristic (ROC) curve. Furthermore, correlations between the signature risk score (RS) and immune cell infiltration, immune checkpoint molecules, somatic gene mutations, and anticancer drug sensitivity were analyzed. Results: In the present study, a 12-NRLs signature comprising REPIN1-AS1, UBL7-AS1, LINC00460, LINC02773, CHROMR, LINC01094, FLNB-AS1, ITFG1-AS1, LASTR, PINK1-AS, LINC01638, and PVT1 was developed to improve the prognosis prediction of STAD patients. Unsupervised methods, including principal component analysis and t-distributed stochastic neighbor embedding, confirmed the capability of the present signature to separate samples with RS. Kaplan-Meier and ROC curves revealed that the signature had an acceptable predictive potency in the TCGA training and testing sets. Cox regression and stratified survival analysis indicated that the 12-NRLs signature were risk factors independent of various clinical parameters. Additionally, immune cell infiltration, immune checkpoint molecules, somatic gene mutations, and half-inhibitory concentration differed significantly among different risk subtypes, which implied that the signature could assess the clinical efficacy of chemotherapy and immunotherapy. Conclusion: This 12-NRLs risk signature may help assess the prognosis and molecular features of patients with STAD and improve treatment modalities, thus can be further applied clinically.
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Affiliation(s)
- Lianghua Luo
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Leyan Li
- Queen Mary School, Medical Department of Nanchang University, Nanchang, China
| | - Li Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Zongfeng Feng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Qingwen Zeng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Xufeng Shu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Yi Cao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Zhengrong Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, China
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Hu M, Tan J, Liu Z, Li L, Zhang H, Zhao D, Li B, Gao X, Che N, Zhang T. Comprehensive Comparative Molecular Characterization of Young and Old Lung Cancer Patients. Front Oncol 2022; 11:806845. [PMID: 35096611 PMCID: PMC8789686 DOI: 10.3389/fonc.2021.806845] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/13/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Young lung cancer as a small subgroup of lung cancer has not been fully studied. Most of the previous studies focused on the clinicopathological features, but studies of molecular characteristics are still few and limited. Here, we explore the characteristics of prognosis and variation in young lung cancer patients with NSCLC. METHODS A total of 5639 young lung cancer samples (NSCLC, age ≤40) were screened from the SEER and the same number of the old (NSCLC, age ≥60) were screened by propensity score matching to evaluate the prognosis of two groups. 165 treatment-naïve patients diagnosed with NSCLC were enrolled to explore the molecular feature difference between two age-varying groups. CCLE cell line expression data was used to verify the finding from the cohort of 165 patients. RESULTS The overall survival of the young lung cancer group was significantly better than the old. Germline analysis showed a trend that the young group contained a higher incidence of germline alterations. The TMB of the young group was lower. Meanwhile, the heterogeneity and evolutionary degrees of the young lung cancer group were also lower than the old. The mutation spectrums of two groups exhibited variance with LRP1B, SMARCA4, STK11, FAT2, RBM10, FANCM mutations, EGFR L858R more recurrent in the old group and EML4-ALK fusions, BCL2L11 deletion polymorphism, EGFR 19DEL, 20IN more recurrent in the young group. For the base substitution, the young showed a lower fraction of transversion. Further, we performed a pathway analysis and found the EGFR tyrosine kinase inhibitor resistance pathway enriched in the young lung cancer group, which was validated in gene expression data later. CONCLUSIONS There were significantly different molecular features of the young lung cancer group. The young lung cancer group had a more simple alteration structure. Alteration spectrums and base substitution types varied between two groups, implying the different pathogenesis. The young lung cancer group had more potential treatment choices. Although young lung patients had better outcomes, there were still adverse factors of them, suggesting that the young group still needs more caution for treatment choice and monitoring after the treatment to further improve the prognosis.
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Affiliation(s)
- Mingming Hu
- Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Tumor Research Institute, Beijing, China
| | - Jinjing Tan
- Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Tumor Research Institute, Beijing, China
| | - Zhentian Liu
- Department of Tranlational Medicine, Geneplus-Beijing, Beijing, China
| | - Lifeng Li
- Department of Tranlational Medicine, Geneplus-Beijing, Beijing, China
| | - Hongmei Zhang
- Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Tumor Research Institute, Beijing, China
| | - Dan Zhao
- Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Tumor Research Institute, Beijing, China
| | - Baolan Li
- Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Tumor Research Institute, Beijing, China
| | - Xuan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Department of Tranlational Medicine, Geneplus-Shenzhen Clinical Laboratory, Shenzhen, China
| | - Nanying Che
- Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Tumor Research Institute, Beijing, China
| | - Tongmei Zhang
- Beijing Chest Hospital, Capital Medical University & Beijing Tuberculosis and Tumor Research Institute, Beijing, China
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Meng X, Huang X, Peng Z, Wang Y, Liu S, Zeng C, Duan J, Wen X, Fu C, Wu A, Li C. Antibiotic Resistances and Molecular Characteristics of Clostridioides difficile in ICUs in a Teaching Hospital From Central South China. Front Med (Lausanne) 2021; 8:745383. [PMID: 34938744 PMCID: PMC8685378 DOI: 10.3389/fmed.2021.745383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/01/2021] [Indexed: 11/21/2022] Open
Abstract
Clostridioides (C.) difficile is a major healthcare-associated pathogen inducing infectious diarrhea. Approximately 25–33% of patients with antibiotic-associated diarrhea (AAD) and 90% of patients with pseudomembranous enteritis are caused by C. difficile infection (CDI). Stool samples were collected from hospitalized adults with presumptive AAD in four nonneonatal intensive care units (ICUs). Diagnosis of CDI was based on both clinical symptoms and laboratory results. The stool specimens were transferred onto CDIF (C. difficile agar), and C. difficile was finally confirmed by the latex agglutination test. Toxin-producing genes tcdA (A), tcdB (B), and cdt (CDT) were detected by PCR, and all isolates were performed multilocus sequence typing analysis. The antibiotic susceptibility of C. difficile isolates was assessed by the agar dilution method. A total of 184 C. difficile were isolated from 857 specimens in our study, the isolation rate of C. difficile was 21.5% (184/857). The 184 C. difficile were isolated from 179 patients, among these 115 patients were toxin-positive, giving the incidence of CDI being 58.0/10,000 patient days in the four ICUs. Among these 115 toxin-positive C. difficile isolates, 100 (87.0%) isolates produced two toxins (A+B+CDT-), three (2.6%) isolates were A+B+ with binary toxin-producing (A+B+CDT+), and 12 (10.4%) isolates only produced one toxin (A-B+CDT-). A total of 27 sequencing types (STs) were obtained. The most prevalent was ST3 (34 isolates), followed by ST39 (27 isolates), ST54 (19 isolates), ST26 (16 isolates), ST35 (15 isolates), and ST2 (13 isolates). All the ST26 isolates were nontoxigenic. Meanwhile, five STs were newly discovered. Although multidrug resistance was present in ≥50% of these C. difficile isolates, all of them were susceptible to tigecycline, fidaxomicin, metronidazole, and vancomycin. In conclusion, C. difficile isolates producing two toxins (A+B+CDT-) were dominant in our hospital. The most prevalent was ST3, and all ST26 isolates were NTCD. Although multidrug resistance was present in ≥50% of the C. difficile isolates, metronidazole, tigecycline, fidaxomicin, and vancomycin were still effective treatments for CDI in our hospital.
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Affiliation(s)
- Xiujuan Meng
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, China
| | - Xun Huang
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, China
| | - Zhong Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yaowang Wang
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, China
| | - Sidi Liu
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, China
| | - Cui Zeng
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, China
| | - Juping Duan
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, China
| | - Ximao Wen
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, China
| | - Chenchao Fu
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, China
| | - Anhua Wu
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital of Central South University, Changsha, China
| | - Chunhui Li
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital of Central South University, Changsha, China
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Li CX, Gao J, Zhang Z, Chen L, Li X, Zhou M, Wheelock ÅM. Multiomics integration-based molecular characterizations of COVID-19. Brief Bioinform 2021; 23:6447675. [PMID: 34864875 PMCID: PMC8769889 DOI: 10.1093/bib/bbab485] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/04/2021] [Accepted: 10/23/2021] [Indexed: 01/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), rapidly became a global health challenge, leading to unprecedented social and economic consequences. The mechanisms behind the pathogenesis of SARS-CoV-2 are both unique and complex. Omics-scale studies are emerging rapidly and offer a tremendous potential to unravel the puzzle of SARS-CoV-2 pathobiology, as well as moving forward with diagnostics, potential drug targets, risk stratification, therapeutic responses, vaccine development and therapeutic innovation. This review summarizes various aspects of understanding multiomics integration-based molecular characterizations of COVID-19, which to date include the integration of transcriptomics, proteomics, genomics, lipidomics, immunomics and metabolomics to explore virus targets and developing suitable therapeutic solutions through systems biology tools. Furthermore, this review also covers an abridgment of omics investigations related to disease pathogenesis and virulence, the role of host genetic variation and a broad array of immune and inflammatory phenotypes contributing to understanding COVID-19 traits. Insights into this review, which combines existing strategies and multiomics integration profiling, may help further advance our knowledge of COVID-19.
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Affiliation(s)
- Chuan-Xing Li
- Respiratory Medicine Unit, Department of Medicine & Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,The First Hospital of Lanzhou University, Lanzhou, China
| | - Jing Gao
- Respiratory Medicine Unit, Department of Medicine & Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Heart and Lung Centre, Department of Pulmonary Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Zicheng Zhang
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Lu Chen
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xun Li
- The First Hospital of Lanzhou University, Lanzhou, China.,The First School of Clinical Medicine, Lanzhou University, Lanzhou, China.,Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, China.,Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Meng Zhou
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Åsa M Wheelock
- Respiratory Medicine Unit, Department of Medicine & Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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Fan Y, Shan Q, Gong J, Qin J, Lu H. Molecular and Clinical Characteristics of Primary Pulmonary Lymphoepithelioma-Like Carcinoma. Front Mol Biosci 2021; 8:736940. [PMID: 34760925 PMCID: PMC8573970 DOI: 10.3389/fmolb.2021.736940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/07/2021] [Indexed: 11/22/2022] Open
Abstract
Objectives: Primary pulmonary lymphoepithelioma-like carcinoma (PPLELC) is an extremely rare subtype of non-small cell lung cancer (NSCLC). Currently, there are no established treatment protocols due to rarity of the cancer. Thus, this study aimed to explore the molecular and clinical characteristics of PPLELC. Study design and setting: Data from patients with PPLELC who were admitted to Zhejiang Cancer Hospital from August 2009 to September 2020 were retrospectively collected. Next-generation sequencing was performed to obtain a genomic profile and tumor mutation burden (TMB) value of patients with adequate tissue and divided them into two groups according to the expression level of PD-L1. The correlation of PD-L1 expression and the clinicopathological characteristics was evaluated by Pearson Chi-square test. Kaplan-Meier curves was applied to present the probability of survival between PD-L1 expression level and overall survival (OS). Moreover, the literature on the immunotherapy of advanced PPLELC published in PubMed between 2016 and 2020 were reviewed and the efficacy of immunotherapy were analyzed. Results: A total of 18 patients pathologically diagnosed as PPLELC were included. After a follow-up period of 8.8–138 months, 14 patients survived, three patients died and one patient lost, the median OS was 45.3 months Seven samples (tissue-available) tested by NGS and the median TMB was 2.5 mutations/Mb. 19 somatic mutated genes were recognized and TP53 (43%) and CYLD (43%) were the two most commonly mutated genes. Only seven patients who underwent NGS were tested for PD-L1. Three patients with high PD-L1 expression (PD-L1≥ 50%) and four patients with low PD-L1 expression (PD-L1 <50%) were included. No significant correlation was observed between PD-L1 expression and clinical characteristics (age, gender, smoking status, tumor stage, lymph node metastasis) (p > 0.05) and OS (p = 1). What’s more, 10 PPLELC patients involved in previous studies and one patient received nivolumab in the current study were collected retrospectively. 4/11 (36.4%) patients achieved PR, 6/11 (54.5%) patients achieved SD, and 1/11 (9.1%) patients achieved PD and the disease control rate (DCR) was 90.9%. Conclusions: The prognosis of PPLELC is better than that of other NSCLC, and immunotherapy may be a promising treatment to prolong the survival of advanced PPLELC patients. Whether the immunotherapy efficacy of PPLELC can be predicted by PD-L1 and TMB needs further clinical investigation. CYLD genetic alterations may participate in Epstein–Barr virus-mediated tumorigenesis in PPLELC, providing a novel therapeutic target.
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Affiliation(s)
- Ying Fan
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Department of Thoracic Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China.,The First Clinical Medical College, Wenzhou Medical University, Wenzhou, China
| | - Qianyun Shan
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Department of Thoracic Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China.,The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jiali Gong
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Department of Thoracic Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China.,The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jing Qin
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Department of Thoracic Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Hongyang Lu
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Department of Thoracic Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China.,The First Clinical Medical College, Wenzhou Medical University, Wenzhou, China.,The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
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Wang H, Wu Y, Chen S, Hou M, Yang Y, Xie M. Construction and Validation of a Ferroptosis-Related Prognostic Model for Endometrial Cancer. Front Genet 2021; 12:729046. [PMID: 34650597 PMCID: PMC8505971 DOI: 10.3389/fgene.2021.729046] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/18/2021] [Indexed: 01/21/2023] Open
Abstract
Endometrial cancer (EC) is one of the most common female reproductive system tumors, with close to 200,000 new cases each year. It accounts for approximately 7% of the total number of female cancers, but until now the cause of EC has remained unclear. Ferroptosis is regulated cell death that distinguishes apoptosis and caused by oxidative damage. The process has unique biological effects on metabolism and redox biology. In this study, we analyzed the relationship between EC and ferroptosis. According to the different expression levels of related genes, we first divided 544 EC samples into four clusters and found that most of the infiltrating immune cells were significantly different among the four groups. A differential gene expression analysis between Fe.cluster groups was performed, and the samples were again divided into three Fe.gene.cluster groups. The molecular characteristics and clinical characteristics of the groups were significantly different. Finally, 13 characteristic genes were selected as ferroptosis gene signatures, and the Fe.score was obtained by calculation. The Fe.score is closely related to the clinical and molecular characteristics of EC, and a low Fe.score has a significant survival advantage. The GDSC predicts that the IC50 of multiple chemotherapeutic drugs is also significantly different between the two groups. In conclusion, our research has explored the relationship between EC and ferroptosis in detail, provides comprehensive insights for ferroptosis-mediated EC mechanism research, and emphasizes the clinical application potential of Fe.score-based immunotherapy strategies.
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Affiliation(s)
- Hao Wang
- Department of Gynecology and Obstetrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yingchen Wu
- Department of Gynecology and Obstetrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shengfu Chen
- Department of Gynecology and Obstetrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Minzhi Hou
- Department of Gynecology and Obstetrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanning Yang
- Department of Gynecology and Obstetrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Meiqing Xie
- Department of Gynecology and Obstetrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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Zhang J, Zhang G, Miao Y. Identification, Molecular Characterization, and Tissue Expression Profiles of Three Smad Genes from Water Buffalo ( Bubalus bubalis). Genes (Basel) 2021; 12:genes12101536. [PMID: 34680931 PMCID: PMC8535384 DOI: 10.3390/genes12101536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/14/2021] [Accepted: 09/24/2021] [Indexed: 11/26/2022] Open
Abstract
Smads are involved in a variety of biological activities by mediating bone morphogenetic protein (BMP) signals. The full-length coding sequences (CDSs) of buffalo Smads 1, 4, and 5 were isolated and identified through RT-PCR in this study. Their lengths are 1398 bp, 1662 bp, and 1398 bp, respectively. In silico analysis showed that their transcriptional region structures, as well as their amino acid sequences, physicochemical characteristics, motifs, conserved domains, and three-dimensional structures of their encoded proteins are highly consistent with their counterparts in the species of Bovidae. The three Smad proteins are all hydrophilic without the signal peptides and transmembrane regions. Each of them has an MH1 domain and an MH2 domain. A nuclear localization sequence was found in the MH1 domain of buffalo Smads 1 and 5. Prediction showed that the function of the three Smads is mainly protein binding, and they can interact with BMPs and their receptors. The three genes were expressed in all 10 buffalo tissues assayed, and their expression in the mammary gland, gonad, and spleen was relatively high. The results here indicate that the three buffalo Smads may be involved in the transcriptional regulation of genes in a variety of tissues.
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Yuan C, Li C, Zhao X, Yan C, Wang J, Mou Y, Sun Q, Shan S. Genome-Wide Identification and Characterization of HSP90-RAR1-SGT1-Complex Members From Arachis Genomes and Their Responses to Biotic and Abiotic Stresses. Front Genet 2021; 12:689669. [PMID: 34512718 PMCID: PMC8430224 DOI: 10.3389/fgene.2021.689669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/05/2021] [Indexed: 11/13/2022] Open
Abstract
The molecular chaperone complex HSP90-RAR1-SGT1 (HRS) plays important roles in both biotic and abiotic stress responses in plants. A previous study showed that wild peanut Arachis diogoi SGT1 (AdSGT1) could enhance disease resistance in transgenic tobacco and peanut. However, no systematic analysis of the HRS complex in Arachis has been conducted to date. In this study, a comprehensive analysis of the HRS complex were performed in Arachis. Nineteen HSP90, two RAR1 and six SGT1 genes were identified from the allotetraploid peanut Arachis hypogaea, a number close to the sum of those from the two wild diploid peanut species Arachis duranensis and Arachis ipaensis. According to phylogenetic and chromosomal location analyses, thirteen orthologous gene pairs from Arachis were identified, all of which except AhHSP90-A8, AhHSP90-B9, AdHSP90-9, and AiHSP90-9 were localized on the syntenic locus, and they shared similar exon-intron structures, conserved motifs and expression patterns. Phylogenetic analysis showed that HSP90 and RAR1 from dicot and monocot plants diverged into different clusters throughout their evolution. Chromosomal location analysis indicated that AdSGT1 (the orthologous gene of AhSGT1-B3 in this study) might provide resistance to leaf late spot disease dependent on the orthologous genes of AhHSP90-B10 and AhRAR1-B in the wild peanut A. diogoi. Several HRS genes exhibited tissue-specific expression patterns, which may reflect the sites where they perform functions. By exploring published RNA-seq data, we found that several HSP90 genes play major roles in both biotic and abiotic stress responses, especially salt and drought responses. Autoactivation assays showed that AhSGT1-B1 could not be used as bait for yeast two-hybrid (Y2H) library screening. AhRAR1 and AhSGT1 could strongly interact with each other and interact with AhHSP90-B8. The present study represents the first systematic analysis of HRS complex genes in Arachis and provides valuable information for functional analyses of HRS complex genes. This study also offers potential stress-resistant genes for peanut improvement.
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Affiliation(s)
- Cuiling Yuan
- Shandong Peanut Research Institute, Qingdao, China
| | - Chunjuan Li
- Shandong Peanut Research Institute, Qingdao, China
| | - Xiaobo Zhao
- Shandong Peanut Research Institute, Qingdao, China
| | - Caixia Yan
- Shandong Peanut Research Institute, Qingdao, China
| | - Juan Wang
- Shandong Peanut Research Institute, Qingdao, China
| | - Yifei Mou
- Shandong Peanut Research Institute, Qingdao, China
| | - Quanxi Sun
- Shandong Peanut Research Institute, Qingdao, China
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao, China
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41
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Shao H, Li J, Yuan H, Ji L, Zhang J, Jin W, Qian K, Ye J, Qin A. Isolation and Molecular Characteristics of a CIAV Isolate From Pigeons, China. Front Vet Sci 2021; 8:669154. [PMID: 34458350 PMCID: PMC8385301 DOI: 10.3389/fvets.2021.669154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/09/2021] [Indexed: 11/13/2022] Open
Abstract
Chicken infectious anemia virus (CIAV) mainly infects chickens and causes immunosuppression. In this study, a CIAV isolate, designated as Pigeon-CIAV-1906, was efficiently isolated from two sick pigeons by inoculating the samples into MSB1 cells. The genome of Pigeon-CIAV-1906 was amplified by PCR and analyzed. The genome size of Pigeon-CIAV-1906 was 2,298 bp with the highest homology (99.5%) to Jilin strain (JL14023) and the lowest homology (91.5%) to Brazil strain (KY024579), which phylogenetically clustered into Group A. Notably, several amino acids such as 139K and 394Q related with high virulence were found in the VP1 of Pigeon-CIAV-1906. The isolation of Pigeon-CIAV-1906 and its molecular characteristics provide evidence for the cross-transmission of CIAV from chicken to pigeon and give novel insights into the molecular epidemiology of CIAV.
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Affiliation(s)
- Hongxia Shao
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Jinzhi Li
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Huisha Yuan
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Lifei Ji
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Jun Zhang
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Wenjie Jin
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Kun Qian
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Jianqiang Ye
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Aijian Qin
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
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Gunduz M, Ünal-Uzun Ö, Koç N, Ceylaner S, Özaydın E, Kasapkara ÇS. Molecular and clinical findings of Turkish patients with hereditary fructose intolerance. J Pediatr Endocrinol Metab 2021; 34:1017-1022. [PMID: 34162028 DOI: 10.1515/jpem-2021-0303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 05/25/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Hereditary fructose intolerance (HFI) is an autosomal recessive disorder caused by a deficiency in aldolase B that can result in hypoglycemia, nausea, vomiting, abdominal pain, liver and kidney dysfunction, coma, and even death. This study aims to represent the clinical features and molecular genetic analysis data of the patients diagnosed with HFI in our study population. METHODS The medical records of the 26 patients with HFI were evaluated retrospectively. Age, gender, clinical findings, metabolic crises, and the results of molecular analyses were recorded. RESULTS The patients with HFI had a good prognosis and the aversion to sugar-containing foods was the main complaint. Seven different variants were identified in the Aldolase B (ALDOB) gene in HFI patients. The most frequent mutations were p.Ala150Pro, p.Ala175Asp had a prevalence of 61 and 30%, respectively, in agreement with the literature and other known variants were found with minor frequencies c.360-363del4(3.8%), p.Asn335Lys(3.8%), and three novel mutations c.113-1_15del4 (3.8%), p.Ala338Val(7.6%), and p.Asp156His(3.8%) were identified at a heterozygous, homozygous, or compound heterozygous level. CONCLUSIONS This study results revealed three novel mutations in patients with HFI. On the basis of age of presentation, clinical symptoms, and metabolic crisis, there was no clear-cut genotype-phenotype correlation. This article also demonstrates the importance of screening suspected infants in cases of acute liver failure for prompt diagnosis and treatment of HFI.
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Affiliation(s)
- Mehmet Gunduz
- Ankara City Hospital, Department of Pediatric Metabolism, Ankara, Turkey
| | - Özlem Ünal-Uzun
- Kocaeli University, Department of Pediatric Metabolism, Kocaeli, Turkey
| | - Nevra Koç
- University of Health Sciences, Gulhane Health Sciences Faculty, Department of Nutrition and Dietetics, Ankara, Turkey
| | - Serdar Ceylaner
- Genetics, İntergen Genetic Diseases Diagnostic Center, Ankara, Turkey
| | - Eda Özaydın
- Ankara City Hospital, Department of Pediatrics, Ankara, Turkey
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Liu X, Yan N, Yue H, Wang Y, Zhang B, Tang C. Detection and molecular characteristics of bovine rotavirus A in dairy calves in China. J Vet Sci 2021; 22:e69. [PMID: 34423605 PMCID: PMC8460460 DOI: 10.4142/jvs.2021.22.e69] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/11/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022] Open
Abstract
Background Bovine group A rotavirus (BoRVA) is a major cause of severe gastroenteritis in newborn dairy calves. Only one study has investigated the G and P genotypes among dairy calves in a few regions of China, which were G6 and P[5]. Therefore, data on the prevalence and molecular characteristics of BoRVA in dairy calves in China remains limited. Objectives The purpose of this study was to investigate the prevalence and molecular characteristics of BoRVA in dairy calves in China. Methods 269 dairy calves diarrheic samples from 23 farms in six provinces in China were collected to detect BoRVA using reverse transcription polymerase chain reaction. Results 71% of samples were determined to be BoRVA-positive. Two G genotypes (G6, G10) and two P genotypes (P[1], P[5]) were identified, and G6P[1] BoRVA was the predominant strain. Moreover, the VP7 and VP4 gene sequences of these dairy calf BoRVA strains revealed abundant genetic diversity. Interestingly, eight out of 17 complete G6 VP7 sequences were clustered into G6 lineage VI and analysis showed the strains were closely related to Chinese yak BoRVA strains. Conclusions The results of this study show that BoRVA circulates widely among dairy calves in China, and the dominant genotype in circulation is G6P[1], first report on molecular characteristics of complete P[5] VP4 genes in chinese dairy calves. These results will help us to further understand the prevalence and genetic evolution of BoRVA among dairy calves in China and, thus, prevent the disease more effectively.
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Affiliation(s)
- Xiaoying Liu
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Nan Yan
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Hua Yue
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu 610041, China
| | - Yuanwei Wang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Bin Zhang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Cheng Tang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu 610041, China.
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Li Z, Ding Z, Yang J, Liu Y, Jin X, Xie J, Li T, Ding Y, Zeng Z, Liu J. Carbapenem-Resistant Klebsiella pneumoniae in Southwest China: Molecular Characteristics and Risk Factors Caused by KPC and NDM Producers. Infect Drug Resist 2021; 14:3145-3158. [PMID: 34413658 PMCID: PMC8370685 DOI: 10.2147/idr.s324244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/04/2021] [Indexed: 12/19/2022] Open
Abstract
Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) infection has attracted worldwide concern and became a serious challenge for clinical treatment. The aims of this study were to evaluate the molecular characteristics and risk factors for CRKP infection. Methods All the CRKP strains were screened for antimicrobial resistance genes, virulence genes, and integron by polymerase chain reaction (PCR). Plasmid typing was performed by plasmid conjugation assay and PCR-based replicon typing (PBRT). The genetic environments of blaKPC-2 and blaNDM-1 were analyzed by using overlapping PCR and molecular typing was performed by multi-locus sequence typing (MLST). Risk factors for CRKP infection were analyzed by logistic regression model. Results All the 66 CRKP isolates were multidrug-resistant, but all of them were susceptible to tigecycline and polymyxin B. Among the CRKP isolates, 42 blaKPC-2-positive strains were identified carrying IncFII plasmids. Meanwhile, 24 blaNDM-positive strains were found on lncX3 plasmids, including 20 blaNDM-1 isolates and 4 blaNDM-5 isolates. Most of CRKP isolates contained several virulence genes and the class I integron (intl1). The genetic environments of blaKPC-2 and blaNDM-1 revealed that the conserved regions (tnpA-tnpR-ISkpn8-blaKPC-2) and (blaNDM-1-bleMBL-trpF-tat) were associated with the dissemination of KPC-2 and NDM-1. ST11 was the most common type in this work. Hematological disease, tracheal cannula, and use of β-lactams and β-lactamase inhibitor combination were identified as independent risk factors for CRKP infection. Conclusion This study established the resistance pattern, molecular characteristics, clonal relatedness, and risk factors of CRKP infection. The findings of the novel strain that co-harboring blaNDM-5 and blaIMP-4, and the novel ST4495 indicated that the brand-new types have spread in Southwest China, emphasizing the prevent and control the further dissemination of CRKP isolates are highly needed.
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Affiliation(s)
- Zhaoyinqian Li
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Zixuan Ding
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Jia Yang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Yao Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Xinrui Jin
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Jingling Xie
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Tingting Li
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Yinhuan Ding
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Zhangrui Zeng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
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Lu Y, Huang W, Zhong L, Qin Y, Liu X, Yang C, Wang R, Su X, Du C, Mi X, Wang H, He Y, Zhao W, Chen Y, Wei Z, Ouyang K. Comparative Characterization and Pathogenicity of a Novel Porcine Epidemic Diarrhea Virus (PEDV) with a Naturally Occurring Truncated ORF3 Gene Coinfected with PEDVs Possessing an Intact ORF3 Gene in Piglets. Viruses 2021; 13:v13081562. [PMID: 34452427 PMCID: PMC8402686 DOI: 10.3390/v13081562] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022] Open
Abstract
Coinfection caused by various genotypes of porcine epidemic diarrhea virus (PEDV) is a new disease situation. We previously reported the coexistence of PEDV strains containing different ORF3 genotypes in China. In this study, the PEDV strains 17GXCZ-1ORF3d and 17GXCZ-1ORF3c were isolated and plaque-purified from the same piglet, which had a natural large deletion at the 172–554 bp position of the ORF3 gene or possessed a complete ORF3 gene, respectively. Meanwhile, 17GXCZ-1ORF3d had >99% nt identity with 17GXCZ-1ORF3c in the 5′UTR, ORF1a/1b, S, E, M, N and 3′UTR regions but only demonstrated low nucleotide identities (80.5%) in the ORF3 gene. To elucidate the pathogenicity, 7-day-old piglets were infected. Piglets infected with these two PEDV strains exhibited severe clinical signs and shed the virus at the highest level within 96 hpi. Compared with the piglets inoculated with the 17GXCZ-1ORF3c strain, the piglets inoculated with the 17GXCZ-1ORF3d strain had higher mortality rates (75% vs. 50%), an earlier onset of clinical signs with a significantly higher diarrhea score, lower VH:CD ratios and a higher percentage of PEDV-positive enterocytes. This study is the first to report PEDV coinfections with different ORF3 genotypes, and a PEDV strain with a large deletion in the ORF3 gene might have the advantage of a potential genetic marker, which would be useful during vaccine development.
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Affiliation(s)
- Ying Lu
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China; (Y.L.); (W.H.); (L.Z.); (X.L.); (C.Y.); (R.W.); (X.S.); (C.D.); (X.M.); (H.W.); (Y.C.); (Z.W.)
| | - Weijian Huang
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China; (Y.L.); (W.H.); (L.Z.); (X.L.); (C.Y.); (R.W.); (X.S.); (C.D.); (X.M.); (H.W.); (Y.C.); (Z.W.)
| | - Lian Zhong
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China; (Y.L.); (W.H.); (L.Z.); (X.L.); (C.Y.); (R.W.); (X.S.); (C.D.); (X.M.); (H.W.); (Y.C.); (Z.W.)
| | - Yibin Qin
- Guangxi Veterinary Research Institute, Nanning 530005, China; (Y.Q.); (Y.H.); (W.Z.)
| | - Xueting Liu
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China; (Y.L.); (W.H.); (L.Z.); (X.L.); (C.Y.); (R.W.); (X.S.); (C.D.); (X.M.); (H.W.); (Y.C.); (Z.W.)
| | - Chunjie Yang
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China; (Y.L.); (W.H.); (L.Z.); (X.L.); (C.Y.); (R.W.); (X.S.); (C.D.); (X.M.); (H.W.); (Y.C.); (Z.W.)
| | - Ruomu Wang
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China; (Y.L.); (W.H.); (L.Z.); (X.L.); (C.Y.); (R.W.); (X.S.); (C.D.); (X.M.); (H.W.); (Y.C.); (Z.W.)
| | - Xueli Su
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China; (Y.L.); (W.H.); (L.Z.); (X.L.); (C.Y.); (R.W.); (X.S.); (C.D.); (X.M.); (H.W.); (Y.C.); (Z.W.)
| | - Chen Du
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China; (Y.L.); (W.H.); (L.Z.); (X.L.); (C.Y.); (R.W.); (X.S.); (C.D.); (X.M.); (H.W.); (Y.C.); (Z.W.)
| | - Xue Mi
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China; (Y.L.); (W.H.); (L.Z.); (X.L.); (C.Y.); (R.W.); (X.S.); (C.D.); (X.M.); (H.W.); (Y.C.); (Z.W.)
| | - Hejie Wang
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China; (Y.L.); (W.H.); (L.Z.); (X.L.); (C.Y.); (R.W.); (X.S.); (C.D.); (X.M.); (H.W.); (Y.C.); (Z.W.)
| | - Ying He
- Guangxi Veterinary Research Institute, Nanning 530005, China; (Y.Q.); (Y.H.); (W.Z.)
| | - Wu Zhao
- Guangxi Veterinary Research Institute, Nanning 530005, China; (Y.Q.); (Y.H.); (W.Z.)
| | - Ying Chen
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China; (Y.L.); (W.H.); (L.Z.); (X.L.); (C.Y.); (R.W.); (X.S.); (C.D.); (X.M.); (H.W.); (Y.C.); (Z.W.)
| | - Zuzhang Wei
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China; (Y.L.); (W.H.); (L.Z.); (X.L.); (C.Y.); (R.W.); (X.S.); (C.D.); (X.M.); (H.W.); (Y.C.); (Z.W.)
| | - Kang Ouyang
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China; (Y.L.); (W.H.); (L.Z.); (X.L.); (C.Y.); (R.W.); (X.S.); (C.D.); (X.M.); (H.W.); (Y.C.); (Z.W.)
- Correspondence:
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Zheng Z, Lei Y, Wang Y, Lin C, Lin J. Occurrence of mcr Positive Strains and Molecular Characteristics of Two mcr-1 Positive Salmonella typhimurium and Escherichia coli from a Chinese Women's and Children's Hospital. Infect Drug Resist 2021; 14:2925-2932. [PMID: 34349527 PMCID: PMC8327187 DOI: 10.2147/idr.s322686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/22/2021] [Indexed: 12/18/2022] Open
Abstract
Background The purpose of this study was to evaluate the prevalence of mobile colistin resistance genes (mcr) in Gram-negative bacteria and to analyze the molecular characteristics of mcr-1 positive Salmonella typhimurium strain 75 and Escherichia coli strain 107 from the Quanzhou Women’s and Children’s Hospital in China. Methods The genes mcr-1 through mcr-9 were screened via multiplex PCR. Antibiotic susceptibility was detected using a GN11 card with the VITEK-2 compact automated system. Whole genomes were sequenced using PacBio’s single molecule real-time (SMRT) technology. Results In this study, mcr-1 was detected in only four strains, with a positivity rate of 0.65% (4/616). All the four strains were resistant to more than three different kinds of antibiotics. The mcr-1 positive S. typhimurium strain 75 harbored IncHI2 plasmid, which carried mcr-1 gene, while the mcr-1 positive E. coli strain 107 contained four plasmids including one mcr-1 harboring IncHI2 plasmid, one IncFII plasmid and two IncI1-I (Alpha) plasmids. Mobile elements carrying mcr-1 in the 75_plasmid and 107_plasmid-1 were located in the IS1086(ISApl1)-IS30A(ISApl1)-mcr-1-hp and IS1086(ISApl1)-mcr-1-hp regions, respectively. Tn6010 carrying drug efflux pump genes was found in 75_plasmid, while cn_31611_IS26 carrying multi-drug resistance (MDR) genes were found in 107_plasmid-1. Conclusion This study found that mcr-1 was prevalent at a low frequency in the Quanzhou Women’s and Children’s Hospital. A similar genetic pattern of mcr-1 transmission was found in both E. coli and S. typhimurium.
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Affiliation(s)
- Zhenzhu Zheng
- Department of Laboratory Medicine, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
| | - Ying Lei
- Department of Laboratory Medicine, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
| | - Yinna Wang
- Department of Laboratory Medicine, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
| | - Chunli Lin
- Department of Laboratory Medicine, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
| | - Jiansheng Lin
- Department of Laboratory Medicine, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
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Szymankiewicz M, Stefaniuk E, Baraniak A, Nowikiewicz T. Clinical and Molecular Findings of Infections Caused by Extended-Spectrum β-Lactamase-Producing Enterobacterales in Patients with Solid Tumors: A Single-Center Study. Microb Drug Resist 2021; 27:1470-1481. [PMID: 34264754 DOI: 10.1089/mdr.2020.0530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Infectious complications caused by multidrug-resistant bacteria are a serious clinical and therapeutic problem. Our study aimed to analyze the genetic characteristics of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) that cause multidrug-resistant infections in patients with solid tumors. Identification of ESBL-encoding genes was performed by polymerase chain reaction (PCR) and sequencing. The clonal relationship of the isolates was evaluated by pulsed-field gel electrophoresis. Multilocus sequence typing (MLST) was carried out for selected Escherichia coli and Klebsiella pneumoniae isolates. All E. coli strains were classified into phylogenetic groups using the PCR-based approach. There were 735 patients with clinical symptoms of infections tested, of which 44 (6.0%) were positive for ESBL-E on genotypic testing. The most frequent organism was E. coli (n = 24, 54.5%), followed by K. pneumoniae (n = 13, 29.5%), Proteus mirabilis (n = 3, 6.8%), Enterobacter cloacae cplx (n = 2, 4.5%), and Klebsiella oxytoca (n = 2, 4.5%). Overall, 31 (70.5%) of the ESBL-E isolates carried only blaCTX-M-1-like genes, and the genes were found to be blaCTX-M-15 (n = 30, 68.2%) or blaCTX-M-3 (n = 1, 2.3%). Eleven strains (25%) had blaCTX-M-9-like genes, mostly blaCTX-M-27 (n = 10, 22.7%) and unique blaCTX-M-65 (n = 1, 2.3%). One isolate possessed both blaCTX-M-15 and blaCTX-M-27 genes, and another one produced TEM-12 ESBL. MLST analysis revealed E. coli sequence type (ST) 131 and ST361, and K. pneumoniae ST16, ST307, and ST437. Among E. coli isolates, the B2 phylogenetic group was predominant. Most of the strains showed resistance to third-generation cephalosporins and fluoroquinolones, and susceptibility to aminoglycosides and carbapenems. Patients with solid cancer and ESBL-E infections require special management since they are a population with a high threat of antibiotic-resistant infections. Carbapenems and aminoglycosides remain active antibiotics against these infections.
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Affiliation(s)
- Maria Szymankiewicz
- Department of Microbiology, prof. F. Łukaszczyk Centre of Oncology in Bydgoszcz, Bydgoszcz, Poland
| | - Elżbieta Stefaniuk
- Department of Antibiotics and Microbiology, National Medicines Institute, Warsaw, Poland
| | - Anna Baraniak
- Department of Molecular Microbiology, and National Medicines Institute, Warsaw, Poland.,Department of Drug Biotechnology and Bioinformatics, National Medicines Institute, Warsaw, Poland
| | - Tomasz Nowikiewicz
- Department of Surgical Oncology, Nicolaus Copernicus University Ludwik Rydygier's Collegium Medicum, Bydgoszcz, Poland.,Clinical Department of Breast Cancer and Reconstructive Surgery, prof. F. Łukaszczyk Centre of Oncology in Bydgoszcz, Bydgoszcz, Poland
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Duan Y, Xu B, Li C, Bao Y, An S, Zhou Y, Chen A, Deng L, Ning L, Zhu Y, Wang W, Zhang M, Xu L, Chen X, Xie Z. Molecular Characteristics of Human Adenovirus Type 3 Circulating in Parts of China During 2014-2018. Front Microbiol 2021; 12:688661. [PMID: 34267738 PMCID: PMC8276179 DOI: 10.3389/fmicb.2021.688661] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/20/2021] [Indexed: 12/22/2022] Open
Abstract
Human adenoviruses (HAdVs) are important pathogens causing respiratory infections; 3.5-11% of childhood community-acquired pneumonia is associated with HAdV infection. Human adenovirus type 3 (HAdV-3), leading to severe morbidity and mortality, is one of the most prevalent genotype among adenoviruses responsible for acute respiratory infections (ARIs) in children in China. To identify the genetic variation of HAdV-3 in children with ARIs in China, a molecular epidemiological study was conducted. A total of 54 HAdV-3 isolated strains were obtained from children with ARIs in Beijing, Wenzhou, Shanghai, Shijiazhuang, Hangzhou, Guangzhou, and Changchun from 2014 to 2018. Thirty-two strains of which were selected for whole-genome sequencing, while the hexon, penton base, and fiber genes were sequenced for remaining strains. Bioinformatics analysis was performed on the obtained sequences. The phylogenetic analyses based on whole-genome sequences, major capsid protein genes (hexon, penton base, and fiber), and early genes (E1, E2, E3, and E4) showed that the HAdV-3 strains obtained in this study always clustered together with the reference strains from Chinese mainland, while the HAdV-3 prototype strain formed a cluster independently. Compared with the prototype strain, all strains possessed nine amino acid (AA) substitutions at neutralization antigenic epitopes of hexon. The homology models of the hexon protein of the HAdV-3 prototype and strain BJ20160214 showed that there was no evident structural change at the AA mutation sites. Two AA substitutions were found at the Arg-Gly-Asp (RGD) loop and hypervariable region 1 (HVR1) region of the penton base. A distinct AA insertion (20P) in the highly conserved PPPSY motif of the penton base that had never been reported before was observed. Recombination analysis indicated that partial regions of protein IIIa precursor, penton base, and protein VII precursor genes among all HAdV-3 strains in this study were from HAdV-7. This study showed that the genomes of the HAdV-3 strains in China were highly homologous. Some AA mutations were found at antigenic sites; however, the significance needs further study. Our data demonstrated the molecular characteristics of HAdV-3 circulating in China and was highly beneficial for further epidemiological exploration and the development of vaccines and drugs against HAdV-3.
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Affiliation(s)
- Yali Duan
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Baoping Xu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Changchong Li
- The 2nd Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yixiao Bao
- Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuhua An
- Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Yunlian Zhou
- The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Aihuan Chen
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Deng
- Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Limin Ning
- Children's Hospital of Changchun, Changchun, China
| | - Yun Zhu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Wei Wang
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Meng Zhang
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Lili Xu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xiangpeng Chen
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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Zhang P, Liu X, Zhang J, Fu X, Wan Y, Pan H, Wu C, Wang X. Prevalence and characterization of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus isolated from retail yak butter in Tibet, China. J Dairy Sci 2021; 104:9596-9606. [PMID: 34176628 DOI: 10.3168/jds.2020-19604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 05/07/2021] [Indexed: 11/19/2022]
Abstract
This study aimed to investigate the prevalence, molecular characteristics and antibiotic resistance of Staphylococcus aureus isolates from yak butter in Tibet, China. A total of 218 yak butter samples were collected from retail stores in Tibet and screened for Staph. aureus. Furthermore, the virulence genes, resistance genes, antimicrobial susceptibility, and molecular typing [pulsed-field gel electrophoresis (PFGE), multilocus sequence typing, and staphylococcal protein A (spa) typing] of Staph. aureus isolates were detected. The results showed that 12.4% of yak butter samples were contaminated with Staph. aureus, including 5 samples positive for methicillin-resistant Staph. aureus (MRSA). Among all isolates, 96.3% harbored one or more virulence genes, including classical (sea and sec), novel enterotoxin-encoding genes (seh, sek, sel, and seq), and hemolysin genes (hla and hld). All isolates were resistant to at least 2 different antibiotic classes, and the isolates were most commonly resistant to sulfonamides, β-lactams, and erythromycin. For resistance genes, blaZ (74.1%) was most frequently detected, followed by dfrG (51.9%), erm(B) (22.2%), mecA (18.5%), tet(K) (14.8%), aph(2″)-Ia, aph(3')-III, and ant(6)-Ia (11.1% for each), and erm(C) (7.4%). We detected 8 spa types, 6 sequence types (ST), and 5 clonal complex (CC) types. In addition, 1 isolate of Staph. aureus was nontypeable. We found that CC1-ST1-t559 (55.6%) was the most predominant clone, followed by CC59-ST59-t437 (11.1%), CC5-ST5-t002 (7.4%), CC1-ST1, CC1-ST1-t114, CC1-ST573-t4938, CC1-ST573-t8915, CC30-ST30-t021, and CC25-ST25-t167 (3.7% for each). For PFGE typing, a total of 5 clusters and 15 pulsotypes were generated, and some isolates from different samples showed indistinguishable pulsotypes. Our findings suggest that yak butter produced in Tibet, China, could be contaminated by Staph. aureus strains, including MRSA strains, carrying various virulence and resistance genes, representing multiple antimicrobial resistance phenotypes. The presence of potentially virulent and antibiotic-resistant Staph. aureus strains in yak butter poses a potential threat to consumers, and appropriate measures need to be taken in the production chain to reduce the occurrence of Staph. aureus in yak butter.
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Affiliation(s)
- Pengfei Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinyu Liu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xueting Fu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yangli Wan
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hu Pan
- Institute of Agricultural Product Quality Standard and Testing Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa Tibet 850032, China
| | - Congming Wu
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xin Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Tada H, Nagata Y, Takahashi H, Matsuyama T, Ida S, Mito I, Chikamatsu K. Systemic immune responses are associated with molecular characteristics of circulating tumor cells in head and neck squamous cell carcinoma. Mol Clin Oncol 2021; 15:147. [PMID: 34094545 DOI: 10.3892/mco.2021.2309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/21/2021] [Indexed: 12/16/2022] Open
Abstract
Systemic immunity mediated by circulating immune cells may affect clinical features, as well as the characteristics of circulating tumor cells (CTCs) in patients with head and neck squamous cell carcinoma (HNSCC). The present study aimed to analyze the influence of circulating immune cells, using their markers, on clinical features to investigate the association between systemic immunity and the molecular characteristics of CTCs. Circulating immune-cell markers were associated with disease progression and clinical outcomes in patients with HNSCC. Meanwhile, there was no significant association between the presence of CTCs and systemic immune-related markers. Moreover, phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit a expression in CTCs was significantly associated with higher lymphocyte counts (P=0.035) and an increased prognostic nutrition index (P=0.0157). Patients with CTCs expressing CD47 exhibited significantly higher neutrophil (P=0.0031) and monocyte (P=0.0016) counts. Patients with CTCs expressing programmed cell death 1 ligand 2 exhibited lower C-reactive protein (CRP) levels (P=0.0271) and a decreased CRP/albumin ratio (P=0.0207). The current results suggested that the interaction between CTCs and circulating immune cells may provide survival advantages via molecular alterations to CTCs.
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Affiliation(s)
- Hiroe Tada
- Department of Otolaryngology-Head and Neck Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 3718511, Japan
| | - Yurino Nagata
- Department of Otolaryngology-Head and Neck Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 3718511, Japan
| | - Hideyuki Takahashi
- Department of Otolaryngology-Head and Neck Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 3718511, Japan
| | - Toshiyuki Matsuyama
- Department of Otolaryngology-Head and Neck Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 3718511, Japan
| | - Shota Ida
- Department of Otolaryngology-Head and Neck Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 3718511, Japan
| | - Ikko Mito
- Department of Otolaryngology-Head and Neck Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 3718511, Japan
| | - Kazuaki Chikamatsu
- Department of Otolaryngology-Head and Neck Surgery, Gunma University Graduate School of Medicine, Maebashi, Gunma 3718511, Japan
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