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Li S, Wang Z, Li Z, Xie S, Shan X, Cai Z. Intraosseous schwannoma of the mandible: new case series, literature update, and proposal of a classification. Int J Oral Maxillofac Surg 2024; 53:205-211. [PMID: 37716827 DOI: 10.1016/j.ijom.2023.08.006] [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: 06/03/2023] [Revised: 08/15/2023] [Accepted: 08/29/2023] [Indexed: 09/18/2023]
Abstract
Intraosseous schwannoma of the mandible is rare, with diagnostic and therapeutic challenges. The aims of this study were to report new cases of intraosseous schwannoma of the mandible and to propose a clinical classification, providing suggestions for treatment methods. The cases of 13 patients treated at the authors' hospital and 86 cases reported previously in the literature were reviewed. The most common clinical feature was facial swelling (60/93). The rate of cortical thinning or expansion was 44.8% (43/96); widening of the inferior alveolar nerve canal on radiographs was observed in 15 patients.
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Affiliation(s)
- S Li
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Haidian District, Beijing, PR China
| | - Z Wang
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Haidian District, Beijing, PR China
| | - Z Li
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Haidian District, Beijing, PR China
| | - S Xie
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Haidian District, Beijing, PR China
| | - X Shan
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Haidian District, Beijing, PR China
| | - Z Cai
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Haidian District, Beijing, PR China.
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Yuan XL, Wu YB, Song XL, Chen Y, Lu Y, Lai XY, Shi JM, Liu LZ, Zhao YM, Yu J, Yang LX, Lan JP, Cai Z, Huang H, Luo Y. [Efficacy and prognostic factors of allogeneic hematopoietic stem cell transplantation in the treatment of secondary acute myeloid leukemia]. Zhonghua Xue Ye Xue Za Zhi 2024; 45:41-47. [PMID: 38527837 DOI: 10.3760/cma.j.cn121090-20230929-00151] [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] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Objective: To evaluate the efficacy and prognostic factors of allogeneic hematopoietic stem cell transplantation (allo-HSCT) in patients with secondary acute myeloid leukemia (sAML) . Methods: In this multicenter, retrospective clinical study, adult patients aged ≥18 years who underwent allo-HSCT for sAML at four centers of the Zhejiang Hematopoietic Stem Cell Transplantation Collaborative Group from January 2014 to November 2022 were included, and the efficacy and prognostic factors of allo-HSCT were analyzed. Results: A total of 95 patients were enrolled; 66 (69.5%) had myelodysplastic syndrome-acute myeloid leukemia (MDS-AML) , 4 (4.2%) had MDS/MPN-AML, and 25 (26.3%) had therapy-related AML (tAML) . The 3-year CIR, LFS, and overall survival (OS) rates were 18.6% (95% CI 10.2%-27.0%) , 70.6% (95% CI 60.8%-80.4%) , and 73.3% (95% CI 63.9%-82.7%) , respectively. The 3-year CIRs of the M-AML group (including MDS-AML and MDS/MPN-AML) and the tAML group were 20.0% and 16.4%, respectively (P=0.430) . The 3-year LFSs were 68.3% and 75.4%, respectively (P=0.176) . The 3-year OS rates were 69.7% and 75.4%, respectively (P=0.233) . The 3-year CIRs of the groups with and without TP53 mutations were 60.0% and 13.7%, respectively (P=0.003) ; the 3-year LFSs were 20.0% and 76.5%, respectively (P=0.002) ; and the 3-year OS rates were 40.0% and 77.6%, respectively (P=0.002) . According to European LeukmiaNet 2022 (ELN2022) risk stratification, the 3-year CIRs of patients in the low-, intermediate-, and high-risk groups were 8.3%, 17.8%, and 22.6%, respectively (P=0.639) . The three-year LFSs were 91.7%, 69.5%, and 65.6%, respectively (P=0.268) . The 3-year OS rates were 91.7%, 71.4%, and 70.1%, respectively (P=0.314) . Multivariate analysis revealed that advanced disease at allo-HSCT and TP53 mutations were independent risk factors for CIR, LFS, and OS. Conclusion: There was no significant difference in the prognosis of patients who underwent allo-HSCT among the MDS-AML, MDS/MPN-AML, and tAML groups. Advanced disease at transplantation and TP53 mutations were poor prognostic factors. ELN2022 risk stratification had limited value for predicting the prognosis of patients with sAML following allo-HSCT.
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Affiliation(s)
- X L Yuan
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - Y B Wu
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - X L Song
- Zhejiang Provincial People's Hospital, Hangzhou 310014, China
| | - Y Chen
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, China
| | - Y Lu
- People's Hospital Affiliated to Ningbo University, Ningbo 315000, China
| | - X Y Lai
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - J M Shi
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - L Z Liu
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - Y M Zhao
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - J Yu
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - L X Yang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - J P Lan
- Zhejiang Provincial People's Hospital, Hangzhou 310014, China
| | - Z Cai
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - H Huang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - Y Luo
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
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Fu P, Cai Z, Zhang Z, Meng X, Peng Y. An updated database of virus circular RNAs provides new insights into the biogenesis mechanism of the molecule. Emerg Microbes Infect 2023; 12:2261558. [PMID: 37725485 PMCID: PMC10557547 DOI: 10.1080/22221751.2023.2261558] [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: 06/28/2023] [Accepted: 09/17/2023] [Indexed: 09/21/2023]
Abstract
Virus circular RNAs (circRNA) have been reported to be extensively expressed and play important roles in viral infections. Previously we build the first database of virus circRNAs named VirusCircBase which has been widely used in the field. This study significantly improved the database on both the data quantity and database functionality: the number of virus circRNAs, virus species, host organisms was increased from 46440, 23, 9 to 60859, 43, 22, respectively, and 1902 full-length virus circRNAs were newly added; new functions were added such as visualization of the expression level of virus circRNAs and visualization of virus circRNAs in the Genome Browser. Analysis of the expression of virus circRNAs showed that they had low expression levels in most cells or tissues and showed strong expression heterogeneity. Analysis of the splicing of virus circRNAs showed that they used a much higher proportion of non-canonical back-splicing signals compared to those in animals and plants, and mainly used the A5SS (alternative 5' splice site) in alternative-splicing. Most virus circRNAs have no more than two isoforms. Finally, human genes associated with the virus circRNA production were investigated and more than 1000 human genes exhibited moderate correlations with the expression of virus circRNAs. Most of them showed negative correlations including 42 genes encoding RNA-binding proteins. They were significantly enriched in biological processes related to cell cycle and RNA processing. Overall, the study provides a valuable resource for further studies of virus circRNAs and also provides new insights into the biogenesis mechanisms of virus circRNAs.
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Affiliation(s)
- Ping Fu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Zena Cai
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Zhiyuan Zhang
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Xiangxian Meng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
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Sahana G, Cai Z, Sanchez MP, Bouwman AC, Boichard D. Invited review: Good practices in genome-wide association studies to identify candidate sequence variants in dairy cattle. J Dairy Sci 2023:S0022-0302(23)00357-0. [PMID: 37349208 DOI: 10.3168/jds.2022-22694] [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: 08/24/2022] [Accepted: 02/01/2023] [Indexed: 06/24/2023]
Abstract
Genotype data from dairy cattle selection programs have greatly facilitated GWAS to identify variants related to economic traits. Results can enhance the accuracy of genomic prediction, analyze more complex models that go beyond additive effects, elucidate the genetic architecture of a trait, and finally, decipher the underlying biology of traits. The entire process, comprising data generation, quality control, statistical analyses, interpretation of association results, and linking results to biology should be designed and executed to minimize the generation of false-positive and false-negative associations and misleading links to biological processes. This review aims to provide general guidelines for data analysis that address data quality control, association tests, adjustment for population stratification, and significance evaluation to improve the reliability of conclusions. We also provide guidance on post-GWAS strategy and the interpretation of results. These guidelines are tailored to dairy cattle, which are characterized by long-range linkage disequilibrium, large half-sib families, and routinely collected phenotypes, requiring different approaches than those applied in human GWAS. We discuss common limitations and challenges that have been overlooked in the analysis and interpretation of GWAS to identify candidate sequence variants in dairy cattle.
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Affiliation(s)
- G Sahana
- Aarhus University, Center for Quantitative Genetic and Genomics, 8830 Tjele, Denmark.
| | - Z Cai
- Aarhus University, Center for Quantitative Genetic and Genomics, 8830 Tjele, Denmark
| | - M P Sanchez
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - A C Bouwman
- Wageningen University & Research, Animal Breeding and Genomics, 6700 AH Wageningen, the Netherlands
| | - D Boichard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
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5
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Xiong YF, Cai Z, Li SC, Song YJ, Hu XM, Zheng L. [Bioinformatics analysis in metagenomic next-generation sequencing of pathogenic microorganisms: current status and challenges]. Zhonghua Yi Xue Za Zhi 2023; 103:1098-1102. [PMID: 37055228 DOI: 10.3760/cma.j.cn112137-20221208-02598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
The clinical application of metagenomic next-generation sequencing (mNGS) in the diagnosis of unknown pathogenic infections and critical infections has become increasingly valuable. Due to the huge volume of mNGS data and the complexity of clinical diagnosis and treatment, mNGS has difficulties in data analysis and interpretation in practical application. Therefore, in the process of clinical practice, it is crucial to grasp the key points of bioinformatics analysis and establish a standardized bioinformatics analysis process, which is an important step in the transformation of mNGS from laboratory to clinic. At present, bioinformatics analysis of mNGS has made great progress, but with the high requirements of clinical standardization of bioinformatics analysis and the development of computer technology, bioinformatics analysis of mNGS is also facing new challenges. This article mainly elaborates on quality control, and identification and visualization of pathogenic bacteria.
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Affiliation(s)
- Y F Xiong
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Z Cai
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - S C Li
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Y J Song
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - X M Hu
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - L Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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6
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Huang JC, Yu ZZ, Zou F, Li M, Cai Z, Liu GL, Li GY. [Progress in the clinical research of malignant melanoma in nasal cavity and paranasal sinuses]. Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2023; 58:297-302. [PMID: 36878516 DOI: 10.3760/cma.j.cn115330-20220608-00337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Affiliation(s)
- J C Huang
- Postgraduate Training Base of Shiyan Taihe Hospital of Hubei Medical College, Shiyan 442000, China
| | - Z Z Yu
- Department of Otorhinolaryngology Head and Neck Surgery, Shiyan Taihe Hospital (Affiliated Hospital of Hubei Medical College), Shiyan 442000, China
| | - F Zou
- Department of Otorhinolaryngology Head and Neck Surgery, Shiyan Taihe Hospital (Affiliated Hospital of Hubei Medical College), Shiyan 442000, China
| | - M Li
- Department of Otorhinolaryngology Head and Neck Surgery, Shiyan Taihe Hospital (Affiliated Hospital of Hubei Medical College), Shiyan 442000, China
| | - Z Cai
- Department of Otorhinolaryngology Head and Neck Surgery, Shiyan Taihe Hospital (Affiliated Hospital of Hubei Medical College), Shiyan 442000, China
| | - G L Liu
- Department of Otorhinolaryngology Head and Neck Surgery, Shiyan Taihe Hospital (Affiliated Hospital of Hubei Medical College), Shiyan 442000, China
| | - G Y Li
- Department of Otorhinolaryngology Head and Neck Surgery, Shiyan Taihe Hospital (Affiliated Hospital of Hubei Medical College), Shiyan 442000, China
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Cai Z, Fu P, Xu L, Deng L, Peng Y. Systematic identification and characterization of viral small RNAs from small RNA-Seq data. J Med Virol 2023; 95:e28617. [PMID: 36840404 DOI: 10.1002/jmv.28617] [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: 12/15/2022] [Revised: 02/03/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
Virus-encoded small RNAs (vsRNAs) have been reported to play an important role in viral infection. Unfortunately, there is still a lack of a systematic characterization and resource of vsRNAs. Herein, we identified a total of 19,734 high-confidence vsRNAs including 2,746 miRNAs in 64 viral species from more than 800 samples of public small RNA-Seq data. The number of vsRNAs identified in viruses varied from 1 to 2,489 with a median of 170. The length distribution of vsRNAs peaked at 21 and 22 nt. Plant viruses were found to express larger number and higher levels of vsRNAs than those of animal viruses. Besides, the number of vsRNAs identified increased as the viral infection persisted. Interestingly, the vsRNA showed strong expression specificity as little overlap was observed among vsRNAs identified in different strains of a virus, or in different hosts, cells, or tissues infected by the same virus. Little conservation was observed among vsRNAs of different viruses. The viral miRNAs were found to interact with host genes involved in multiple biological processes related to organization, development, action potential, polarity establishment, methylation, immune response, gene regulation, localization, and so on. To facilitate the usage of vsRNAs, a database named vsRNAdb was built to organize and store vsRNAs which is available at http://www.computationalbiology.cn/vsRNAdb/#/. Overall, the study deepens our understanding about the diversity and complexity of vsRNAs and provides a rich resource for further studies of vsRNAs. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Zena Cai
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Ping Fu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Lihua Xu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Li Deng
- Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, 410015, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
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Cai Z, Fu P, Qiu Y, Wu A, Zhang G, Wang Y, Jiang T, Ge XY, Zhu H, Peng Y. vsRNAfinder: a novel method for identifying high-confidence viral small RNAs from small RNA-Seq data. Brief Bioinform 2022; 23:6827719. [PMID: 36377755 DOI: 10.1093/bib/bbac496] [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: 07/01/2022] [Revised: 09/23/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Virus-encoded small RNAs (vsRNA) have been reported to play an important role in viral infection. Unfortunately, there is still a lack of an effective method for vsRNA identification. Herein, we presented vsRNAfinder, a de novo method for identifying high-confidence vsRNAs from small RNA-Seq (sRNA-Seq) data based on peak calling and Poisson distribution and is publicly available at https://github.com/ZenaCai/vsRNAfinder. vsRNAfinder outperformed two widely used methods namely miRDeep2 and ShortStack in identifying viral miRNAs with a significantly improved sensitivity. It can also be used to identify sRNAs in animals and plants with similar performance to miRDeep2 and ShortStack. vsRNAfinder would greatly facilitate effective identification of vsRNAs from sRNA-Seq data.
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Affiliation(s)
- Zena Cai
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Ping Fu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Ye Qiu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Gaihua Zhang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Yirong Wang
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | | | - Xing-Yi Ge
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Haizhen Zhu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
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van Egmond S, Cai Z, Nava V, Rapaport B, Ko J, Chiou A, Sarin K, Tang J, Bousheri S, Zhang L, Linos E. 349 Development of a digital tool for home-based monitoring of skin disease for older adults. J Invest Dermatol 2022. [PMCID: PMC9296962 DOI: 10.1016/j.jid.2022.05.358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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van Egmond S, de Vere Hunt I, Cai Z, Rizk N, Wakkee M, Chren M, Goldfarb N, Simard J, Linos E. 374 529 dermatologists’ perspectives on active surveillance for low-risk basal cell carcinoma. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Wang Z, Zhao Z, Xia Y, Cai Z, Wang C, Shen Y, Liu R, Qin H, Jia J, Yuan G. Potential biomarkers in the fibrosis progression of nonalcoholic steatohepatitis (NASH). J Endocrinol Invest 2022; 45:1379-1392. [PMID: 35226336 DOI: 10.1007/s40618-022-01773-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 12/14/2021] [Accepted: 02/17/2022] [Indexed: 12/13/2022]
Abstract
PURPOSE Fibrosis is the only histological feature reflecting the severity and prognosis of nonalcoholic steatohepatitis (NASH). We aim to explore novel genes associated with fibrosis progression in NASH. METHODS Two human RNA-seq datasets were downloaded from the public database. Weighted gene co-expression network analysis (WGCNA) was used to identify their co-expressed modules and further bioinformatics analysis was performed to identify hub genes within the modules. Finally, based on two single-cell RNA-seq datasets from mice and one microarray dataset from human, we further observed the expression of hub genes in different cell clusters and liver tissues. RESULTS 7 hub genes (SPP1, PROM1, SOX9, EPCAM, THY1, CD34 and MCAM) associated with fibrosis progression were identified. Single-cell RNA-seq analysis revealed that those hub genes were expressed by different cell clusters such as cholangiocytes, natural killer (NK) cells, and hepatic stellate cells (HSCs). We also found that SPP1 and CD34 serve as markers of different HSCs clusters, which are associated with inflammatory response and fibrogenesis, respectively. Further study suggested that SPP1, SOX9, MCAM and THY1 might be related to NASH-associated hepatocellular carcinoma (HCC). Receiver operating characteristic (ROC) analysis showed that the high expression of these genes could well predict the occurrence of HCC. At the same time, there were significant differences in metabolism-related pathway changes between different HCC subtypes, and SOX9 may be involved in these changes. CONCLUSIONS The present study identified novel genes associated with NASH fibrosis and explored their effects on fibrosis from a single-cell perspective that might provide new ideas for the early diagnosis, monitoring, evaluation, and prediction of fibrosis progression in NASH.
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Affiliation(s)
- Z Wang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Z Zhao
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Y Xia
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Z Cai
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - C Wang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Y Shen
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - R Liu
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - H Qin
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - J Jia
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China.
| | - G Yuan
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China.
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Cai Z, Mu M, Zhang B. P-223 An eleven-lncRNA signature predicts overall survival in patients with gastric cancer. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Mu M, Cai Z, Shen C, Wang J, Zhao Z, Zhang B. P-220 The efficacy of preoperative imatinib in locally advanced gastrointestinal stromal tumors: A single-center retrospective analysis. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Cai Z, Zhao Z, Mu M, Shen C, Zhang B. P-215 Liver transplantation for hilar cholangiocarcinoma: A systematic review and meta-analysis. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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15
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Cai Z, Chen WM. [Interpretation of treatment of relapsed/refractory multiple myeloma patients in the guidelines for the diagnosis and management of multiple myeloma in China(2022 revision)]. Zhonghua Nei Ke Za Zhi 2022; 61:469-473. [PMID: 35488595 DOI: 10.3760/cma.j.cn112138-20220414-00278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Z Cai
- Department of Bone Marrow Transplantation,the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - W M Chen
- Department of Hematology,Beijing Chao-yang Hospital,Capital Medical University, Beijing 100020, China
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16
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Cai Z, Huang Y, Tang JH, Zhang R, Chen JK, Wang J, Ma YY. [Heparin-binding hemagglutinin as a composition antigen of tuberculosis vaccine exerts protective immune effects by inducing IL-17]. Zhonghua Yu Fang Yi Xue Za Zhi 2022; 56:370-376. [PMID: 35381662 DOI: 10.3760/cma.j.cn112150-20211206-01122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
To explore the protective immune effect induced by mucosal delivery heparin-binding hemagglutinin (HBHA)-a candidate vaccine antigen of Mycobacterium tuberculosis. Female C57BL/6 mice were between 6 and 8 weeks of age before experimental use. Thirty mice received different immunization strategies and were randomly divided into the control group, the early secreting antigen target-6 (ESAT-6) intranasal immunization group, the HBHA intranasal immunization group, the BCG priming PBS control group, or BCG priming HBHA boost group, 6 mice in each group. In order to analyzed the immune effect, the concentrations of plasma Interleukin-17A (IL-17A) and other cytokines were measured by ELISA. Quantitative real-time PCR analyses were performed to detect the relative quantity (RQ) mRNA of IL-17A in the lung. The lung tissue sections were stained to detect the formation of the tertiary lymphoid structures. The chemokines contributed to formation of the tertiary lymphoid structures were also measured. Flow cytometry was used to detect the frequency of Th1 and Th17 cells in the system. Sixty mice in the BCG priming PBS control group and the BCG priming HBHA boost group were sacrificed at different time points after infection to count the lung bacterial burden. The concentrations of plasma IL-17A and relative quantity of lung IL-17A mRNA were highest in the BCG priming HBHA boost group [(14.76±4.73) pg/mL,RQ (12.27±6.71)], which was significantly higher than the control group [(5.57±2.95) pg/mL,RQ (1.30±0.97)] (t=4.213, P<0.001; t=5.984, P<0.001), and also significantly higher than the BCG priming PBS control group [(6.81±2.18) pg/mL,RQ (1.44±1.16)] (t=3.646 P=0.001; t=6.185 P<0.001). Compared with the BCG priming PBS control group (0.38±0.38)% the frequency of spleen Th17 cells were also significantly increased (t=-0.280, P=0.048) in the BCG-primary HBHA boost group (1.02±0.34)%. In addition, HBHA boosting could promote better formation of the tertiary lymphoid structures in the lung, and decrease the bacterial load on the early stage after BCG challenge. Collectively, mucosal delivery of HBHA can effectively enhance the protective effect after BCG vaccination, and it is a potential candidate vaccine component.
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Affiliation(s)
- Z Cai
- Department of Clinical Laboratory, Air Force Medical Center, Beijing 100142, China
| | - Y Huang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - J H Tang
- Department of Clinical Laboratory, Air Force Medical Center, Beijing 100142, China
| | - R Zhang
- Department of Clinical Laboratory, the First Affiliated Hospital, Air Force Medical University, Xi'an 710032, China
| | - J K Chen
- Department of Clinical Laboratory, the First Affiliated Hospital, Air Force Medical University, Xi'an 710032, China
| | - J Wang
- Department of Clinical Laboratory, the First Affiliated Hospital, Air Force Medical University, Xi'an 710032, China
| | - Y Y Ma
- Department of Clinical Laboratory, Air Force Medical Center, Beijing 100142, China
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Zhu Z, Ge S, Cai Z, Wu Y, Lu C, Zhang Z, Fu P, Mao L, Wu X, Peng Y. Systematic identification and characterization of repeat sequences in African swine fever virus genomes. Vet Res 2022; 53:101. [PMID: 36461107 PMCID: PMC9717548 DOI: 10.1186/s13567-022-01119-9] [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: 05/17/2022] [Accepted: 07/19/2022] [Indexed: 12/03/2022] Open
Abstract
African swine fever virus (ASFV) is a large DNA virus that infects domestic pigs with high morbidity and mortality rates. Repeat sequences, which are DNA sequence elements that are repeated more than twice in the genome, play an important role in the ASFV genome. The majority of repeat sequences, however, have not been identified and characterized in a systematic manner. In this study, three types of repeat sequences, including microsatellites, minisatellites and short interspersed nuclear elements (SINEs), were identified in the ASFV genome, and their distribution, structure, function, and evolutionary history were investigated. Most repeat sequences were observed in noncoding regions and at the 5' end of the genome. Noncoding repeat sequences tended to form enhancers, whereas coding repeat sequences had a lower ratio of alpha-helix and beta-sheet and a higher ratio of loop structure and surface amino acids than nonrepeat sequences. In addition, the repeat sequences tended to encode penetrating and antimicrobial peptides. Further analysis of the evolution of repeat sequences revealed that the pan-repeat sequences presented an open state, showing the diversity of repeat sequences. Finally, CpG islands were observed to be negatively correlated with repeat sequence occurrences, suggesting that they may affect the generation of repeat sequences. Overall, this study emphasizes the importance of repeat sequences in ASFVs, and these results can aid in understanding the virus's function and evolution.
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Affiliation(s)
- Zhaozhong Zhu
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Shengqiang Ge
- grid.414245.20000 0004 6063 681XChina Animal Health and Epidemiology Center, Qingdao, 266032 China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Animal Biosafety Risk Prevention and Control (South), Ministry of Agriculture and Rural Affairs, Qingdao, China
| | - Zena Cai
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Yifan Wu
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Congyu Lu
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Zheng Zhang
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Ping Fu
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Longfei Mao
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Xiaodong Wu
- grid.414245.20000 0004 6063 681XChina Animal Health and Epidemiology Center, Qingdao, 266032 China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Animal Biosafety Risk Prevention and Control (South), Ministry of Agriculture and Rural Affairs, Qingdao, China
| | - Yousong Peng
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
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18
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Zhang Y, Betran AP, Li X, Liu D, Yuan N, Shang L, Lin W, Tu S, Wang L, Wu X, Zhu T, Zhang Y, Lu Z, Zheng L, Gu C, Fang J, Liu Z, Ma L, Cai Z, Yang X, Li H, Zhang H, Zhao X, Yan L, Wang L, Sun X, Luo Q, Liu L, Zhu J, Qin W, Yao Q, Dong S, Yang Y, Cui Z, He Y, Feng X, He L, Zhang H, Zhang L, Wang X, Souza JP, Qi H, Duan T, Zhang J. What is an appropriate caesarean delivery rate for China: a multicentre survey. BJOG 2021; 129:138-147. [PMID: 34559941 PMCID: PMC9297886 DOI: 10.1111/1471-0528.16951] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Accepted: 08/15/2021] [Indexed: 11/30/2022]
Abstract
Objective To assess the current status of caesarean delivery (CD) in China, propose reference CD rates for China overall, and by regions, investigate the main indications for CDs and identify possible areas for safe reduction. Design A multicentre cross‐sectional study. Setting A total of 94 hospitals across 23 provinces in China. Population A total of 73 977 randomly selected deliveries. Methods We used a modified Robson classification to characterise CDs in subgroups and by regions, and the World Health Organization (WHO) C‐Model to calculate reference CD rates. Main outcome measures CD rates in China. Results In 2015–2016, the overall CD rate in China was 38.9% (95% CI 38.6–39.3%). Considering the obstetric characteristics of the population, the multivariable model‐based reference CD rate was estimated at 28.5% (95% CI 28.3–28.8%). Accordingly, an absolute reduction of 10.4% (or 26.7% relative reduction) may be considered. The CD rate varied substantially by region. Previous CD was the most common indication in all regions, accounting for 38.2% of all CDs, followed by maternal request (9.8%), labour dystocia (8.3%), fetal distress (7.7%) and malpresentation (7.6%). Overall, 12.7% of women had prelabour CDs, contributing to 32.8% of the total CDs. Conclusions Nearly 39% of births were delivered by caesarean in China but a reduction of this rate by a quarter may be considered attainable. Repeat CD contributed more than one‐third of the total CDs. Given the large variation in maternal characteristics, region‐specific or even hospital‐specific reference CD rates are needed for precision management of CD. Tweetable abstract The caesarean rate in 2015–2016 in China was 38.9%, whereas the reference rate was 28.5%. The caesarean rate in 2015–2016 in China was 38.9%, whereas the reference rate was 28.5%. Linked article This article is commented on by M Varner, p. 148 in this issue. To view this mini commentary visit https://doi.org/10.1111/1471-0528.16953.
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Affiliation(s)
- Y Zhang
- Ministry of Education - Shanghai Key Laboratory of Children's Environmental Health, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - A P Betran
- UNDP/UNFPA/UNICEF/WHO/World Bank Special Programme of Research, Development and Research Training in Human Reproduction, Department of Reproductive Health and Research, World Health Organization (WHO), Geneva, Switzerland
| | - X Li
- Obstetrics and Gynaecology Hospital of Fudan University, Shanghai, China
| | - D Liu
- Dongguan City Maternal and Child Health Hospital, Southern Medical University, Guangdong, China
| | - N Yuan
- Department of Obstetrics and Gynaecology, The Second Hospital Affiliated to Shaanxi University of Chinese Medicine, Shaanxi, China
| | - L Shang
- Department of Obstetrics, The Maternal and Child Health Hospital of Xinxiang, Henan, China
| | - W Lin
- Department of Obstetrics, The Maternal and Child Health Hospital of Dalian, Liaoning, China
| | - S Tu
- Department of Obstetrics and Gynaecology, Southwest Medical University, Sichuan, China
| | - L Wang
- Department of Obstetrics and Gynaecology, The First Hospital Affiliated to Kunming Medical University, Yunnan, China
| | - X Wu
- Department of Obstetrics, Jiangsu Women and Child Health Hospital, Jiangsu, China
| | - T Zhu
- The First People's Hospital of Zhaotong, Kunming Medical University, Yunnan, China
| | - Y Zhang
- Department of Obstetrics, The Maternal and Child Health Hospital of Qujing, Yunnan, China
| | - Z Lu
- Suining Central Hospital, Chongqing Medical University, Sichuan, China
| | - L Zheng
- Taizhou Hospital of Zhejiang Province, Zhejiang, China
| | - C Gu
- Yangzhou Maternal and Child Care Service Centre, Jiangsu, China
| | - J Fang
- Qingdao Chengyang People's Hospital, Shandong First Medical University, Shandong, China
| | - Z Liu
- Department of Obstetrics, The Maternal and Child Health Hospital of Baoji, Shaanxi, China
| | - L Ma
- Yanshi City People's Hospital, Henan, China
| | - Z Cai
- Department of Obstetrics and Gynaecology, Aviation Hospital of Beijing, China Medical University, Beijing, China
| | - X Yang
- Department of Obstetrics, The Maternal and Child Health Hospital of Luohu District, Shenzhen, China
| | - H Li
- Yanan University Affiliated Hospital, Shaanxi, China
| | - H Zhang
- Haikou Hospital of the Maternal and Child Health, Hainan, China
| | - X Zhao
- The First People's Hospital of Taizhou, Wenzhou Medical University, Zhejiang, China
| | - L Yan
- The Second Affiliated Hospital of Hebei North University, Hebei, China
| | - L Wang
- Department of Obstetrics and Gynaecology, The 174th Hospital of the Chinese People's Liberation Army, Xiamen University, Fujian, China
| | - X Sun
- Puyang Maternal and Child Care Centres, Henan, China
| | - Q Luo
- Luzhou People's Hospital, Sichuan, China
| | - L Liu
- Affiliated Hospital of Jiangsu University, Jiangsu, China
| | - J Zhu
- The Second People's Hospital of Tongxiang, Zhejiang, China
| | - W Qin
- Department of Obstetrics and Gynaecology, Aviation Hospital of Beijing, China Medical University, Beijing, China
| | - Q Yao
- The Central Hospital of Shaoyang, University of South China, Hunan, China
| | - S Dong
- Affiliated Hospital of Zunyi Medical University, Guizhou, China
| | - Y Yang
- The First Affiliated Hospital of Anhui Medical University, Anhui, China
| | - Z Cui
- Department of Obstetrics, The Maternal and Child Health Hospital of Cangzhou, Hebei, China
| | - Y He
- The Second People's Hospital of Qingyuan City, Guangdong, China
| | - X Feng
- Department of Obstetrics and Gynaecology, Fujian Medical University Union Hospital, Fujian Medical University, Fujian, China
| | - L He
- The People's Hospital of Pengzhou, Sichuan, China
| | - H Zhang
- Department of Obstetrics, Eastern District of the Fourth Hospital of Hebei Medical University, Hebei, China
| | - L Zhang
- Ministry of Education - Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - X Wang
- Department of Obstetrics and Gynaecology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - J P Souza
- Department of Social Medicine, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
| | - H Qi
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - T Duan
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - J Zhang
- Ministry of Education - Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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James R, Admire B, Sisserson T, Cai Z, Dumas M, Inge L, Baumann J, Towne P, Dalvi D, ElGabry E. 1125P Analytical assessment of a diagnostic immunohistochemical assay for the detection of folate receptor-ɑ in epithelial ovarian cancers. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Cai Z, Wang W, Pan BH, Xie C, Yang P, Wang XW, Ouyang Y, Liu GQ, Wu KM, Le TM, Huang JH. [Choices of emergency treatment and surgical method for ruptured abdominal aortic aneurysms]. Zhonghua Yi Xue Za Zhi 2021; 101:2288-2292. [PMID: 34333943 DOI: 10.3760/cma.j.cn112137-20201216-03368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the emergency management process of ruptured abdominal aortic aneurysm (RAAA), and analyze the perioperative mortality factors of different surgical methods. Methods: The emergency data and hospitalization data of 91 patients with ruptured abdominal aortic aneurysm in Xiangya Hospital of Central South University from June 2010 to June 2019 were retrospectively analyzed.Twelve of the patients died preoperatively due to excessive blood loss, and the remaining 79 patients were hospitalized for open surgery (OSR) or endovascular repair (EVAR).The differences in age, time to hospital arrival, emergency preparation time, first creatinine value, emergency infusion volume, preoperative drop in blood pressure, preoperative use of vasoactive drugs and iliac artery involvement were compared between preoperative death group (n=12) and preoperative survival group (n=79), OSR group (n=50) and EVAR group (n=29), postoperative death group (n=23) and postoperative survival group (n=56). Results: Seventy-nine patients received open surgery or endovascular repair, and 23 died after operation. Age, time to hospital arrival, first creatinine value and emergency infusion volume were (77±11) years, (18±5)h, (469±150) μmol/L, (4 140±1 743) ml in the preoperative death group and (70±10) years, (12±8) h, (228±174) μmol/L, (1 358±1 211) ml in the preoperative survival group, respectively, and the differences were statistically significant (all P<0.05). There were no significant differences in preoperative data, intraoperative treatment and postoperative perioperative mortality between the open surgery group and the endovascular repair group (all P>0.05). The intraoperative blood loss, operation time and aortic occlusion rate in the endovascular repair group were 100 (50, 175) ml, (3.2±0.9) h, 13.8%, respectively, which were better than that in the open surgery group 1700 (600, 3425) ml, (5.2±1.1) h, 100%. The differences were statistically significant (all P<0.05). Age, emergency preparation time, first creatinine value, emergency infusion volume, blood pressure decline rate and vasoactive drug utilization rate in the death group were (77±8) years, (4.1±1.7) h, (456±172) μmol/L, (2 024±1 687) ml, 100%, 100%, respectively, and (68±10) years, (2.7±2.2) h, (135±26) μmol/L, (1 085±825) ml, 21.4%, 12.5% in the survival group, respectively. The differences were statistically significant (all P<0.05). Conclusions: Age, emergency preparation time, first creatinine value, emergency infusion volume, decreased blood pressure and use of vasoactive drugs are all associated with perioperative death in patients with ruptured abdominal aortic aneurysm. EVAR surgery is a better choice if conditions exist.
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Affiliation(s)
- Z Cai
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - W Wang
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - B H Pan
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - C Xie
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - P Yang
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - X W Wang
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - Y Ouyang
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - G Q Liu
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - K M Wu
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - T M Le
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - J H Huang
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
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Mu M, Cai Z, Shen C, Wang J, Zhang B. P-93 The characteristics and prognosis of extragastrointestinal stromal tumors: A single center retrospective analysis of 31 patients. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.05.148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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22
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Cai Z, Liu C, Shen C, Jiang Z, Mu M, Zhang B. P-227 Comparative safety and tolerability of approved PARP inhibitors in cancer: A systematic review and network meta-analysis. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.05.281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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23
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Vicente-Serrano SM, Peña-Angulo D, Murphy C, López-Moreno JI, Tomas-Burguera M, Domínguez-Castro F, Tian F, Eklundh L, Cai Z, Alvarez-Farizo B, Noguera I, Camarero JJ, Sánchez-Salguero R, Gazol A, Grainger S, Conradt T, Boincean B, El Kenawy A. The complex multi-sectoral impacts of drought: Evidence from a mountainous basin in the Central Spanish Pyrenees. Sci Total Environ 2021; 769:144702. [PMID: 33736257 DOI: 10.1016/j.scitotenv.2020.144702] [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] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/18/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
We analyzed the impacts of drought severity on a variety of sectors in a topographically complex basin (the upper Aragón basin 2181 km2) in the Central Spanish Pyrenees. Using diverse data sources including meteorological and hydrological observations, remote sensing and tree rings, we analyze the possible hydrological implications of drought occurrence and severity on water availability in various sectors, including downstream impacts on irrigation water supply for crop production. Results suggest varying responses in forest activity, secondary growth, plant phenology, and crop yield to drought impacts. Specifically, meteorological droughts have distinct impacts downstream, mainly due to water partitioning between streamflow and irrigation channels that transport water to crop producing areas. This implies that drought severity can extend beyond the physical boundaries of the basin, with impacts on crop productivity. This complex response to drought impacts makes it difficult to develop objective basin-scale operational definitions for monitoring drought severity. Moreover, given the high spatial variability in responses to drought across sectors, it is difficult to establish reliable drought thresholds from indices that are relevant across all socio-economic sectors. The anthropogenic impacts (e.g. water regulation projects, ecosystem services, land cover and land use changes) pose further challenges to assessing the response of different systems to drought severity. This study stresses the need to consider the seasonality of drought impacts and appropriate drought time scales to adequately assess and understand their complexity.
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Affiliation(s)
- S M Vicente-Serrano
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciones Científicas (IPE-CSIC), Zaragoza, Spain.
| | - D Peña-Angulo
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciones Científicas (IPE-CSIC), Zaragoza, Spain
| | - C Murphy
- Irish Climate Analysis and Research UnitS (ICARUS), Department of Geography, Maynooth University, Maynooth, Ireland
| | - J I López-Moreno
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciones Científicas (IPE-CSIC), Zaragoza, Spain
| | - M Tomas-Burguera
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain
| | - F Domínguez-Castro
- Aragonese Agency for Research and Development Researcher (ARAID), Spain; Department of Geography, University of Zaragoza, Zaragoza, Spain
| | - F Tian
- Department of Geography, Lund University, Lund, Sweden
| | - L Eklundh
- Department of Geography, Lund University, Lund, Sweden
| | - Z Cai
- Department of Geography, Lund University, Lund, Sweden
| | - B Alvarez-Farizo
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciones Científicas (IPE-CSIC), Zaragoza, Spain
| | - I Noguera
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciones Científicas (IPE-CSIC), Zaragoza, Spain
| | - J J Camarero
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciones Científicas (IPE-CSIC), Zaragoza, Spain
| | - R Sánchez-Salguero
- Departamento Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - A Gazol
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciones Científicas (IPE-CSIC), Zaragoza, Spain
| | - S Grainger
- Irish Climate Analysis and Research UnitS (ICARUS), Department of Geography, Maynooth University, Maynooth, Ireland
| | - T Conradt
- Potsdam Institute for Climate Impact Research, Potsdam, Germany
| | - B Boincean
- Selectia Research Institute Of Field Crops, Balti, Republic of Moldova
| | - A El Kenawy
- Department of Geography, Mansoura University, Mansoura, Egypt; Department of Geography, Sultan Qaboos University, Al Khoud, Muscat, Oman
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Lun MH, Jin XY, Wang MY, Cai Z, Du W, Huang ZQ. Ulinastatin improves myocardial ischemia-reperfusion injury in rats through endoplasmic reticulum stress-induced apoptosis pathway. Eur Rev Med Pharmacol Sci 2021; 24:5742-5749. [PMID: 32495910 DOI: 10.26355/eurrev_202005_21366] [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] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE To investigate the protective role of ulinastatin (UTI) on myocardial ischemia-reperfusion (I/R) injury in rats via endoplasmic reticulum stress (ERS)-induced apoptosis pathway. MATERIALS AND METHODS A total of 60 rats were randomly divided into normal group (n=20), myocardial I/R model group (model group, n=20), and myocardial I/R model+UTI treatment group (treatment group, n=20). The myocardial function indicators [creatinine (Scr) and creatine kinase (CK)] were detected. Enzyme-linked immunosorbent assay (ELISA) was performed to measure serum levels of tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and matrix metalloproteinase-9 (MMP-9). Meanwhile, the contents of reactive oxygen species (ROS), superoxide dismutase (SOD), and malondialdehyde (MDA) in rat left ventricular tissues were determined by ELISA as well. The cardiac function indexes were determined via magnetic resonance imaging (MRI) and echocardiography (ECG). Terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate-biotin nick end labeling (TUNEL) staining assay was carried out to detect the apoptosis of myocardial tissues. Additionally, the expression levels of endoplasmic reticulum stress and apoptosis genes were measured through quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR) assay and Western blotting analysis, respectively. RESULTS Serum levels of alanine aminotransferase (ALT), CK, and Scr in model group were significantly higher than those in normal group (p<0.05). Besides, rats in model group had significantly lowered SOD, ejection fraction (EF, %), and fractional shortening (FS, %) than those in normal group (p<0.05). In addition, remarkably increased contents of TNF-α, IL-6, MMP-9, MDA, and ROS, as well as higher left ventricular end-diastolic diameter (LVEDd) and left ventricular end-systolic diameter (LVESd) were observed in model group in comparison with normal group (p<0.05). TUNEL staining results revealed that there were more apoptotic cells in model group than that in the other two groups (p<0.05). Expression levels of cysteine aspartic acid-specific protease 12 (Caspase-12) and glucose-regulated protein 78 (GRP78) were evidently higher in model group than those in normal group (p<0.05), while the expression level of B-cell lymphoma 2 (Bcl-2) was clearly lower in model group than that in normal group (p<0.05). UTI treatment partially reversed the above expression changes (p<0.05). CONCLUSIONS UTI has a protective effect against myocardial I/R injury in rats by repressing the occurrence of ERS-induced apoptosis.
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Affiliation(s)
- M-H Lun
- Department of Anesthesiology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China.
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Cai Z, Lu C, He J, Liu L, Zou Y, Zhang Z, Zhu Z, Ge X, Wu A, Jiang T, Zheng H, Peng Y. Identification and characterization of circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2. Brief Bioinform 2021; 22:1297-1308. [PMID: 33757279 PMCID: PMC7799257 DOI: 10.1093/bib/bbaa334] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/28/2020] [Accepted: 10/23/2020] [Indexed: 12/17/2022] Open
Abstract
The life-threatening coronaviruses MERS-CoV, SARS-CoV-1 and SARS-CoV-2 (SARS-CoV-1/2) have caused and will continue to cause enormous morbidity and mortality to humans. Virus-encoded noncoding RNAs are poorly understood in coronaviruses. Data mining of viral-infection-related RNA-sequencing data has resulted in the identification of 28 754, 720 and 3437 circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2, respectively. MERS-CoV exhibits much more prominent ability to encode circRNAs in all genomic regions than those of SARS-CoV-1/2. Viral circRNAs typically exhibit low expression levels. Moreover, majority of the viral circRNAs exhibit expressions only in the late stage of viral infection. Analysis of the competitive interactions of viral circRNAs, human miRNAs and mRNAs in MERS-CoV infections reveals that viral circRNAs up-regulated genes related to mRNA splicing and processing in the early stage of viral infection, and regulated genes involved in diverse functions including cancer, metabolism, autophagy, viral infection in the late stage of viral infection. Similar analysis in SARS-CoV-2 infections reveals that its viral circRNAs down-regulated genes associated with metabolic processes of cholesterol, alcohol, fatty acid and up-regulated genes associated with cellular responses to oxidative stress in the late stage of viral infection. A few genes regulated by viral circRNAs from both MERS-CoV and SARS-CoV-2 were enriched in several biological processes such as response to reactive oxygen and centrosome localization. This study provides the first glimpse into viral circRNAs in three deadly coronaviruses and would serve as a valuable resource for further studies of circRNAs in coronaviruses.
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Affiliation(s)
- Zena Cai
- College of Biology, Hunan University
| | - Congyu Lu
- College of Biology, Hunan University
| | | | - Li Liu
- Hunan Yuelu mountain data science and Technology Research Institute Co., Ltd, Changsha, China
| | | | | | | | - Xingyi Ge
- College of Biology, Hunan University
| | - Aiping Wu
- Suzhou Institute of Systems Medicine
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Cai Z, Zhang J, He Y, Xia L, Dong X, Chen G, Zhou Y, Hu X, Zhong S, Wang Y, Chen H, Xie D, Liu X, Liu J. Liquid biopsy by combining 5-hydroxymethylcytosine signatures of plasma cell-free DNA and protein biomarkers for diagnosis and prognosis of hepatocellular carcinoma. ESMO Open 2021; 6:100021. [PMID: 33508734 PMCID: PMC7841321 DOI: 10.1016/j.esmoop.2020.100021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 09/16/2020] [Revised: 10/29/2020] [Accepted: 11/14/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Liquid biopsy based on 5-hydroxymethylcytosine (5hmC) signatures of plasma cell-free DNA (cfDNA) originating from tumor cells provides a novel approach for early diagnosis in hepatocellular carcinoma (HCC). Here, we sought to develop a reliable model using cfDNA 5hmC signatures and protein biomarkers for diagnosis and prognosis of HCC. PATIENTS AND METHODS We carried out genome-wide 5hmC sequencing of cfDNA samples collected from 165 healthy volunteers, 62 liver cirrhosis (LC) patients and 135 HCC patients. A sensitive 5hmC diagnostic model was developed based on 5hmC signatures selected by sparse Partial Least Squares Discriminant Analysis and cross-validation to define the weighted diagnostic score (wd-score). Then, we combined protein biomarkers with the wd-score to build a more robust score (HCC score) by logistic regression. RESULTS The distribution pattern of differential 5hmC regions could clearly distinguish HCC patients, LC patients and healthy volunteers. The wd-score based on 64 5hmC signatures in cfDNA achieves 93.24% of area under the curve (AUC) to distinguish HCC patients from non-HCC patients, and the HCC score by combing protein biomarkers achieves 92.75% of AUC to distinguish HCC patients from LC patients. Meanwhile, the HCC score showed high capacity for screening high recurrence risk patients after receiving surgical resection, and appeared to be an independent indicator for both relapse-free survival (P = 0.00865) and overall survival (P = 0.000739). Furthermore, the values of the HCC score in patients' longitudinal plasma samples were positively associated with tumor burden dynamics during follow-up. CONCLUSION We have developed and validated a novel non-invasive liquid biopsy strategy for HCC diagnosis, prognosis and surveillance during HCC progression.
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Affiliation(s)
- Z Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China; Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - J Zhang
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, P. R. China
| | - Y He
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, P. R. China; Laboratory of Nervous System Disease and Brain Functions, Clinical Research Institute, The Affiliated Hospital of Southwest Medical University, Luzhou, P. R. China
| | - L Xia
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, P. R. China
| | - X Dong
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China; Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - G Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China; Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - Y Zhou
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China; Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - X Hu
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, P. R. China
| | - S Zhong
- Tailai Inc., Shanghai, P. R. China
| | - Y Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China; Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - H Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
| | - D Xie
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, P. R. China.
| | - X Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China; Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China.
| | - J Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China; Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China.
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Lu C, Zhang Z, Cai Z, Zhu Z, Qiu Y, Wu A, Jiang T, Zheng H, Peng Y. Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics. BMC Biol 2021; 19:5. [PMID: 33441133 PMCID: PMC7807511 DOI: 10.1186/s12915-020-00938-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 02/29/2020] [Accepted: 12/09/2020] [Indexed: 12/19/2022] Open
Abstract
Background Viruses are ubiquitous biological entities, estimated to be the largest reservoirs of unexplored genetic diversity on Earth. Full functional characterization and annotation of newly discovered viruses requires tools to enable taxonomic assignment, the range of hosts, and biological properties of the virus. Here we focus on prokaryotic viruses, which include phages and archaeal viruses, and for which identifying the viral host is an essential step in characterizing the virus, as the virus relies on the host for survival. Currently, the method for determining the viral host is either to culture the virus, which is low-throughput, time-consuming, and expensive, or to computationally predict the viral hosts, which needs improvements at both accuracy and usability. Here we develop a Gaussian model to predict hosts for prokaryotic viruses with better performances than previous computational methods. Results We present here Prokaryotic virus Host Predictor (PHP), a software tool using a Gaussian model, to predict hosts for prokaryotic viruses using the differences of k-mer frequencies between viral and host genomic sequences as features. PHP gave a host prediction accuracy of 34% (genus level) on the VirHostMatcher benchmark dataset and a host prediction accuracy of 35% (genus level) on a new dataset containing 671 viruses and 60,105 prokaryotic genomes. The prediction accuracy exceeded that of two alignment-free methods (VirHostMatcher and WIsH, 28–34%, genus level). PHP also outperformed these two alignment-free methods much (24–38% vs 18–20%, genus level) when predicting hosts for prokaryotic viruses which cannot be predicted by the BLAST-based or the CRISPR-spacer-based methods alone. Requiring a minimal score for making predictions (thresholding) and taking the consensus of the top 30 predictions further improved the host prediction accuracy of PHP. Conclusions The Prokaryotic virus Host Predictor software tool provides an intuitive and user-friendly API for the Gaussian model described herein. This work will facilitate the rapid identification of hosts for newly identified prokaryotic viruses in metagenomic studies.
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Affiliation(s)
- Congyu Lu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Zheng Zhang
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Zena Cai
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Zhaozhong Zhu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Ye Qiu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Aiping Wu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Taijiao Jiang
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Heping Zheng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China.
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Qiu L, Han XY, He DH, Zhu F, Zhao Y, Zhu WW, Zheng GF, Yang Y, Wu WW, Cai Z, Yang XC, He JS. [The effect of peripheral blood cell score on the prognosis of multiple myeloma patients treated with bortezomib]. Zhonghua Xue Ye Xue Za Zhi 2021; 41:756-761. [PMID: 33113608 PMCID: PMC7595856 DOI: 10.3760/cma.j.issn.0253-2727.2020.09.009] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
目的 评估外周血细胞检测结果在以硼替佐米为一线治疗的多发性骨髓瘤(MM)患者中的预后作用。 方法 回顾性分析2014年1月至2016年12月浙江大学医学院附属第一医院和浙江省舟山医院收治的155例初诊MM患者的临床数据,患者均一线接受以硼替佐米为基础方案的治疗。分析外周血细胞检测结果,包括ANC、单核细胞计数(AMC)、HGB、红细胞平均体积(MCV)、PLT以及其他临床特征对MM患者的预后评估作用。 结果 AMC(>0.6×109/L)、MCV(>99.1fl)以及PLT(<150×109/L)明显影响MM患者无进展生存(PFS)和总生存(OS),以上3个因子分别赋值1分,形成血细胞积分。结果显示,64例(41.3%)积分0,57例(36.8%)积分1,32例(20.6%)积分2,2例(1.3%)积分3,4组患者中位PFS时间分别为42.8、26.5、15.8、6.4个月(P<0.001),中位OS时间分别为未达到和48.2、31.1、31.4个月(P=0.001)。多因素分析提示,血细胞积分(2~3对0~1)和骨髓浆细胞比例(>30%对≤30%)为PFS的独立预后因素(HR分别为1.95和1.76),而患者年龄(>65岁对≤65岁)、R-ISS分期(Ⅲ期对Ⅰ~Ⅱ期)和血细胞积分(2~3对0~1)是OS的独立预后因素(HR分别为2.08、2.13和2.12)。 结论 血细胞积分简单易得,可用于新药时代初治MM患者的预后评估,但仍需扩大病例并进行前瞻性研究进一步明确。
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Affiliation(s)
- L Qiu
- Department of Hematological Oncology and Chemotherapy, Zhoushan Hospital, Zhoushan 316004, China
| | - X Y Han
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - D H He
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - F Zhu
- Department of Hematological Oncology and Chemotherapy, Zhoushan Hospital, Zhoushan 316004, China
| | - Y Zhao
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - W W Zhu
- Department of Hematological Oncology and Chemotherapy, Zhoushan Hospital, Zhoushan 316004, China
| | - G F Zheng
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Y Yang
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - W W Wu
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Z Cai
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - X C Yang
- Department of Hematological Oncology and Chemotherapy, Zhoushan Hospital, Zhoushan 316004, China
| | - J S He
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
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Yang D, Boesch H, Liu Y, Somkuti P, Cai Z, Chen X, Di Noia A, Lin C, Lu N, Lyu D, Parker RJ, Tian L, Wang M, Webb A, Yao L, Yin Z, Zheng Y, Deutscher NM, Griffith DWT, Hase F, Kivi R, Morino I, Notholt J, Ohyama H, Pollard DF, Shiomi K, Sussmann R, Té Y, Velazco VA, Warneke T, Wunch D. Toward High Precision XCO 2 Retrievals From TanSat Observations: Retrieval Improvement and Validation Against TCCON Measurements. J Geophys Res Atmos 2020; 125:e2020JD032794. [PMID: 33777605 PMCID: PMC7983077 DOI: 10.1029/2020jd032794] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 06/12/2023]
Abstract
TanSat is the 1st Chinese carbon dioxide (CO2) measurement satellite, launched in 2016. In this study, the University of Leicester Full Physics (UoL-FP) algorithm is implemented for TanSat nadir mode XCO2 retrievals. We develop a spectrum correction method to reduce the retrieval errors by the online fitting of an 8th order Fourier series. The spectrum-correction model and its a priori parameters are developed by analyzing the solar calibration measurement. This correction provides a significant improvement to the O2 A band retrieval. Accordingly, we extend the previous TanSat single CO2 weak band retrieval to a combined O2 A and CO2 weak band retrieval. A Genetic Algorithm (GA) has been applied to determine the threshold values of post-screening filters. In total, 18.3% of the retrieved data is identified as high quality compared to the original measurements. The same quality control parameters have been used in a footprint independent multiple linear regression bias correction due to the strong correlation with the XCO2 retrieval error. Twenty sites of the Total Column Carbon Observing Network (TCCON) have been selected to validate our new approach for the TanSat XCO2 retrieval. We show that our new approach produces a significant improvement on the XCO2 retrieval accuracy and precision when compared to TCCON with an average bias and RMSE of -0.08 ppm and 1.47 ppm, respectively. The methods used in this study can help to improve the XCO2 retrieval from TanSat and subsequently the Level-2 data production, and hence will be applied in the TanSat operational XCO2 processing.
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Affiliation(s)
- D. Yang
- Earth Observation Science, School of Physics and AstronomyUniversity of LeicesterUK
- Institute of Atmospheric PhysicsChinese Academy of SciencesChina
- Shanghai Advanced Research InstituteChinese Academy of SciencesShanghaiChina
| | - H. Boesch
- Earth Observation Science, School of Physics and AstronomyUniversity of LeicesterUK
- National Centre for Earth ObservationUniversity of LeicesterUK
| | - Y. Liu
- Institute of Atmospheric PhysicsChinese Academy of SciencesChina
- Shanghai Advanced Research InstituteChinese Academy of SciencesShanghaiChina
| | - P. Somkuti
- Earth Observation Science, School of Physics and AstronomyUniversity of LeicesterUK
- National Centre for Earth ObservationUniversity of LeicesterUK
- Colorado State UniversityFort CollinsCOUSA
| | - Z. Cai
- Institute of Atmospheric PhysicsChinese Academy of SciencesChina
| | - X. Chen
- Institute of Atmospheric PhysicsChinese Academy of SciencesChina
| | - A. Di Noia
- Earth Observation Science, School of Physics and AstronomyUniversity of LeicesterUK
- National Centre for Earth ObservationUniversity of LeicesterUK
| | - C. Lin
- Changchun Institute of Optics, Fine Mechanics and PhysicsChina
| | - N. Lu
- National Satellite Meteorological Center, China Meteorological AdministrationChina
| | - D. Lyu
- Institute of Atmospheric PhysicsChinese Academy of SciencesChina
| | - R. J. Parker
- Earth Observation Science, School of Physics and AstronomyUniversity of LeicesterUK
- National Centre for Earth ObservationUniversity of LeicesterUK
| | - L. Tian
- Shanghai Engineering Center for MicrosatellitesChina
| | - M. Wang
- Shanghai Advanced Research InstituteChinese Academy of SciencesShanghaiChina
| | - A. Webb
- Earth Observation Science, School of Physics and AstronomyUniversity of LeicesterUK
- National Centre for Earth ObservationUniversity of LeicesterUK
| | - L. Yao
- Institute of Atmospheric PhysicsChinese Academy of SciencesChina
| | - Z. Yin
- Shanghai Engineering Center for MicrosatellitesChina
| | - Y. Zheng
- Changchun Institute of Optics, Fine Mechanics and PhysicsChina
| | - N. M. Deutscher
- Centre for Atmospheric Chemistry, School of Earth, Atmospheric and Life SciencesUniversity of WollongongNSWAustralia
| | - D. W. T. Griffith
- Centre for Atmospheric Chemistry, School of Earth, Atmospheric and Life SciencesUniversity of WollongongNSWAustralia
| | - F. Hase
- Karlsruhe Institute of Technology, IMK‐IFUGarmisch‐PartenkirchenGermany
| | - R. Kivi
- Space and Earth Observation CentreFinnish Meteorological InstituteFinland
| | - I. Morino
- National Institute for Environmental Studies (NIES)TsukubaIbarakiJapan
| | - J. Notholt
- Institute of Environmental Physics (IUP)University of BremenBremenGermany
| | - H. Ohyama
- National Institute for Environmental Studies (NIES)TsukubaIbarakiJapan
| | - D. F. Pollard
- National Institute of Water and Atmospheric Research Ltd (NIWA)LauderNew Zealand
| | - K. Shiomi
- Japan Aerospace Exploration AgencyJapan
| | - R. Sussmann
- Karlsruhe Institute of Technology, IMK‐IFUGarmisch‐PartenkirchenGermany
| | - Y. Té
- Laboratoire d'Etudes du Rayonnement et de la Matière en Astrophysique et Atmosphères (LERMA‐IPSL)Sorbonne Université, CNRS, Observatoire de Paris, PSL UniversitéParisFrance
| | - V. A. Velazco
- Centre for Atmospheric Chemistry, School of Earth, Atmospheric and Life SciencesUniversity of WollongongNSWAustralia
| | - T. Warneke
- Institute of Environmental Physics (IUP)University of BremenBremenGermany
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Cai Z, Klein T, Geenen L, Tu L, Tian S, Van Den Bosch A, De Rijke Y, Reiss I, Boersma E, Duncker D, Boomars K, Guignabert C, Merkus D. Lower plasma melatonin levels predict worse long-term survival in pulmonary arterial hypertension. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.3815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Exogenous melatonin has been reported to be beneficial in the treatment of pulmonary hypertension (PH) in animal models. Multiple mechanisms may be involved, with melatonin exerting anti-oxidant and anti-inflammatory effects, as well as inducing vasodilation and cardio-protection. However, endogenous levels of melatonin in treatment-naïve pulmonary arterial hypertension (PAH) patients and their clinical significance are still unknown.
Methods and results
Plasma levels of endogenous melatonin were measured by liquid chromatography-tandem mass spectrometry in treatment-naïve PAH patients (n=43) and healthy controls (n=111). Melatonin levels were higher in PAH patients when compared with controls (Median 118.9 [IQR 109.3–147.7] versus 108.0 [102.3–115.2] pM, P<0.001) (Figure 1A). The overall mortality was 26% (11/43) during a median long-term follow-up of 42 [IQR: 32–58] months. When PAH patients were stratified into 4 groups according to the quartiles of melatonin levels, the mortality from below 1st quartile to above 4th quartile was 55% (6/11), 10% (1/10), 0% (0/12), and 40% (4/10), respectively (Figure 1B). Kaplan-Meier analysis further showed that patients with melatonin levels below the 1st quartile (<109.3 pM) had a worse long-term survival than patients with melatonin levels above the 1st quartile (Mean survival times were 46 [95% CI: 30–65] versus 68 [58–77] months, Log-rank, p=0.026) (Figure 1C).
Conclusion
Endogenous melatonin levels were increased in treatment-naïve PAH patients, and lower levels of melatonin were associated with worse long-term survival in patient with PAH, however, whether exogenous melatonin supplements may be effective as a therapeutic strategy in human PAH remains to be established.
Figure 1
Funding Acknowledgement
Type of funding source: Foundation. Main funding source(s): This work was supported by the China Scholarship Council (201606230252) as well as the Netherlands CardioVascular Research Initiative: an initiative with support of the Dutch Heart Foundation (CVON2014-11, RECONNECT), and German Center for Cardiovascular Research (DZHK81Z0600207). Instrumentation support was received from AB Sciex, ltd. for LC-MS/MS analyses performed in this study.
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Affiliation(s)
- Z Cai
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | - T Klein
- Erasmus Medical Center, Clinical Chemistry, Rotterdam, Netherlands (The)
| | - L.W Geenen
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | - L Tu
- INSERM UMR_S 999 Hôpital Marie Lannelongue and Université Paris-Saclay School of Medicine, Paris, France
| | - S Tian
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | | | - Y.B De Rijke
- Erasmus Medical Center, Clinical Chemistry, Rotterdam, Netherlands (The)
| | - I.K.M Reiss
- Erasmus Medical Center, Pediatrics/Neonatology, Rotterdam, Netherlands (The)
| | - E Boersma
- Erasmus University Medical Centre, Clinical Epidemiology, Rotterdam, Netherlands (The)
| | - D.J Duncker
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | - K.A Boomars
- Erasmus Medical Center, Pulmonary Medicine, Rotterdam, Netherlands (The)
| | - C Guignabert
- INSERM UMR_S 999 Hôpital Marie Lannelongue and Université Paris-Saclay School of Medicine, Paris, France
| | - D Merkus
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
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Cai Z, Klein T, Tu L, Geenen L, Tian S, Van Der Ley C, Van Faassen M, Kema I, Van Den Bosch A, De Rijke J, Reiss I, Duncker D, Boomars K, Guignabert C, Merkus D. Different tryptophan-kynurenine metabolism profiles in human pulmonary arterial hypertension and animal models of pulmonary hypertension. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.3814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
De novo NAD+ synthesis through the tryptophan-kynurenine (TK) metabolism was recognized as an important pathway in improving mitochondrial function and survival of injury or apoptotic cells, which are key processes involved in the pathogenesis of pulmonary arterial hypertension (PAH). Although abnormal TK metabolism has been reported in human PAH, the difference between human and animal models of pulmonary hypertension (PH) are currently unknown.
Objective
Determine and compare TK metabolism profiles in plasma from human PAH and 3 animal models of PH.
Methods
Human plasma was collected from treatment naïve patients with PAH (n=43) and healthy controls (n=111). Animal plasma was collected from 3 animal models of PH and corresponding controls, including monocrotaline (MCT) induced PH in rat (n=7, control n=6), Sugen + hypoxia (SuHx) induced PH in rat (n=5, control n=6), and pulmonary vein banding (PVB) induced PH in swine (n=7, control n=6). TK metabolites were determined using liquid chromatography-tandem mass spectrometry (LC-MS/MS).
Results
TK metabolism was altered in the plasma from of PAH compared to healthy controls (Figure 1A). Lower tryptophan (0.8 fold vs Control, p<0.0001), maintained 3-hydroxyanthranilic acid, and higher kynurenine, 3-hydroxykynurenine, anthranilic acid, and quinolinic acid (1.5, 2.6, 2.0, 2.6 fold vs Control, respectively, p all<0.0001) were seen in the plasma from human PAH. In the rat SuHx-PH model, kynurenine (0.7 fold, p<0.01) and quinolinic acid (0.5 fold, p<0.001) were lower, while 3-hydroxyanthranilic acid (4.3 fold, p<0.001) was higher in PH compared to control (Figure 1B). However, the TK metabolism was unaltered in MCT-PH model in rat (Figure 1C), and PVB-PH model in swine (Figure 1D).
Conclusions
TK metabolism was altered in the plasma from human PAH. The TK metabolism profiles were different among 3 animal models of PH, but did not mimic the profile in human PAH. Further research is required to determine the mechanism(s) behind the abnormal TK metabolism in human PAH as well as whether these mechanisms relate to disease onset or progression.
Figure 1
Funding Acknowledgement
Type of funding source: Foundation. Main funding source(s): This work was supported by the China Scholarship Council (201606230252) as well as the Netherlands CardioVascular Research Initiative: an initiative with support of the Dutch Heart Foundation (CVON2014-11, RECONNECT), and German Center for Cardiovascular Research (DZHK81Z0600207). Instrumentation support was received from AB Sciex, ltd. for LC-MS/MS analyses performed in this study.
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Affiliation(s)
- Z Cai
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | - T Klein
- Erasmus Medical Center, Clinical Chemistry, Rotterdam, Netherlands (The)
| | - L Tu
- INSERM UMR_S 999 Hôpital Marie Lannelongue and Université Paris-Saclay School of Medicine, Paris, France
| | - L.W Geenen
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | - S Tian
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | - C Van Der Ley
- University Medical Center Groningen, Laboratory Medicine, Groningen, Netherlands (The)
| | - M Van Faassen
- University Medical Center Groningen, Laboratory Medicine, Groningen, Netherlands (The)
| | - I Kema
- University Medical Center Groningen, Laboratory Medicine, Groningen, Netherlands (The)
| | | | - J.B De Rijke
- Erasmus Medical Center, Clinical Chemistry, Rotterdam, Netherlands (The)
| | - I.K.M Reiss
- Erasmus Medical Center, Pediatrics/Neonatology, Rotterdam, Netherlands (The)
| | - D.J Duncker
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | - K.A Boomars
- Erasmus Medical Center, Pulmonary Medicine, Rotterdam, Netherlands (The)
| | - C Guignabert
- INSERM UMR_S 999 Hôpital Marie Lannelongue and Université Paris-Saclay School of Medicine, Paris, France
| | - D Merkus
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
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Lu C, Cai Z, Zou Y, Zhang Z, Chen W, Deng L, Du X, Wu A, Yang L, Wang D, Shu Y, Jiang T, Peng Y. FluPhenotype-a one-stop platform for early warnings of the influenza A virus. Bioinformatics 2020; 36:3251-3253. [PMID: 32049310 DOI: 10.1093/bioinformatics/btaa083] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 01/06/2020] [Accepted: 02/04/2020] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Newly emerging influenza viruses keep challenging global public health. To evaluate the potential risk of the viruses, it is critical to rapidly determine the phenotypes of the viruses, including the antigenicity, host, virulence and drug resistance. RESULTS Here, we built FluPhenotype, a one-stop platform to rapidly determinate the phenotypes of the influenza A viruses. The input of FluPhenotype is the complete or partial genomic/protein sequences of the influenza A viruses. The output presents five types of information about the viruses: (i) sequence annotation including the gene and protein names as well as the open reading frames, (ii) potential hosts and human-adaptation-associated amino acid markers, (iii) antigenic and genetic relationships with the vaccine strains of different HA subtypes, (iv) mammalian virulence-related amino acid markers and (v) drug resistance-related amino acid markers. FluPhenotype will be a useful bioinformatic tool for surveillance and early warnings of the newly emerging influenza A viruses. AVAILABILITY AND IMPLEMENTATION It is publicly available from: http://www.computationalbiology.cn : 18888/IVEW. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Congyu Lu
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Zena Cai
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | | | - Zheng Zhang
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Wenjun Chen
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Lizong Deng
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong 510275, China
| | - Aiping Wu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong 510275, China
| | - Taijiao Jiang
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Yousong Peng
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
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Ueda K, Jung S, Chen Y, Cai Z, Nakamura T. PND16 Quantifying the Burden of Migraine in JAPAN: A Propensity-Score Matched Analysis of a Population-Based Survey. Value Health Reg Issues 2020. [DOI: 10.1016/j.vhri.2020.07.404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Cai Z, Wu Y, Zhang F, Wu H. A three-gene signature and clinical outcome in pediatric acute myeloid leukemia. Clin Transl Oncol 2020; 23:866-873. [PMID: 32862280 DOI: 10.1007/s12094-020-02480-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 06/28/2020] [Accepted: 08/12/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND Although the 5-year survival rates in pediatric acute myeloid leukemia (AML) have improved over the last decades, there is a high relapse rate for Pediatric AML patients. METHODS In the present study, we mainly combine PCA with the LASSO technique to identify prognostic markers for Pediatric AML patients coming from the NCI TARGET database. RESULTS Three key genes (EEF1A1, RPLP2, RPL19) associated with poor prognosis of pediatric AML has been screened by both PCA and LASSO Cox regression analysis. Simultaneously, we developed a risk score model to predict the prognosis of pediatric AML, according to risk scores, the patients were divided into high- and low-risk groups based on the median risk score. Kaplan-Meier survival analysis indicated that Pediatric AML patients with the high-risk group have a poorer survival rate than those with a low-risk group (p < 0.000). The receiver operating characteristic (ROC) analysis showed that the risk model has a good performance (AUC:0.669). Moreover, the clinicopathologic correlation showed that the expression levels of three genes were related to the central nervous system (CNS) disease and chloroma. GSEA identified that those pathways including oxidative phosphorylation, apoptosis and TGFB signaling pathway were differentially enriched. CONCLUSION Taken together, those studies suggested that a gene panel that consists of three genes (EEF1A1, RPLP2, RPL19) may act as a potential prognostic marker.
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Affiliation(s)
- Z Cai
- Department of Pediatrics, The First Affiliated Hospital of University of South China, Hengyang, 421001, Hunan, China
| | - Y Wu
- Department of Pathology, The First People's Hospital of Xiangtan City, No.100 Shuyuan Road, Yuetang District, Xiangtan, 421001, Hunan, China
| | - F Zhang
- Department of Pathology, The Rushan People's Hospital of Weihai City, Shandong, 264500, China
| | - H Wu
- Department of Pathology, The First People's Hospital of Xiangtan City, No.100 Shuyuan Road, Yuetang District, Xiangtan, 421001, Hunan, China.
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Zhang EF, Yang L, Cai Z. [Prognosis of multiple myeloma: current situation, challenges and contemplation]. Zhonghua Nei Ke Za Zhi 2020; 59:493-495. [PMID: 32594681 DOI: 10.3760/cma.j.cn112138-20200318-00256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- E F Zhang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - L Yang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Z Cai
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
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Deng S, Li D, Liu X, Cai Z, Wei W, Chen J, Zhang L. Serum metabolomic investigations of mulberry leaf powder supplementation in Chinese Erhualian pigs. J Anim Feed Sci 2020. [DOI: 10.22358/jafs/124043/2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Nowell WB, Kannowski CL, Gavigan K, Cai Z, Cardoso A, Hunter T, Venkatachalam S, Birt J, Workman J, Curtis J. PARE0026 WHICH PATIENT-REPORTED OUTCOMES DO RHEUMATOLOGY PATIENTS FIND IMPORTANT TO TRACK DIGITALLY? A REAL-WORLD LONGITUDINAL STUDY IN ARTHRITISPOWER. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.1016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Background:Development of a standardized approach to assess key elements of disease activity in rheumatology clinical trials has been the goal of Outcome Measures in Rheumatology Clinical Trials (OMERACT), American College of Rheumatology (ACR), and European League Against Rheumatism (EULAR).1,2,3The core sets of measures developed include assessments and composite indices incorporating use of patient-reported outcomes (PROs) and clinical measures and clinicians’ assessments to quantify disease activity over time.2PROs are important indicators of disease activity and variability, and they are increasingly used to evaluate treatment effectiveness. Little is known about PROs that patients with rheumatic conditions find most important to convey their experience with their condition and its treatment.Objectives:To examine PROs selected by patients with rheumatic conditions in the ArthritisPower registry to identify symptoms they found most important to track digitally.Methods:Adult US patients within the ArthritisPower registry with rheumatoid arthritis (RA), psoriatic arthritis (PsA), ankylosing spondylitis (AS), systemic lupus erythematosus (SLE), osteoporosis (OP), osteoarthritis (OA), and fibromyalgia syndrome (FMS) were invited via email to participate in this study. Enrolled participants (pts) were prompted to select ≤10 PRO symptom measures they felt were important to track for their condition at baseline via the ArthritisPower app. At 3 subsequent time points (Month [m] 1, m2, m3), pts were given the option to continue tracking their previously selected PRO measures or to add, remove and/or select different measures. At m3, pts completed an exit survey to prioritize ≤5 measures from all measures selected during study participation and to specify other symptoms not available that they would have wanted to track. Measures were rank-ordered based on number of pts rating the item as their 1st, 2nd, 3rd, 4th or 5th choice and weighted by multiplying the rank number by its inverse for a single, weighted summary score for each measure. Values were summed across all pts to produce a summary score for each measure.Results:Among pts who completed initial selection of PRO assessments at baseline (N=253), 184 pts confirmed or changed PRO selections across m1-3. Mean (SD) age of pts was 55.7 (9.2) yrs, 89.3% female, 91.3% White, mean disease duration of 11.6 (10.6) yrs. The majority (64.8%) self-reported OA, followed by RA (48.6%), FMS (40.3%), PsA (26.1%), OP (21.0%), AS (15.8%) and SLE (5.9%), not mutually exclusive, and were similar to the overall ArthritisPower population. The average number of instruments (SD) selected for baseline completion was 7.0 (2.5), 7.1 (2.4) at m1, 7.2 (2.4) at m2, and 7.0 (2.5) at m3. The top 5 PROs ranked by pts overall as most important (weighted summary score) for tracking were Fatigue (71), Physical Function (58), Pain Intensity (50), Pain Interference (49), Duration of Morning Joint Stiffness (41) (Figure 1). Fatigue, Physical Function, and Pain were consistently in the top 5 across diseases while Depression was more frequent among pts with OA, AS and FMS. Pts’ PRO selections showed stability over time except for the RA Flare measure which decreased from 70.5% of RA pts at baseline to 13.6% at m3.Conclusion:The symptoms prioritized by pts included fatigue, physical function, pain, and joint stiffness. Pts‘ choices were consistent over time. These findings provide insights into symptoms rheumatology patients find most important and will be useful to inform design of future patient-centric clinical trials and real-world evidence generation.References:[1]Boers M, et al. J Rheumatol Suppl. 1994;41:86–89.[2]Felson DT, et al. Arthritis Rheum. 1993;36:729–740.[3]Tugwell P, et al. J Rheumatol. 1993;20:555–556.Disclosure of Interests:W. Benjamin Nowell: None declared, Carol L. Kannowski Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Kelly Gavigan: None declared, Zhihong Cai Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Anabela Cardoso Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Theresa Hunter Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Shilpa Venkatachalam: None declared, Julie Birt Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Jennifer Workman Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Jeffrey Curtis Grant/research support from: AbbVie, Amgen, Bristol-Myers Squibb, Corrona, Janssen, Lilly, Myriad, Pfizer, Regeneron, Roche, UCB, Consultant of: AbbVie, Amgen, Bristol-Myers Squibb, Corrona, Janssen, Lilly, Myriad, Pfizer, Regeneron, Roche, UCB
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Cai Z, Fan Y, Zhang Z, Lu C, Zhu Z, Jiang T, Shan T, Peng Y. VirusCircBase: a database of virus circular RNAs. Brief Bioinform 2020; 22:2182-2190. [PMID: 32349124 DOI: 10.1093/bib/bbaa052] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) are covalently closed long noncoding RNAs critical in diverse cellular activities and multiple human diseases. Several cancer-related viral circRNAs have been identified in double-stranded DNA viruses (dsDNA), yet no systematic study about the viral circRNAs has been reported. Herein, we have performed a systematic survey of 11 924 circRNAs from 23 viral species by computational prediction of viral circRNAs from viral-infection-related RNA sequencing data. Besides the dsDNA viruses, our study has also revealed lots of circRNAs in single-stranded RNA viruses and retro-transcribing viruses, such as the Zika virus, the Influenza A virus, the Zaire ebolavirus, and the Human immunodeficiency virus 1. Most viral circRNAs had reverse complementary sequences or repeated sequences at the flanking sequences of the back-splice sites. Most viral circRNAs only expressed in a specific cell line or tissue in a specific species. Functional enrichment analysis indicated that the viral circRNAs from dsDNA viruses were involved in KEGG pathways associated with cancer. All viral circRNAs presented in the current study were stored and organized in VirusCircBase, which is freely available at http://www.computationalbiology.cn/ViruscircBase/home.html and is the first virus circRNA database. VirusCircBase forms the fundamental atlas for the further exploration and investigation of viral circRNAs in the context of public health.
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Dong S, Nie H, Li D, Cai Z, Sun X, Huo Z, Yan X. Molecular cloning and characterization of Y-box gene (Rpybx) from Manila clam and its expression analysis in different strains under low-temperature stress. Anim Genet 2020; 51:430-438. [PMID: 32091145 DOI: 10.1111/age.12919] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2020] [Indexed: 12/28/2022]
Abstract
Manila clam, Ruditapes philippinarum, is an economically important marine bivalve species. Y-box proteins are members of the cold shock proteins family and highly conserved from bacteria to humans. In this study, a novel Y-box gene (Rpybx) was cloned from the Manila clam and gene expression profiling was performed on three shell color strains (white, zebra and white zebra) and two wild populations (Southern and Northern) of R. philippinarum. The complete ORF length of Rpybx is 1367 bp, encoding 253 amino acids residues. Based on the amino acid sequence analysis and phylogenetic analysis, the Rpybx gene was identified as a member of the invertebrate Y-box proteins family. Rpybx has a similar tertiary structure to human Y-box protein YB-1. The Rpybx mRNA levels were analyzed by qPCR under acute and gradually varied cold stress. Under acute low-temperature stress, the expression of Rpybx mRNA in gills and hepatopancreas was significantly increased in all selected strains and populations (P < 0.05). The Northern population showed the lowest relative expression level of Rpybx. The expressions of Rpybx were greatly upregulated in gills and hepatopancreas of different stains and populations at 5 or -2°C under gradually varied temperature stress (P < 0.05). The results shed light on the biological function of the Rpybx gene in defending against low-temperature challenge and further exploring the molecular mechanism of cold tolerance and resistance in R. philippinarum.
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Affiliation(s)
- S Dong
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding of Liaoning Province, Dalian Ocean University, Dalian, 116023, China
| | - H Nie
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding of Liaoning Province, Dalian Ocean University, Dalian, 116023, China
| | - D Li
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding of Liaoning Province, Dalian Ocean University, Dalian, 116023, China
| | - Z Cai
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding of Liaoning Province, Dalian Ocean University, Dalian, 116023, China
| | - X Sun
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding of Liaoning Province, Dalian Ocean University, Dalian, 116023, China
| | - Z Huo
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding of Liaoning Province, Dalian Ocean University, Dalian, 116023, China
| | - X Yan
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding of Liaoning Province, Dalian Ocean University, Dalian, 116023, China
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Zhang Z, Zhu Z, Chen W, Cai Z, Xu B, Tan Z, Wu A, Ge X, Guo X, Tan Z, Xia Z, Zhu H, Jiang T, Peng Y. Cell membrane proteins with high N-glycosylation, high expression and multiple interaction partners are preferred by mammalian viruses as receptors. Bioinformatics 2019; 35:723-728. [PMID: 30102334 PMCID: PMC7109886 DOI: 10.1093/bioinformatics/bty694] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/12/2018] [Accepted: 08/08/2018] [Indexed: 01/03/2023] Open
Abstract
Motivation Receptor mediated entry is the first step for viral infection. However, the question of how viruses select receptors remains unanswered. Results Here, by manually curating a high-quality database of 268 pairs of mammalian virus–host receptor interaction, which included 128 unique viral species or sub-species and 119 virus receptors, we found the viral receptors are structurally and functionally diverse, yet they had several common features when compared to other cell membrane proteins: more protein domains, higher level of N-glycosylation, higher ratio of self-interaction and more interaction partners, and higher expression in most tissues of the host. This study could deepen our understanding of virus–receptor interaction. Availability and implementation The database of mammalian virus–host receptor interaction is available at http://www.computationalbiology.cn: 5000/viralReceptor. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zheng Zhang
- College of Biology, Hunan University, Changsha, China
| | - Zhaozhong Zhu
- College of Biology, Hunan University, Changsha, China
| | - Wenjun Chen
- College of Biology, Hunan University, Changsha, China
| | - Zena Cai
- College of Biology, Hunan University, Changsha, China
| | - Beibei Xu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Zhiying Tan
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Aiping Wu
- Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Xingyi Ge
- College of Biology, Hunan University, Changsha, China
| | - Xinhong Guo
- College of Biology, Hunan University, Changsha, China
| | - Zhongyang Tan
- College of Biology, Hunan University, Changsha, China
| | - Zanxian Xia
- School of Life Sciences, Central South University, Changsha, China
| | - Haizhen Zhu
- College of Biology, Hunan University, Changsha, China.,State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
| | - Taijiao Jiang
- Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Yousong Peng
- College of Biology, Hunan University, Changsha, China
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Zhang Z, Cai Z, Tan Z, Lu C, Jiang T, Zhang G, Peng Y. Rapid identification of human-infecting viruses. Transbound Emerg Dis 2019; 66:2517-2522. [PMID: 31373773 PMCID: PMC7168554 DOI: 10.1111/tbed.13314] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/01/2019] [Accepted: 07/26/2019] [Indexed: 01/08/2023]
Abstract
Viruses have caused much mortality and morbidity to humans and pose a serious threat to global public health. The virome with the potential of human infection is still far from complete. Novel viruses have been discovered at an unprecedented pace as the rapid development of viral metagenomics. However, there is still a lack of methodology for rapidly identifying novel viruses with the potential of human infection. This study built several machine learning models to discriminate human-infecting viruses from other viruses based on the frequency of k-mers in the viral genomic sequences. The k-nearest neighbor (KNN) model can predict the human-infecting viruses with an accuracy of over 90%. The performance of this KNN model built on the short contigs (≥1 kb) is comparable to those built on the viral genomes. We used a reported human blood virome to further validate this KNN model with an accuracy of over 80% based on very short raw reads (150 bp). Our work demonstrates a conceptual and generic protocol for the discovery of novel human-infecting viruses in viral metagenomics studies.
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Affiliation(s)
- Zheng Zhang
- College of BiologyHunan UniversityChangshaChina
| | - Zena Cai
- College of BiologyHunan UniversityChangshaChina
| | - Zhiying Tan
- College of Computer Science and Electronic EngineeringHunan UniversityChangshaChina
| | - Congyu Lu
- College of BiologyHunan UniversityChangshaChina
| | - Taijiao Jiang
- Suzhou Institute of Systems MedicineSuzhouChina
- Center of System Medicine, Institute of Basic Medical SciencesChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Gaihua Zhang
- College of Life SciencesHunan Normal UniversityChangshaChina
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Liu X, Li Z, Cai Z, Chen G, Liu J. Neoantigen profile of hepatocellular carcinoma reveals its correlation with tumour progression and clonal evolution. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz438.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Chi Y, Yao Y, Fang Z, Wang S, Huang G, Cai Q, Shang G, Wang G, Qu G, Wu Q, Jiang Y, Song J, Chen J, Zhu X, Cai Z, Bai C, Lu Y, Yu Z, Shen J, Cai J. Efficacy and safety of anlotinib in advanced leiomyosarcoma: Subgroup analysis of a phase IIB trial (ALTER0203). Ann Oncol 2019. [DOI: 10.1093/annonc/mdz283.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Fang Z, Yao Y, Cai J, Chi Y, Wang S, Huang G, Cai Q, Shang G, Wang G, Qu G, Wu Q, Jiang Y, Song J, Chen J, Cai Z, Zhu X, Bai C, Lu Y, Yu Z, Shen J. The effect of treatment line on the efficacy of anlotinib hydrochloride in advanced alveolar soft part sarcoma patients. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz283.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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Huang J, Ma C, Yin J, Bai Y, Zhang G, Wang J, Yu J, Cai Z. Anatomy research of the bifrontal decompressive craniectomy with coronal incision. J Neurol Sci 2019. [DOI: 10.1016/j.jns.2019.10.423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Cai Z, Zhang B, Yin Y, Cao D. Efficacy and safety of apatinib for advanced gastrointestinal stromal tumours after failure of imatinib and sunitinib: An open-label, multicenter, single-arm, phase II trial. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz283.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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47
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Cai Z, Wang C, Chen Y, He W. An Antioxidant Role by Minocycline Via Enhancing the Activation of LKB1/AMPK Signaling in the Process of Cerebral Ischemia Injury. Curr Mol Med 2019; 18:142-151. [PMID: 30198433 DOI: 10.2174/1566524018666180907161504] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 05/12/2018] [Revised: 07/22/2018] [Accepted: 09/04/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND LKB1/AMPK signaling pathway, as a metabolic checkpoint, is involved in the pathogenesis of cerebral ischemia injury. Minocycline, a tetracycline derivative, protects against cerebral ischemia via reducing inflammation, oxidative stress, and apoptosis. The aim of the study was to evaluate the influence of minocycline on oxidative biomarkers and LKB1/AMPK signaling pathway in Wistar rats with focal cerebral ischemia injury and to clarify the neuroprotective mechanism of minocycline against focal cerebral ischemia injury. METHODS The focal cerebral ischemia injury of Wistar rats was established by inserting a thread into the left middle cerebral artery. 2,3,5-Triphenyltetrazolium chloride (TTC) staining was used to label infarct volume. The levels of MDA and LPO were measured with a biochemical assay. All other items were determined by Western blotting. RESULTS Minocycline decreased cerebral infarct volume, but had no effects on neurological scores. Minocycline improved the biological activity of GPx-1/2, GSS and GR, while limited the GGT1 activity in the hippocampus of cerebral ischemia-reperfusion rats. Minocycline also elevated the biological activity of SOD and counteracted lipid peroxidation. Minocycline enhanced the activity of both LKB1 and the levels of the three AMPK subunits in the hippocampus of cerebral ischemia-reperfusion rats. CONCLUSION Minocycline effectively inhibits oxidative stress via modulating antioxidative enzymes and activating the LKB1/AMPK signaling pathway in the process of acute cerebral infarct.
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Affiliation(s)
- Z Cai
- Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing 400013, Chongqing, China
| | - C Wang
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan 442000, Hubei Province, China
| | - Y Chen
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan 442000, Hubei Province, China
| | - W He
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan 442000, Hubei Province, China
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48
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Zhu Z, Xiao CT, Fan Y, Cai Z, Lu C, Zhang G, Jiang T, Tan Y, Peng Y. Homologous recombination shapes the genetic diversity of African swine fever viruses. Vet Microbiol 2019; 236:108380. [PMID: 31500735 PMCID: PMC7172151 DOI: 10.1016/j.vetmic.2019.08.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 04/05/2019] [Revised: 07/23/2019] [Accepted: 08/05/2019] [Indexed: 11/24/2022]
Abstract
The African swine fever virus (ASFV) has severely influenced the swine industry of the world. Currently, there is no effective vaccine or drugs against the ASFV. How to effectively control the virus is challenging. In this study, we have analyzed all the publicly available ASFV genomes and demonstrated that there was a large genetic diversity of ASFV genomes. Interestingly, the genetic diversity was mainly caused by extensive genomic insertions and/or deletions (indels) instead of the point mutations. Further analyses showed that the indels may be attributed much to the homologous recombination, as supported by significant associations between the occurrence of extensive recombination events and the indels in the ASFV genomes. Besides, the homologous recombination also led to changes of gene content of ASFVs. Finally, repeated elements of dozens of nucleotides in length were observed to widely distribute and cluster in the adjacent positions of ASFV genomes, which may facilitate the occurrence of homologous recombination. This work highlighted the importance of homologous recombination in shaping the genetic diversity of the ASFVs, and could help understand the evolution of the virus.
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Affiliation(s)
- Zhaozhong Zhu
- College of Biology, Hunan University, Changsha, China
| | | | - Yunshi Fan
- College of Biology, Hunan University, Changsha, China
| | - Zena Cai
- College of Biology, Hunan University, Changsha, China
| | - Congyu Lu
- College of Biology, Hunan University, Changsha, China
| | - Gaihua Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Taijiao Jiang
- Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Suzhou Institute of Systems Medicine, Suzhou, China
| | - Yongjun Tan
- College of Biology, Hunan University, Changsha, China
| | - Yousong Peng
- College of Biology, Hunan University, Changsha, China.
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49
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Gao H, Chi X, Qin W, Wang L, Song P, Cai Z, Zhang J, Zhang T. Comparison of the gut microbiota composition between the wild and captive Tibetan wild ass (Equus kiang). J Appl Microbiol 2019; 126:1869-1878. [PMID: 30825354 PMCID: PMC6849810 DOI: 10.1111/jam.14240] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 12/26/2018] [Revised: 02/11/2019] [Accepted: 02/18/2019] [Indexed: 12/20/2022]
Abstract
Aims The gut microbiota has a great effect on the health and nutrition of the host. Manipulation of the intestinal microbiota may improve animal health and growth performance. The objectives of our study were to characterize the faecal microbiota between wild and captive Tibetan wild asses and discuss the differences and their reasons. Methods and Results Through high‐throughput sequencing of the 16S rRNA V4‐V5 region, we studied the gut microbiota composition and structure of Tibetan wild asses in winter, and analysed the differences between wild and captive groups. The results showed that the most common bacterial phylum in Tibetan wild ass faeces samples was Bacteroidetes, while the phylum Firmicutes was dominant in captive Tibetan wild ass faecal samples. The relative abundance of Firmicutes, Tenericutes and Spirochaetes were significantly higher (P < 0·01) than in the wild groups. Conclusions Captivity reduces intestinal microbial diversity, evenness and operational taxonomic unit number due to the consumption of industrial food, therefore, increasing the risk of disease prevalence and affecting the health of wildlife. Significance and Impact of the Study We studied the effect of the captive environment on intestinal micro‐organisms. This article provides a theoretical basis for the ex‐situ conservation of wild animals in the future.
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Affiliation(s)
- H Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province, China.,University of Chinese Academy of Sciences, Beijing, China
| | - X Chi
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province, China.,University of Chinese Academy of Sciences, Beijing, China
| | - W Qin
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province, China.,University of Chinese Academy of Sciences, Beijing, China
| | - L Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, Province, China
| | - P Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Z Cai
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province, China.,University of Chinese Academy of Sciences, Beijing, China
| | - J Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province, China.,University of Chinese Academy of Sciences, Beijing, China
| | - T Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai Province, China
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50
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Feng K, Cai Z, Ding T, Yan H, Liu X, Zhang Z. Effects of potassium‐solubulizing and photosynthetic bacteria on tolerance to salt stress in maize. J Appl Microbiol 2019; 126:1530-1540. [DOI: 10.1111/jam.14220] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/02/2019] [Accepted: 02/07/2019] [Indexed: 11/29/2022]
Affiliation(s)
- K. Feng
- Department of Biological Technology Institute of Chemistry and Biological Engineering University of Science and Technology Beijing BeijingPeople's Republic of China
| | - Z. Cai
- Department of Biological Technology Institute of Chemistry and Biological Engineering University of Science and Technology Beijing BeijingPeople's Republic of China
| | - T. Ding
- Department of Biological Technology Institute of Chemistry and Biological Engineering University of Science and Technology Beijing BeijingPeople's Republic of China
| | - H. Yan
- Department of Biological Technology Institute of Chemistry and Biological Engineering University of Science and Technology Beijing BeijingPeople's Republic of China
| | - X. Liu
- Department of Biological Technology Institute of Chemistry and Biological Engineering University of Science and Technology Beijing BeijingPeople's Republic of China
| | - Z. Zhang
- Beijing Agro‐Biotechnology Research Center Beijing Academy of Agriculture and Forestry Sciences Beijing People's Republic of China
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