1
|
Wang J, Han Y, Sam FE, Wang Q, Zhang B, Ma T, Li J, Feng L, Jiang Y. Application of benzothiadiazole to Cabernet Gernischt grapes (Vitis vinifera L.) for quality improvement: Effects on aroma metabolism precursors and related genes expression. Plant Physiol Biochem 2024; 208:108537. [PMID: 38513517 DOI: 10.1016/j.plaphy.2024.108537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024]
Abstract
Pre-harvest spraying of benzothiadiazole (BTH) can improve the winemaking properties of grapes, especially their aroma compounds and phenolics. Limited research has explored the molecular mechanisms by which BTH influences the accumulation of grape aroma precursors during early grape development. This study investigated the effects and putative molecular mechanisms of applying 0.37 mM BTH through whole-plant spraying on the accumulation of aroma metabolism precursors and gene expression in Cabernet Gernischt grapes during ripening. The results showed that BTH treatment increased the levels of fructose, alanine, aspartate, threonine, myristic acid, myristoleic acid, palmitic acid, β-cryptoxanthin, norisoprenoids and methoxypyrazines. Contrarily, it decreased the levels of glucose, sucrose, phenylalanine, tyrosine, leucine, valine, glycine, arginine, histidine, total unsaturated fatty acids (particularly linoleic acid), zeaxanthin, lutein, and organic acids. Additionally, BTH upregulated the expression of genes associated with the production and degradation of amino acids, fatty acids, and carotenoids while decreasing the expression of genes involved in the synthesis and degradation of soluble sugars and organic acids. Ten different metabolites, including fumaric acid, were identified as potential biological markers for distinguishing BTH-treated grapes from control grapes. The study demonstrates that BTH treatment had a substantial impact on the concentration and developmental patterns of aroma metabolism precursors. Furthermore, it altered the winemaking characteristics of Cabernet Gernischt grapes by modulating genes associated with the production and breakdown of metabolites.
Collapse
Affiliation(s)
- Jianfeng Wang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuqi Han
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, China
| | - Faisal Eudes Sam
- College of Enology, Northwest A&F University, Xianyang, 712100, China
| | - Qihui Wang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, China
| | - Bo Zhang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, China
| | - Tengzhen Ma
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jixin Li
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lidan Feng
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yumei Jiang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, China.
| |
Collapse
|
2
|
Wu Y, Gong Y, Liu Y, Chen F, Chen S, Zhang F, Wang C, Li S, Hu M, Huang R, Guo X, Wang X, Ning Y, Yang L. Comparative Analysis of Differentially Expressed Genes in Chondrocytes from Rats Exposed to Low Selenium and T-2 Toxin. Biol Trace Elem Res 2024; 202:1020-1030. [PMID: 37326932 DOI: 10.1007/s12011-023-03725-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/03/2023] [Indexed: 06/17/2023]
Abstract
The aim of this study was to construct rat models of environmental risk factors for Kashin-Beck disease (KBD) with low selenium and T-2 toxin levels and to screen the differentially expressed genes (DEGs) between the rat models exposed to environmental risk factors. The Se-deficient (SD) group and T-2 toxin exposure (T-2) group were constructed. Knee joint samples were stained with hematoxylin-eosin, and cartilage tissue damage was observed. Illumina high-throughput sequencing technology was used to detect the gene expression profiles of the rat models in each group. Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway enrichment analysis were performed and five differential gene expression results were verified by quantitative real-time polymerase chain reaction (qRT‒PCR). A total of 124 DEGs were identified from the SD group, including 56 upregulated genes and 68 downregulated genes. A total of 135 DEGs were identified in the T-2 group, including 68 upregulated genes and 67 downregulated genes. The DEGs were significantly enriched in 4 KEGG pathways in the SD group and 9 KEGG pathways in the T-2 group. The expression levels of Dbp, Pc, Selenow, Rpl30, and Mt2A were consistent with the results of transcriptome sequencing by qRT‒PCR. The results of this study confirmed that there were some differences in DEGs between the SD group and the T-2 group and provided new evidence for further exploration of the etiology and pathogenesis of KBD.
Collapse
Affiliation(s)
- Yifan Wu
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Yi Gong
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Yanli Liu
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Feihong Chen
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Sijie Chen
- School of Public Health, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Feiyu Zhang
- School of Public Health, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Chaowei Wang
- School of Public Health, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Shujin Li
- School of Public Health, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Minhan Hu
- School of Public Health, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Ruitian Huang
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Xiong Guo
- School of Public Health, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi, 710061, People's Republic of China
- Clinical Research Center for Endemic Disease of Shaanxi Province, The Second Affiliated Hospital of Xi'an Jiaotong University, No.157 Xi Wu Road, Xi'an, 710004, Shaanxi, People's Republic of China
| | - Xi Wang
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, People's Republic of China.
- School of Public Health, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi, 710061, People's Republic of China.
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an Jiaotong University, Xi'an, China.
| | - Yujie Ning
- School of Public Health, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi, 710061, People's Republic of China.
| | - Lei Yang
- School of Nursing, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| |
Collapse
|
3
|
Beler M, Cansız D, Ünal İ, Emekli-Alturfan E. Quantitative Real-Time PCR Method to Evaluate Gene Expression in Zebrafish Embryos. Methods Mol Biol 2024; 2753:553-561. [PMID: 38285367 DOI: 10.1007/978-1-0716-3625-1_36] [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] [Indexed: 01/30/2024]
Abstract
The fast zebrafish embryonic development offers an opportunity for the study of genes crucial for developmental processes. Several genes associated with human diseases have orthologs in zebrafish. Enhanced comprehension of a gene's function can be achieved by knowing when and where it is expressed. This knowledge also makes it possible to alter a gene-by-gene knockdown in a time- and place-specific manner. Moreover, gene expression analyses contribute greatly to teratogenicity studies in zebrafish embryos. Therefore, the importance of examining the differences between the expressions of these genes has increased day by day. The incorporation of reverse transcription (RT) as the initial step prior to thermal cycling in quantitative real-time polymerase chain reaction (RT-qPCR) has made a significant contribution to RNA research. RT-qPCR is the gold standard and an effective method for gene expression analysis. Quick readout, high sensitivity, reproducibility, as well as high potential throughput, along with reliable quantification, are just a few advantages of RT-qPCR. However, there are drawbacks to its application, such as RNA's inherent variability, impurities during RNA extraction, and variations in reverse transcription and PCR efficiencies. Implementing a precise normalization technique is crucial to account for these inaccuracies. In this chapter, the protocol for gene expression analysis by RT-qPCR for zebrafish embryos is explained.
Collapse
Affiliation(s)
- Merih Beler
- Department of Biochemistry, Institute of Health Sciences, Marmara University, Istanbul, Turkey
| | - Derya Cansız
- Department of Biochemistry, Faculty of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - İsmail Ünal
- Department of Biochemistry, Institute of Health Sciences, Marmara University, Istanbul, Turkey
| | - Ebru Emekli-Alturfan
- Department of Basic Medical Sciences, Faculty of Dentistry, Marmara University, Istanbul, Turkey.
| |
Collapse
|
4
|
Qu D, Hu D, Zhang J, Yang G, Guo J, Zhang D, Qi C, Fu H. Identification and Validation of Ferroptosis-Related Genes in Patients with Acute Spinal Cord Injury. Mol Neurobiol 2023; 60:5411-5425. [PMID: 37316756 DOI: 10.1007/s12035-023-03423-7] [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: 03/16/2023] [Accepted: 06/03/2023] [Indexed: 06/16/2023]
Abstract
Ferroptosis plays crucial roles in the pathology of spinal cord injury (SCI). The purpose of this study was to identify differentially expressed ferroptosis-related genes (DE-FRGs) in human acute SCI by bioinformatics analysis and validate the hub DE-FRGs in non-SCI and SCI patients. The GSE151371 dataset was downloaded from the Gene Expression Omnibus and difference analysis was performed. The differentially expressed genes (DEGs) in GSE151371 overlapped with the ferroptosis-related genes (FRGs) obtained from the Ferroptosis Database. A total of 41 DE-FRGs were detected in 38 SCI samples and 10 healthy samples in GSE151371. Then, enrichment analyses of these DE-FRGs were performed for functional annotation. The GO enrichment results showed that upregulated DE-FRGs were mainly associated with reactive oxygen species and redox reactions, and the KEGG enrichment analysis indicated involvement in some diseases and ferroptosis pathways. Protein-protein interaction (PPI) analysis and lncRNA-miRNA-mRNA regulatory network were performed to explore the correlations between genes and regulatory mechanisms. The relationship between DE-FRGs and differentially expressed mitochondria-related genes (DE-MRGs) was also analyzed. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the hub DE-FRGs in clinical blood samples from acute SCI patients and healthy controls. Consistent with the bioinformatics results, qRT-PCR of the clinical samples indicated similar expression levels of TLR4, STAT3, and HMOX1. This study identified DE-FRGs in blood samples from SCI patients, and the results could improve our understanding of the molecular mechanisms of ferroptosis in SCI. These candidate genes and pathways could be therapeutic targets for SCI.
Collapse
Affiliation(s)
- Di Qu
- Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, 16 Jiangsu Road, Qingdao, 266003, China
- Medical Department of Qingdao University, 308 Ningxia Road, Qingdao, 266071, China
| | - Die Hu
- Qingdao Eye Hospital of Shandong First Medical University, 5 Yan'er Island Road, Qingdao, 266071, China
| | - Jing Zhang
- Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, 16 Jiangsu Road, Qingdao, 266003, China
- Medical Department of Qingdao University, 308 Ningxia Road, Qingdao, 266071, China
| | - Guodong Yang
- Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, 16 Jiangsu Road, Qingdao, 266003, China
- Medical Department of Qingdao University, 308 Ningxia Road, Qingdao, 266071, China
| | - Jia Guo
- Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, 16 Jiangsu Road, Qingdao, 266003, China
- Medical Department of Qingdao University, 308 Ningxia Road, Qingdao, 266071, China
| | - Dongfang Zhang
- Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, 16 Jiangsu Road, Qingdao, 266003, China
| | - Chao Qi
- Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, 16 Jiangsu Road, Qingdao, 266003, China.
| | - Haitao Fu
- Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, 16 Jiangsu Road, Qingdao, 266003, China.
| |
Collapse
|
5
|
Chen L, Qin Y, Lin Y, Du M, Li Y, Fan M. Salivary levels of five microorganisms of root caries in nursing home elderly: a preliminary investigation. BMC Oral Health 2023; 23:355. [PMID: 37270529 DOI: 10.1186/s12903-023-02953-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 04/07/2023] [Indexed: 06/05/2023] Open
Abstract
BACKGROUND Streptococcus, Bifidobacteria, Lactobacillus and Actinomyces are acidogenic aciduria that may be associated with root caries (RC). The aim of the study was to analyze Streptococcus mutans (S. mutans), Streptococcus sobrinus (S. sobrinus), Bifidobacterium spp., Lactobacillus spp. and Actinomyces naeslundii (A. naeslundii) in the saliva of nursing home elderly, to assess the correlation between bacterial composition and RC for five putative catiogenic organisms. METHODS In this study, we collected 43 saliva samples and divided into two groups: the root caries group (RCG, n = 21) and the caries-free group (CFG, n = 22). Bacterial DNA was extracted from the saliva samples. The presence and abundance of the five microorganisms were detected by Quantitative real-time PCR (qPCR). Spearman correlation test was performed to evaluate the relationship between the numbers of root decayed filled surfaces (RDFS) and root caries index (RCI) and salivary levels of the bacteria. RESULTS The salivary levels of S. mutans, S. sobrinus, Bifidobacterium spp. and Lactobacillus spp. were significantly higher in RCG than in CFG (p < 0.05). RDFS and RCI (RDFS/RCI) were positively associated with salivary levels of S. mutans, S. sobrinus and Bifidobacterium spp. (r = 0.658/0.635, r = 0.465/0.420 and r = 0.407/0.406, respectively). No significant differences in presence and amounts of A. naeslundii was observed between the two groups (p > 0.05). CONCLUSION S. mutans, S. sobrinus and Bifidobacterium spp. in saliva appear to be associated with RC in the elderly. Taken together, the findings indicate that specific salivary bacteria may be involved in the progression of RC.
Collapse
Affiliation(s)
- Lin Chen
- Stomatological Hospital, School of Stomatology, Southern Medical University, No. 366, South of Jiangnan Avenue, Guangzhou, China
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Microbiology Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yuandong Qin
- Stomatological Hospital, School of Stomatology, Southern Medical University, No. 366, South of Jiangnan Avenue, Guangzhou, China
| | - Yuhong Lin
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Microbiology Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Endodontics, Yantai Stomatological Hospital Affiliated to Binzhou Medical College, Yantai, China
| | - Minquan Du
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Microbiology Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yuhong Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Microbiology Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Mingwen Fan
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Microbiology Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
- First dental hospital , Jean Han University, Wuhan, China.
| |
Collapse
|
6
|
Li B, Ding T, Chen H, Li C, Chen B, Xu X, Huang P, Hu F, Guo L. CircStrn3 targeting microRNA-9-5p is involved in the regulation of cartilage degeneration and subchondral bone remodelling in osteoarthritis. Bone Joint Res 2023; 12:33-45. [PMID: 36642417 PMCID: PMC9872037 DOI: 10.1302/2046-3758.121.bjr-2022-0231.r1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
AIMS Circular RNA (circRNA) is involved in the regulation of articular cartilage degeneration induced by inflammatory factors or oxidative stress. In a previous study, we found that the expression of circStrn3 was significantly reduced in chondrocytes of osteoarthritis (OA) patients and OA mice. Therefore, the aim of this paper was to explore the role and mechanism of circStrn3 in osteoarthritis. METHODS Minus RNA sequencing, fluorescence in situ hybridization, and quantitative real-time polymerase chain reaction (qRT-PCR) were used to detect the expression of circStrn3 in human and mouse OA cartilage tissues and chondrocytes. Chondrocytes were then stimulated to secrete exosomal miR-9-5p by cyclic tensile strain. Intra-articular injection of exosomal miR-9-5p into the model induced by destabilized medial meniscus (DMM) surgery was conducted to alleviate OA progression. RESULTS Tensile strain could decrease the expression of circStrn3 in chondrocytes. CircStrn3 expression was significantly decreased in human and mouse OA cartilage tissues and chondrocytes. CircStrn3 could inhibit matrix metabolism of chondrocytes through competitively 'sponging' miRNA-9-5p targeting Kruppel-like factor 5 (KLF5), indicating that the decrease in circStrn3 might be a protective factor in mechanical instability-induced OA. The tensile strain stimulated chondrocytes to secrete exosomal miR-9-5p. Exosomes with high miR-9-5p expression from chondrocytes could inhibit osteoblast differentiation by targeting KLF5. Intra-articular injection of exosomal miR-9-5p alleviated the progression of OA induced by destabilized medial meniscus surgery in mice. CONCLUSION Taken together, these results demonstrate that reduction of circStrn3 causes an increase in miR-9-5p, which acts as a protective factor in mechanical instability-induced OA, and provides a novel mechanism of communication among joint components and a potential application for the treatment of OA.Cite this article: Bone Joint Res 2023;12(1):33-45.
Collapse
Affiliation(s)
- Bin Li
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tao Ding
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haoyi Chen
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Changwei Li
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Chen
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xing Xu
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Huang
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fangqiong Hu
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Guo
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, Lei Guo. E-mail:
| |
Collapse
|
7
|
Yuan W, Yang M, Zhu Y. Development and validation of a gene signature predicting the risk of postmenopausal osteoporosis. Bone Joint Res 2022; 11:548-560. [PMID: 35920104 PMCID: PMC9396926 DOI: 10.1302/2046-3758.118.bjr-2021-0565.r1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
AIMS We aimed to develop a gene signature that predicts the occurrence of postmenopausal osteoporosis (PMOP) by studying its genetic mechanism. METHODS Five datasets were obtained from the Gene Expression Omnibus database. Unsupervised consensus cluster analysis was used to determine new PMOP subtypes. To determine the central genes and the core modules related to PMOP, the weighted gene co-expression network analysis (WCGNA) was applied. Gene Ontology enrichment analysis was used to explore the biological processes underlying key genes. Logistic regression univariate analysis was used to screen for statistically significant variables. Two algorithms were used to select important PMOP-related genes. A logistic regression model was used to construct the PMOP-related gene profile. The receiver operating characteristic area under the curve, Harrell's concordance index, a calibration chart, and decision curve analysis were used to characterize PMOP-related genes. Then, quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the expression of the PMOP-related genes in the gene signature. RESULTS We identified three PMOP-related subtypes and four core modules. The muscle system process, muscle contraction, and actin filament-based movement were more active in the hub genes. We obtained five feature genes related to PMOP. Our analysis verified that the gene signature had good predictive power and applicability. The outcomes of the GSE56815 cohort were found to be consistent with the results of the earlier studies. qRT-PCR results showed that RAB2A and FYCO1 were amplified in clinical samples. CONCLUSION The PMOP-related gene signature we developed and verified can accurately predict the risk of PMOP in patients. These results can elucidate the molecular mechanism of RAB2A and FYCO1 underlying PMOP, and yield new and improved treatment strategies, ultimately helping PMOP monitoring.Cite this article: Bone Joint Res 2022;11(8):548-560.
Collapse
Affiliation(s)
- Wei Yuan
- Department of Orthopedics, The First Hospital of China Medical University, Shenyang, China
| | - Maowei Yang
- Department of Orthopedics, The First Hospital of China Medical University, Shenyang, China
| | - Yue Zhu
- Department of Orthopedics, The First Hospital of China Medical University, Shenyang, China
| |
Collapse
|
8
|
Abstract
Aims Circular RNA (circRNA) S-phase cyclin A-associated protein in the endoplasmic reticulum (ER) (circSCAPER, ID: hsa_circ_0104595) has been found to be highly expressed in osteoarthritis (OA) patients and has been associated with the severity of OA. Hence, the role and mechanisms underlying circSCAPER in OA were investigated in this study. Methods In vitro cultured human normal chondrocyte C28/I2 was exposed to interleukin (IL)-1β to mimic the microenvironment of OA. The expression of circSCAPER, microRNA (miR)-140-3p, and enhancer of zeste homolog 2 (EZH2) was detected using quantitative real-time polymerase chain reaction and Western blot assays. The extracellular matrix (ECM) degradation, proliferation, and apoptosis of chondrocytes were determined using Western blot, cell counting kit-8, and flow cytometry assays. Targeted relationships were predicted by bioinformatic analysis and verified using dual-luciferase reporter and RNA immunoprecipitation (RIP) assays. The levels of phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) pathway-related protein were detected using Western blot assays. Results CircSCAPER was highly expressed in OA cartilage tissues and IL-1β-induced chondrocytes. Knockdown of circSCAPER reduced IL-1β-evoked ECM degradation, proliferation arrest, and apoptosis enhancement in chondrocytes. Mechanistically, circSCAPER directly bound to miR-140-3p, and miR-140-3p inhibition reversed the effects of circSCAPER knockdown on IL-1β-induced chondrocytes. miR-140-3p was verified to target EZH2, and overexpression of miR-140-3p protected chondrocytes against IL-1β-induced dysfunction via targeting EZH2. Additionally, we confirmed that circSCAPER could regulate EZH2 through sponging miR-140-3p, and the circSCAPER/miR-140-3p/EZH2 axis could activate the PI3K/AKT pathway. Conclusion CircSCAPER promoted IL-1β-evoked ECM degradation, proliferation arrest, and apoptosis enhancement in chondrocytes via regulating miR-140-3p/EZH2 axis, which gained a new insight into the pathogenesis of OA. Cite this article: Bone Joint Res 2022;11(2):61–72.
Collapse
Affiliation(s)
- Zhaxi Luobu
- Department of Orthopedics, Lhasa People's Hospital, Lhasa City, Tibet, China
| | - Lei Wang
- Department of Orthopedics, Tiantan Hospital Affiliated to Capital Medical University, Beijing, China
| | - Dahai Jiang
- Department of Orthopedics, Lhasa People's Hospital, Lhasa City, Tibet, China
| | - Tao Liao
- Department of Orthopedics, Lhasa People's Hospital, Lhasa City, Tibet, China
| | - Ciren Luobu
- Department of Orthopedics, Lhasa People's Hospital, Lhasa City, Tibet, China
| | - Luosong Qunpei
- Department of Orthopedics, Lhasa People's Hospital, Lhasa City, Tibet, China
| |
Collapse
|
9
|
Abstract
Real-time quantitative polymerase chain reaction (qPCR) is a powerful tool for analyzing and quantifying gene expression, and its primer design is the first and most important step. In order to improve the efficiency and effectiveness of primer design, we designed a database qPrimerDB, based on thermodynamics gene-specific for multispecies qPCR primers design.In this chapter, we explained the working principle of the database and detailed the step-by-step practical steps with examples. The valuable and time-saving qPrimerDB database is publicly accessible at http://biodb.swu.edu.cn/qprimerdb and will be routinely updated.
Collapse
|
10
|
Maralani M, Shanehbandi D, Asadi M, Hashemzadeh S, Hajiasgharzadeh K, Mashhadi Abdolahi H, Baradaran B, Peeters M. Expression profiles of miR-196, miR-132, miR-146a, and miR-134 in human colorectal cancer tissues in accordance with their clinical significance : Comparison regarding KRAS mutation. Wien Klin Wochenschr 2021. [PMID: 34463887 DOI: 10.1007/s00508-021-01933-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/25/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is among the most widespread malignancies in the world. MicroRNA (miRNA) has been identified as an important modulator of the biological processes of the cells. This group of noncoding RNAs also has a pivotal function in the growth and development of human cancers, including CRC. Among these miRNAs, miR-196, miR-132, miR-146a, and miR-134 have fundamental impacts on the regulation of cancers. The current study aimed to investigate the involvement of these miRNAs in CRC patients. METHODS In this study, 50 pairs of tumor and tumor margin samples of CRC patients were investigated to assess the expression levels of miR-196, miR-132, miR-146a, and miR-134 in this cancer. For this purpose, firstly, quantitative real-time PCR (qRT-PCR) was applied. Also, KRAS mutation and clinicopathological characteristics of the CRC patients were analyzed in the study groups. RESULTS The findings demonstrated the overexpression of miR-196 (P-value = 0.0045) and miR-146a (P-value = 0.0033) in tumor tissues compared to controls. Conversely, the expression levels of miR-132 (P-value = 0.00032) and miR-134 (P-value < 0.0001) were downregulated in tumor tissues. Also, miR-146a was the only miRNA with significant expression change in the case of the KRAS gene mutation. Interestingly, the expression ratio of these miRNAs was significantly associated with some of the clinicopathological features of the patients, such as lymph node and distant metastases. CONCLUSION Our data demonstrated that these miRNAs appear to be promising novel biomarkers for early diagnosis of CRC and may pave the way for the future establishment of novel therapeutic options for CRC.
Collapse
|
11
|
Abstract
Aims Circular RNAs (circRNAs) are a novel type of non-coding RNA that plays major roles in the development of diverse diseases including osteonecrosis of the femoral head (ONFH). Here, we explored the impact of hsa_circ_0066523 derived from forkhead box P1 (FOXP1) (also called circFOXP1) on bone mesenchymal stem cells (BMSCs), which is important for ONFH development. Methods RNA or protein expression in BMSCs was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR) or western blot, respectively. Cell Counting Kit 8 (CCK8) and 5-ethynyl-2’-deoxyuridine (EdU) were used to analyze cell proliferation. Alkaline phosphatase (ALP) activity, ALP staining, and Alizarin Red S staining were employed to evaluate the osteoblastic differentiation. Chromatin immunoprecipitation (ChIP), luciferase reporter, RNA pull down, and RNA immunoprecipitation (RIP) assays were combined for exploring molecular associations. Results Circ_0066523 was upregulated in osteogenic induction process of BMSCs. Silencing circ_0066523 restrained the proliferation and osteogenic differentiation of BMSCs. Mechanistically, circ_0066523 activated phosphatidylinositol-4,5-bisphosphate 3-kinase / AKT serine/threonine kinase 1 (PI3K/AKT) pathway via recruiting lysine demethylase 5B (KDM5B) to epigenetically repress the transcription of phosphatase and tensin homolog (PTEN). Functionally, AKT signalling pathway agonist or PTEN knockdown counteracted the effects of silenced circ_0066523 on BMSC proliferation and differentiation. Conclusion Circ_0066523 promotes the proliferation and differentiation of BMSCs by epigenetically repressing PTEN and therefore activating AKT pathway. This finding might open new avenues for the identification of therapeutic targets for osteoblast differentiation related diseases such as ONFH. Cite this article: Bone Joint Res 2021;10(8):526–535.
Collapse
Affiliation(s)
- Wei Xin
- Department of Orthopedics, Changzheng Hospital, Shanghai, China
| | - Shuai Yuan
- Department of Orthopedics, Changzheng Hospital, Shanghai, China
| | - Bo Wang
- Department of Orthopedics, Changzheng Hospital, Shanghai, China
| | - Qirong Qian
- Department of Orthopedics, Changzheng Hospital, Shanghai, China
| | - Yi Chen
- Department of Orthopedics, Changzheng Hospital, Shanghai, China
| |
Collapse
|
12
|
Ge C, Yu P, Fang M, Wang H, Zhang Y. Selection of reliable reference genes for analysis of gene expression in the rat placenta. Mol Cell Biochem 2021; 476:2613-22. [PMID: 33660185 DOI: 10.1007/s11010-021-04115-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/18/2021] [Indexed: 12/21/2022]
Abstract
The selection of suitable reference genes (RGs), especially the identification of the proper combination of RGs is the key to obtain reliable results of gene expression for quantitative real-time polymerase chain reaction (qRT-PCR). To date, there is no relevant study dealing with the stability of RGs in rat placenta. In this study, the geNorm, NormFinder, and BestKeeper software were used to analyze the expression stability of the candidate RGs in placenta under physiological and prenatal caffeine exposure (PCE) conditions. The expression of Tbp, Gapdh and Ywhaz in female and Polr2a, Gapdh and Ywhaz in male placenta were highly stable under physiological conditions, and there was no obvious gender difference. We further found that two RGs were sufficient for reliable normalization in female and male placenta and the combination of Ywhaz and Gapdh was the most suitable compound RGs under physiological conditions. Under PCE conditions, Ywhaz, Gapdh and Polr2a were the most stable genes in both female and male placenta. Among them, Ywhaz and Gapdh were chosen as the best paring. Finally, selected RGs were employed for normalization of the expression of a clear target gene and the results of standardization supported our choice. In conclusion, our study confirmed that Ywhaz/Gapdh combination was the most suitable RGs in rat placenta under physiological and PCE pathological conditions and provided a theoretical and experimental basis for physiological and pathological research of the rat placenta.
Collapse
|
13
|
Bakry O, Shoeib M, Soliman S, Kamal L. Neutrophil Cytosolic Factor-1 Genotyping in Acne Vulgaris. Skin Pharmacol Physiol 2021; 34:51-56. [PMID: 33596590 DOI: 10.1159/000513053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 11/13/2020] [Indexed: 11/19/2022]
Abstract
Acne vulgaris (AV) is a very common inflammatory dermatosis. It has a complex pathogenesis in which oxidative stress plays an important role. Neutrophil cytosolic factor (NCF)-1 gene encodes for NCF1 protein which shares in reactive oxygen species (ROS) production. Copy number variation (CNV) is a type of genetic variance in which gene copies are duplicated or deleted. The current work aimed to detect the association between NCF1 CNV and NCF-1 genotypes and AV to explore their possible role in increased disease risk or influencing its clinical presentation. Twenty-five cases with AV and 25 age- and gender-matched healthy volunteers were selected. NCF1 CNV and genotypes were determined using quantitative real-time polymerase chain reaction. NCF1 copy number was significantly increased in patients compared to the control group (p = 0.02). Higher copy number increased the risk of occurrence of AV by about 4-fold. The NCF1 genotype was more prevalent in patients (72%) compared to NCF1B (24%) and NCF1C (4%) variants, while NCF1B and NCF1C variants (68%) were more prevalent in the control group. The NCF1B genotype decreased the risk of occurrence of AV by 0.2-fold. NCF1 was significantly associated with cases more than controls (p = 0.005). It increased the risk of occurrence of acne by 5.4-fold. There was significant association between NCF1 copy number and disease duration where higher number was associated with long disease duration (p = 0.03). Higher copy number was also associated with the NCF1 genotype (p = 0.01). This study suggests that increased copy number of NCF1 gene may be a predisposing factor for AV development. However, the presence of NCF1B and NCF1C variants lowers ROS production and subsequently decreases the risk of development of AV.
Collapse
Affiliation(s)
- Ola Bakry
- Department of Dermatology, Andrology and STDs, Faculty of Medicine, Menoufiya University, Shibeen El Koom, Egypt,
| | - Mohamed Shoeib
- Department of Dermatology, Andrology and STDs, Faculty of Medicine, Menoufiya University, Shibeen El Koom, Egypt
| | - Shimaa Soliman
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Menoufiya University, Shibeen El Koom, Egypt.,Medical Biochemistry Unit, Department of Pathology, College of Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Lamiaa Kamal
- Department of Dermatology, Andrology and STDs, Faculty of Medicine, Menoufiya University, Shibeen El Koom, Egypt
| |
Collapse
|
14
|
Partap M, Kumar P, Ashrita, Kumar P, Kumar D, Warghat AR. Growth Kinetics, Metabolites Production and Expression Profiling of Picrosides Biosynthetic Pathway Genes in Friable Callus Culture of Picrorhiza kurroa Royle ex Benth. Appl Biochem Biotechnol 2020; 192:1298-317. [PMID: 32725372 DOI: 10.1007/s12010-020-03391-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022]
Abstract
The rising demand for picrosides commercially and over-exploitation of Picrorhiza kurroa from natural habitat has to initiate alternative strategies for sustainable production of metabolites. In the present research, wild leaf explant of P. kurroa was used to produce friable callus under different culture condition, i.e., dark and light with two temperature variants (15 °C and 25 °C). Afterward, callus cell lines were screened based on growth biomass and metabolites content accumulation. The results revealed, maximum callus growth index along with antioxidant potential (IC50-40.88 μg/mL) and total phenol content (41.35 μg/mg) were observed under dark 25 °C. However, under light 15 °C, highest accumulation of picroside II (0.58 μg/mg), cinnamic acid (0.15 μg/mg), p-hydroxy acetophenone (0.30 μg/mg), total flavonoids (77.30 μg/mg), nitrogen (7.06%), carbohydrates (18.03%), and protein (44.12%) were detected. Major reported metabolite in callus was picroside I (1.63 μg/mg) under dark 15 °C. For the first time, picroside III content (range 0.15-0.56 μg/mg) was also detected and quantified in leaf-derived calli. Expression profiling of picroside biosynthetic pathway genes showed a positive correlation with the observed metabolites. Furthermore, an optimized protocol of metabolites enriched callus biomass could be used as potential strategy for sustainable production of picrosides at commercial scale.
Collapse
|
15
|
Cai GF, Sun ZR, Zhuang Z, Zhou HC, Gao S, Liu K, Shang LL, Jia KP, Wang XZ, Zhao H, Cai GL, Song WL, Xu SN. Cross electro-nape-acupuncture ameliorates cerebral hemorrhage-induced brain damage by inhibiting necroptosis. World J Clin Cases 2020; 8:1848-1858. [PMID: 32518774 PMCID: PMC7262720 DOI: 10.12998/wjcc.v8.i10.1848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/01/2020] [Accepted: 04/21/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Receptor interacting protein kinase 1 (RIPK1)-mediated cell death, including apoptosis and necroptosis, belongs to programmed cell death. It has been reported that RIPK1-mediated necroptosis exists in lesions of cerebral hemorrhage (CH). Electroacupuncture, a treatment derived from traditional Chinese medicine, could improve neurological impairment in patients with brain injury.
AIM To investigate the protective role of cross electro-nape acupuncture (CENA) in CH, and clarify the potential mechanism.
METHODS CH rat models were established, and CENA was applied to the experimental rats. Neurological functions and encephaledema were then measured. Necrotic cells in the brain of rats with CH were evaluated by propidium iodide staining. Necroptosis was assessed by immunofluorescence. Activation of the necroptosis-related pathway was detected by western blot. Extraction of brain tissue, cerebrospinal fluid and serum samples was conducted to measure the expression and secretion of inflammatory cytokines by quantitative real-time polymerase chain reaction and enzyme-linked immunosorbent assay.
RESULTS The necroptotic marker p-MLKL was detectable in the brains of rats with CH. Next, we found that CENA could ameliorate neurological functions in rat models of CH. Moreover, the upregulation of RIPK1-mediated necroptosis-related molecules in the brains of rats with CH were inhibited by CENA. Further investigation revealed that CENA partially blocked the interaction between RIPK1 and RIPK3. Finally, in vivo assays showed that CENA decreased the expression of the inflammatory cytokines tumor necrosis factor-α, interleukin-6 and interleukin-8 in CH rat models.
CONCLUSION These findings revealed that CENA exerts a protective role in CH models by inhibiting RIPK1-mediated necroptosis.
Collapse
Affiliation(s)
- Guo-Feng Cai
- Hanan Branch of Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin 150001, Heilongjiang Province, China
- Postdoctoral Research Station of Heilongjiang Academy of Traditional Chinese Medicine, Harbin 150001, Heilongjiang Province, China
| | - Zhong-Ren Sun
- Heilongjiang University of Traditional Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Zhe Zhuang
- Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin 150000, Heilongjiang Province, China
| | - Hai-Chun Zhou
- Hanan Branch of Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin 150001, Heilongjiang Province, China
| | - Shan Gao
- First Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Kai Liu
- Hanan Branch of Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin 150001, Heilongjiang Province, China
| | - Li-Li Shang
- Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin 150000, Heilongjiang Province, China
| | - Kun-Ping Jia
- Hanan Branch of Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin 150001, Heilongjiang Province, China
| | - Xiu-Zhen Wang
- Hanan Branch of Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin 150001, Heilongjiang Province, China
| | - Hui Zhao
- Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin 150000, Heilongjiang Province, China
| | - Guo-Liang Cai
- Harbin Sport University, Harbin 150001, Heilongjiang Province, China
| | - Wen-Li Song
- Harbin Sport University, Harbin 150001, Heilongjiang Province, China
| | - Sheng-Nan Xu
- Graduate School of Heilongjiang University of Traditional Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| |
Collapse
|
16
|
Dreier M, Berthoud H, Shani N, Wechsler D, Junier P. SpeciesPrimer: a bioinformatics pipeline dedicated to the design of qPCR primers for the quantification of bacterial species. PeerJ 2020; 8:e8544. [PMID: 32110486 PMCID: PMC7034379 DOI: 10.7717/peerj.8544] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 01/10/2020] [Indexed: 01/21/2023] Open
Abstract
Background Quantitative real-time PCR (qPCR) is a well-established method for detecting and quantifying bacteria, and it is progressively replacing culture-based diagnostic methods in food microbiology. High-throughput qPCR using microfluidics brings further advantages by providing faster results, decreasing the costs per sample and reducing errors due to automatic distribution of samples and reagents. In order to develop a high-throughput qPCR approach for the rapid and cost-efficient quantification of microbial species in complex systems such as fermented foods (for instance, cheese), the preliminary setup of qPCR assays working efficiently under identical PCR conditions is required. Identification of target-specific nucleotide sequences and design of specific primers are the most challenging steps in this process. To date, most available tools for primer design require either laborious manual manipulation or high-performance computing systems. Results We developed the SpeciesPrimer pipeline for automated high-throughput screening of species-specific target regions and the design of dedicated primers. Using SpeciesPrimer, specific primers were designed for four bacterial species of importance in cheese quality control, namely Enterococcus faecium, Enterococcus faecalis, Pediococcus acidilactici and Pediococcus pentosaceus. Selected primers were first evaluated in silico and subsequently in vitro using DNA from pure cultures of a variety of strains found in dairy products. Specific qPCR assays were developed and validated, satisfying the criteria of inclusivity, exclusivity and amplification efficiencies. Conclusion In this work, we present the SpeciesPrimer pipeline, a tool to design species-specific primers for the detection and quantification of bacterial species. We use SpeciesPrimer to design qPCR assays for four bacterial species and describe a workflow to evaluate the designed primers. SpeciesPrimer facilitates efficient primer design for species-specific quantification, paving the way for a fast and accurate quantitative investigation of microbial communities.
Collapse
Affiliation(s)
- Matthias Dreier
- Agroscope, Bern, Switzerland.,Laboratory of Microbiology, University of Neuchâtel, Neuchâtel, Switzerland
| | | | | | | | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Neuchâtel, Switzerland
| |
Collapse
|
17
|
Li Y, Wang T, Hu X, Zhang H, Chen L, Bao X, He J. Study of KIR gene expression at the mRNA level in specific donor-derived NK cells after allogeneic HSCT. Immunogenetics 2020; 72:135-141. [PMID: 31900503 DOI: 10.1007/s00251-019-01153-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/03/2019] [Indexed: 02/07/2023]
Abstract
The function of natural killer (NK) cells after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is regulated by the balance between inhibitory KIRs (iKIRs) and activating KIRs (aKIRs). However, few studies have examined the subsequent expression of KIR genes unique to the donor. We defined the set of KIR genes expressed only in the donor and designed a method for measuring the expression of these KIR genes by quantitative real-time polymerase chain reaction (RT-qPCR) based on genetic cloning techniques. In this study, we evaluated the recovery pattern of KIR genes in 252 donor-recipient pairs. The expression of each KIR unique to the donor was in line with that of KIR genes shared by the donor and recipient, such as KIR2DS1, KIR3DS1, KIR2DS4, or KIR2DS3. The timing of the peak mRNA expression of aKIRs unique to the donor was inconsistent but occurred within the first 3 months posttransplantation, whereas the peak mRNA expression of iKIRs was consistently observed in the third month after transplantation. The expression of KIR2DL2 in the third month posttransplantation was significantly higher in the transplant recipients than in the donors (p = 0.01). The KIR2DL1 and KIR3DL1 levels in the transplant recipients in the second and third months posttransplantation were also obviously higher than the donor levels (p < 0.0001). Thus, these observations should be considered when attempting to predict the correlation between mRNA expression and prognosis after allo-HSCT.
Collapse
Affiliation(s)
- Ying Li
- HLA Laboratory of Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Building 15, No. 708 Renmin Road, Suzhou, 215007, Jiangsu, China
| | - Tian Wang
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, No. 708 Renmin Road, Suzhou, 215007, Jiangsu, China
| | - Xing Hu
- HLA Laboratory of Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Building 15, No. 708 Renmin Road, Suzhou, 215007, Jiangsu, China
| | - Huanhuan Zhang
- HLA Laboratory of Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Building 15, No. 708 Renmin Road, Suzhou, 215007, Jiangsu, China
| | - Luyao Chen
- HLA Laboratory of Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Building 15, No. 708 Renmin Road, Suzhou, 215007, Jiangsu, China
| | - Xiaojing Bao
- HLA Laboratory of Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Building 15, No. 708 Renmin Road, Suzhou, 215007, Jiangsu, China
| | - Jun He
- HLA Laboratory of Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Building 15, No. 708 Renmin Road, Suzhou, 215007, Jiangsu, China. .,Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, No. 708 Renmin Road, Suzhou, 215007, Jiangsu, China.
| |
Collapse
|
18
|
Jiayuan S, Junyan Y, Xiangzhen W, Zuping L, Jian N, Baowei H, Lifang J. Gant61 ameliorates CCl 4-induced liver fibrosis by inhibition of Hedgehog signaling activity. Toxicol Appl Pharmacol 2019; 387:114853. [PMID: 31816328 DOI: 10.1016/j.taap.2019.114853] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/27/2019] [Accepted: 12/05/2019] [Indexed: 02/08/2023]
Abstract
As an intercellular signaling molecule, Hedgehog (Hh) plays a critical role in liver fibrosis/regeneration. Transcription effectors Gli1 and Gli2 are key components of the Hh signaling pathway. However, whether inhibition of Gli1/2 activity can affect liver fibrogenesis is largely unknown. In the present study, we investigated the effect of Gant61 (a Gli1/2 transcription factor inhibitor) on liver fibrosis and its possible mechanism. Wild-type and Shh-EGFP-Cre male mice were exposed to CCl4, and then treated with or without Gant61 for four weeks. The level of liver injury/fibrosis and expression levels of mRNA and protein related to the Hh ligand/pathway were assessed. In our study, CCl4 treatment induced liver injury/fibrosis and promoted activation of hepatic stellate cells (HSCs). In addition, CCl4 induced the expression of Shh ligands in and around the fibrotic lesion, accompanied by induction of mRNA and protein expression of Hh components (Smo, Gli1 and Gli2). However, administration of Gant61 decreased liver fibrosis by reduction in HSC number, down-regulation of mRNA and protein expression of Hh components (Smo, Gli1 and Gli2), and cell-cycle arrest of HSCs. Our data highlight the importance of the Shh pathway for the development of liver fibrosis, and also suggest Glis as potential therapeutic targets for the treatment of liver fibrosis.
Collapse
Affiliation(s)
- Shen Jiayuan
- College of Life Science, Shaoxing University, Shaoxing, Zhejiang, China; Department of pathology, Affliliated hospital of Shaoxing University, Shaoxing, Zhejiang, China
| | - Yan Junyan
- College of Life Science, Shaoxing University, Shaoxing, Zhejiang, China
| | | | - Liu Zuping
- College of Life Science, Shaoxing University, Shaoxing, Zhejiang, China; Department of pathology, Affliliated hospital of Shaoxing University, Shaoxing, Zhejiang, China
| | - Ni Jian
- College of Life Science, Shaoxing University, Shaoxing, Zhejiang, China
| | - Hu Baowei
- College of Life Science, Shaoxing University, Shaoxing, Zhejiang, China.
| | - Jin Lifang
- College of Life Science, Shaoxing University, Shaoxing, Zhejiang, China.
| |
Collapse
|
19
|
Molina CE, Jacquet E, Ponien P, Muñoz-Guijosa C, Baczkó I, Maier LS, Donzeau-Gouge P, Dobrev D, Fischmeister R, Garnier A. Identification of optimal reference genes for transcriptomic analyses in normal and diseased human heart. Cardiovasc Res 2019; 114:247-258. [PMID: 29036603 DOI: 10.1093/cvr/cvx182] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 09/20/2017] [Indexed: 11/13/2022] Open
Abstract
Aims Quantitative real-time RT-PCR (RT-qPCR) has become the method of choice for mRNA quantification, but requires an accurate normalization based on the use of reference genes showing invariant expression across various pathological conditions. Only few data exist on appropriate reference genes for the human heart. The objective of this study was to determine a set of suitable reference genes in human atrial and ventricular tissues, from right and left cavities in control and in cardiac diseases. Methods and results We assessed the expression of 16 reference genes (ACTB, B2M, GAPDH, GUSB, HMBS, HPRT1, IPO8, PGK1, POLR2A, PPIA, RPLP0, TBP, TFRC, UBC, YWHAZ, 18S) in tissues from: right and left ventricles from healthy controls and heart failure (HF) patients; right-atrial tissue from patients in sinus rhythm with (SRd) or without (SRnd) atrial dilatation, patients with paroxysmal (pAF) or chronic (cAF) atrial fibrillation or with HF; and left-atrial tissue from patients in SR or cAF. Consensual analysis (by geNorm and Normfinder algorithms, BestKeeper software tool and comparative delta-Ct method) of the variability scores obtained for each reference gene expression shows that the most stably expressed genes are: GAPDH, GUSB, IPO8, POLR2A, and YWHAZ when comparing either right and left ventricle or ventricle from healthy controls and HF patients; GAPDH, IPO8, POLR2A, PPIA, and RPLP0 when comparing either right and left atrium or right atria from all pathological groups. ACTB, TBP, TFRC, and 18S genes were identified as the least stable. Conclusions The overall most stable reference genes across different heart cavities and disease conditions were GAPDH, IPO8, POLR2A and PPIA. YWHAZ or GUSB could be added to this set for some specific experiments. This study should provide useful guidelines for reference gene selection in RT-qPCR studies in human heart.
Collapse
Affiliation(s)
- Cristina E Molina
- Inserm, UMR-S 1180, University of Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France.,Institute of Pharmacology and Toxicology, Heart Research Center Göttingen, University Medical Center, Georg-August University Göttingen, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, UPR 2301, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Prishila Ponien
- Institut de Chimie des Substances Naturelles, UPR 2301, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Istvan Baczkó
- Department Pharmacology and Pharmacotherapy, University of Szeged, Hungary
| | - Lars S Maier
- Department Internal Medicine II, University Heart Center, University Hospital Regensburg, Regensburg, Germany
| | | | - Dobromir Dobrev
- West German Heart and Vascular Center, Institute of Pharmacology, University Duisburg-Essen, Essen, Germany
| | - Rodolphe Fischmeister
- Inserm, UMR-S 1180, University of Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Anne Garnier
- Inserm, UMR-S 1180, University of Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| |
Collapse
|
20
|
Mohammadi M, Amirmahani F, Goharrizi KJ, Pakzad R, Dolat H. Evaluating the expression level of Survivin gene in different groups of B-cell acute lymphoblastic leukemia patients of Iran. Mol Biol Rep 2019; 46:2679-2684. [PMID: 31037549 DOI: 10.1007/s11033-019-04703-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 11/13/2018] [Accepted: 02/12/2019] [Indexed: 01/17/2023]
Abstract
Survivin is one of the major members of Inhibitory Apoptotic Proteins (IAP) family. The functional anti-apoptotic and regulatory role of Survivin in the cell cycle had made it as an interesting candidate for tumor studies. Acute lymphoblastic leukemia is one of the most common malignancies of children that accounts for 30% of all the childhood malignancies. The purpose of this study was to investigate the prognostic importance of Survivin level in B-cell acute lymphoblastic leukemia patients of Iran in four different steps of disease in order to follow up its impact on various treatment ways, the development of the disease, and the response to treatment in the patients. The expression level of Survivin was evaluated in 85 patients with B-cell acute lymphoblastic leukemia and 85 healthy controls using Quantitative Real-Time Polymerase Chain Reaction. Also, western blot analysis was done to confirm the results. Based on our findings, the expression of Survivin showed a significant up-regulation in patients compared to controls. Therefore, a correlation between Survivin expression and the development pattern of B-cell acute lymphoblastic leukemia with a strong diagnostic efficiency (AUC-ROC, 0.8562) was observed. Therefore, it can be introduced as a potential marker for prognosis B-cell Acute Lymphoblastic Leukemia in the future.
Collapse
Affiliation(s)
- Mahan Mohammadi
- Department of Molecular Genetics, Faculty of Science, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Farzane Amirmahani
- Genetic Division, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran.
| | | | - Rambod Pakzad
- Department of Plant Breeding, Yazd Branch, Islamic Azad University, Yazd, Iran
| | - Hossein Dolat
- Department of Urology, Shahid Beheshti University of Medical Science, Tehran, Iran
| |
Collapse
|
21
|
Zhao Y, Han HY, Fan L, Tian RB, Cui JT, Li JY, Chen HY, Yang MF, Zheng LL. Development of a TB green II-based duplex real-time fluorescence quantitative PCR assay for the simultaneous detection of porcine circovirus 2 and 3. Mol Cell Probes 2019; 45:31-36. [PMID: 30980890 DOI: 10.1016/j.mcp.2019.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/28/2019] [Accepted: 04/07/2019] [Indexed: 11/30/2022]
Abstract
Porcine circovirus 3 (PCV3), as a newly emerged circovirus, is widely distributed in pig populations worldwide. Co-infection of PCV2 and PCV3 has been reported frequently in clinical samples. In the present study, a TB Green II-based duplex real-time polymerase chain reaction (qPCR) was developed to rapidly and differentially detect PCV2 and PCV3. The assay specifically detected PCV2 and PCV3, with no fluorescence signals being detected for other non-targeted pig pathogens. The duplex qPCR showed a high degree of linearity (R2 > 0.998), and its limits of detection were 10 and 78 copies/μL for PCV2 and PCV3, respectively. The duplex qPCR could detect and differentiate PCV2 (melting peaks at 85.5 °C) and PCV3 (melting peaks at 82.5 °C), and showed high repeatability and reproducibility, with intra- and inter-assay coefficients of variation of less than 2.0%. Fifty-six tissue samples from 18 pig farms were used to evaluate the duplex qPCR method. The results revealed infection rates of 66.07% (37/56) and 39.28% (22/56) for PCV2 and PCV3, respectively. The PCV2 + PCV3 co-infection rate was 39.28% (22/56). The developed method could be used as an efficient molecular biology tool for epidemiological investigations of PCV2 and PCV3.
Collapse
Affiliation(s)
- Yu Zhao
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China
| | - Hao-Ying Han
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China
| | - Lin Fan
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China
| | - Run-Bo Tian
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China
| | - Jian-Tao Cui
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China
| | - Jing-Yi Li
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China
| | - Hong-Ying Chen
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China.
| | - Ming-Fan Yang
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China.
| | - Lan-Lan Zheng
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China
| |
Collapse
|
22
|
Jin K, Xie X, Pan Y, Wang K, Chen B, Wu D, Shen Z, Wang M, Zhang H. [Applicable Value of AMSS-PCR in Lung Cancer Gene Mutation Detection]. Zhongguo Fei Ai Za Zhi 2018; 21:815-820. [PMID: 30454542 PMCID: PMC6247010 DOI: 10.3779/j.issn.1009-3419.2018.11.02] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
背景与目的 肺癌驱动基因检测具有重要意义,目前检测方法多样,临床适用性有差异。本研究旨在比较基于扩增阻碍突变系统-聚合酶链反应(Amplification Refractory Mutation System-polymerase chain reaction, ARMS-PCR)技术的试剂盒与一代测序及ARMS-qPCR检测肺癌突变基因的敏感性和特异性,探究突变位点特异扩增法(Amplification Mutation Specific System, AMSS)-PCR技术在肺癌突变基因检测中的应用价值。 方法 对前期已行ARMS-PCR检测的肿瘤标本进行一代测序及试剂盒检测,比较各种方法的检测结果,并对检测结果进行统计学分析。 结果 本研究共收集了309例肺癌标本。试剂盒与一代测序符合率97.41%,ARMS-PCR的符合率97.73%。试剂盒与一代测序、试剂盒与实时定量聚合酶链反应(quantitative real-time polymerase chain reaction, qPCR)、qPCR与一代测序一致性检验的Kappa值分别为0.946、0.953、0.913。试剂盒以一代测序为参照的受试者工作特征曲线(receiver operating characteristic curve, ROC)曲线下面积为0.976,以qPCR为参照的ROC曲线下面积为0.975。 结论 AMSS-qPCR技术能够有效检测肺癌突变基因,具有较好的临床应用价值。
Collapse
Affiliation(s)
- Ke Jin
- Department of Thoracic Surgery, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510120, China
| | - Xuan Xie
- Department of Thoracic Surgery, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510120, China
| | - Yuejiang Pan
- Department of Thoracic Surgery, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510120, China
| | - Kexi Wang
- Department of Thoracic Surgery, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510120, China
| | - Baishen Chen
- Department of Thoracic Surgery, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510120, China
| | - Duoguang Wu
- Department of Thoracic Surgery, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510120, China
| | - Zhuojian Shen
- Department of Thoracic Surgery, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510120, China
| | - Minghui Wang
- Department of Thoracic Surgery, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510120, China
| | - Huizhong Zhang
- Department of Thoracic Surgery, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510120, China
| |
Collapse
|
23
|
Zhang C, Du Z, Li B, Sun X, Wang J, Wang J, Zhu L. Evaluating toxicity of 1-octyl-3-methylimidazolium hexafluorophosphate to microorganisms in soil. Chemosphere 2018; 210:762-768. [PMID: 30036824 DOI: 10.1016/j.chemosphere.2018.07.105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
Ionic liquids (ILs) were widely applied because of their excellent properties. The present investigation studied the toxicity of the IL 1-octyl-3-methylimidazolium hexafluorophosphate ([Omim]PF6) to the soil microbial population and community diversity with dose (1.0, 2.0, 4.0, 6.0, and 8.0 mg kg-1) and exposure time (7, 10, and 13 d). The results show the IL was stable during the entire experimental period. The Biolog-ECO plate results indicated that the average well color development (AWCD) in the 6.0 and 8.0 mg kg-1 treatments was lower than these in the other treatments. The diversity indices of the Biolog analysis were significantly reduced. The abundance of the ammonia-oxidizing archaea (AOA-) and the ammonia-oxidizing bacteria (AOB-) ammonia monooxygenase (amoA) genes was measured by the real-time polymerase chain reaction (RT-PCR). In the treatments of 4.0, 6.0 and 8.0 mg kg-1, the abundance of amoA genes of the AOA- and AOB- were inhibited by IL [Omim]PF6.
Collapse
Affiliation(s)
- Cheng Zhang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Taian, 271018, China.
| | - Zhongkun Du
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Taian, 271018, China.
| | - Bing Li
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Taian, 271018, China.
| | - Xi Sun
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Taian, 271018, China.
| | - Jun Wang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Taian, 271018, China.
| | - Jinhua Wang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Taian, 271018, China.
| | - Lusheng Zhu
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Taian, 271018, China.
| |
Collapse
|
24
|
Udomsinprasert W, Vejchapipat P, Klaikeaw N, Chongsrisawat V, Poovorawan Y, Honsawek S. Hepatic autotaxin overexpression in infants with biliary atresia. PeerJ 2018; 6:e5224. [PMID: 30065861 PMCID: PMC6063256 DOI: 10.7717/peerj.5224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/22/2018] [Indexed: 12/21/2022] Open
Abstract
Background Autotaxin (ATX) is a secreted glycoprotein that is involved in the development of hepatic fibrogenesis via the enzymatic production of lysophosphatidic acid. The aim of this study was to investigate hepatic expression of ATX in biliary atresia (BA) compared with non-BA liver controls and to examine the association between ATX expression and clinical outcome in BA. Methods Liver specimens from BA infants (n = 20) were compared with samples from infants who underwent liver biopsy for reasons other than BA (n = 14) and served as controls. Relative mRNA and protein expression of ATX were quantified using real-time polymerase chain reaction (PCR) and immunohistochemistry. Masson’s Trichrome staining was performed to determine the degree of liver fibrosis. Results Quantitative real-time PCR demonstrated overexpression of ATX mRNA in BA livers. In immunohistochemical evaluation, ATX was positively stained on the hepatic parenchyma and the biliary epithelium in BA patients, as compared to non-BA controls. The immunostaining score of ATX in BA livers was also significantly higher than that observed in non-BA livers (P < 0.001). Subgroup analysis revealed that ATX expression in the patients with poor outcomes was significantly greater than in those with good outcomes (P = 0.03). Additionally, there was a positive correlation between hepatic ATX expression and Metavir fibrosis stage in BA livers (r = 0.79, P < 0.001). Discussion This study found that mRNA and protein expression of ATX were increased in BA livers. High hepatic ATX expression at the time of Kasai operation was associated with liver fibrosis and outcome in BA, suggesting that ATX may serve a role as a promising biomarker of the prognosis in biliary atresia.
Collapse
Affiliation(s)
- Wanvisa Udomsinprasert
- Osteoarthritis and Musculoskeleton Research Unit, Department of Biochemistry, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Chulalongkorn University, Bangkok, Thailand.,Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Paisarn Vejchapipat
- Department of Surgery, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Chulalongkorn University, Bangkok, Thailand
| | - Naruemon Klaikeaw
- Department of Pathology, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Chulalongkorn University, Bangkok, Thailand
| | - Voranush Chongsrisawat
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Chulalongkorn University, Bangkok, Thailand
| | - Sittisak Honsawek
- Osteoarthritis and Musculoskeleton Research Unit, Department of Biochemistry, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Chulalongkorn University, Bangkok, Thailand
| |
Collapse
|
25
|
Zhang C, Wang J, Zhu L, Du Z, Wang J, Sun X, Zhou T. Effects of 1-octyl-3-methylimidazolium nitrate on the microbes in brown soil. J Environ Sci (China) 2018; 67:249-259. [PMID: 29778159 DOI: 10.1016/j.jes.2017.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/25/2017] [Accepted: 09/01/2017] [Indexed: 06/08/2023]
Abstract
The toxicity of ionic liquids (ILs) on soil organisms has aroused wide attention due to their high-solubility. The present investigation focused on the toxicity of 1-octyl-3-methylimidazolium nitrate ([C8mim]NO3) on the microbial populations (bacteria, fungi, and actinomycetes), soil enzyme (urease, dehydrogenase, acid phosphatase, and β-glucosidase) activities, microbial community diversity using terminal restriction fragment length polymorphism (T-RFLP), and abundance of the ammonia monooxygenase (amoA) genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) using quantitative real-time polymerase chain reaction (q-PCR) in brown soil at each trial with doses of 0, 1.0, 5.0, and 10.0mg/kg on days 10, 20, 30, and 40. The contents of [C8mim]NO3 in soil were measured using high performance liquid chromatography with recoveries of 84.3% to 85.2%, and changed less than 10% during the experimental period. A significant decrease was observed from the bacteria, fungi and actinomycetes populations at 10.0mg/kg, at which the urease activity was inhibited and the β-glucosidase activity was stimulated on days 20, 30, and 40. In addition, [C8mim]NO3 inhibited the dehydrogenase activity at 10mg/kg on days 30 and 40 and the acid phosphatase activity on day 20. The diversity of the soil microbial community and the gene abundance of AOA- and AOB- amoA were also inhibited. Furthermore, the present investigation provided more scientific information for the toxicity evaluation of ILs in soil.
Collapse
Affiliation(s)
- Cheng Zhang
- Key Laboratory of Agriculture Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong 271018, China.
| | - Jun Wang
- Key Laboratory of Agriculture Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong 271018, China.
| | - Lusheng Zhu
- Key Laboratory of Agriculture Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong 271018, China.
| | - Zhongkun Du
- Key Laboratory of Agriculture Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Jinhua Wang
- Key Laboratory of Agriculture Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong 271018, China.
| | - Xi Sun
- Key Laboratory of Agriculture Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Tongtong Zhou
- Key Laboratory of Agriculture Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong 271018, China
| |
Collapse
|
26
|
Heerema JL, Jackman KW, Miliano RC, Li L, Zaborniak TSM, Veldhoen N, van Aggelen G, Parker WJ, Pyle GG, Helbing CC. Behavioral and molecular analyses of olfaction-mediated avoidance responses of Rana (Lithobates) catesbeiana tadpoles: Sensitivity to thyroid hormones, estrogen, and treated municipal wastewater effluent. Horm Behav 2018; 101:85-93. [PMID: 28964734 DOI: 10.1016/j.yhbeh.2017.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 08/04/2017] [Revised: 09/25/2017] [Accepted: 09/25/2017] [Indexed: 10/18/2022]
Abstract
Olfaction is critical for survival, facilitating predator avoidance and food location. The nature of the olfactory system changes during amphibian metamorphosis as the aquatic herbivorous tadpole transitions to a terrestrial, carnivorous frog. Metamorphosis is principally dependent on the action of thyroid hormones (THs), l-thyroxine (T4) and 3,5,3'-triiodothyronine (T3), yet little is known about their influence on olfaction during this phase of postembryonic development. We exposed Taylor Kollros stage I-XIII Rana (Lithobates) catesbeiana tadpoles to physiological concentrations of T4, T3, or 17-beta-estradiol (E2) for 48h and evaluated a predator cue avoidance response. The avoidance response in T3-exposed tadpoles was abolished while T4- or E2-exposed tadpoles were unaffected compared to control tadpoles. qPCR analyses on classic TH-response gene transcripts (thra, thrb, and thibz) in the olfactory epithelium demonstrated that, while both THs produced molecular responses, T3 elicited greater responses than T4. Municipal wastewater feed stock was spiked with a defined pharmaceutical and personal care product (PPCP) cocktail and treated with an anaerobic membrane bioreactor (AnMBR). Despite substantially reduced PPCP levels, exposure to this effluent abolished avoidance behavior relative to AnMBR effluent whose feed stock was spiked with vehicle. Thibz transcript levels increased upon exposure to either effluent indicating TH mimic activity. The present work is the first to demonstrate differential TH responsiveness of the frog tadpole olfactory system with both behavioral and molecular alterations. A systems-based analysis is warranted to further elucidate the mechanism of action on the olfactory epithelium and identify further molecular bioindicators linked to behavioral response disruption.
Collapse
Affiliation(s)
- Jody L Heerema
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Kevin W Jackman
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Rachel C Miliano
- Environment Canada, Pacific Environmental Science Centre, 2645 Dollarton Highway, North Vancouver, British Columbia V7H 1V2, Canada
| | - Linda Li
- Department of Civil and Environmental Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Tristan S M Zaborniak
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Nik Veldhoen
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Graham van Aggelen
- Environment Canada, Pacific Environmental Science Centre, 2645 Dollarton Highway, North Vancouver, British Columbia V7H 1V2, Canada
| | - Wayne J Parker
- Department of Civil and Environmental Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Gregory G Pyle
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Caren C Helbing
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada.
| |
Collapse
|
27
|
Kook SY, Kim Y, Kang B, Choe YH, Kim YH, Kim S. Characterization of the fecal microbiota differs between age groups in Koreans. Intest Res 2018; 16:246-254. [PMID: 29743837 PMCID: PMC5934597 DOI: 10.5217/ir.2018.16.2.246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 02/06/2023] Open
Abstract
Background/Aims Tens of trillions of microorganisms constitute the gut microbiota of the human body. The microbiota plays a critical role in maintaining host immunity and metabolism. Analyses of the gut microbial composition in Korea are limited to a few studies consisting of small sample sizes. To investigate the gut microbial community in a large sample of healthy Koreans, we analyzed the 16S ribosomal RNA of 4 representative bacterial genera Lactobacillus, Bifidobacterium, Bacteroides, and Clostridium. Methods A total of 378 DNA samples extracted from 164 infants and 214 adults were analyzed using quantitative real-time polymerase chain reaction. Results Analysis of 16S ribosomal RNA of 4 representative bacterial genera Lactobacillus, Bifidobacterium, Bacteroides, and Clostridium showed that the gut microbiota in infants had higher relative abundances of Bifidobacterium and Lactobacillus than that in adults, which was dominated by Bacteroides and Clostridium. Conclusions To the best of our knowledge, this was the first study evaluating the distinct characteristics of the microbial community of Korean infants and adults. The differences between the 2 populations suggest that external factors such as age, diet, and the environment are important contributing factors to the change in gut microbial composition during development.
Collapse
Affiliation(s)
- Sun-Young Kook
- Probioticslab R&D Institute, Bioeleven Co., Seoul, Korea
| | - Yunjeong Kim
- Probioticslab R&D Institute, Bioeleven Co., Seoul, Korea
| | - Ben Kang
- Department of Pediatric, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yon Ho Choe
- Department of Pediatric, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young-Ho Kim
- Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seokjin Kim
- Probioticslab R&D Institute, Bioeleven Co., Seoul, Korea
| |
Collapse
|
28
|
Zhang D, Lin G, Zhang K, Yi L, Zhang R, Xie J, Li J. Implications of and lessons learned from external assurance of eight influenza diagnostics in China. Virus Res 2018; 249:110-115. [PMID: 29608994 DOI: 10.1016/j.virusres.2018.03.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 08/24/2017] [Revised: 02/19/2018] [Accepted: 03/29/2018] [Indexed: 11/16/2022]
Abstract
This study evaluated the ability of laboratories in the Chinese mainland to conduct molecular detection of seasonal A(H1N1), A(H1N1)pdm09, A(H3N2), A(H5N1), A(H7N9), A(H9N2), B(Victoria), and B(Yamagata). Based on a genetically engineered system of virus-like particles (VLPs), the National Center for Clinical Laboratories of China (NCCLs) developed an external quality assessment (EQA) panel. The panel was distributed to 35 laboratories in mainland China to investigate the proficiency of the 16 assays for influenza molecular detection. Using genetic engineering technology, VLPs encapsulating the 37 target genes of 8 influenza viruses were generated. After verification and quantification, 26 influenza virus surrogates with different concentrations were prepared for EQA. Among the 35 participating laboratories, 319 datasets were returned to the NCCLs. Overall, 95.6% (305/319) of datasets correctly reported all 30 samples, while 2.2% (7/319) of datasets with more than one incorrect result were considered as "improvable". A total of 16 misdiagnosed and 18 undiagnosed results were reported. The data analyzed in this study showed good reproducibility in China, but improvements are needed to decrease misdiagnosed and undiagnosed cases, particularly for the A(H9N2) NA gene. Moreover, VLPs are a good alternative specimen type for assay training and proficiency testing purposes.
Collapse
Affiliation(s)
- Dong Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Lang Yi
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.
| |
Collapse
|
29
|
Fu Y, Wang G, Wu Q, Yang X, Zhang R, Zhang K, Lin G, Han Y, Bao L, Li Z, Li J. Preparation of MS2-based nanoparticles as control and standard materials for the molecular detection of dengue virus serotypes. Virus Res 2017; 233:42-50. [PMID: 28288812 DOI: 10.1016/j.virusres.2017.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/14/2017] [Accepted: 02/23/2017] [Indexed: 11/20/2022]
Abstract
To quantify dengue virus (DENV) and evaluate the performance of clinical laboratories using quantitative real-time polymerase chain reaction (qRT-PCR) assays, we constructed high-efficiency expression systems to produce DENV-1 to 4 nanoparticles and assessed their suitability as standard and control materials in 20 laboratories across China. Targeted gene sequences of DENV-1 to 4 were synthesized and inserted into pACYC-Duet 1-MS2 recombinant plasmids to generate corresponding nanoparticle expression systems. After collection, verification, and quantification by digital PCR (dPCR), DENV-1 to 4 nanoparticles were prepared as control and standard materials. Five positive and three negative samples of each DENV serotype in every panel were used for assessing the performance of the participating laboratories across China, as well as standard materials for the quantitative detection of DENV using qRT-PCR assays. The accuracy, sensitivity, and specificity of qRT-PCR used by the 20 evaluated laboratories were 89.6 (569/635), 85.1 (336/395), and 97.1% (233/240), respectively. Overall, sixteen (80.0%) laboratories were qualified in detecting DENV, among which five (25.0%) were designated as "competent", eleven (55.0%) were defined as "acceptable", and four (20%) were considered to be "improvable". The results generated from the DENV standard samples were significantly positively correlated with those generated by dPCR (r2=0.8698, P<0.001). In summary, DENV nanoparticles could potentially be used as controls for improving the performance of laboratories and as standards for the quantitative detection of DENV.
Collapse
|
30
|
Pan D, Pan M, Xu YM. Mir-29a expressions in peripheral blood mononuclear cell and cerebrospinal fluid: Diagnostic value in patients with pediatric tuberculous meningitis. Brain Res Bull 2017; 130:231-235. [PMID: 28109794 DOI: 10.1016/j.brainresbull.2017.01.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 11/24/2016] [Accepted: 01/12/2017] [Indexed: 11/29/2022]
Abstract
To evaluate the value of miR-29a expression in peripheral blood mononuclear cell (PBMC) and cerebrospinal fluid (CSF) in the diagnosis of pediatric tuberculous meningitis (TBM). Our study enrolled 112 children with TBM and 130 healthy children, from which PBMC and CSF were collected. The quantitative real-time polymerase chain reaction (qRT-PCR) was used to measure the expression of miR-29a in PBMC and CSF, and then analyze the diagnostic value. Compared with control group, the miR-29a expressions in PBMC and CSF were increased in TBM children (both P<0.05), and the expressions were associated with following factors: intracranial hypertension, conscious disturbance, focal cerebral symptoms, meningeal irritation, hydrocrania, abnormal electroencephalogram and extra-cerebral tuberculous (all P<0.05). The receiver operating characteristic (ROC) curve showed that the sensitivity, specificity and area under the curve (AUC) of miR-29a in PBMC was 67.20%, 88.50% and 0.852, respectively, and that in CSF was 81.10%, 90.00% and 0.890, respectively, and that in combination of PBMC and CSF was 84.40%, 95.38% and 0.934, respectively. miR-29a expression in PBMC and CSF may provide a reference for the diagnosis of pediatric TBM.
Collapse
Affiliation(s)
- Deng Pan
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, P.R. China; 2nd Department of Neurology, The First People's Hospital of Xinxiang, Xinxiang, 453000, PR China
| | - Miao Pan
- The Second Affiliated Hospital of Xinxiang Medical University, Henan Mental Hospital, Xinxiang, 453000, PR China
| | - Yu-Ming Xu
- 3rd Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, PR China.
| |
Collapse
|
31
|
Wu J, Lin Y, He X, Yang H, He P, Fu X, Li G, Gu X. Comparison of detection methods and follow-up study on the tyrosine kinase inhibitors therapy in non-small cell lung cancer patients with ROS1 fusion rearrangement. BMC Cancer 2016; 16:599. [PMID: 27488371 PMCID: PMC4973062 DOI: 10.1186/s12885-016-2582-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 07/19/2016] [Indexed: 01/15/2023] Open
Abstract
Background The screening of ROS proto-oncogene 1, receptor tyrosine kinase(ROS1) fusion rearrangement might be potentially beneficial for an effective therapy against non-small cell lung cancer (NSCLC). However, the three main ROS1 rearrangement detection methods have limitations, and no routine protocol for the detection of ROS1 rearrangement in NSCLC is available. In this study, our aims were to compare immunohistochemistry (IHC), fluorescent in situ hybridization (FISH) and quantitative real-time polymerase chain reaction (qRT-PCR) in their ability to detect ROS1 rearrangement in NSCLC, and discuss the clinical characteristics and histopathology of the patients with ROS1 rearrangement. Moreover, the effects of tyrosine kinase inhibitors (TKIs) therapy on the patients with ROS1 rearrangement and advanced stage disease (III b–IV) were investigated. Methods Patients with a previously diagnosed NSCLC were recruited in this study from November 2013 to October 2015. IHC was performed using the D4D6 monoclonal antibody (mAb) in an automatic IHC instrument, while FISH and qRT-PCR were carried out to confirm the IHC results. FISH and qRT-PCR positive cases underwent direct sequencing. After detection, patients with advanced ROS1 rearranged NSCLC had received TKI therapy. Results Two hundred and thirty-eight patients were included in this study. ROS1 rearrangement was detected in 10 patients. The concordant rate of FISH and qRT-PCR results was 100 %, while in the FISH and IHC results high congruence was present when IHC showed a diffusely (≥60 % tumor cells) 2–3+ cytoplasmic reactivity pattern. Patients harboring ROS1 rearrangement were mostly young (8/10), females (7/10) and non-smokers (7/10) with adenocarcinoma (10/10) and acinar pattern. Most of their tumor were in intermediate grade (6/8). Among these 10 patients, three of them in stage IV with ROS1 rearrangement gained benefits from ROS1 TKI therapy. Conclusions IHC, FISH and qRT-PCR can reliably detect ROS1 rearrangement in NSCLC, while IHC can be used as a preliminary screening tool. These results supported the efficacy of ROS1 TKI therapy in treating advanced NSCLC patients with ROS1 rearrangement. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2582-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jieyu Wu
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, No. 151, Yanjiangxi Road, Guangzhou, 510120, China
| | - Yunen Lin
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, No. 151, Yanjiangxi Road, Guangzhou, 510120, China
| | - Xinming He
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, No. 151, Yanjiangxi Road, Guangzhou, 510120, China
| | - Haihong Yang
- Department of Cardiothoracic Surgery, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ping He
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, No. 151, Yanjiangxi Road, Guangzhou, 510120, China
| | - Xinge Fu
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, No. 151, Yanjiangxi Road, Guangzhou, 510120, China
| | - Guangqiu Li
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, No. 151, Yanjiangxi Road, Guangzhou, 510120, China
| | - Xia Gu
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, No. 151, Yanjiangxi Road, Guangzhou, 510120, China.
| |
Collapse
|
32
|
Irshad M, Gupta P, Mankotia DS, Ansari MA. Multiplex qPCR for serodetection and serotyping of hepatitis viruses: A brief review. World J Gastroenterol 2016; 22:4824-4834. [PMID: 27239109 PMCID: PMC4873875 DOI: 10.3748/wjg.v22.i20.4824] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/09/2016] [Accepted: 03/30/2016] [Indexed: 02/06/2023] Open
Abstract
The present review describes the current status of multiplex quantitative real time polymerase chain reaction (qPCR) assays developed and used globally for detection and subtyping of hepatitis viruses in body fluids. Several studies have reported the use of multiplex qPCR for the detection of hepatitis viruses, including hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), and hepatitis E virus (HEV). In addition, multiplex qPCR has also been developed for genotyping HBV, HCV, and HEV subtypes. Although a single step multiplex qPCR assay for all six hepatitis viruses, i.e., A to G viruses, is not yet reported, it may be available in the near future as the technologies continue to advance. All studies use a conserved region of the viral genome as the basis of amplification and hydrolysis probes as the preferred chemistries for improved detection. Based on a standard plot prepared using varying concentrations of template and the observed threshold cycle value, it is possible to determine the linear dynamic range and to calculate an exact copy number of virus in the specimen. Advantages of multiplex qPCR assay over singleplex or other molecular techniques in samples from patients with co-infection include fast results, low cost, and a single step investigation process.
Collapse
MESH Headings
- DNA, Viral/blood
- DNA, Viral/genetics
- Hepatitis Viruses/classification
- Hepatitis Viruses/genetics
- Hepatitis Viruses/immunology
- Hepatitis, Viral, Human/blood
- Hepatitis, Viral, Human/diagnosis
- Hepatitis, Viral, Human/genetics
- Hepatitis, Viral, Human/immunology
- Humans
- Multiplex Polymerase Chain Reaction
- Predictive Value of Tests
- Reproducibility of Results
- Serogroup
- Serologic Tests/methods
- Serotyping
Collapse
|
33
|
Abstract
Acute promyelocytic leukemia (APL) is a molecularly well-defined disease, characterized by a specific chromosomal translocation; the improvement in biologic and clinical
knowledge and subsequent introduction of molecularly targeted therapies have transformed the management of APL, with survival rates now exceeding 80%. Minimal residual disease (MRD) assessment in APL is the most important tool for its treatment; the prognostic role of the molecular detection of promyelocytic leukemia retinoic acid receptor α (PML-RARα) transcript after consolidation therapy in the early identification of the following hematologic relapse is now well established and guides preemptive therapy. First experiences performed with a qualitative polymerase chain reaction (PCR) approach were replaced with more accurate real-time quantitative PCR (RQ-PCR), which guarantees a numeric quantification of MRD. The identification of arsenic trioxide (ATO) as a valid therapy not only in relapsed patients but also as an alternative to standard therapy alone or in association with all-trans-retinoic acid enlarges the setting of validation of MRD evaluation in APL patients, considering a possible different clearance of PML-RARα with innovative therapy different from the standard ones. MRD monitoring demonstrated its validity also in the setting of relapsed patients with interesting results in the autologous and allogeneic stem cell transplantation setting or with the use of other biological agents. The aim of this review is to report and discuss the actual state of the art of MRD in APL.
Collapse
Affiliation(s)
- Federico De Angelis
- Department of Cellular Biotechnologies and Hematology, Sapienza University, Via Benevento 6, 00161 Rome, Italy
| | - Massimo Breccia
- Department of Cellular Biotechnologies and Hematology, Sapienza University, Via Benevento 6, 00161 Rome, Italy
| |
Collapse
|
34
|
Shukla R, Ghoshal U, Dhole TN, Ghoshal UC. Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis. Dig Dis Sci 2015; 60:2953-62. [PMID: 25784074 DOI: 10.1007/s10620-015-3607-y] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/21/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND Dysbiosis may play a role in irritable bowel syndrome (IBS), hitherto an enigmatic disorder. We evaluated selected fecal microbes in IBS patients and healthy controls (HC). METHODS Fecal 16S rRNA copy number of selected bacteria was studied using qPCR in 47 patients with IBS (Rome III) and 30 HC. RESULTS Of 47 patients, 20 had constipation (IBS-C), 20 diarrhea (IBS-D), and seven unclassified IBS (IBS-U). Relative difference in 16S rRNA copy number of Bifidobacterium (P = 0.042) was lower, while those of Ruminococcus productus-Clostridium coccoides (P = 0.016), Veillonella (P = 0.008), Bacteroides thetaiotamicron (P < 0.001), Pseudomonas aeruginosa (P < 0.001), and Gram-negative bacteria (GNB, P = 0.001) were higher among IBS patients than HC. Number of Lactobacillus (P = 0.002) was lower, while that of Bacteroides thetaiotamicron (P < 0.001) and segmented filamentous bacteria (SFB, P < 0.001) was higher among IBS-D than IBS-C. Numbers of Bacteroides thetaiotamicron (P < 0.001), P. aeruginosa (P < 0.001), and GNB (P < 0.01) were higher among IBS-C and IBS-D than HC. Quantity of SFB was higher among IBS-D (P = 0.011) and lower among IBS-C (P = 0.002) than HC. Number of Veillonella species was higher among IBS-C than HC (P = 0.002). P. aeruginosa was frequently detected among IBS than HC (46/47 [97.9 %] vs. 10/30 [33.3 %], P < 0.001). Abdominal distension (n = 34/47) was associated with higher number of Bacteroides thetaiotamicron, Clostridium coccoides, P. aeruginosa, SFB, and GNB; bloating (n = 22/47) was associated with Clostridium coccoides and GNB. Microbial flora was different among IBS than HC on principal component analysis. CONCLUSION Fecal microbiota was different among IBS than HC, and different sub-types were associated with different microbiota. P. aeruginosa was more frequent and higher in number among IBS patients.
Collapse
|
35
|
Tan SK, Waggoner JJ, Pinsky BA. Cytomegalovirus load at treatment initiation is predictive of time to resolution of viremia and duration of therapy in hematopoietic cell transplant recipients. J Clin Virol 2015; 69:179-83. [PMID: 26209403 DOI: 10.1016/j.jcv.2015.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Preemptive antiviral therapy relies on viral load measurements and is the mainstay of cytomegalovirus (CMV) prevention in hematopoietic cell transplant (HCT) recipients. However, optimal CMV levels for the initiation of preemptive therapy have not been defined. OBJECTIVES The objectives of our work were to evaluate the relationship between plasma CMV DNA levels at initiation of preemptive therapy with time to resolution of viremia and duration of treatment. STUDY DESIGN Retrospective analysis of HCT recipients undergoing serial CMV PCR testing between June 2011 and June 2014 was performed. RESULTS 221 HCT recipients underwent preemptive therapy for 305 episodes of CMV viremia. Median time to resolution was shorter when treatment was initiated at lower CMV levels (15 days at 135-440 international units (IU)/mL, 18 days at 441-1000 IU/mL, and 21 days at >1000 IU/mL, P<.001). Prolonged viremia lasting >30 days occurred less frequently when treatment was initiated at 135-440 IU/mL compared to 441-1000 IU/mL and >1000 IU/mL (1%, 15%, 24%, P<.001). Median treatment duration was also shorter in the lower viral load groups (28, 34, 37 days, P<.001). CONCLUSION Initiation of preemptive therapy at low CMV levels was associated with shorter episodes of viremia and courses of antiviral therapy. These data support the utility of initiating preemptive CMV therapy at viral loads as low as 135 IU/mL in HCT recipients.
Collapse
|
36
|
Park YS, Na YS, Ryu MH, Lee CW, Park HJ, Lee JK, Park SR, Ryoo BY, Kang YK. FGFR2 Assessment in Gastric Cancer Using Quantitative Real-Time Polymerase Chain Reaction, Fluorescent In Situ Hybridization, and Immunohistochemistry. Am J Clin Pathol 2015; 143:865-72. [PMID: 25972329 DOI: 10.1309/ajcpnflsmwwpp8dr] [Citation(s) in RCA: 16] [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] [Indexed: 01/13/2023] Open
Abstract
OBJECTIVES Fibroblast growth factor receptor 2 (FGFR2) amplification has been reported to be a target for treatment in gastric cancer. However, an optimal tissue source and method for evaluating FGFR2 have yet to be established. METHODS Copy numbers were compared by quantitative polymerase chain reaction (qPCR) using frozen vs formalin-fixed, paraffin-embedded (FFPE) tissue and biopsy vs surgical specimens. We correlated the results of qPCR and immunohistochemistry (IHC) with fluorescence in situ hybridization (FISH) using stage IV gastric cancer biopsy specimens and validated the results in surgical specimens. RESULTS FFPE tissues were suitable for qPCR, and biopsy specimens were equivalent to or better than surgical specimens. qPCR and IHC results exhibited an excellent correlation with FISH at eight or more copies by qPCR in any kind of tissue, 5% or more by IHC in biopsy specimens, and 10% or more by IHC in surgical specimens. FGFR2 amplification was 6.6% in stage IV gastric cancers, and 42% of these showed heterogeneous amplification and overexpression. IHC indicated a good correlation with FISH even in the heterogeneous cases. CONCLUSIONS FFPE biopsy tissues are an adequate source for FGFR2 evaluation in gastric carcinomas, and a qPCR-based copy number assay can be used for screening. IHC is also a valid and practical method for evaluating FGFR2, considering frequent heterogeneity.
Collapse
Affiliation(s)
- Young Soo Park
- Department of Pathology, University of Ulsan College of Medicine, Republic of Korea
| | - Young-Soon Na
- Asan Institute for Life Science, University of Ulsan College of Medicine, Republic of Korea
| | - Min-Hee Ryu
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Republic of Korea
| | - Chae-Won Lee
- Asan Institute for Life Science, University of Ulsan College of Medicine, Republic of Korea
| | - Hye Jin Park
- Department of Pathology, University of Ulsan College of Medicine, Republic of Korea
| | - Ju-Kyung Lee
- Asan Institute for Life Science, University of Ulsan College of Medicine, Republic of Korea
| | - Sook Ryun Park
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Republic of Korea
| | - Baek-Yeol Ryoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Republic of Korea
| | - Yoon-Koo Kang
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Republic of Korea
| |
Collapse
|
37
|
Han Q, Deng ZQ, Xin L, Cao JQ, Hu XY, Mao SX. Clinical significance of dopa decarboxylase expression in gastric peritoneal lavage in patients with gastric adenocarcinoma. Shijie Huaren Xiaohua Zazhi 2015; 23:959-963. [DOI: 10.11569/wcjd.v23.i6.959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To detect the mRNA expression of dopa decarboxylase (DDC) in intraperitoneal lavage fluid from patients with gastric adenocarcinoma, and to evaluate the possibility of using DDC expression in intraperitoneal lavage fluid as a new predictor of peritoneal micrometastasis of gastric adenocarcinoma.
METHODS: Intraperitoneal lavage fluid samples were collected from 87 patients with gastric adenocarcinoma treated in the Second Affiliated Hospital of Nanchang University. Quantitative real-time polymerase chain reaction (QRT-PCR) was used to detect the DDC mRNA expression in intraperitoneal lavage fluid. Intraperitoneal lavage fluid samples from 12 non-cancer patients were used as negative controls.
RESULTS: In the 87 patients with gastric adenocarcinoma, the number of patients with T1, T2, T3 and T4 stage disease was 6, 14, 28 and 39, respectively. The relative expression levels (×107) of DDC mRNA in different T stages (invasion grade) were: T1, 168 ± 21; T2, 283 ± 87; T3, 31162 ± 4261; T4, 35310 ± 6593; and 60.28 ± 19.00 in non-cancer group. The expression of DDC was also correlated with the degree of tumor differentiation, pathological type and lymph node metastasis. Conventional intraperitoneal cytology (CY) revealed positive results (CY+) in 11 patients, and the positive rate was 13% (11/87). In 9 of 11 CY+ cases, the DDC mRNA expression was higher than the critical value (classified as DDC+), and the sensitivity of DDC detection was 86% (9/11). In addition, only two DDC+ cases were found in the 10 patients with T1 and 14 with T2 disease, and no DDC+ result was observed in the non-cancer group. The DDC specificity was 92% (22/24). Differential expression of DDC in intraperitoneal lavage fluid was noted in gastric adenocarcinoma with different depth of invasion (P < 0.05).
CONCLUSION: QRT-PCR can effectively detect DDC mRNA expression in intraperitoneal lavage fluid, which may become a new reliable predictor of peritoneal metastasis of gastric adenocarcinoma.
Collapse
|
38
|
Ciccocioppo R, Racca F, Paolucci S, Campanini G, Pozzi L, Betti E, Riboni R, Vanoli A, Baldanti F, Corazza GR. Human cytomegalovirus and Epstein-Barr virus infection in inflammatory bowel disease: Need for mucosal viral load measurement. World J Gastroenterol 2015; 21:1915-1926. [PMID: 25684960 PMCID: PMC4323471 DOI: 10.3748/wjg.v21.i6.1915] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/03/2014] [Accepted: 11/19/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To evaluate the best diagnostic technique and risk factors of the human Cytomegalovirus (HCMV) and Epstein-Barr virus (EBV) infection in inflammatory bowel disease (IBD).
METHODS: A cohort of 40 IBD patients (17 refractory) and 40 controls underwent peripheral blood and endoscopic colonic mucosal sample harvest. Viral infection was assessed by quantitative real-time polymerase chain reaction and immunohistochemistry, and correlations with clinical and endoscopic indexes of activity, and risk factors were investigated.
RESULTS: All refractory patients carried detectable levels of HCMV and/or EBV mucosal load as compared to 13/23 (56.5%) non-refractory and 13/40 (32.5%) controls. The median DNA value was significantly higher in refractory (HCMV 286 and EBV 5.440 copies/105 cells) than in non-refractory (HCMV 0 and EBV 6 copies/105 cells; P < 0.05 and < 0.001) IBD patients and controls (HCMV and EBV 0 copies/105 cells; P < 0.001 for both). Refractory patients showed DNA peak values ≥ 103 copies/105 cells in diseased mucosa in comparison to non-diseased mucosa (P < 0.0121 for HCMV and < 0.0004 for EBV), while non-refractory patients and controls invariably displayed levels below this threshold, thus allowing us to differentiate viral colitis from mucosal infection. Moreover, the mucosal load positively correlated with the values found in the peripheral blood, whilst no correlation with the number of positive cells at immunohistochemistry was found. Steroid use was identified as a significant risk factor for both HCMV (P = 0.018) and EBV (P = 0.002) colitis. Finally, a course of specific antiviral therapy with ganciclovir was successful in all refractory patients with HCMV colitis, whilst refractory patients with EBV colitis did not show any improvement despite steroid tapering and discontinuation of the other medications.
CONCLUSION: Viral colitis appeared to contribute to mucosal lesions in refractory IBD, and its correct diagnosis and management require quantitative real-time polymerase chain reaction assay of mucosal specimens.
Collapse
|
39
|
Shi H, Han J, Yue S, Zhang T, Zhu W, Zhang D. Prognostic significance of combined microRNA-206 and CyclinD2 in gastric cancer patients after curative surgery: A retrospective cohort study. Biomed Pharmacother 2015; 71:210-5. [PMID: 25960238 DOI: 10.1016/j.biopha.2014.12.037] [Citation(s) in RCA: 16] [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: 11/29/2014] [Accepted: 12/30/2014] [Indexed: 12/22/2022] Open
Abstract
AIM To investigate associations of microRNA (miR)-206 and CyclinD2 (CCND2) expression, alone or in combination, with clinicopathological characteristics and patients' prognosis in gastric cancer. METHODS MiR-206 and CCND2 mRNA expression levels were detected by real-time quantitative RT-PCR in 220 self-pairs of gastric cancer and adjacent non-cancerous tissues. RESULTS Compared with the adjacent non-cancerous tissues, the expression levels of miR-206 and CCND2 mRNA were respectively reduced and elevated in gastric cancer tissues dramatically (both P<0.001). Notably, the expression levels of miR-206 in gastric cancer tissues were negatively correlated with those of CCND2 mRNA significantly (r=-0.463, P<0.001). Then, statistical analysis showed that low miR-206 expression and high CCND2 expression, alone or in combination, were all significantly associated with great depth of invasion, positive lymph node and distant metastases, and advanced TNM stage of human gastric cancer (all P<0.05). After that, we also found that the overall survivals of the patients with low miR-206 expression and high CCND2 expression were respectively shorter than those with high miR-206 expression and low CCND2 expression. More interestingly, miR-206-low/CCND2-high expression was associated with a significantly worst overall survival of all miR-206/CCND2 groups (P<0.001). Furthermore, multivariate analysis identified miR-206 and/or CCND2 expression as independent prognostic factors for overall survival in patients with gastric cancer. CONCLUSION Our data provide evidence that the dysregulation of miR-206-CCND2 axis may contribute to the aggressive progression and poor prognosis of human gastric cancer in clinical settings. Combined detection of their expression might be particularly helpful for surveillance of disease progression and treatment stratification.
Collapse
Affiliation(s)
- Huichang Shi
- Department of Oncology, First Hospital of Huai'an, Nanjing Medical University, Huai'an 223300, China
| | - Jun Han
- Department of Oncology, First Hospital of Huai'an, Nanjing Medical University, Huai'an 223300, China
| | - Shun Yue
- Department of Oncology, First Hospital of Huai'an, Nanjing Medical University, Huai'an 223300, China
| | - Tiecheng Zhang
- Department of Oncology, First Hospital of Huai'an, Nanjing Medical University, Huai'an 223300, China
| | - Weiguo Zhu
- Department of Oncology, First Hospital of Huai'an, Nanjing Medical University, Huai'an 223300, China
| | - Dahong Zhang
- Department of Oncology, First Hospital of Huai'an, Nanjing Medical University, Huai'an 223300, China.
| |
Collapse
|
40
|
Bach C, Tomova E, Goldmann K, Weisbach V, Roesler W, Mackensen A, Winkler J, Spriewald BM. Monitoring of hematopoietic chimerism by real-time quantitative PCR of micro insertions/deletions in samples with low DNA quantities. Transfus Med Hemother 2014; 42:38-45. [PMID: 25960714 DOI: 10.1159/000370255] [Citation(s) in RCA: 18] [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: 02/18/2014] [Accepted: 12/22/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Sensitive and accurate methods to detect hematopoietic chimerism after hematopoietic stem cell transplantation (HSCT) are essential to evaluate engraftment and to monitor response to therapeutic procedures such as donor lymphocyte infusion. Continuous long-term follow up, however, requires large amounts of pre-HSCT samples limiting the application of many widely used techniques for sensitive chimerism monitoring. METHODS DNAs from 42 normal healthy donors and 16 HSCT donor/recipient pairs were employed to validate the use of allele-specific insertion/deletion (indel) quantitative real-time polymerase chain reaction (qPCR) to quantify chimerism in samples with low amounts of DNA. Consequently, indel-qPCR analyses of samples from 16 HSCT patients were compared to short-tandem repeat (STR) specific PCR analyses. RESULTS Typing with reduced amounts of input DNA (15 vs. 60 ng) allowed for the reliable distinction of positive (mean threshold cycle (ct) 28.05) and negative (ct >36) signals. The high informativity of primer/probe sets, with 12 out of 19 markers exceeding 20% informativity, was confirmed in our cohort (n = 74). Importantly, a fourfold reduction of input DNA compared to published protocols did not alter PCR efficiencies and allowed for a more sensitive detection of chimerism in 7 of 16 HSCT patients compared to results obtained by STR-PCR. CONCLUSIONS Our data suggest that indel-qPCR is a more sensitive technique for the detection of hematopoietic chimerism compared to STR-PCR and works efficiently for samples with low amounts of DNA.
Collapse
Affiliation(s)
- Christian Bach
- Department of Internal Medicine 5, Hematology/Oncology, University Hospital Erlangen, Erlangen, Germany
| | - Elmira Tomova
- Department of Internal Medicine 5, Hematology/Oncology, University Hospital Erlangen, Erlangen, Germany
| | - Katja Goldmann
- Department of Internal Medicine 5, Hematology/Oncology, University Hospital Erlangen, Erlangen, Germany
| | - Volker Weisbach
- Department of Transfusion Medicine and Hemostaseology, University Hospital Erlangen, Erlangen, Germany
| | - Wolf Roesler
- Department of Internal Medicine 5, Hematology/Oncology, University Hospital Erlangen, Erlangen, Germany
| | - Andreas Mackensen
- Department of Internal Medicine 5, Hematology/Oncology, University Hospital Erlangen, Erlangen, Germany
| | - Julia Winkler
- Department of Internal Medicine 5, Hematology/Oncology, University Hospital Erlangen, Erlangen, Germany
| | - Bernd M Spriewald
- Department of Internal Medicine 5, Hematology/Oncology, University Hospital Erlangen, Erlangen, Germany
| |
Collapse
|
41
|
Borowczyk M, Wojtaszewska M, Lewandowski K, Gil L, Lewandowska M, Lehmann-Kopydłowska A, Kroll-Balcerzak R, Balcerzak A, Iwoła M, Michalak M, Komarnicki M. The JAK2 V617F mutational status and allele burden may be related with the risk of venous thromboembolic events in patients with Philadelphia-negative myeloproliferative neoplasms. Thromb Res 2014; 135:272-80. [PMID: 25559461 DOI: 10.1016/j.thromres.2014.11.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [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: 06/02/2014] [Revised: 11/03/2014] [Accepted: 11/10/2014] [Indexed: 01/24/2023]
Abstract
INTRODUCTION Patients with Philadelphia-negative myeloproliferative neoplasms (Ph(-) MPNs) are at increased risk of thromboembolic and hemorrhagic complications. The aim of the study was to determine the relationship between JAK2 V617F mutational status, JAK2 V617F allele burden and the risk of vascular complications occurrence. MATERIALS AND METHODS Analysis was performed in a cohort of 186 patients diagnosed with polycythemia vera (53), essential thrombocythemia (114), primary myelofibrosis (11), and unclassified MPN (8). The risk of vascular complications development was analyzed in 126 JAK2 V617F-positive patients with respect to allele burden assessed with allele-specific 'real-time' quantitative polymerase chain reaction (AS RQ-PCR). RESULTS Overall prevalence of any vascular complications was 44.6%. Arterial thrombosis occurred in 20.4%, venous thromboembolism (VTE) in 11.3%, bleeding episodes in 24.7% of patients. Individuals harboring JAK2 V617F mutation, regardless of MPN type, were at higher risk of VTE (OR=5.15, 95%CI: 1.16-22.90, P=0.024), mainly deep vein thrombosis (DVT). JAK2 allele burden higher than 20% identified patients with 7.4-fold increased risk of VTE (95%CI: 1.6-33.7, P=0.004), but not of arterial thrombosis, neither of bleeding complications, and remained the only significant VTE risk factor in multivariate logistic regression. High allele burdens (over 50%) were strikingly associated with proximal DVT cases, but not with distal DVT. CONCLUSIONS The group of MPN patients with JAK2 V617F allele burden higher than 20% may benefit the most from vigilant monitoring and appropriate prophylaxis against vascular events. Inclusion of JAK2 V617F mutant allele burden in new risk stratifications seems to be justified and requires controlled prospective trials.
Collapse
Affiliation(s)
- Martyna Borowczyk
- Department of Hematology and Bone Marrow Transplantation, Poznań University of Medical Sciences, Poznań, Poland.
| | - Marzena Wojtaszewska
- Department of Hematology and Bone Marrow Transplantation, Poznań University of Medical Sciences, Poznań, Poland
| | - Krzysztof Lewandowski
- Department of Hematology and Bone Marrow Transplantation, Poznań University of Medical Sciences, Poznań, Poland
| | - Lidia Gil
- Department of Hematology and Bone Marrow Transplantation, Poznań University of Medical Sciences, Poznań, Poland
| | - Maria Lewandowska
- Department of Hematology and Bone Marrow Transplantation, Poznań University of Medical Sciences, Poznań, Poland
| | - Agata Lehmann-Kopydłowska
- Department of Hematology and Bone Marrow Transplantation, Poznań University of Medical Sciences, Poznań, Poland
| | - Renata Kroll-Balcerzak
- Department of Hematology and Bone Marrow Transplantation, Poznań University of Medical Sciences, Poznań, Poland
| | - Andrzej Balcerzak
- Department of Hematology and Bone Marrow Transplantation, Poznań University of Medical Sciences, Poznań, Poland
| | - Małgorzata Iwoła
- Department of Hematology and Bone Marrow Transplantation, Poznań University of Medical Sciences, Poznań, Poland
| | - Michał Michalak
- Department of Computer Science and Statistics, Poznań University of Medical Sciences, Poznań, Poland
| | - Mieczysław Komarnicki
- Department of Hematology and Bone Marrow Transplantation, Poznań University of Medical Sciences, Poznań, Poland
| |
Collapse
|
42
|
Han J, Rong LF, Shi CB, Dong XG, Wang J, Wang BL, Wen H, He ZY. Screening of lymph nodes metastasis associated lncRNAs in colorectal cancer patients. World J Gastroenterol 2014; 20:8139-8150. [PMID: 25009386 PMCID: PMC4081685 DOI: 10.3748/wjg.v20.i25.8139] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/15/2014] [Accepted: 05/14/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To screen lymph nodes metastasis associated long noncoding RNAs (lncRNAs) in colorectal cancer through microarray analysis.
METHODS: Metastatic lymph node (MLN), normal lymph node (NLN) and tumor tissues of 3 colorectal cancer (CRC) patients were collected during the operation and validated by pathological examinations. RNAs were extracted from MLN, NLN, and cancer tissues separately. RNA quantity and quality were measured with a NanoDrop ND-1000 spectrophotometer and RNA integrity was assessed by standard denaturing agarose electrophoresis. Agilent Feature Extraction Software (Version 11.0.1.1) was used to analyze acquired array images. Four differently expressed lncRNAs were confirmed by quantitative real-time polymerase chain reaction (qRT-PCR) in 26 subsets of MLN, NLN, and tumor tissues.
RESULTS: Of 33045 lncRNAs, 1133 were differentially expressed in MLN compared with NLN, of which 260 were up-regulated and 873 down-regulated (≥ 2 fold-change). Five hundred and forty-five lncRNAs were differentially expressed in MLN compared with tumor tissues, of which 460 were up-regulated and 85 down-regulated (≥ 2 fold-change). Compared with NLN and cancer tissues, 14 lncRNAs were specifically up-regulated and 5 specifically down-regulated in MLN. AK307796, ENST00000425785, and AK021444 were confirmed to be specifically up-regulated in MLN and ENST00000465846 specifically down-regulated in MLN by qRT-PCR in 26 CRC patients.
CONCLUSION: The specifically expressed lncRNAs in MLN may exert a partial or key role in the progress of lymph nodes metastasis of CRC.
Collapse
|
43
|
Tajadini M, Panjehpour M, Javanmard SH. Comparison of SYBR Green and TaqMan methods in quantitative real-time polymerase chain reaction analysis of four adenosine receptor subtypes. Adv Biomed Res 2014; 3:85. [PMID: 24761393 PMCID: PMC3988599 DOI: 10.4103/2277-9175.127998] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 05/22/2013] [Indexed: 12/14/2022] Open
Abstract
Background: Real-time polymerase chain reaction (PCR) is based on the revolutionary method of PCR. This technique is the result of PCR enormous sensitivity and real-time monitoring combination. In quantitative gene expression analysis, two methods have more popularity, SYBR Green and TaqMan, SYBR Green is relatively cost benefit and easy to use and technically based on binding the fluorescent dye to double-stranded deoxyribonucleic acid (dsDNA) where TaqMan method has more expensive and based on dual labeled oligonucleotide and exonuclease activity of Taq polymerase enzyme. Specificity is the most important concern with the usage of any non-specific dsDNA-binding Dyes such as SYBR Green whiles more specificity showed by labeled oligonucleotide method such as TaqMan. In this study, we compared two common RT PCR methods, TaqMan and SYBR Green in measurement gene expression profile of adenosine receptors. Materials and Methods: Gene expression profiles of A1, A2A, A2B and A3 Adenosine receptors were analyzed by optimized TaqMan and SYBR Green quantitative RT PCR in breast cancer tissues. Primary expression data was normalizing by B. actin reference gene. Results: Efficiencies were calculated more than 95% for TaqMan and SYBR Green methods in all genes. The correlations between means of normalized data of each gene in two methods were positive and significant (P < 0.05). Conclusion: Data analysis showed that with the use of high performance primer and by use proper protocols and material we can make precise data by SYBR Green as TaqMan method. In other word by optimization of SYBR Green method, its performance and quality could be comparable to TaqMan method.
Collapse
Affiliation(s)
- Mohamadhasan Tajadini
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Research Center, Isfahan University of Medical Sciences, Isfahan, Iran ; Physiology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mojtaba Panjehpour
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | | |
Collapse
|
44
|
Wisnieski F, Calcagno DQ, Leal MF, Santos LCD, Gigek CDO, Chen ES, Pontes TB, Assumpção PP, Assumpção MBD, Demachki S, Burbano RR, Smith MDAC. Reference genes for quantitative RT-PCR data in gastric tissues and cell lines. World J Gastroenterol 2013; 19:7121-7128. [PMID: 24222956 PMCID: PMC3819548 DOI: 10.3748/wjg.v19.i41.7121] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 08/06/2013] [Accepted: 08/20/2013] [Indexed: 02/06/2023] Open
Abstract
AIM: To evaluate the suitability of reference genes in gastric tissue samples and cell lines.
METHODS: The suitability of genes ACTB, B2M, GAPDH, RPL29, and 18S rRNA was assessed in 21 matched pairs of neoplastic and adjacent non-neoplastic gastric tissues from patients with gastric adenocarcinoma, 27 normal gastric tissues from patients without cancer, and 4 cell lines using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). The ranking of the best single and combination of reference genes was determined by NormFinder, geNorm™, BestKeeper, and DataAssist™. In addition, GenEx software was used to determine the optimal number of reference genes. To validate the results, the mRNA expression of a target gene, DNMT1, was quantified using the different reference gene combinations suggested by the various software packages for normalization.
RESULTS: ACTB was the best reference gene for all gastric tissues, cell lines and all gastric tissues plus cell lines. GAPDH + B2M or ACTB + B2M was the best combination of reference genes for all the gastric tissues. On the other hand, ACTB + B2M was the best combination for all the cell lines tested and was also the best combination for analyses involving all the gastric tissues plus cell lines. According to the GenEx software, 2 or 3 genes were the optimal number of references genes for all the gastric tissues. The relative quantification of DNMT1 showed similar patterns when normalized by each combination of reference genes. The level of expression of DNMT1 in neoplastic, adjacent non-neoplastic and normal gastric tissues did not differ when these samples were normalized using GAPDH + B2M (P = 0.32), ACTB + B2M (P = 0.61), or GAPDH + B2M + ACTB (P = 0.44).
CONCLUSION: GAPDH + B2M or ACTB + B2M is the best combination of reference gene for all the gastric tissues, and ACTB + B2M is the best combination for the cell lines tested.
Collapse
|
45
|
Rhim EM, Ahn SJ, Kim JY, Chang YR, Kim KH, Lee HW, Jung SH, Kim EC, Park SH. Cryopreservation induces macrophage colony stimulating factor from human periodontal ligament cells in vitro. Cryobiology 2013; 67:156-62. [PMID: 23810633 DOI: 10.1016/j.cryobiol.2013.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 04/05/2013] [Revised: 06/13/2013] [Accepted: 06/13/2013] [Indexed: 11/16/2022]
Abstract
Cryopreservation is used to protect vital periodontal ligaments during the transplantation of teeth. We investigated which gene products implicated in root resorption are upregulated in human periodontal ligament cells by cryopreservation, and whether cryopreservation affects the expression of macrophage-colony stimulating factor (M-CSF) in human periodontal ligament cells. We used customized microarrays to compare gene expression in human periodontal ligament cells cultured from teeth immediately after extraction and from cryopreserved teeth. Based on the result of these assays, we examined M-CSF expression in periodontal ligament cells from the immediately extracted tooth and cryopreserved teeth by real-time PCR, enzyme-linked immunosorbent assay (ELISA), Western blot analysis, and immunofluorescence. We also investigated whether human bone marrow cells differentiate into tartrate-resistant acid phosphatase (TRAP) positive osteoclasts when stimulated with RANKL (Receptor Activator for Nuclear Factor κ B Ligand) together with any secreted M-CSF present in the supernatants of the periodontal ligament cells cultured from the various groups of teeth. M-CSF was twofold higher in the periodontal ligament cells from the rapid freezing teeth than in those from the immediately extracted group (p < 0.05). Cryopreservation increased M-CSF expression in the periodontal ligament cells when analyzed by real time PCR, ELISA, Western blotting, and immunofluorescence (p < 0.05). TRAP positive osteoclasts were formed in response to RANKL and the secreted M-CSF present in the supernatants of all the experimental groups except negative control. These results demonstrate that cryopreservation promotes the production of M-CSF, which plays an important role in root resorption by periodontal ligament cells.
Collapse
Affiliation(s)
- E-M Rhim
- Department of Conservative Dentistry, St. Paul's Hospital, Seoul, South Korea
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Lee TH, Lee JY, Park S, Shin SH, Yahng SA, Yoon JH, Lee SE, Cho BS, Kim YJ, Lee S, Min CK, Kim DW, Lee JW, Min WS, Park CW, Kim HJ. Expression of SOCS1 and SOCS3 genes in human graft-versus-host disease after allogeneic hematopoietic stem cell transplantation. Blood Res 2013; 48:16-23. [PMID: 23589790 PMCID: PMC3625005 DOI: 10.5045/br.2013.48.1.16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [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: 09/26/2012] [Revised: 10/22/2012] [Accepted: 02/13/2013] [Indexed: 12/22/2022] Open
Abstract
Background Suppressor of cytokine signaling genes (SOCS) are regarded as pivotal negative feedback regulators of cytokine signals, including the interferon-gamma (IFN-γ), granulocyte-colony stimulating factor, and interleukin families, released by T cells. A detailed understanding of the involvement of SOCS genes in graft-versus-host disease (GVHD) is critical to effectively manage GVHD, yet their expression patterns among recipients remain largely unexplored. Methods Expression levels of SOCS1 and SOCS3 were determined by real-time quantitative reverse transcription PCR (qRT-PCR) in patients with acute GVHD (aGVHD) and chronic GVHD (cGVHD), in a severity-dependent manner, after allogeneic hematopoietic stem cell transplantation (HSCT). A total of 71 recipients with AML (N=40), ALL (N=12), myelodysplastic syndromes (MDS; N=10), chronic myelogenous leukemia (CML; N=2), severe aplastic anemia (SAA; N=5), or others (N=2), who received allogeneic HSCT from human leukocyte antigen-identical siblings or unrelated donors between 2009 and 2011, were included in the present study. Results Overall, the expression levels of SOCS1 decreased in recipients with grade II to IV aGVHD and cGVHD when compared to normal donors and non-GVHD recipients. Interestingly, the expressions of SOCS1 decreased significantly more in cGVHD than in aGVHD recipients (P=0.0091). In contrast, SOCS3 expressions were similarly reduced in all the recipients. Conclusion This is the first study to show that SOCS1 and SOCS3 are differentially expressed in recipients following allogeneic HSCT, suggesting a prognostic correlation between SOCS genes and the development of GVHD. This result provides a new platform to study GVHD immunobiology and potential diagnostic and therapeutic targets for GVHD.
Collapse
Affiliation(s)
- Tae Hyang Lee
- Division of Hematology, Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
F S Teixeira T, Grześkowiak LM, Salminen S, Laitinen K, Bressan J, Gouveia Peluzio MDC. Faecal levels of Bifidobacterium and Clostridium coccoides but not plasma lipopolysaccharide are inversely related to insulin and HOMA index in women. Clin Nutr 2013; 32:1017-22. [PMID: 23538004 DOI: 10.1016/j.clnu.2013.02.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [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: 02/01/2013] [Accepted: 02/16/2013] [Indexed: 01/14/2023]
Abstract
BACKGROUND & AIMS The abundance of specific microbes might be associated with plasma lipopolysaccharide and insulin levels. The aims were to quantify the abundance of specific microbes and plasma LPS in females and assess their association with anthropometric, body composition and biochemical measurements. METHODS Seventeen lean (BMI 19-24.99 kg/m(2)) and fifteen obese females (BMI > 30 kg/m(2)) participated. Anthropometry, body composition, food intake and biochemical analyses were assessed. Bacterial groups in faeces were analysed by qPCR method. RESULTS Lactobacillus plantarum prevalence was higher (p = 0.005) and its counts tended to be higher in lean vs. obese group (p = 0.06). Bifidobacterium genus, Bifidobacterium longum, Clostridium coccoides and Clostridium leptum counts were higher in lean women (p < 0.05); prevalence and counts of Akkermansia muciniphila tended to be higher in lean group (p = 0.09, p = 0.06, respectively). Plasma LPS levels were similar between the study groups (p > 0.05). No association was found between LPS and bacterial levels or insulin. Bifidobacteria and C. coccoides counts were inversely associated with insulin and HOMA index. CONCLUSIONS Abundance of specific microbes is distinct between obese and lean women, but is not associated with LPS level. Bifidobacterial and C. coccoides levels are associated with insulin sensitivity. These bacterial groups may be capable of modulating insulin action.
Collapse
Affiliation(s)
- T F S Teixeira
- Laboratory of Nutritional Biochemistry, Department of Nutrition and Health, Federal University of Viçosa, University Campus, 36.570-000 Viçosa, Minas Gerais, Brazil.
| | | | | | | | | | | |
Collapse
|
48
|
Cieśla A, Kuśmider M, Faron-Górecka A, Dziedzicka-Wasylewska M, Bociąga-Jasik M, Owczarek D, Ciećko-Michalska I, Cibor D, Mach T. Intrahepatic expression of genes related to metabotropic receptors in chronic hepatitis. World J Gastroenterol 2012; 18:4156-61. [PMID: 22919248 PMCID: PMC3422796 DOI: 10.3748/wjg.v18.i31.4156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 04/23/2012] [Accepted: 04/27/2012] [Indexed: 02/06/2023] Open
Abstract
AIM: To screen for genes related to metabotropic receptors that might be involved in the development of chronic hepatitis.
METHODS: Assessment of 20 genes associated with metabotropic receptors was performed in liver specimens obtained by punch biopsy from 12 patients with autoimmune and chronic hepatitis type B and C. For this purpose, a microarray with low integrity grade and with oligonucleotide DNA probes complementary to target transcripts was used. Evaluation of gene expression was performed in relation to transcript level, correlation between samples and grouping of clinical parameters used in chronic hepatitis assessment. Clinical markers of chronic hepatitis included alanine and aspartate aminotransferase, γ-glutamyltranspeptidase, alkaline phosphatase and cholinesterase activity, levels of iron ions, total cholesterol, triglycerides, albumin, glucose, hemoglobin, platelets, histological analysis of inflammatory and necrotic status, fibrosis according to METAVIR score, steatosis, as well as anthropometric body mass index, waist/hip index, percentage of adipose tissue and liver size in ultrasound examination. Gender, age, concomitant diseases and drugs were also taken into account. Validation of oligonucleotide microarray gene expression results was done with the use of quantitative real-time polymerase chain reaction (qRT-PCR).
RESULTS: The highest (0.002 < P < 0.046) expression among genes encoding main components of metabotropic receptor pathways, such as the α subunit of G-coupled protein, phosphoinositol-dependent protein kinase or arrestin was comparable to that of angiotensinogen synthesized in the liver. Carcinogenesis suppressor genes, such as chemokine ligand 4, transcription factor early growth response protein 1 and lysophosphatidic acid receptor, were characterized by the lowest expression (0.002 < P < 0.046), while the factor potentially triggering hepatic cancer, transcription factor JUN-B, had a 20-fold higher expression. The correlation between expression of genes of protein kinases PDPK1, phosphoinositide 3-kinase and protein kinase A (Spearman’s coefficient range: 0.762-0.769) confirmed a functional link between these enzymes. Gender (P = 0.0046) and inflammation severity, measured by alanine aminotransferase activity (P = 0.035), were characterized by diverse metabotropic receptor gene expression patterns. The Pearson’s coefficient ranging from -0.35 to 0.99 from the results of qRT-PCR and microarray indicated that qRT-PCR had certain limitations as a validation tool for oligonucleotide microarray studies.
CONCLUSION: A microarray-based analysis of hepatocyte metabotropic G-protein-related gene expression can reveal the molecular basis of chronic hepatitis.
Collapse
|
49
|
Malinen E, Krogius-Kurikka L, Lyra A, Nikkilä J, Jääskeläinen A, Rinttilä T, Vilpponen-Salmela T, Wright AJV, Palva A. Association of symptoms with gastrointestinal microbiota in irritable bowel syndrome. World J Gastroenterol 2010; 16:4532-40. [PMID: 20857523 PMCID: PMC2945484 DOI: 10.3748/wjg.v16.i36.4532] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the correlations between self-reported symptoms of irritable bowel syndrome (IBS) and the gastrointestinal (GI) microbiota composition.
METHODS: Fecal samples were collected from a total of 44 subjects diagnosed with IBS. Their symptoms were monitored with a validated inflammatory bowel disease questionnaire adjusted for IBS patients. Thirteen quantitative real-time polymerase chain reaction assays were applied to evaluate the GI microbiota composition. Eubacteria and GI bacterial genera (Bifidobacterium, Lactobacillus and Veillonella), groups (Clostridium coccoides/Eubacterium rectale, Desulfovibrio desulfuricans) and distinct bacterial phylotypes [closest 16S rDNA sequence resemblance to species Bifidobacterium catenulatum, Clostridium cocleatum, Collinsella aerofaciens (C. aerofaciens), Coprococcus eutactus (C. eutactus), Ruminococcus torques and Streptococcus bovis] with a suspected association with IBS were quantified. Correlations between quantities or presence/absence data of selected bacterial groups or phylotypes and various IBS-related symptoms were investigated.
RESULTS: Associations were observed between subjects’ self-reported symptoms and the presence or quantities of certain GI bacteria. A Ruminococcus torques (R. torques)-like (94% similarity in 16S rRNA gene sequence) phylotype was associated with severity of bowel symptoms. Furthermore, among IBS subjects with R. torques 94% detected, the amounts of C. cocleatum 88%, C. aerofaciens-like and C. eutactus 97% phylotypes were significantly reduced. Interesting observations were also made concerning the effect of a subject’s weight on GI microbiota with regard to C. aerofaciens-like phylotype, Bifidobacterium spp. and Lactobacillus spp.
CONCLUSION: Bacteria seemingly affecting the symptom scores are unlikely to be the underlying cause or cure of IBS, but they may serve as biomarkers of the condition.
Collapse
|
50
|
Sampieri CL, de la Peña S, Ochoa-Lara M, Zenteno-Cuevas R, León-Córdoba K. Expression of matrix metalloproteinases 2 and 9 in human gastric cancer and superficial gastritis. World J Gastroenterol 2010; 16:1500-5. [PMID: 20333791 PMCID: PMC2846256 DOI: 10.3748/wjg.v16.i12.1500] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To assess expression of matrix metalloproteinases 2 (MMP2) and MMP9 in gastric cancer, superficial gastritis and normal mucosa, and to measure metalloproteinase activity.
METHODS: MMP2 and MMP9 mRNA expression was determined by quantitative real-time polymerase chain reaction. Normalization was carried out using three different factors. Proteins were analyzed by quantitative gelatin zymography (qGZ).
RESULTS: 18S ribosomal RNA (18SRNA) was very highly expressed, while hypoxanthine ribosyltransferase-1 (HPRT-1) was moderately expressed. MMP2 was highly expressed, while MMP9 was not detected or lowly expressed in normal tissues, moderately or highly expressed in gastritis and highly expressed in cancer. Relative expression of 18SRNA and HPRT-1 showed no significant differences. Significant differences in MMP2 and MMP9 were found between cancer and normal tissue, but not between gastritis and normal tissue. Absolute quantification of MMP9 echoed this pattern, but differential expression of MMP2 proved conflictive. Analysis by qGZ indicated significant differences between cancer and normal tissue in MMP-2, total MMP-9, 250 and 110 kDa bands.
CONCLUSION: MMP9 expression is enhanced in gastric cancer compared to normal mucosa; interpretation of differential expression of MMP2 is difficult to establish.
Collapse
|