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Kong X, Xiong Y, Li L. LINC01605 promotes malignant phenotypes of cervical cancer via miR-149-3p/WNT7B axis. Gene 2024; 921:148518. [PMID: 38734188 DOI: 10.1016/j.gene.2024.148518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Long non-coding RNAs (LncRNA) play a pivotal role in the progression of various malignancies. Despite recent identification as an oncogene associated with tumorigenesis. The precise role of LINC01605 in cervical cancer (CC) remains unclear. Therefore, the objective of this study was to investigate the influence of LINC01605 on proliferation and invasion of CC cells, while also exploring its potential underlying mechanisms. METHODS The expression of LINC01605 in CC cell lines was analyzed using the TCGA database and qRT-PCR. Various assays, including CCK-8 and transwell analysis, were conducted on CC cells to assess the influence of LINC01605 on their proliferation, migration, and invasion capabilities. Bioinformatics and dual luciferase reporter gene assays were employed to analyze the target genes of LINC01605 and miR-149-3p. To further investigate the mechanism of action, transfection and investigation were performed using specific siRNA, miRNA mimics, or inhibitors. RESULTS The expression of LINC01605 exhibited a significant increase in CC cell lines, and this upregulation was associated with an unfavorable prognosis. Modulating the expression of LINC01605, either by down-regulating or up-regulating it, exerted suppressive or stimulatory effects on the growth and invasion of HeLa and Siha cells. LINC01605 functioned as a competitive endogenous RNA (ceRNA) for miR-149-3p, with WNT7B being identified as a target gene of miR-149-3p. The involvement of LINC01605 in CC development is facilitated by its ability to regulate the expression of WNT7B through sequestering miR-149-3p. CONCLUSION Our study demonstrates that LINC01605 acts as a competitive endogenous RNA in modulating the effects of WNT7B on the proliferation and invasion of CC cells by sequestering miR-149-3p. This research provides novel insights into the involvement of LINC01605 in the advancement of CC.
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Affiliation(s)
- Xiaoyu Kong
- School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Yuanpeng Xiong
- Department of General Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Liping Li
- School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China; The First Hospital of Nanchang (also known as the Third Affiliated Hospital of Nanchang University), Nanchang, 330006, China.
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2
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Sogore T, Guo M, Sun N, Jiang D, Shen M, Ding T. Microbiological and chemical hazards in cultured meat and methods for their detection. Compr Rev Food Sci Food Saf 2024; 23:e13392. [PMID: 38865212 DOI: 10.1111/1541-4337.13392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/23/2024] [Accepted: 05/19/2024] [Indexed: 06/14/2024]
Abstract
Cultured meat, which involves growing meat in a laboratory rather than breeding animals, offers potential benefits in terms of sustainability, health, and animal welfare compared to conventional meat production. However, the cultured meat production process involves several stages, each with potential hazards requiring careful monitoring and control. Microbial contamination risks exist in the initial cell collection from source animals and the surrounding environment. During cell proliferation, hazards may include chemical residues from media components such as antibiotics and growth factors, as well as microbial issues from improper bioreactor sterilization. In the differentiation stage where cells become muscle tissue, potential hazards include residues from scaffolding materials, microcarriers, and media components. Final maturation and harvesting stages risk environmental contamination from nonsterile conditions, equipment, or worker handling if proper aseptic conditions are not maintained. This review examines the key microbiological and chemical hazards that must be monitored and controlled during the manufacturing process for cultured meats. It describes some conventional and emerging novel techniques that could be applied for the detection of microbial and chemical hazards in cultured meat. The review also outlines the current evolving regulatory landscape around cultured meat and explains how thorough detection and characterization of microbiological and chemical hazards through advanced analytical techniques can provide crucial data to help develop robust, evidence-based food safety regulations specifically tailored for the cultured meat industry. Implementing new digital food safety methods is recommended for further research on the sensitive and effective detection of microbiological and chemical hazards in cultured meat.
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Affiliation(s)
- Tahirou Sogore
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Meimei Guo
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Na Sun
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Donglei Jiang
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, China
| | - Mofei Shen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Zhongyuan Institute, Zhejiang University, Zhengzhou, China
| | - Tian Ding
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, China
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3
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Goncu B. Identification of suitable reference genes for RT-qPCR studies in human parathyroid tissue glandular cells. Gene 2024; 912:148380. [PMID: 38490511 DOI: 10.1016/j.gene.2024.148380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/06/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024]
Abstract
Identifying a proper reference gene allows us to understand fundamental changes in many biological processes. Normalization during gene expression analyses is essential for every tissue/cell type, including parathyroid tissue glandular cells. Quantitative method of gene expression analyses via qRT-PCR method provides the accurate examination of every target gene. There are limited reports to present commonly used reference genes in human parathyroid tissues rather than for glandular cell types. This study aims to determine and compare the most stable to least stable genes for parathyroid tissue cells. 43 human parathyroid tissue obtained from primary and secondary hyperparathyroidism patients and glandular cells isolated enzymatically by the removal of extracellular matrix components. After extraction of the total RNA, cDNA synthesis was performed, then qRT-PCR evaluated 14 candidate reference genes. Stability was determined by RefFinder software (Delta ct, BestKeeper, Genorm, and NormFinder algorithms), and the outcome was evaluated for five groups. Even if assessed with different groups, the most stable genes were RPLP0 and GAPDH, while the CLTC and RNA 18S were the least stable. We have confirmed the comprehensive ranking of the most stable three genes alone with the NormFinder algorithm to understand intergroup variation and found out that RPLP0>GAPDH>PGK1. Lastly, comparisons of relative target gene (GCM2) expression revealed similar expression patterns for the most stable reference genes. The most stable reference gene is recommended for the stages where stability is evaluated using the results of four different approaches using RefFinder. We aspire for this study to assist future research to conduct thorough assessments of appropriate reference genes before engaging in gene expression analyses for parathyroid tissue.
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Affiliation(s)
- Beyza Goncu
- Bezmialem Vakif University, Vocational School of Health Services, Department of Medical Services and Techniques, Istanbul, Turkiye; Bezmialem Vakif University Hospital, Organ Transplantation Center, Parathyroid Transplantation Unit, Istanbul, Turkiye.
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4
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Safdari H, Bagheri S, Talkhi N, Saberi Teymourian E, Hosseini Bafghi M, Ahmadi MH. Cq values as an indicator for COVID-19 outcomes: A study of the correlation between laboratory parameters. Immun Inflamm Dis 2024; 12:e1326. [PMID: 38923849 PMCID: PMC11194972 DOI: 10.1002/iid3.1326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/26/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
OBJECTIVE The ongoing outbreak of the respiratory disease coronavirus disease 2019 (COVID-19) is currently presenting a major global health threat. This pandemic is unprecedented in recent human history. The objective of this study was to examine the relationship between cycle quantitation (Cq) and laboratory parameters in COVID-19 patients, aiming to determine if Cq levels can provide valuable insights into the COVID-19 disease. METHODS This study involved 234 participants who were divided into case and control groups. Real-time PCR tests were used to diagnose COVID-19 cases in the study participants. Blood tests, including complete blood count, C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), lactate dehydrogenase (LDH), D-dimer, IgG, and IgM, were also conducted. Statistical analysis was performed using SPSS 22 software. RESULTS The findings showed that COVID-19-positive cases had significantly higher levels of the neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), D-dimer, ESR, CRP, and LDH compared to normal cases. Additionally, the case group had significantly lower lymphocyte and platelet counts. There was a statistically significant positive correlation between Cq levels and lymphocyte count (r = .124, p = .014). Conversely, there was a statistically significant inverse correlation between Cq levels and NLR (r = -.208, p = .017). Furthermore, the evaluation of hematological, inflammatory, and biochemical indexes in COVID-19 patients using the receiver-operating characteristics curve demonstrated statistically appropriate sensitivity and specificity. CONCLUSION Our outcomes indicated a significant association between Cq levels and PLR, NLR, D-dimer, CRP, and ESR in COVID-19 patients. Consequently, including the report of laboratory parameters alongside Cq values offers a promising prognosis.
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Affiliation(s)
- Hadi Safdari
- Department of Laboratory Sciences, School of Paramedical Sciences, Faculty of Paramedical and Rehabilitation SciencesMashhad University of Medical SciencesMashhadIran
| | - Saeede Bagheri
- Department of Laboratory Sciences, School of Paramedical Sciences, Faculty of Paramedical and Rehabilitation SciencesMashhad University of Medical SciencesMashhadIran
| | - Nasrin Talkhi
- Department of Biostatistics, School of Allied Medical SciencesShahid Beheshti University of Medical SciencesTehranIran
| | - Elahe Saberi Teymourian
- Department of Laboratory Sciences, School of Paramedical Sciences, Faculty of Paramedical and Rehabilitation SciencesMashhad University of Medical SciencesMashhadIran
| | - Mahdi Hosseini Bafghi
- Department of Laboratory Sciences, School of Paramedical Sciences, Faculty of Paramedical and Rehabilitation SciencesMashhad University of Medical SciencesMashhadIran
| | - Mohammad Hossein Ahmadi
- Department of Laboratory Sciences, School of Paramedical Sciences, Faculty of Paramedical and Rehabilitation SciencesMashhad University of Medical SciencesMashhadIran
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Wang B, Chen X, Huang S, Tan J, Zhang H, Wang J, Chen R, Zhang M. Bulk Segregant Analysis Sequencing and RNA-Seq Analyses Reveal Candidate Genes Associated with Sepal Color Phenotype of Eggplant ( Solanum melongena L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1385. [PMID: 38794455 PMCID: PMC11124939 DOI: 10.3390/plants13101385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Eggplant is a highly significant vegetable crop and extensively cultivated worldwide. Sepal color is considered one of the major commercial traits of eggplant. Eggplant sepals develop from petals, and sepals have the ability to change color by accumulating anthocyanins, but whether the eggplants in sepal and their biosynthetic pathways are the same as those in petals is not known. To date, little is known about the underlying mechanisms of sepal color formation. In this study, we performed bulked segregant analysis and transcriptome sequencing using eggplant sepals and obtained 1,452,898 SNPs and 182,543 InDel markers, respectively, as well as 123.65 Gb of clean data using transcriptome sequencing. Through marker screening, the genes regulating eggplant sepals were localized to an interval of 2.6 cM on chromosome 10 by bulked segregant analysis sequencing and transcriptome sequencing and co-analysis, combined with screening of molecular markers by capillary electrophoresis. Eight possible candidate genes were then screened to further interpret the regulatory incentives for the eggplant sepal color.
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Affiliation(s)
| | | | | | | | | | | | | | - Min Zhang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China; (B.W.); (X.C.); (S.H.); (J.T.); (H.Z.); (J.W.); (R.C.)
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6
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Li F, Xiang R, Liu Y, Hu G, Jiang Q, Jia T. Approaches and challenges in identifying, quantifying, and manipulating dynamic mitochondrial genome variations. Cell Signal 2024; 117:111123. [PMID: 38417637 DOI: 10.1016/j.cellsig.2024.111123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/14/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Mitochondria, the cellular powerhouses, possess their own unique genetic system, including replication, transcription, and translation. Studying these processes is crucial for comprehending mitochondrial disorders, energy production, and their related diseases. Over the past decades, various approaches have been applied in detecting and quantifying mitochondrial genome variations with also the purpose of manipulation of mitochondria or mitochondrial genome for therapeutics. Understanding the scope and limitations of above strategies is not only fundamental to the understanding of basic biology but also critical for exploring disease-related novel target(s), as well to develop innovative therapies. Here, this review provides an overview of different tools and techniques for accurate mitochondrial genome variations identification, quantification, and discuss novel strategies for the manipulation of mitochondria to develop innovative therapeutic interventions, through combining the insights gained from the study of mitochondrial genetics with ongoing single cell omics combined with advanced single molecular tools.
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Affiliation(s)
- Fei Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Run Xiang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yue Liu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Guoliang Hu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Quanbo Jiang
- Light, Nanomaterials, Nanotechnologies (L2n) Laboratory, CNRS EMR 7004, University of Technology of Troyes, 12 rue Marie Curie, 10004 Troyes, France
| | - Tao Jia
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; CNRS-UMR9187, INSERM U1196, PSL-Research University, 91405 Orsay, France; CNRS-UMR9187, INSERM U1196, Université Paris Saclay, 91405 Orsay, France.
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7
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Newman T, Chang HFK, Jabbari H. DinoKnot: Duplex Interaction of Nucleic Acids With PseudoKnots. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:348-359. [PMID: 38345958 DOI: 10.1109/tcbb.2024.3362308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Interaction of nucleic acid molecules is essential for their functional roles in the cell and their applications in biotechnology. While simple duplex interactions have been studied before, the problem of efficiently predicting the minimum free energy structure of more complex interactions with possibly pseudoknotted structures remains a challenge. In this work, we introduce a novel and efficient algorithm for prediction of Duplex Interaction of Nucleic acids with pseudoKnots, DinoKnot follows the hierarchical folding hypothesis to predict the secondary structure of two interacting nucleic acid strands (both homo- and hetero-dimers). DinoKnot utilizes the structure of molecules before interaction as a guide to find their duplex structure allowing for possible base pair competitions. To showcase DinoKnots's capabilities we evaluated its predicted structures against (1) experimental results for SARS-CoV-2 genome and nine primer-probe sets, (2) a clinically verified example of a mutation affecting detection, and (3) a known nucleic acid interaction involving a pseudoknot. In addition, we compared our results against our closest competition, RNAcofold, further highlighting DinoKnot's strengths. We believe DinoKnot can be utilized for various applications including screening new variants for potential detection issues and supporting existing applications involving DNA/RNA interactions, adding structural considerations to the interaction to elicit functional information.
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8
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Li W, He Y, Li Y, Li X, Bian T, Liu T, Liu X, Jiang W. Metagenomic next-generation sequencing for the diagnosis of neurobrucellosis. Future Microbiol 2024; 19:509-518. [PMID: 38629898 DOI: 10.2217/fmb-2023-0177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 12/06/2023] [Indexed: 06/27/2024] Open
Abstract
Objective: This study investigates the application of metagenomic next-generation sequencing (mNGS) in the diagnosis of neurobrucellosis (NB). Methods: We retrospectively analyzed patients diagnosed with NB who underwent cerebrospinal fluid (CSF) mNGS testing in Xijing Hospital from 2015 to 2021. Results: Among the 20 individuals included in the study, the serum rose bengal test was positive in 11 out of 16 cases, serum agglutination test was positive in 13 out of 16 cases, CSF culture was positive in 6 out of 11 cases, and CSF mNGS tests were positive in 18 out of 20 cases. Conclusion: CSF mNGS demonstrates superior sensitivity; therefore, it is recommended to collect CSF for mNGS testing prior to antibiotic therapy when NB is suspected.
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Affiliation(s)
- Wen Li
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Ying He
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yanyan Li
- Department of Neurology, Ordnance Industry No. 521 Hospital, Xi'an, China
| | - Xiaona Li
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Ting Bian
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Tingting Liu
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xuedong Liu
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Wen Jiang
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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Shi K, Qian X, Shi Y, Wei H, Pan Y, Long F, Zhou Q, Mo S, Hu L, Li Z. A triplex crystal digital PCR for the detection of genotypes I and II African swine fever virus. Front Vet Sci 2024; 11:1351596. [PMID: 38628942 PMCID: PMC11019002 DOI: 10.3389/fvets.2024.1351596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
African swine fever (ASF) is a highly contagious and lethal viral disease that causes severe hemorrhagic fever in pigs. It keeps spreading around the world, posing a severe socioeconomic risk and endangering biodiversity and domestic food security. ASF first outbroke in China in 2018, and has spread to most provinces nationwide. Genotypes I and II ASF virus (ASFV) as the etiological pathogens have been found in China. In this study, three pairs of specific primers and probes targeting the ASFV B646L gene, F1055L gene, and E183L gene were designed to detect universal, genotype I, and genotype II strains, respectively. A triplex crystal digital PCR (cdPCR) was established on the basis of optimizing various reaction conditions. The assay demonstrated remarkably sensitive with low limits of detection (LODs) of 5.120, 4.218, 4.588 copies/reaction for B646L, F1055L, and E183L gene, respectively; excellent repeatability with 1.24-2.01% intra-assay coefficients of variation (CVs) and 1.32-2.53% inter-assay CVs; good specificity for only detection of genotypes I and II ASFV, without cross-reactivity with PCV2, PRV, SIV, PRRSV, PEDV, FMDV, and CSFV. The triplex cdPCR was used to test 1,275 clinical samples from Guangxi province of China, and the positivity rates were 5.05, 3.22, and 1.02% for genotype I, genotype II, and co-infection of genotypes I and II, respectively. These 1,275 clinical samples were also detected using a reported reference triplex real-time quantitative PCR (qPCR), and the agreements of detection results between these two methods were more than 98.98%. In conclusion, the developed triplex cdPCR could be used as a rapid, sensitive, and accurate method to detect and differentiate genotypes I and II strains of ASFV.
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Affiliation(s)
- Kaichuang Shi
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
- College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Xinxiu Qian
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yuwen Shi
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Haina Wei
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Yi Pan
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Feng Long
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Qingan Zhou
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Shenglan Mo
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Liping Hu
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Zongqiang Li
- College of Animal Science and Technology, Guangxi University, Nanning, China
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10
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Zeng R, Du Z, Ma H, Meng X, Li E, Li J. The 60 nm gold nanoparticles improve qPCR amplification efficiency through specific palindromic sequences (GGATCC or ACCGGT) in primers. Biochim Biophys Acta Gen Subj 2024; 1868:130560. [PMID: 38211821 DOI: 10.1016/j.bbagen.2024.130560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND Polymerase chain reaction (PCR) technology and quantitative real-time PCR (qPCR) technology are widely used in clinical diagnosis and research, but amplification efficiency and sensitivity are still key problems for researchers. An increasing number of reports show that gold nanoparticles (AuNPs) can be used to improve the sensitivity and amplification efficiency of PCR. Here, we found that 60 nm gold nanoparticles with a positive charge (60 nm- Au+) can enhance the amplification efficiency of qPCR. METHODS Mouse DNA was extracted by the alkaline lysis method. Primer 5.0 software was used to design primers and mutation primers, and the DNA fragments were obtained by the method of synthesizing plasmids. The qPCR was applied to amplify target gene fragments. RESULTS The amplification efficiency of qPCR was improved by about 1.828 times in the experimental group with 60 nm- Au+ compared with the control group without 60 nm- Au+. The primer pair contains a specific palindromic sequence (GGATCC or ACCGGT). And 60 nm Au+ did not enhance the amplification efficiency of qPCR when the above primer was mutated. CONCLUSIONS The primers contain special palindrome sequences (GGATCC or ACCGGT) with 60 nm- Au+ can enhance the amplification efficiency of qPCR. Therefore, it suggests a more in-depth understanding of the mechanism and function of gold nanoparticles and primer sequences. This study has presented some implications for gold nanoparticles application in the development of qPCR technology.
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Affiliation(s)
- Ruyu Zeng
- The Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Zhiqun Du
- The Department of Pathology, Dongyang People's Hospital, Zhejiang, China
| | - Hongliang Ma
- The Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Xiuqiong Meng
- The Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Erhua Li
- Guangzhou BDS Biological Technology Co., Ltd. Guangzhou, China
| | - Jiangchao Li
- The Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
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11
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Amini A, Esmaeili F, Golpich M. Possible role of lncRNAs in amelioration of Parkinson's disease symptoms by transplantation of dopaminergic cells. NPJ Parkinsons Dis 2024; 10:56. [PMID: 38472261 PMCID: PMC10933336 DOI: 10.1038/s41531-024-00661-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are biomarkers for diagnosis and treatment of Parkinson's disease (PD). Since dopaminergic cell transplantation is a clinical method to treat PD, this study investigated the effects of dopaminergic cell therapy on the expression of some lncRNAs and genes related to PD. In this study, Twenty-eight rats were randomly assigned to four experimental groups. The control group (Sal group) received saline injections. The Par group was a PD rat model with 6-hydroxydopamine (6-OHDA) injection in right striatum (ST). PD animals were transplanted by undifferentiated P19 stem cells (Par-E group), and P19-derived dopaminergic cells (Par-N group). Cell transplant effects were evaluated using behavioral tests (cylinder, open field, and rotarod tests), and histological methods (H&E and Nissl staining, and immunohistochemistry). Moreover, the expression of lncRNAs MALAT1, MEG3, and SNHG1, alongside specific neuronal (synaptophysin) and dopaminergic (tyrosine hydroxylase) markers was evaluated by qRT-PCR. Behavioral and histopathological examinations revealed that cell transplantation partially compensated dopaminergic cell degeneration in ST and substantia nigra (SN) of PD rats. The expression of MALAT1, SNHG1, and MEG3 was decreased in the ST of the Par group, while MEG3 and SNHG1 gene expression was increased in PBMC relative to the Sal group. In PBMC of the Par-N group, all three lncRNAs showed a reduction in their expression. Conversely, MALAT1 and SNHG1 expression was increased in ST tissue, while MEG3 gene expression was decreased compared to the Sal group. In conclusion, dopaminergic cell transplantation could change the lncRNAs expression. Furthermore, it partially improves symptoms in PD rats.
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Affiliation(s)
- A Amini
- Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - F Esmaeili
- Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - M Golpich
- Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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12
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Alsaleh S, Alhussien A, Alyamani A, Alhussain F, Alhijji A, Binkhamis K, Khan A, Javer A, Alshahrani FS. Efficacy of povidone-iodine nasal rinse and mouth wash in COVID-19 management: a prospective, randomized pilot clinical trial (povidone-iodine in COVID-19 management). BMC Infect Dis 2024; 24:271. [PMID: 38429662 PMCID: PMC10905910 DOI: 10.1186/s12879-024-09137-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/14/2024] [Indexed: 03/03/2024] Open
Abstract
OBJECTIVES/HYPOTHESIS To assess the efficacy of 0.23% povidone-iodine (PVP-I) nasal rinses and mouth washes on detectability of the coronavirus disease 2019 (COVID-19) virus and cycle threshold (Ct) values in nasopharyngeal swabs. STUDY DESIGN This was an open-label, prospective, randomized, placebo-controlled clinical trial. SETTING The study was conducted in King Saud University Medical City, Riyadh, Saudi Arabia, from August 2021 to July 2022. METHODS Participants diagnosed with SARS-CoV-2 were randomly assigned to one of three groups, with participants receiving either 0.23% PVP-I, 0.9% normal saline (NS) nasal rinses and mouth washes, or no intervention (control group). Nasopharyngeal swabs were taken 4, 8, 12, and 18 days after the first swab to measure the detectability of the virus and the Ct. RESULTS A total of 19 participants were involved in this study. The mean viral survival was 9.8, 12, and 12.6 days for the PVP-I, NS, and control groups, respectively, with a statistically significant difference (p = 0.046). The Ct mean values were 23 ± 3.4, 23.5 ± 6.3, and 26.3 ± 5.9 at the time of recruitment and 25.2 ± 3.5, 15 ± 11.7, and 26.9 ± 6.4 after 4 days for the PVP-I, NS, and control groups, respectively. CONCLUSIONS When used continuously at a concentration of 0.23%, PVP-I showed promising results in terms of decreasing the pandemic burden by reducing the period of infectiousness and viral load. However, the use of PVP-I did not result in significantly different changes in the quality-of-life parameters in recently vaccinated and mild COVID-19 patients.
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Affiliation(s)
- Saad Alsaleh
- Otolaryngology - Head & Neck Surgery Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Alhussien
- Otolaryngology - Head & Neck Surgery Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia.
| | - Abduljabbar Alyamani
- Department of Otolaryngology - Head and Neck Surgery, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fahad Alhussain
- Department of Urology, King Faisal Specialist Hospital and Research center, Riyadh, Saudi Arabia
| | - Ali Alhijji
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, King Saud University and King Saud University Medical City, Riyadh, Saudi Arabia
| | - Khalifa Binkhamis
- Department of Pathology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Anas Khan
- Department of Emergency Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Amin Javer
- Division of Otolaryngology- Head and Neck Surgery, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Fatimah S Alshahrani
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, King Saud University and King Saud University Medical City, Riyadh, Saudi Arabia
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13
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Bustin SA, Kirvell S, Nolan T, Shipley GL. FlashPCR: Revolutionising qPCR by Accelerating Amplification through Low ∆T Protocols. Int J Mol Sci 2024; 25:2773. [PMID: 38474020 DOI: 10.3390/ijms25052773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/08/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Versatility, sensitivity, and accuracy have made the real-time polymerase chain reaction (qPCR) a crucial tool for research, as well as diagnostic applications. However, for point-of-care (PoC) use, traditional qPCR faces two main challenges: long run times mean results are not available for half an hour or more, and the requisite high-temperature denaturation requires more robust and power-demanding instrumentation. This study addresses both issues and revises primer and probe designs, modified buffers, and low ∆T protocols which, together, speed up qPCR on conventional qPCR instruments and will allow for the development of robust, point-of-care devices. Our approach, called "FlashPCR", uses a protocol involving a 15-second denaturation at 79 °C, followed by repeated cycling for 1 s at 79 °C and 71 °C, together with high Tm primers and specific but simple buffers. It also allows for efficient reverse transcription as part of a one-step RT-qPCR protocol, making it universally applicable for both rapid research and diagnostic applications.
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Affiliation(s)
- Stephen A Bustin
- Medical Technology Research Centre, Faculty of Health, Medicine and Social Care Anglia, Ruskin University, Chelmsford CB1 1PT, UK
| | - Sara Kirvell
- Medical Technology Research Centre, Faculty of Health, Medicine and Social Care Anglia, Ruskin University, Chelmsford CB1 1PT, UK
| | - Tania Nolan
- Medical Technology Research Centre, Faculty of Health, Medicine and Social Care Anglia, Ruskin University, Chelmsford CB1 1PT, UK
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14
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Geng Y, Han Y, Wang S, Qi J, Bi X. Screening and Validation of Key Genes of Autophagy in Acute Myocardial Infarction Based on Bioinformatics. Evol Bioinform Online 2024; 20:11769343241227331. [PMID: 38314309 PMCID: PMC10832399 DOI: 10.1177/11769343241227331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/04/2024] [Indexed: 02/06/2024] Open
Abstract
Aims Autophagy plays a significant role in the development of acute myocardial infarction (AMI), and cardiomyocyte autophagy is of major importance in maintaining cardiac function. We aimed to identify key genes associated with autophagy in AMI through bioinformatics analysis and verify them through clinical validation. Materials and Methods We downloaded an AMI expression profile dataset GSE166780 from Gene Expression Omnibus (GEO). Autophagy-associated genes potentially differentially expressed in AMI were screened using R software. Then, to identify key autophagy-related genes, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, protein-protein interaction (PPI) analysis, Receiver Operating Characteristic (ROC) curve analysis, and correlation analysis were performed on the differentially expressed autophagy-related genes in AMI. Finally, we used quantificational real-time polymerase chain reaction (qRT-PCR) to verify the RNA expression of the screened key genes. Results TSC2, HSPA8, and HIF1A were screened out as key autophagy-related genes. qRT-PCR results showed that the expression levels of HSPA8 and TSC2 in AMI blood samples were lower, while the expression level of HIF1A was higher than that in the healthy controls. Conclusions TSC2, HSPA8, and HIF1A were identified as key autophagy-related genes in this study. They may influence the development of AMI through autophagy. These findings may help deepen our understanding of AMI and may be useful for the treatment of AMI.
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Affiliation(s)
- Yingjie Geng
- Department of Cardiology, Zibo Central Hospital, Zibo, Shandong Province, China
| | - Yu’e Han
- Department of Pulmonary and Critical Care Medicine, Zibo Central Hospital, Zibo, Shandong Province, China
| | - Shujuan Wang
- Department of Cardiology, Zibo Central Hospital, Zibo, Shandong Province, China
| | - Jia Qi
- Department of Cardiology, Zibo Central Hospital, Zibo, Shandong Province, China
| | - Xiaoli Bi
- Department of Cardiology, Zibo First Hospital, Zibo, Shandong Province, China
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15
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Zhang Q, Lin B, Chen H, Ye Y, Huang Y, Chen Z, Li J. Lipid metabolism-related gene expression in the immune microenvironment predicts prognostic outcomes in renal cell carcinoma. Front Immunol 2023; 14:1324205. [PMID: 38090559 PMCID: PMC10712371 DOI: 10.3389/fimmu.2023.1324205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Background Rates of renal cell carcinoma (RCC) occurrence and mortality are steadily rising. In an effort to address this issue, the present bioinformatics study was developed with the goal of identifying major lipid metabolism biomarkers and immune infiltration characteristics associated with RCC cases. Methods The Cancer Genome Atlas (TCGA) and E-MTAB-1980 were used to obtain matched clinical and RNA expression data from patients diagnosed with RCC. A LASSO algorithm and multivariate Cox regression analyses were employed to design a prognostic risk model for these patients. The tumor immune microenvironment (TIME) in RCC patients was further interrogated through ESTIMATE, TIMER, and single-cell gene set enrichment analysis (ssGSEA) analyses. Gene Ontology (GO), KEGG, and GSEA enrichment approaches were further employed to gauge the mechanistic basis for the observed results. Differences in gene expression and associated functional changes were then validated through appropriate molecular biology assays. Results Through the approach detailed above, a risk model based on 8 genes associated with RCC patient overall survival and lipid metabolism was ultimately identified that was capable of aiding in the diagnosis of this cancer type. Poorer prognostic outcomes in the analyzed RCC patients were associated with higher immune scores, lower levels of tumor purity, greater immune cell infiltration, and higher relative immune status. In GO and KEGG enrichment analyses, genes that were differentially expressed between risk groups were primarily related to the immune response and substance metabolism. GSEA analyses additionally revealed that the most enriched factors in the high-risk group included the stable internal environment, peroxisomes, and fatty acid metabolism. Subsequent experimental validation in vitro and in vivo revealed that the most significantly differentially expressed gene identified herein, ALOX5, was capable of suppressing RCC tumor cell proliferation, invasivity, and migration. Conclusion In summary, a risk model was successfully established that was significantly related to RCC patient prognosis and TIME composition, offering a robust foundation for the development of novel targeted therapeutic agents and individualized treatment regimens. In both immunoassays and functional analyses, dysregulated lipid metabolism was associated with aberrant immunological activity and the reprogramming of fatty acid metabolic activity, contributing to poorer outcomes.
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Affiliation(s)
- Qian Zhang
- Department of Rehabilitation Medicine, Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Bingbiao Lin
- Department of Urology, Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Huikun Chen
- Department of Urology, Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Yinyan Ye
- Department of Rehabilitation Medicine, Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Yijie Huang
- Department of Rehabilitation Medicine, Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Zhen Chen
- Department of Rehabilitation Medicine, Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Jun Li
- Department of Urology, Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
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16
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Ren Q, Jiang L, Ma S, Li T, Zhu Y, Qiu R, Xing Y, Yin F, Li Z, Ye X, Zhang Y, Zhang M. Multi-Body Biomarker Entrapment System: An All-Encompassing Tool for Ultrasensitive Disease Diagnosis and Epidemic Screening. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2304119. [PMID: 37486783 DOI: 10.1002/adma.202304119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/18/2023] [Indexed: 07/26/2023]
Abstract
Ultrasensitive identification of biomarkers in biofluids is essential for the precise diagnosis of diseases. For the gold standard approaches, polymerase chain reaction and enzyme-linked immunosorbent assay, cumbersome operational steps hinder their point-of-care applications. Here, a bionic biomarker entrapment system (BioES) is implemented, which employs a multi-body Y-shaped tetrahedral DNA probe immobilized on carbon nanotube transistors. Clinical identification of endometriosis is successfully realized by detecting an estrogen receptor, ERβ, from the lesion tissue of endometriosis patients and establishing a standard diagnosis procedure. The multi-body Y-shaped BioES achieves a theoretical limit of detection (LoD) of 6.74 aM and a limit of quantification of 141 aM in a complex protein milieu. Furthermore, the BioES is optimized into a multi-site recognition module for enhanced binding efficiency, realizing the first identification of monkeypox virus antigen A35R and unamplified detection of circulating tumor DNA of breast cancer in serum. The rigid and compact probe framework with synergy effect enables the BioES to target A35R and DNA with a LoD down to 991 and 0.21 aM, respectively. Owing to its versatility for proteins and nucleic acids as well as ease of manipulation and ultra-sensitivity, the BioES can be leveraged as an all-encompassing tool for population-wide screening of epidemics and clinical disease diagnosis.
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Affiliation(s)
- Qinqi Ren
- School of Electronic and Computer Engineering, Peking University, Shenzhen, 518055, China
| | - Leying Jiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University, Shenzhen, 518055, China
| | - Shenhui Ma
- School of Electronic and Computer Engineering, Peking University, Shenzhen, 518055, China
| | - Tong Li
- Department of Gynecology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, 518020, China
| | - Yang Zhu
- School of Electronic and Computer Engineering, Peking University, Shenzhen, 518055, China
| | - Rui Qiu
- School of Electronic and Computer Engineering, Peking University, Shenzhen, 518055, China
| | - Yun Xing
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University, Shenzhen, 518055, China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University, Shenzhen, 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Xiyang Ye
- Department of Gynecology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, 518020, China
| | - Yaping Zhang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Min Zhang
- School of Electronic and Computer Engineering, Peking University, Shenzhen, 518055, China
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17
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Scott LE, Hsiao NY, Dor G, Hans L, Marokane P, da Silva MP, Preiser W, Vreede H, Tsoka J, Mlisana K, Stevens WS. How South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality. Diagnostics (Basel) 2023; 13:2554. [PMID: 37568917 PMCID: PMC10416981 DOI: 10.3390/diagnostics13152554] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/24/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
The high demand for SARS-CoV-2 tests but limited supply to South African laboratories early in the COVID-19 pandemic resulted in a heterogenous diagnostic footprint of open and closed molecular testing platforms being implemented. Ongoing monitoring of the performance of these multiple and varied systems required novel approaches, especially during the circulation of variants. The National Health Laboratory Service centrally collected cycle threshold (Ct) values from 1,497,669 test results reported from 6 commonly used PCR assays in 36 months, and visually monitored changes in their median Ct within a 28-day centered moving average for each assays' gene targets. This continuous quality monitoring rapidly identified delayed hybridization of RdRp in the Allplex™ SARS-CoV-2 assay due to the Delta (B.1.617.2) variant; S-gene target failure in the TaqPath™ COVID-19 assay due to B.1.1.7 (Alpha) and the B.1.1.529 (Omicron); and recently E-gene delayed hybridization in the Xpert® Xpress SARS-CoV-2 due to XBB.1.5. This near "real-time" monitoring helped inform the need for sequencing and the importance of multiplex molecular nucleic acid amplification technology designs used in diagnostics for patient care. This continuous quality monitoring approach at the granularity of Ct values should be included in ongoing surveillance and with application to other disease use cases that rely on molecular diagnostics.
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Affiliation(s)
- Lesley Erica Scott
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa (L.H.); (M.P.d.S.); (J.T.); (W.S.S.)
| | - Nei-yuan Hsiao
- Division of Medical Virology, Faculty of Heath Sciences, University of Cape Town, Cape Town 7700, South Africa;
- The National Health Laboratory Service, Johannesburg, Private Bag X8, Sandringham 2131, South Africa; (W.P.); (H.V.); (K.M.)
| | - Graeme Dor
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa (L.H.); (M.P.d.S.); (J.T.); (W.S.S.)
| | - Lucia Hans
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa (L.H.); (M.P.d.S.); (J.T.); (W.S.S.)
- The National Priority Program of the National Health Laboratory Service, Johannesburg, Private Bag X8, Sandringham 2131, South Africa;
| | - Puleng Marokane
- The National Priority Program of the National Health Laboratory Service, Johannesburg, Private Bag X8, Sandringham 2131, South Africa;
| | - Manuel Pedro da Silva
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa (L.H.); (M.P.d.S.); (J.T.); (W.S.S.)
- The National Priority Program of the National Health Laboratory Service, Johannesburg, Private Bag X8, Sandringham 2131, South Africa;
| | - Wolfgang Preiser
- The National Health Laboratory Service, Johannesburg, Private Bag X8, Sandringham 2131, South Africa; (W.P.); (H.V.); (K.M.)
- Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Helena Vreede
- The National Health Laboratory Service, Johannesburg, Private Bag X8, Sandringham 2131, South Africa; (W.P.); (H.V.); (K.M.)
- Division of Chemical Pathology, Faculty of Heath Sciences, University of Cape Town, Cape Town 7700, South Africa
| | - Jonathan Tsoka
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa (L.H.); (M.P.d.S.); (J.T.); (W.S.S.)
| | - Koleka Mlisana
- The National Health Laboratory Service, Johannesburg, Private Bag X8, Sandringham 2131, South Africa; (W.P.); (H.V.); (K.M.)
| | - Wendy Susan Stevens
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa (L.H.); (M.P.d.S.); (J.T.); (W.S.S.)
- The National Priority Program of the National Health Laboratory Service, Johannesburg, Private Bag X8, Sandringham 2131, South Africa;
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18
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Liang Y, Xiao M, Xie J, Li J, Zhang Y, Liu H, Zhang Y, He J, Zhang G, Wei N, Peng LM, Ke Y, Zhang ZY. Amplification-Free Detection of SARS-CoV-2 Down to Single Virus Level by Portable Carbon Nanotube Biosensors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2208198. [PMID: 37046180 DOI: 10.1002/smll.202208198] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/18/2023] [Indexed: 06/19/2023]
Abstract
The rapid and sensitive detection of trace-level viruses in a simple and reliable way is of great importance for epidemic prevention and control. Here, a multi-functionalized floating gate carbon nanotube field effect transistor (FG-CNT FET) based biosensor is reported for the single virus level detection of SARS-CoV-2 virus antigen and RNA rapidly with a portable sensing platform. The aptamers functionalized sensors can detect SARS-CoV-2 antigens from unprocessed nasopharyngeal swab samples within 1 min. Meanwhile, enhanced by a multi-probe strategy, the FG-CNT FET-based biosensor can detect the long chain RNA directly without amplification down to single virus level within 1 min. The device, constructed with packaged sensor chips and a portable sensing terminal, can distinguish 10 COVID-19 patients from 10 healthy individuals in clinical tests both by the RNAs and antigens by a combination detection strategy with an combined overall percent agreement (OPA) close to 100%. The results provide a general and simple method to enhance the sensitivity of FET-based biochemical sensors for the detection of nucleic acid molecules and demonstrate that the CNT FG FET biosensor is a versatile and reliable integrated platform for ultrasensitive multibiomarker detection without amplification and has great potential for point-of-care (POC) clinical tests.
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Affiliation(s)
- Yuqi Liang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, School of Electronics, Peking University, Beijing, 100871, China
| | - Mengmeng Xiao
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, School of Electronics, Peking University, Beijing, 100871, China
- Hunan Institute of Advanced Sensing and Information Technology, Xiangtan University, Hunan, 411105, China
| | - Jing Xie
- Chinese PLA Center for Disease Control and Prevention, Beijing, 100071, China
| | - Jiahao Li
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Huangjia Lake West Road, Wuhan, 430065, China
| | - Yuyan Zhang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, School of Electronics, Peking University, Beijing, 100871, China
| | - Haiyang Liu
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, School of Electronics, Peking University, Beijing, 100871, China
| | - Yang Zhang
- Hunan Institute of Advanced Sensing and Information Technology, Xiangtan University, Hunan, 411105, China
| | - Jianping He
- Hunan Institute of Advanced Sensing and Information Technology, Xiangtan University, Hunan, 411105, China
| | - Guojun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Huangjia Lake West Road, Wuhan, 430065, China
| | - Nan Wei
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, School of Electronics, Peking University, Beijing, 100871, China
| | - Lian-Mao Peng
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, School of Electronics, Peking University, Beijing, 100871, China
- Hunan Institute of Advanced Sensing and Information Technology, Xiangtan University, Hunan, 411105, China
| | - Yuehua Ke
- Chinese PLA Center for Disease Control and Prevention, Beijing, 100071, China
| | - Zhi-Yong Zhang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, School of Electronics, Peking University, Beijing, 100871, China
- Hunan Institute of Advanced Sensing and Information Technology, Xiangtan University, Hunan, 411105, China
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Li J, Mai J, Zhang M, Ma Y, He Q, Gong D, Xiao J, Li M, Chen W, Li Z, Chen S, Pan Z, Li S, Wang H. Myricitrin promotes osteogenesis and prevents ovariectomy bone mass loss via the PI3K/AKT signalling pathway. J Cell Biochem 2023; 124:1155-1172. [PMID: 37357411 DOI: 10.1002/jcb.30439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/27/2023]
Abstract
This study aimed to explore the effect of myricitrin on osteoblast differentiation in mice immortalised bone marrow mesenchymal stem cells (imBMSCs). Additionally, ovariectomy (OVX) mice were employed to examine the effect of myricitrin on bone trabecular loss in vivo. The effect of myricitrin on the proliferation of imBMSCs was evaluated using a cell counting kit-8 assay. Alizarin red staining, alkaline phosphatase staining were performed to elucidate osteogenesis. Furthermore, qRT-PCR and western blot determined the expression of osteo-specific genes and proteins. To screen for candidate targets, mRNA transcriptome genes were sequenced using bioinformatics analyses. Western blot and molecular docking analysis were used to examine target signalling markers. Moreover, rescue experiments were used to confirm the effect of myricitrin on the osteogenic differentiation of imBMSCs. OVX mice were also used to estimate the delay capability of myricitrin on bone trabecular loss in vivo using western blot, micro-CT, tartaric acid phosphatase (Trap) staining, haematoxylin and eosin staining, Masson staining and immunochemistry. In vitro, myricitrin significantly enhanced osteo-specific genes and protein expression and calcium deposition. Moreover, mRNA transcriptome gene sequencing and molecular docking analysis revealed that this enhancement was accompanied by an upregulation of the PI3K/AKT signalling pathway. Furthermore, copanlisib, a PI3K inhibitor, partially reversed the osteogenesis promotion induced by myricitrin. In vivo, western blot, micro-CT, hematoxylin and eosin staining, Masson staining, Trap staining and immunochemistry revealed that bone trabecular loss rate was significantly alleviated in the myricitrin low- and high-dose groups, with an increased expression of osteopontin, osteoprotegerin, p-PI3K and p-AKT compared to the OVX group. Myricitrin enhances imBMSC osteoblast differentiation and attenuate bone mass loss partly through the upregulation of the PI3K/AKT signalling pathway. Thus, myricitrin has therapeutic potential as an antiosteoporosis drug.
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Affiliation(s)
- Jianliang Li
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
- The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangzhou First People's Hospital, Second Affiliated Hospital of South China University of Technology, Guangzhou, China
| | - Jiale Mai
- The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
- Eighth Clinical School of Guangzhou University of Chinese Medicine, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Meng Zhang
- Department of Orthopedics, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, Zhengzhou, China
| | - Yanhuai Ma
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
- The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qi He
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
- The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dawei Gong
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
- The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Orthopaedic Surgery, Wendeng Orthopedic and Traumatologic Hospital of Shandong Province, Weihai, China
| | - Jiacong Xiao
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
- The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Miao Li
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
- The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weijian Chen
- The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
- Fifth Clinical School of Guangzhou University of Chinese Medicine, Guangdong Second Tradmonal Chinese Medicine Hostpital, Guangzhou, China
| | - Zhen Li
- The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
- Second School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shuai Chen
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
- The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Orthopaedic Surgery, Guangzhou Hospital of Integrated Traditional and West Medicine, Guangzhou, China
| | - Zhaofeng Pan
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
- The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shaocong Li
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
- The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haibin Wang
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
- The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
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20
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Ansari S, Verma M. Control of Ph + and additional chromosomal abnormalities in chronic myeloid leukemia by tyrosine kinase inhibitors. Med Oncol 2023; 40:237. [PMID: 37439908 DOI: 10.1007/s12032-023-02116-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023]
Abstract
Chronic myeloid leukemia (CML) is a type of blood cancer that is known to affect hematopoietic stem cells. The presence of the Philadelphia chromosome (Ph+) is the major characteristic of CML. A protein expressed by the Philadelphia chromosome shows elevated tyrosine kinase activity and is considered a tumorigenic factor. The first line of therapy that had been established for CML was "imatinib," a potent tyrosine kinase inhibitor. Various other second- and third-generation TKIs are taken into account in cases of imatinib failure/resistance. With the subsequent rise in the development of tyrosine kinase inhibitors, optimization in the treatment of CML and amplified total survival were observed throughout TKI dosage. As the disease progresses, additional chromosomal abnormalities (ACAs) have been reported, but their prognostic effect and impact on the response to treatment are still unknown. However, some substantial understandings have been achieved into the disease transformation mechanisms, including the role of somatic mutations, ACAs, and several different genomic mutations that occur during diagnosis or have evolved during treatment. The acquisition of ACAs impedes CML treatment. Due to additional chromosomal lesions, there are greater chances of future disease progression at the time of CML diagnosis beyond the Ph+ translocation. The synchronous appearance of two or more ACAs leads to lower survival and is classified as a poor prognostic group. The key objective of this review is to provide detailed insights into TKIs and their role in controlling Ph+ and ACAs, along with their response, treatment, overall persistence, and survival rate.
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Affiliation(s)
- Sana Ansari
- School of Biotechnology, Banaras Hindu University, Varanasi, U.P., 221005, India
| | - Malkhey Verma
- School of Biotechnology, Banaras Hindu University, Varanasi, U.P., 221005, India.
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21
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Li S, Zhang H, Zhu M, Kuang Z, Li X, Xu F, Miao S, Zhang Z, Lou X, Li H, Xia F. Electrochemical Biosensors for Whole Blood Analysis: Recent Progress, Challenges, and Future Perspectives. Chem Rev 2023. [PMID: 37262362 DOI: 10.1021/acs.chemrev.1c00759] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Whole blood, as one of the most significant biological fluids, provides critical information for health management and disease monitoring. Over the past 10 years, advances in nanotechnology, microfluidics, and biomarker research have spurred the development of powerful miniaturized diagnostic systems for whole blood testing toward the goal of disease monitoring and treatment. Among the techniques employed for whole-blood diagnostics, electrochemical biosensors, as known to be rapid, sensitive, capable of miniaturization, reagentless and washing free, become a class of emerging technology to achieve the target detection specifically and directly in complex media, e.g., whole blood or even in the living body. Here we are aiming to provide a comprehensive review to summarize advances over the past decade in the development of electrochemical sensors for whole blood analysis. Further, we address the remaining challenges and opportunities to integrate electrochemical sensing platforms.
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Affiliation(s)
- Shaoguang Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Hongyuan Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Man Zhu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Zhujun Kuang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xun Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Siyuan Miao
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Zishuo Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xiaoding Lou
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Hui Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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22
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Nevone A, Lattarulo F, Russo M, Panno G, Milani P, Basset M, Avanzini MA, Merlini G, Palladini G, Nuvolone M. A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets. Biomedicines 2023; 11:biomedicines11041079. [PMID: 37189697 DOI: 10.3390/biomedicines11041079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels of nucleic acids of interest due to its popularity, versatility, and limited costs. The measurement of transcriptional levels through RT-qPCR critically depends on reference genes used for normalization. Here, we devised a strategy to select appropriate reference genes for a specific clinical/experimental setting based on publicly available transcriptomic datasets and a pipeline for RT-qPCR assay design and validation. As a proof-of-principle, we applied this strategy to identify and validate reference genes for transcriptional studies of bone-marrow plasma cells from patients with AL amyloidosis. We performed a systematic review of published literature to compile a list of 163 candidate reference genes for RT-qPCR experiments employing human samples. Next, we interrogated the Gene Expression Omnibus to assess expression levels of these genes in published transcriptomic studies on bone-marrow plasma cells from patients with different plasma cell dyscrasias and identified the most stably expressed genes as candidate normalizing genes. Experimental validation on bone-marrow plasma cells showed the superiority of candidate reference genes identified through this strategy over commonly employed “housekeeping” genes. The strategy presented here may apply to other clinical and experimental settings for which publicly available transcriptomic datasets are available.
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Affiliation(s)
- Alice Nevone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Francesca Lattarulo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Monica Russo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giada Panno
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Paolo Milani
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Marco Basset
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Maria Antonietta Avanzini
- Pediatric Hematology Oncology, Cell Factory, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giampaolo Merlini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giovanni Palladini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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23
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Meng L, Cao X, Li C, Li J, Xie H, Shi J, Han M, Shen H, Liu C. Housekeeping gene stability in Pesudomonas aeruginosa PAO1 under the pressure of commonly used antibiotics in molecular microbiology assays. Front Microbiol 2023; 14:1140515. [PMID: 36992935 PMCID: PMC10040570 DOI: 10.3389/fmicb.2023.1140515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/14/2023] [Indexed: 03/16/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen notorious for its remarkable capacity of multi-drug resistance, and has become one of the most important model bacteria in clinical bacteriology research. Quantitative real-time PCR is a reliable method widely used in gene expression analysis, for which the selection of a set of appropriate housekeeping genes is a key prerequisite for the accuracy of the results. However, it is easy to overlook that the expression level of housekeeping gene may vary in different conditions, especially in the condition of molecular microbiology assays, where tested strains are generally cultured under the pre-set antibiotic selection pressures, and how this affects the stability of commonly used housekeeping genes remains unclear. In this study, the expression stability of ten classic housekeeping genes (algD, gyrA, anr, nadB, recA, fabD, proC, ampC, rpoS, and rpsL) under the pressure of eight laboratory commonly used antibiotics (kanamycin, gentamycin, tetracycline, chloramphenicol, hygromycin B, apramycin, tellurite, and zeocin) were tested. Results showed that the stability of housekeeping gene expression was indeed affected by the types of antibiotics added, and of course the best reference gene set varied for different antibiotics. This study provides a comprehensive summary of the effects of laboratory antibiotics on the stability of housekeeping genes in P. aeruginosa, highlighting the necessity to select housekeeping genes according to the type of antibiotics used in the initial stage of experiment.
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Affiliation(s)
- Lingning Meng
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Xiaoli Cao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Chuchu Li
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jia Li
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Hui Xie
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Jiping Shi
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Mei Han
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
- Han Shen,
| | - Chang Liu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
- *Correspondence: Chang Liu,
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24
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Evaluation of the Diagnostic Performance of a SARS-CoV-2 and Influenza A/B Combo Rapid Antigen Test in Respiratory Samples. Diagnostics (Basel) 2023; 13:diagnostics13050972. [PMID: 36900116 PMCID: PMC10000510 DOI: 10.3390/diagnostics13050972] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
This study aimed to evaluate the performance characteristics of a rapid antigen test developed to detect SARS-CoV-2 (COVID-19), influenza A virus (IAV), and influenza B virus (IBV) (flu) compared with those of the real-time reverse transcription-polymerase chain reaction (rRT-PCR) method. One hundred SARS-CoV-2, one hundred IAV, and twenty-four IBV patients whose diagnoses were confirmed by clinical and laboratory methods were included in the patient group. Seventy-six patients, who were negative for all respiratory tract viruses, were included as the control group. The Panbio™ COVID-19/Flu A&B Rapid Panel test kit was used in the assays. The sensitivity values of the kit were 97.5%, 97.9%, and 33.33% for SARS-CoV-2, IAV, and IBV, respectively, in samples with a viral load below 20 Ct values. The sensitivity values of the kit were 16.7%, 36.5%, and 11.11% for SARS-CoV-2, IAV, and IBV, respectively, in samples with a viral load above 20 Ct. The kit's specificity was 100%. In conclusion, this kit demonstrated high sensitivity to SARS-CoV-2 and IAV for viral loads below 20 Ct values, but the sensitivity values were not compatible with PCR positivity for lower viral loads over 20 Ct values. Rapid antigen tests may be preferred as a routine screening tool in communal environments, especially in symptomatic individuals, when diagnosing SARS-CoV-2, IAV, and IBV with high caution.
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25
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Huber LB, Betz K, Marx A. Reverse Transcriptases: From Discovery and Applications to Xenobiology. Chembiochem 2023; 24:e202200521. [PMID: 36354312 DOI: 10.1002/cbic.202200521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/09/2022] [Indexed: 11/12/2022]
Abstract
Reverse transcriptases are DNA polymerases that can use RNA as a template for DNA synthesis. They thus catalyze the reverse of transcription. Although discovered in 1970, reverse transcriptases are still of great interest and are constantly being further developed for numerous modern research approaches. They are frequently used in biotechnological and molecular diagnostic applications. In this review, we describe the discovery of these fascinating enzymes and summarize research results and applications ranging from molecular cloning, direct virus detection, and modern sequencing methods to xenobiology.
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Affiliation(s)
- Luisa B Huber
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
| | - Karin Betz
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
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26
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Electrochemical biosensors for analysis of DNA point mutations in cancer research. Anal Bioanal Chem 2023; 415:1065-1085. [PMID: 36289102 DOI: 10.1007/s00216-022-04388-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 02/07/2023]
Abstract
Cancer is a genetic disease induced by mutations in DNA, in particular point mutations in important driver genes that lead to protein malfunctioning and ultimately to tumorigenesis. Screening for the most common DNA point mutations, especially in such genes as TP53, BRCA1 and BRCA2, EGFR, KRAS, or BRAF, is crucial to determine predisposition risk for cancer or to predict response to therapy. In this review, we briefly depict how these genes are involved in cancer, followed by a description of the most common techniques routinely applied for their analysis, including high-throughput next-generation sequencing technology and less expensive low-throughput options, such as real-time PCR, restriction fragment length polymorphism, or high resolution melting analysis. We then introduce benefits of electrochemical biosensors as interesting alternatives to the standard methods in terms of cost, speed, and simplicity. We describe most common strategies involved in electrochemical biosensing of point mutations, relying mostly on PCR or isothermal amplification techniques, and critically discuss major challenges and obstacles that, until now, prevented their more widespread application in clinical settings.
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27
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Yin YW, Xiong C, Shi KC, Xie SY, Long F, Li J, Zheng M, Wei XK, Feng S, Qu S, Lu W, Zhou H, Zhao K, Sun W, Li Z. Development and application of a multiplex qPCR assay for the detection of duck circovirus, duck Tembusu virus, Muscovy duck reovirus, and new duck reovirus. Virus Genes 2023; 59:91-99. [PMID: 36258144 DOI: 10.1007/s11262-022-01946-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/07/2022] [Indexed: 01/13/2023]
Abstract
A multiplex qPCR assay was developed to simultaneously detect duck circovirus (DuCV), duck Tembusu virus (DTMUV), Muscovy duck reovirus (MDRV), and novel duck reovirus (NDRV), but it did not amplify other viruses, including duck virus enteritis (DVE), infectious bursal disease virus (IBDV), avian reovirus (ARV), H5 avian influenza virus (H5 AIV), H7 avian influenza virus (H7 AIV), H9 avian influenza virus (H9 AIV), Newcastle disease virus (NDV), and Muscovy duck parvovirus (MDPV), and the detection limit for DuCV, DTMUV, MDRV, and NDRV was 1.51 × 101 copies/μL. The intra- and interassay coefficients of variation were less than 1.54% in the repeatability test with standard plasmid concentrations of 1.51 × 107, 1.51 × 105, and 1.51 × 103 copies/μL. The developed multiple qPCR assay was used to examine 404 clinical samples to verify its practicability. The positivity rates for DuCV, DTMUV, MDRV, and NDRV were 26.0%, 9.9%, 4.0%, and 4.7%, respectively, and the mixed infection rates for DuCV + DTMUV, DuCV + MDRV, DuCV + NDRV, MDRV + NDRV, DTMUV + MDRV, and DTMUV + NDRV were 2.7%, 1.2%, 1.2%, 1.0%, 0.5%, and 0.7%, respectively.
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Affiliation(s)
- Yan Wen Yin
- Guangxi Center for Animal Disease Control and Prevention, Nanning, 530001, China
| | - Chenyong Xiong
- College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Kai Chuang Shi
- Guangxi Center for Animal Disease Control and Prevention, Nanning, 530001, China
| | - Shou Yu Xie
- Guangxi Center for Animal Disease Control and Prevention, Nanning, 530001, China
| | - Feng Long
- Guangxi Center for Animal Disease Control and Prevention, Nanning, 530001, China
| | - Jun Li
- Guangxi Center for Animal Disease Control and Prevention, Nanning, 530001, China
| | - Min Zheng
- Guangxi Center for Animal Disease Control and Prevention, Nanning, 530001, China
| | - Xian Kai Wei
- Guangxi Center for Animal Disease Control and Prevention, Nanning, 530001, China
| | - Shuping Feng
- Guangxi Center for Animal Disease Control and Prevention, Nanning, 530001, China
| | - Sujie Qu
- Guangxi Center for Animal Disease Control and Prevention, Nanning, 530001, China
| | - Wenjun Lu
- Guangxi Center for Animal Disease Control and Prevention, Nanning, 530001, China
| | - Hongjin Zhou
- College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Kang Zhao
- College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Wenchao Sun
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, 325035, China.
| | - Zongqiang Li
- College of Animal Science and Technology, Guangxi University, Nanning, 530005, China.
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28
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Rodriguez AL, Fowler VL, Huether M, Reddick D, Tait-Burkard C, O’Shea M, Perkins S, Dias N, Buterbaugh R, Benchaoui HA. Effects of a water-soluble formulation of tylvalosin on disease caused by porcine reproductive and respiratory syndrome virus alone in sows or in combination with Mycoplasma hyopneumoniae in piglets. BMC Vet Res 2023; 19:31. [PMID: 36726139 PMCID: PMC9890818 DOI: 10.1186/s12917-023-03571-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 01/09/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The effect of a water-soluble formulation of tylvalosin (Aivlosin® 625 mg/g granules) on disease caused by porcine reproductive and respiratory syndrome virus (PRRSV) and Mycoplasma hyopneumoniae (Mhyop) was investigated in two animal studies. In a PRRSV challenge model in pregnant sows (n = 18), six sows received water medicated at target dose of 5 mg tylvalosin/kg body weight/day from 3 days prior to challenge until the end of gestation. Six sows were left untreated, with a third group remaining untreated and unchallenged. Sows were challenged with PRRSV-2 at approximately 85 days of gestation. Cytokines, viremia, viral shedding, sow reproductive parameters and piglet performance to weaning were evaluated. In a dual infection study (n = 16), piglets were challenged with Mhyop on days 0, 1 and 2, and with PRRSV-1 on day 14 and euthanized on day 24. From day 10 to 20, eight piglets received water medicated at target dose of 20 mg tylvalosin/kg body weight/day and eight piglets were left untreated. Cytokines, viremia, bacteriology and lung lesions were evaluated. RESULTS In the PRRSV challenge study in pregnant sows, tylvalosin significantly reduced the levels of serum IL-8 (P < 0.001), IL-12 (P = 0.032), TNFα (P < 0.001) and GM-CSF (P = 0.001). IL-8 (P = 0.100) tended to be lower in uterus of tylvalosin sows. All piglets from tylvalosin sows surviving to weaning were PRRSV negative in faecal swabs at weaning compared to 33.3% PRRSV positive piglets from untreated sows (P = 0.08). In the dual challenge study in piglet, tylvalosin reduced serum IL1β, IL-4, IL-6, IL-8, IL-10, IL-12, IL-1α, IL-13, IL-17A, IL-18, GM-CSF, TGFβ1, TNFα, CCL3L1, MIG, PEPCAM-1 (P < 0.001) and increased serum IFNα, IL-1ra and MIP-1b (P < 0.001). In the lungs, tylvalosin reduced IL-8, IL-10 and IL-12 compared to untreated pigs (P < 0.001) and tended to reduce TNFα (P = 0.082). Lung lavage samples from all tylvalosin treated piglets were negative for Mhyop (0 cfu/mL) compared to the untreated piglets which had mean Mhyop counts of 2.68 × 104 cfu/mL (P = 0.023). CONCLUSION Overall, tylvalosin reduced both local and systemic proinflammatory cytokines after challenge with respiratory pathogens in sows and in piglets. Tylvalosin was effective in reducing Mhyop recovery from the lungs and may reduce virus shedding in piglets following transplacental PRRSV infection in sows.
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Affiliation(s)
| | | | | | - David Reddick
- Moredun Scientific Ltd, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ UK
| | - Christine Tait-Burkard
- grid.4305.20000 0004 1936 7988The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Marie O’Shea
- grid.4305.20000 0004 1936 7988The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | | | - Nirosh Dias
- grid.505215.6RTI, LLC, 801 32nd Ave, Brookings, SD 57006 USA
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29
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Stopar A, Nicholson AW. Multivalent forms of the ribonuclease H1 hybrid binding domain are high-affinity binders of RNA-DNA hybrids. FEBS Lett 2023; 597:472-482. [PMID: 36443824 DOI: 10.1002/1873-3468.14541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 10/18/2022] [Accepted: 10/22/2022] [Indexed: 11/30/2022]
Abstract
The hybrid binding domain (HBD) is a conserved fold present in ribonucleases H1 that selectively recognizes RNA-DNA hybrids, which are structures present in cellular R-loops and participate in diverse biological processes. We engineered multivalent HBD proteins to create high-affinity hybrid binders. Using EMSA- and SPR-based analyses, we showed that the triple-HBD protein exhibits a ~ 22 000-fold increase in hybrid affinity (KD 370 pm) relative to the single HBD (KD 8.29 μm), with the length and sequence of the linkers enabling optimal function. These findings provide a framework for testing models that correlate multivalency and affinity to understand how multivalent proteins function and also can serve to guide applications that exploit multivalency as a strategy to enhance binding affinity.
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Affiliation(s)
- Alex Stopar
- Department of Biology, Temple University, Philadelphia, PA, USA
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30
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Wilner OI, Yesodi D, Weizmann Y. Point-of-care nucleic acid tests: assays and devices. NANOSCALE 2023; 15:942-952. [PMID: 36515009 DOI: 10.1039/d2nr05385c] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The COVID-19 pandemic (caused by the SARS_CoV_2 virus) has emphasized the need for quick, easy-to-operate, reliable, and affordable diagnostic tests and devices at the Point-of-Care (POC) for homes/fields/clinics. Such tests and devices will contribute significantly to the fight against the COVID-19 pandemic and any future infectious disease epidemic. Often, academic research studies and those from industry lack knowledge of each other's developments. Here, we introduced DNA Polymerase Chain Reaction (PCR) and isothermal amplification reactions and reviewed the current commercially available POC nucleic acid diagnostic devices. In addition, we reviewed the history and the recent advancements in an effort to develop reliable, quick, portable, cost-effective, and automatic point-of-care nucleic acid diagnostic devices, from sample to result. The purpose of this paper is to bridge the gap between academia and industry and to share important knowledge on this subject.
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Affiliation(s)
- Ofer I Wilner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| | - Doron Yesodi
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| | - Yossi Weizmann
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
- Ilse Katz Institute for Nanotechnology Science, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Sommer KM, Lee Y, Donovan SM, Dilger RN. Purification methods to reduce interference by dextran sodium sulfate with quantification of gene expression in intestinal tissue samples from a piglet model of colitis. J Anim Sci 2023; 101:skad202. [PMID: 37330677 PMCID: PMC10317179 DOI: 10.1093/jas/skad202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
Dextran sodium sulfate (DSS) is commonly used to induce intestinal (i.e., colonic) inflammation in a variety of animal models. However, DSS is known to cause interference when using quantitative-real time polymerase chain reaction (qRT-PCR) methods, thereby invalidating accurate and precise measurement of tissue gene expression. Therefore, the goal of this study was to determine whether different mRNA purification methods would reduce DSS-interference. Colonic tissue samples were collected at postnatal days (PND) 27 or 28 from pigs that had not been administered DSS (Control), and two independent groups of pigs that received 1.25 g of DSS/kg of BW/d (DSS-1 and DSS-2) from PND 14 to 18. Tissue samples collected were subsequently stratified into three purification methods (i.e., 9 total treatment × method combinations), including: 1) no purification, 2) purification with lithium chloride (LiCl), or 3) purification using spin column filtration. All data were analyzed using a one-way ANOVA in the Mixed procedure of SAS. The average RNA concentrations across all treatments were between 1,300 and 1,800 μg/μL for all three in vivo groups. Although there were statistical differences among purification methods, the 260/280 and 260/230 ratios fell between acceptable limits of 2.0 to 2.1 and 2.0 to 2.2, respectively, for all treatment groups. This confirms the RNA quality was adequate and not influenced by purification method in addition to suggesting the absence of phenol, salts, and carbohydrate contamination. For pigs in the Control group that did not receive DSS, qRT-PCR Ct values of four cytokines were achieved, though these values were not altered by purification method. For pigs that had undergone DSS dosing, those tissues subjected to either no purification or purification using LiCl did not generate applicable Ct values. However, when tissues derive from DSS-treated pigs underwent spin column purification, half of the samples from DSS-1 and DSS-2 groups generated appropriate Ct estimates. Therefore, spin column purification appeared to be more effective than LiCl purification, but no method was 100% effective, so caution should be exercised when interpreting gene expression results from studies where animals are exposed to DSS-induced colitis.
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Affiliation(s)
- Kaitlyn M Sommer
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA
| | - Youngsoo Lee
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, Illinois, USA
| | - Sharon M Donovan
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, Illinois, USA
| | - Ryan N Dilger
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA
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Zhao J, Zhao X. Sensitive miRNA Detection for Early Diagnosis of Psoriasis Based on Dual Signal Recycles. Appl Biochem Biotechnol 2023; 195:125-134. [PMID: 36066806 DOI: 10.1007/s12010-022-04114-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2022] [Indexed: 01/13/2023]
Abstract
MicroRNAs (miRNAs) play a pivotal role in regulating a variety of biological processes and can be used as biomarkers for the early diagnosis of various diseases, such as psoriasis. Herein, we depict a simple and sensitive miRNA detection method based on dual signal recycles, which is developed on the basis of strand displacement amplification (SDA). The sensor is successfully applied to the detection of miRNA-21 with a wide linear range from 100 fM to 10 nM and a lower limit of detection (LOD) of 67 fM. Because of the simple operation yet improved detection capability, we thereby believe that the developed fluorescent biosensor can be potentially applied for early clinical diagnosis as well as biological researches.
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Affiliation(s)
- Jiemei Zhao
- Department of Dermatology, Zhuji People's Hospital, Zhuji Affiliated Hospital of Shaoxing University, 9 Jianmin Road, Taozhu Street, Zhuji City, 311800, Zhejiang Province, China
| | - Xiaoqin Zhao
- Department of Dermatology, Zhuji People's Hospital, Zhuji Affiliated Hospital of Shaoxing University, 9 Jianmin Road, Taozhu Street, Zhuji City, 311800, Zhejiang Province, China.
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Performance Evaluation of STANDARD Q COVID/FLU Ag Combo for Detection of SARS-CoV-2 and Influenza A/B. Diagnostics (Basel) 2022; 13:diagnostics13010032. [PMID: 36611324 PMCID: PMC9818676 DOI: 10.3390/diagnostics13010032] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022] Open
Abstract
We evaluated the performance of the STANDARD Q COVID/FLU Ag Combo test (Q Ag combo test) for the detection of SARS-CoV-2, influenza A, and influenza B using a single point-of-care device compared with real-time PCR. A total of 408 individuals, 55 positives with SARS-CoV-2, 90 with influenza A, 68 with influenza B, and 195 negatives for all viruses, participated. The Q Ag combo test demonstrated a high level of sensitivity of 92.73% and a specificity of 99.49% for the detection of SARS-CoV-2. When the number of days from symptom onset (DSO) was restricted to 0 < DSO ≤ 6, the sensitivity of the Q Ag combo test to detect SARS-CoV-2 was 100%, and when the Ct value of RdRp was ≤20, the sensitivity to detect SARS-CoV-2 was 93.10%. The Q Ag combo test results also demonstrated a sensitivity of 92.22% and a specificity of 100% for influenza A, a sensitivity of 91.18%, and a specificity of 99.49% for influenza B. The agreement analysis of the Q Ag combo test with the RT-PCR results demonstrated excellent outcomes, making it useful and efficient for the detection of SARS-CoV-2, influenza A, and influenza B.
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Development of an optimized colorimetric RT-LAMP for SARS-CoV-2 assay with enhanced procedure controls for remote diagnostics. Sci Rep 2022; 12:21424. [PMID: 36503901 PMCID: PMC9741705 DOI: 10.1038/s41598-022-25872-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
The coronavirus pandemic accentuated the need for molecular diagnostic tests. A technique highly used to this end is the Polymerase Chain Reaction (PCR)-a sensitive and specific technique commonly used as the gold standard for molecular diagnostics. However, it demands highly trained personnel and high-maintenance equipment and is relatively time-consuming. An alternative is the Loop-Mediated Isothermal Amplification (LAMP) technique, which doesn't need sample purification or expensive equipment, and is similar to PCR when compared in sensitivity and specificity. In this paper, we developed an optimized colorimetric Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) Point-of-Care test using a portable device to diagnose COVID-19. Variables such as concentration of primers, magnesium sulfate, betaine, hydrochloride guanidine, Bst, and temperature of the reactions were tested. We also created a pipetting quality control system-using a combination of dyes-to avoid false negatives due to a lack of samples added to the reaction test tube. Mineral oil was incorporated in the composition of the RT-LAMP reactions to avoid evaporation when a heating lid isn't available. The final RT-LAMP test is tenfold more sensitive when compared to the WarmStart Colorimetric Master mix from New England Biolabs with a sensitivity of 5 copies per μL.
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Osman NA, Hashish MH, Bakr WMK, Osman NA, Omran EA. "Day 25": a temporal indicator of stabilization of mortality risk among COVID-19 patients with high viral load. Trop Med Health 2022; 50:92. [PMID: 36494866 PMCID: PMC9732988 DOI: 10.1186/s41182-022-00483-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/19/2022] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION The relationship between SARS-CoV-2 viral load and hospitalization and mortality among COVID-19 patients has been established. However, the estimation of the duration of time after which the risk of mortality of these patients stops escalating was not extensively discussed earlier. Stratifying patients according to their risk of mortality would optimize healthcare services and costs and reduce mortality. METHODOLOGY In this retrospective observational study, hospital records were used to collect data of 519 COVID-19 patients from May through November 2020. Data included the clinical condition of patients, their viral loads, their admission chest computed tomography results (CO-RAD scale), and the duration of their hospitalization. A Kaplan-Meier analysis was constructed to estimate mortality risk concerning viral load. RESULTS By the end of the study, 20.42% of patients were deceased. The cumulative mortality was: 36.1% (75/208) among patients with high viral load, 12.6% (28/222) in those with moderate viral load, and 3.4% (3/89) among those with low viral load. Predictors of mortality were: older age [adjusted hazard ratio (aHR) = 1.02, 95% CI: [1.00-1.03], (p = 0.05)], "being female" [aHR = 1.53 with 95% CI: [1.03-2.26], (p = 0.031), "high CO-RAD scale" [aHR = 1.32 (1.06-1.64), p = 0.013], "high viral load" [aHR = 4.59 (2.38-20.92), p = 0.017, ICU admission [aHR = 15.95; 95%CI:7.22-35.20, p < 0.001] and lymphocytosis [aHR = 1.89 45;95%CI:1.04-3.45, p = 0.036]. In the ICU-admitted patients, the median survival was 19 days and mortality stabilized at "day 25". For patients with high viral load, mortality rates stabilized at "day 25 post-admission" after which the risks of mortality did not change until day 40, while patients with low and moderate viral loads reached the peak and stabilized at day "20 post-admission". CONCLUSIONS Initial high SARS-CoV-2 viral load might be used as an indicator of a delayed stabilization of mortality risk among COVID-19 patients.
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Affiliation(s)
- Nancy A. Osman
- grid.415762.3Ministry of Health and Population, Alexandria, Egypt
| | - Mona H. Hashish
- grid.7155.60000 0001 2260 6941Department of Microbiology, High Institute of Public Health, Alexandria University, 165 El-Horreya Avenue, El-Ibrahimia, Alexandria, Egypt
| | - Wafaa M. K. Bakr
- grid.7155.60000 0001 2260 6941Department of Microbiology, High Institute of Public Health, Alexandria University, 165 El-Horreya Avenue, El-Ibrahimia, Alexandria, Egypt
| | - Nermin A. Osman
- grid.7155.60000 0001 2260 6941Biomedical Informatics and Medical Statistics Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Eman A. Omran
- grid.7155.60000 0001 2260 6941Department of Microbiology, High Institute of Public Health, Alexandria University, 165 El-Horreya Avenue, El-Ibrahimia, Alexandria, Egypt
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Dogan L, Allahverdiyeva A, Önel M, Meşe S, Saka Ersin E, Anaklı İ, Sarıkaya ZT, Zengin R, Gucyetmez B, Yurtturan Uyar N, Özcan PE, Kocagöz AS, Uysal HK, Akinci İO, Ağaçfidan A. Is SARS-CoV-2 viral load a predictor of mortality in COVID-19 acute respiratory distress syndrome patients? J Int Med Res 2022; 50:3000605221137443. [DOI: 10.1177/03000605221137443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Objective Viral load varies during infection and is higher during the initial stages of disease. Given the importance of the intensive care unit (ICU) in the late stages of COVID-19 infection, analyzing cycle threshold values to detect viral load upon ICU admission can be a clinically valuable tool for identifying patients with the highest mortality risk. Methods This was a retrospectively designed study. Patients older than 18 years who tested positive for SARS-CoV-2 PCR and had a PaO2/FiO2 ratio <200 were included in the study. The patient population was divided into two groups: survivors and non-survivors. Results Two hundred patients were included in the study. In non-survivors, age, relevant ICU admission scores, and procalcitonin levels were significantly higher whereas PaO2/FiO2 ratios and cycle threshold levels were significantly lower than in survivors. Conclusion Viral load at ICU admission has significant prognostic value. In combination with age, comorbidities, and severity scores, viral load may assist clinicians in identifying individuals who need more intensive monitoring. Increased awareness may improve outcomes by allowing the more effective monitoring and treatment of patients. More prospective studies are needed to determine how a high viral load worsens disease and how to avoid irreversible results.
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Affiliation(s)
- Lerzan Dogan
- Department of Medical Microbiology, Istanbul University, Istanbul, Turkey
- Intensive Care Unit, Acibadem Altunizade Hospital, Istanbul, Turkey
| | | | - Mustafa Önel
- Department of Medical Microbiology, Istanbul University, Istanbul, Turkey
| | - Sevim Meşe
- Department of Medical Microbiology, Istanbul University, Istanbul, Turkey
| | - Esra Saka Ersin
- Department of Anesthesiology and Reanimation, Istanbul University, Istanbul, Turkey
| | - İlkay Anaklı
- Department of Anesthesiology and Reanimation, Istanbul University, Istanbul, Turkey
| | - Zeynep Tuğçe Sarıkaya
- Department of Anesthesiology and Reanimation, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Rehile Zengin
- Department of Infectious Disease and Clinical Microbiology, Acibadem Altunizade Hospital, Istanbul, Turkey
| | - Bulent Gucyetmez
- Department of Anesthesiology and Reanimation, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Neval Yurtturan Uyar
- Department of Medical Microbiology, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Perihan Ergin Özcan
- Department of Anesthesiology and Reanimation, Istanbul University, Istanbul, Turkey
| | - Ayse Sesin Kocagöz
- Department of Infectious Disease and Clinical Microbiology, Acibadem Altunizade Hospital, Istanbul, Turkey
| | | | | | - Ali Ağaçfidan
- Department of Medical Microbiology, Istanbul University, Istanbul, Turkey
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Kumar S, Pany SPP, Sudhakar S, Singh SB, Todankar CS, Pradeepkumar PI. Targeting Parallel Topology of G-Quadruplex Structures by Indole- Fused Quindoline Scaffolds. Biochemistry 2022; 61:2546-2559. [DOI: 10.1021/acs.biochem.2c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Satendra Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | | | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Sushma B. Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Chaitra S. Todankar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - P. I. Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
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Gentile A, Juarez MDV, Lucion MF, Pejito MN, Alexay S, Orqueda AS, Bollon LR, Mistchenko A. COVID-19 in Children: Correlation Between Epidemiologic, Clinical Characteristics, and RT-qPCR Cycle Threshold Values. Pediatr Infect Dis J 2022; 41:666-670. [PMID: 35544738 PMCID: PMC9281424 DOI: 10.1097/inf.0000000000003564] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/31/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND Initially, the impact of SARS-CoV-2 infection on children was unknown. Standard COVID-19 diagnosis is confirmed using real-time qPCR. Cycle threshold (Ct) values of RT-qPCR are inversely proportional to viral load and the test indirectly quantifies viral RNA copy numbers. The objective of this study was to determine the correlation between epidemiology, clinical characteristics, severity of confirmed COVID-19 cases, and Ct values. METHODS An observational, analytical, cross-sectional study. All children with COVID-19 under 18 years old admitted to the Ricardo Gutiérrez Children's Hospital between March 1, 2020, and February 28, 2021, were included. SARS-CoV-2 infection was confirmed using RT-qPCR. RESULTS Median age of patients was 7 years. Ct values were estimated in 419 cases, median Ct value was 23.5 [interquartile range (IQR): 18.9-30.9]. Levels were significantly lower in symptomatic than asymptomatic patients (Ct: 22.1; IQR: 18.4-22.1), in children <2 years of age (Ct: 20.6; IQR: 17.3-27.3) and when sample collection was <4 days after symptom onset (Ct: 21.1; IQR: 18.1-27.5). In children >2 years of age, Ct values were significantly lower in symptomatic (Ct: 22.6; IQR: 18.7-29.3) than asymptomatic (Ct: 31.2; IQR: 24.5-33.3) patients. CONCLUSIONS Children younger than 2 years with COVID-19 have lower values of Ct-as a proxy for higher viral load-than older children. Symptomatic children over 2 years of age had lower Ct values compared with asymptomatic children.
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Affiliation(s)
- Angela Gentile
- From the Epidemiology, Ricardo Gutiérrez Children’s Hospital, Buenos Aires, Argentina
| | | | | | - María Natalia Pejito
- From the Epidemiology, Ricardo Gutiérrez Children’s Hospital, Buenos Aires, Argentina
| | - Sofia Alexay
- Virology, Ricardo Gutiérrez Children’s Hospital, Buenos Aires, Argentina
| | - Ana Sofia Orqueda
- From the Epidemiology, Ricardo Gutiérrez Children’s Hospital, Buenos Aires, Argentina
| | - Lucia Romero Bollon
- From the Epidemiology, Ricardo Gutiérrez Children’s Hospital, Buenos Aires, Argentina
| | - Alicia Mistchenko
- Virology, Ricardo Gutiérrez Children’s Hospital, Buenos Aires, Argentina
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Qin Z, Sun Y, Zhang J, Zhou L, Chen Y, Huang C. Lessons from SARS‑CoV‑2 and its variants (Review). Mol Med Rep 2022; 26:263. [PMID: 35730623 PMCID: PMC9260876 DOI: 10.3892/mmr.2022.12779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/01/2022] [Indexed: 12/15/2022] Open
Abstract
COVID-19 has swept through mainland China by human-to-human transmission. The rapid spread of SARS-CoV-2 and its variants, including the currently prevalent Omicron strain, pose a serious threat worldwide. The present review summarizes epidemiological investigation and etiological analysis of genomic, epidemiological, and pathological characteristics of the original strain and its variants, as well as progress in diagnosis and treatment. Prevention and control measures used during the current Omicron pandemic are discussed to provide further knowledge of SARS-CoV-2.
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Affiliation(s)
- Ziwen Qin
- Department of Respiratory Diseases, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250013, P.R. China
| | - Yan Sun
- Department of Respiratory Diseases, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Jian Zhang
- Department of Respiratory Diseases, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Ling Zhou
- Department of Respiratory Diseases, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Yujuan Chen
- Department of Respiratory Diseases, The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250013, P.R. China
| | - Chuanjun Huang
- Department of Respiratory Diseases, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250013, P.R. China
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Characterization of Butyrate-Resistant Colorectal Cancer Cell Lines and the Cytotoxicity of Anticancer Drugs against These Cells. BIOMED RESEARCH INTERNATIONAL 2022; 2022:6565300. [PMID: 35909471 PMCID: PMC9325644 DOI: 10.1155/2022/6565300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/30/2022] [Indexed: 12/26/2022]
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. The gut microbiota plays a critical role in homeostasis and carcinogenesis. Butyrate, a short-chain fatty acid produced by the gut microbiota, plays a role in intestinal homeostasis and acts as an anticancer agent by inhibiting growth and inducing apoptosis. However, microbiota studies have revealed an abnormally high abundance of butyrate-producing bacteria in patients with CRC and indicated that it leads to chemoresistance. We characterized butyrate resistance in HCT-116 and PMF-K014 CRC cells after treatment with a maximum butyrate concentration of 3.2 mM. The 50% inhibitory concentration of butyrate was increased in butyrate-resistant (BR) cells compared with that in parental (PT) cells. The mechanism of butyrate resistance was initially investigated by determining the expression of butyrate influx- and drug efflux-related genes. We found the increased expression of influx- and efflux-related genes in BR cells compared with that in PT cells. Proteomic data showed both identical and different proteins in PT and BR cells. Further analysis revealed the crossresistance of HCT-116 cells to metformin and oxaliplatin and that of PMF-K014 cells to 5-fluorouracil. Our findings suggest that the acquisition of butyrate resistance induces the development of chemoresistance in CRC cells, which may play an important role in CRC development, treatment, and metastasis.
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Abeysuriya V, Seneviratne SL, de Silva AP, Mowjood R, Mowjood S, de Silva T, de Mel P, de Mel C, Chandrasena L, Wijesinha RS, Fernando A, de Mel S. Combination of cycle threshold time, absolute lymphocyte count and neutrophil:lymphocyte ratio is predictive of hypoxia in patients with SARS-CoV-2 infection. Trans R Soc Trop Med Hyg 2022; 116:628-635. [PMID: 34894631 PMCID: PMC8754692 DOI: 10.1093/trstmh/trab182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/24/2021] [Accepted: 11/16/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND There is currently no clinically validated biomarker to predict respiratory compromise in sudden acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Cycle threshold time (Ct), absolute lymphocyte count (AL) and neutrophil:lymphocyte ratio (NLR) have been previously evaluated for this purpose. We hypothesized that the combination of these parameters at presentation may be predictive of hypoxia (oxygen saturation <92%). METHODS Data were collected on 118 patients with SARS-CoV-2 infection between May 2020 and April 2021. Demographics, clinical parameters and laboratory and radiological investigation results were recorded. Respiratory compromise (RC) was defined based on symptoms and signs, hypoxia and chest X-ray abnormalities. RESULTS RC occurred in 61 (51.7%) of patients. The Ct, AL and NLR at median day 3 of illness were significantly different between patients with and without RC (Ct, RC vs not: 19.46±2.64 vs 22.62±3.37, p=0.0001; AL, RC vs not: 531.49±289.09 vs 764.69±481.79, p=0.0001; NLR, RC vs not: 3.42±0.75 vs 2.59±0.55, p=0.0001). Receiver operating characteristics analysis showed that a Ct <19.9, AL <630.8×103/μL and NLR >3.12 at median day 3 of symptoms was predictive of hypoxia on day 7 of illness (area under the curve 0.805, sensitivity 96.7%, specificity 69.1%). The predictive value for the parameters combined was significantly superior to their individual predictive power. CONCLUSIONS Ct, AL and NLR used in combination on day 3 of symptoms are predictive of hypoxia on day 7 of SARS-CoV-2 illness.
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Affiliation(s)
- Visula Abeysuriya
- Nawaloka Hospital Research and Education Foundation, Nawaloka Hospitals PLC, Colombo, Sri Lanka
| | - Suranjith L Seneviratne
- Nawaloka Hospital Research and Education Foundation, Nawaloka Hospitals PLC, Colombo, Sri Lanka
- Institute of Immunity and Transplantation, Royal Free Hospital and University College London, UK
| | - Arjuna P de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Sri Lanka
| | - Riaz Mowjood
- Department of Respiratory Disease, Nawaloka Hospitals PLC, Colombo, Sri Lanka
| | - Shazli Mowjood
- Department of Respiratory Disease, Nawaloka Hospitals PLC, Colombo, Sri Lanka
| | - Thushara de Silva
- Department of Respiratory Disease, Nawaloka Hospitals PLC, Colombo, Sri Lanka
| | - Primesh de Mel
- Nawaloka Hospital Research and Education Foundation, Nawaloka Hospitals PLC, Colombo, Sri Lanka
| | - Chandima de Mel
- Nawaloka Hospital Research and Education Foundation, Nawaloka Hospitals PLC, Colombo, Sri Lanka
| | - Lal Chandrasena
- Nawaloka Hospital Research and Education Foundation, Nawaloka Hospitals PLC, Colombo, Sri Lanka
| | - R S Wijesinha
- Princess Alexandra Hospital, Princess Alexandra Hospital NHS Trust, UK
| | | | - Sanjay de Mel
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System Singapore, Singapore
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Bohan AE, Purvis KN, Sawyer JT, Bergen WG, Brandebourg TD. Sampling Adipose and Muscle Tissue following Post-Harvest Scalding Does Not Affect RNA Integrity or Real-Time PCR Results in Market Weight Yorkshire Pigs. Foods 2022; 11:foods11121741. [PMID: 35741939 PMCID: PMC9222963 DOI: 10.3390/foods11121741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/06/2022] [Accepted: 06/11/2022] [Indexed: 11/16/2022] Open
Abstract
Improving production efficiency while enhancing pork quality is pivotal for strengthening sustainable pork production. Being able to study both gene expression and indices of pork quality from the same anatomical location of an individual animal would better enable research conducted to study relationships between animal growth and carcass merit. To facilitate gene expression studies, adipose and muscle tissue samples are often collected immediately following exsanguination to maximize RNA integrity, which is a primary determinant of the sensitivity of RNA-based assays, such as real-time PCR. However, collecting soft tissue samples requires cutting through the hide or skin. This leaves the underlying tissue exposed during scalding, poses possible food safety issues, and potentially confounds pork quality measures. To overcome these limitations, the effect of tissue sample timing post-harvest on RNA integrity, real-time PCR results, and pork quality measurements was investigated by sampling subcutaneous adipose tissue and longissimus thoracis et lumborum muscle immediately following either exsanguination, scalding, or chilling. Sampling time did not affect RNA quality, as determined by the RNA integrity number of RNA samples purified from either adipose (RIN; p > 0.54) or muscle tissue (p > 0.43). Likewise, the sampling time did not influence the results of real-time PCR analysis of gene expression when comparing RNA samples prepared from adipose or muscle tissue immediately following either exsanguination or scalding (p > 0.92). However, sampling tissue prior to scalding resulted in a greater visual color score (p < 0.001) and lesser L* (p < 0.001) and b* (p < 0.001) values without impacting the 24 h pH (p < 0.41). These results suggested that if both RNA-based assays and meat quality endpoints are to be performed at the same anatomical location on an animal, tissue sampling to facilitate RNA-based assays should occur at a time point immediately following scalding. These findings demonstrated that sampling of adipose and muscle tissue can be delayed until after scalding/dehairing without decreasing the RNA integrity or altering the results of real-time PCR assays, while doing so was associated with little impact on measures of pork quality.
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Guan L, Crasta KC, Maier AB. Assessment of cell cycle regulators in human peripheral blood cells as markers of cellular senescence. Ageing Res Rev 2022; 78:101634. [PMID: 35460888 DOI: 10.1016/j.arr.2022.101634] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/11/2022] [Accepted: 04/15/2022] [Indexed: 12/12/2022]
Abstract
Cellular senescence has gained increasing interest during recent years, particularly due to causal involvement in the aging process corroborated by multiple experimental findings. Indeed, cellular senescence considered to be one of the hallmarks of aging, is defined as a stable growth arrest predominantly mediated by cell cycle regulators p53, p21 and p16. Senescent cells have frequently been studied in the peripheral blood of humans due to its accessibility. This review summarizes ex vivo studies describing cell cycle regulators as markers of senescence in human peripheral blood cells, along with detection methodologies and associative studies examining demographic and clinical characteristics. The utility of techniques such as the quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), microarray, RNA sequencing and nCounter technologies for detection at the transcriptional level, along with Western blotting, enzyme-linked immunosorbent assay and flow cytometry at the translational level, will be brought up at salient points throughout this review. Notably, housekeeping genes or proteins serving as controls such as GAPDH and β-Actin, were found not to be stably expressed in some contexts. As such, optimization and validation of such genes during experimental design were recommended. In addition, the expression of cell cycle regulators was found to vary not only between different types of blood cells such as T cells and B cells but also between stages of cellular differentiation such as naïve T cells and highly differentiated T cells. On the other hand, the associations of the presence of cell cycle regulators with demographics (age, gender, ethnicity, and socioeconomic status), clinical characteristics (body mass index, specific diseases, disease-related parameters) and lifestyle vary in groups of participants. One envisions that increased understanding and insights into the assessment of cell cycle regulators as markers of senescence in human peripheral blood cells will help inform prognostication and clinical intervention in elderly individuals.
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Affiliation(s)
- Lihuan Guan
- Department of Medicine and Aged Care, @AgeMelbourne, The Royal Melbourne Hospital, The University of Melbourne, Victoria, Australia.
| | - Karen C Crasta
- Healthy Longevity Translational Researc h Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Physiology, National University of Singapore, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Agency for Science, Technology & Research (A⁎STAR), Institute of Molecular and Cell Biology (IMCB), Singapore.
| | - Andrea B Maier
- Department of Medicine and Aged Care, @AgeMelbourne, The Royal Melbourne Hospital, The University of Melbourne, Victoria, Australia; Healthy Longevity Translational Researc h Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Centre for Healthy Longevity, @AgeSingapore, National University Health System, Singapore; Department of Human Movement Sciences, @AgeAmsterdam, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, the Netherlands.
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Kumar S, Reddy Sannapureddi RK, Todankar CS, Ramanathan R, Biswas A, Sathyamoorthy B, Pradeepkumar PI. Bisindolylmaleimide Ligands Stabilize c-MYC G-Quadruplex DNA Structure and Downregulate Gene Expression. Biochemistry 2022; 61:1064-1076. [PMID: 35584037 DOI: 10.1021/acs.biochem.2c00116] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
G-Quadruplex (G4) structures play a pivotal role in diverse biological functions, including essential processes, such as telomere maintenance and gene regulation. G4 structures formed in functional regions of genomes are actively pursued toward therapeutics and are targeted by small-molecule ligands that alter their structure and/or stability. Herein, we report the synthesis of bisindolylmaleimide-based (BIM) ligands, which preferentially stabilize parallel G4 structures of c-MYC and c-KIT oncogenes over the telomeric h-RAS1 G4 and duplex DNAs. The preferential stabilization of parallel G4s with BIM ligands is further validated by the DNA polymerase stop assay, where stop products were only observed for templates containing the c-MYC G4 sequence. Nuclear magnetic resonance (NMR) titration studies indicate that the lead ligand BIM-Pr1 forms a 2:1 complex with c-MYC G4 DNA with a KD of 38 ± 5 μM. The BIM ligand stacks at the 5' and 3' quartets, with molecular modeling and dynamics studies supporting the proposed binding mode. The ligand is cytotoxic to HeLa cells and downregulates c-MYC gene expression. Collectively, the results present bisindolylmaleimide scaffolds as novel and powerful G4 targeting agents.
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Affiliation(s)
- Satendra Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | - Chaitra S Todankar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - R Ramanathan
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Annyesha Biswas
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Bharathwaj Sathyamoorthy
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal 462066, India
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Expression of microRNA-223 and microRNA-146b in serum and liver tissue of mice infected with Schistosoma mansoni. Parasitol Res 2022; 121:1963-1972. [PMID: 35576078 PMCID: PMC9192441 DOI: 10.1007/s00436-022-07542-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/03/2022] [Indexed: 11/21/2022]
Abstract
MicroRNAs (miRNAs) play regulatory roles in several diseases. In schistosomiasis, the main pathological changes are caused by the granulomatous reaction induced by egg deposition. We aimed to study the changes in host miRNA-223 and miRNA-146b expression in relation to egg deposition and development of hepatic pathology in murine schistosomiasis mansoni. Blood and liver tissue samples were collected from non-infected mice (group I), S. mansoni–infected mice at the 4th, 8th, and 12th weeks post-infection (p.i.) (groups II–IV), and 4 weeks after praziquantel treatment (group V). The collected samples were processed for RNA extraction, reverse transcription, and real-time PCR analysis of miRNA-223 and miRNA-146b. miRNAs’ relative expression was estimated by the ΔΔCt method. Liver tissue samples were examined for egg count estimation and histopathological evaluation. Results revealed that miRNA-223 was significantly downregulated in liver tissues 8 and 12 weeks p.i., whereas miRNA-146b expression increased gradually with the progression of infection with a significantly higher level at week 12 p.i. compared to week 4 p.i. Serum expression levels nearly followed the same pattern as the tissue levels. The dysregulated expression of miRNAs correlated with liver egg counts and was more obvious with the demonstration of chronic granulomas, fibrous transformation, and distorted hepatic architecture 12 weeks p.i. Restoration of normal expression levels was observed 4 weeks after treatment. Collectively, these findings provide new insights for in-depth understanding of host-parasite interaction in schistosomiasis and pave a new way for monitoring the progress of hepatic pathology before and after treatment.
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A panoptic review of techniques for finfish disease diagnosis: The status quo and future perspectives. J Microbiol Methods 2022; 196:106477. [DOI: 10.1016/j.mimet.2022.106477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
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Derqaoui S, Oukessou M, Attrassi K, Elftouhy FZ, Nassik S. Detection of Sutterella spp. in Broiler Liver and Breast. Front Vet Sci 2022; 9:859902. [PMID: 35433902 PMCID: PMC9009309 DOI: 10.3389/fvets.2022.859902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/23/2022] [Indexed: 02/03/2023] Open
Abstract
Sutterella sp. is a gram-negative, microaerophilic bacterium that is particularly resistant to bile acids. It has recently been associated with several human pathologies such as inflammatory bowel disease, asthma, diabetes, and autism. Indeed, susceptibility patterns to ciprofloxacin and erythromycin, combined with resistance to metronidazole, indicate that Sutterella wadsworthensis patterns are closer to those of Campylobacter. The objective of this study is to identify, for the first time, Sutterella spp. in the liver and breast of broiler chickens by quantitative real-time PCR (qPCR). Liver, breast, and cecal content samples were taken from 25 birds and frozen at −20°C until analyzed. The main results showed that Sutterella sp. is part of the cecal microbiota of 48% of the birds and present in the liver and breast of, respectively 20 and 40% of the chicks with a variable Cq. We, therefore, conclude that Sutterella sp. exists in poultry and poultry meat and that foodstuffs of poultry origin might be considered as a potential source of contamination for humans.
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Affiliation(s)
- Sophia Derqaoui
- Unit of Avian Pathology, Department of Veterinary Pathology and Public Health, Agronomy and Veterinary Medicine Institute Hassan II, Rabat, Morocco
- *Correspondence: Sophia Derqaoui ; orcid.org/0000-0002-3355-2800
| | - Mohammed Oukessou
- Unit of Physiology and Therapeutics, Department of Veterinary Biological and Pharmaceutical Sciences, Agronomy and Veterinary Medicine Institute Hassan II, Rabat, Morocco
| | - Kawtar Attrassi
- Unit of Avian Pathology, Department of Veterinary Pathology and Public Health, Agronomy and Veterinary Medicine Institute Hassan II, Rabat, Morocco
| | - Fatima Zahra Elftouhy
- Unit of Avian Pathology, Department of Veterinary Pathology and Public Health, Agronomy and Veterinary Medicine Institute Hassan II, Rabat, Morocco
| | - Saadia Nassik
- Unit of Avian Pathology, Department of Veterinary Pathology and Public Health, Agronomy and Veterinary Medicine Institute Hassan II, Rabat, Morocco
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Benchikh S, Bousfiha A, El Hamouchi A, Soro SGC, Malki A, Nassereddine S. Chronic myeloid leukemia: cytogenetics and molecular biology’s part in the comprehension and management of the pathology and treatment evolution. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00248-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Abstract
Background
Chronic myelogenous leukemia (CML) is a type of blood cancer that affects hematopoietic stem cells and is often characterized by the presence of the Philadelphia chromosome. The Philadelphia chromosome encodes for a protein with high tyrosine kinase activity which acts as a tumorigenic factor.
Main body
This review article reports an update on the pathophysiology of CML and highlights the role of cytogenetic and molecular biology in screening, diagnosis, therapeutic monitoring as well as evaluating patients’ response to treatment. Additionally, these genetic tests allow identifying additional chromosomal abnormalities (ACA) and BCR-ABL tyrosine kinase domain mutations in intolerant or resistant patients. Thus, therapeutic advances have enabled this pathology to become manageable and almost curable in its clinical course. The scientific literature search used in the synthesis of this paper was carried out in the PubMed database, and the figures were generated using online software named BioRender.
Conclusion
The role of cytogenetic and molecular biology is crucial for the diagnosis and medical monitoring of patients. In-depth knowledge of molecular mechanisms of the BCR-ABL kinase facilitated the development of new targeted therapies that have improved the vital prognosis in patients. However, the emergence of ACA and new mutations resistant to tyrosine kinase inhibitors constitutes a real challenge in the quest for adequate therapy.
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Zhang L, Su Z, Hong F, Wang L. Identification of a Methylation-Regulating Genes Prognostic Signature to Predict the Prognosis and Aid Immunotherapy of Clear Cell Renal Cell Carcinoma. Front Cell Dev Biol 2022; 10:832803. [PMID: 35309925 PMCID: PMC8924039 DOI: 10.3389/fcell.2022.832803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/04/2022] [Indexed: 12/21/2022] Open
Abstract
Methylation is one of the most extensive modifications of biological macromolecules and affects cell-fate determination, development, aging, and cancer. Several methylation modifications, including 5-methylcytosine and N6-methyladenosine, play an essential role in many cancers. However, little is known about the relationship between methylation and the prognosis of clear cell renal cell carcinoma (ccRCC). Here, we established a methylation-regulating genes prognostic signature (MRGPS) to predict the prognoses of ccRCC patients. We obtained ccRCC samples from The Cancer Genome Atlas and identified methylation-regulatingd genes (MRGs) from the Gene Set Enrichment Analysis database. We also determined differentially expressed genes (DEGs) and performed cluster analysis to identify candidate genes. Subsequently, we established and validated an MRGPS to predict the overall survival of ccRCC patients. This was also verified in 15 ccRCC samples collected from the Fujian Provincial Hospital via quantitative real-time transcription (qRT-PCR). While 95 MRGs were differentially expressed (DEGs1) between tumor and normal tissues, 17 MRGs were differentially expressed (DEGs2) between cluster 1 and 2. Notably, 13 genes common among DEGs1 and DEGs2 were identified as hub genes. In fact, we established three genes (NOP2, NSUN6, and TET2) to be an MRGPS based on their multivariate Cox regression analysis coefficients (p < 0.05). A receiver operating characteristic curve analysis confirmed this MRGPS to have a good prognostic performance. Moreover, the MRGPS was associated with characteristics of the tumor immune microenvironment and responses to inhibitor checkpoint inhibitors. Data from “IMvigor 210” demonstrated that patients with a low MRGPS would benefit more from atelozumab (p < 0.05). Furthermore, a multivariate analysis revealed that MRGPS was an independent risk factor associated with ccRCC prognosis (p < 0.05). Notably, a nomogram constructed by combining with clinical characteristics (age, grade, stage, and MRGPS risk score) to predict the overall survival of a ccRCC patient had a favorable predictive value. Eventually, our qRT-PCR results showed that tumor tissues had higher NOP2 and NSUN6 expression levels and lower TET2 expression than normal tissues of ccRCC samples. While the proposed MRGPS comprising NOP2, NSUN6, and TET2 can be an alternative prognostic biomarker for ccRCC patients, it is a promising index for personalized ICI treatments against ccRCC.
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Affiliation(s)
- Li Zhang
- Department of Nephrology, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Zhixiong Su
- Department of Radiation Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Fuyuan Hong
- Department of Nephrology, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
- *Correspondence: Fuyuan Hong, ; Lei Wang,
| | - Lei Wang
- Department of Radiation Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, China
- *Correspondence: Fuyuan Hong, ; Lei Wang,
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Gao B, Rojas Chavez AA, Malkawi WI, Keefe DW, Smith R, Haim H, Salem AK, Toor F. Sensitive detection of SARS-CoV-2 spike protein using vertically-oriented silicon nanowire array-based biosensor. SENSING AND BIO-SENSING RESEARCH 2022; 36:100487. [PMID: 35340912 PMCID: PMC8937609 DOI: 10.1016/j.sbsr.2022.100487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/23/2022] [Accepted: 03/18/2022] [Indexed: 11/06/2022] Open
Abstract
The COVID-19 pandemic has caused tremendous damage to the world. In order to quickly and accurately diagnose the virus and contain the spread, there is a need for rapid, sensitive, accurate, and cost-effective SARS-CoV-2 biosensors. In this paper, we report on a novel biosensor based on angiotensin converting enzyme 2 (ACE-2)-conjugated vertically-oriented silicon nanowire (vSiNW) arrays that can detect the SARS-CoV-2 spike protein with high sensitivity and selectivity relative to negative controls. First, we demonstrate the efficacy of using ACE-2 receptor to detect the SARS-CoV-2 spike protein via a capture assay test, which confirms high specificity of ACE-2 against the mock protein, and high affinity between the spike and ACE-2. We then report on results for ACE-2-conjugated vSiNW arrays where the biosensor device architecture is based on a p-n junction transducer. We confirm via analytical modeling that the transduction mechanism of the biosensor involves induced surface charge depletion of the vSiNWs due to negative electrostatic surface potential induced by the spike protein after binding with ACE-2. This vSiNW surface charge modulation is measured via current-voltage characteristics of the functionalized biosensor. Calibrated concentration dependent electrical response of the vSiNW sensor confirms the limit-of-detection for virus spike concentration of 100 ng/ml (or 575 pM). The vSiNW sensor also exhibits highly specific response to the spike protein with respect to negative controls, offering a promising point-of-care detection method for SARS-CoV-2.
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