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Li J, Gao H, Li Y, Zhai S, Xiao F, Wu G, Wu Y. The Development of a Series of Genomic DNA Reference Materials with Specific Copy Number Ratios for The Detection of Genetically Modified Maize DBN9936. Foods 2024; 13:747. [PMID: 38472860 DOI: 10.3390/foods13050747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
The genetically modified (GM) maize DBN9936 with a biosafety certificate will soon undergo commercial application. To monitor the safety of DBN9936 maize, three genomic DNA (gDNA) reference materials (RMs) (DBN9936a, DBN9936b, and DBN9936c) were prepared with nominal copy number ratios of 100%, 3%, and 1% for the DBN9936 event, respectively. DBN9936a was prepared from the leaf tissue gDNA of DBN9936 homozygotes, while DBN9936b and DBN9936c were prepared by the quantitative mixing of gDNA from the leaf tissues of DBN9936 homozygotes and non-GM counterparts. Validated DBN9936/zSSIIb duplex droplet digital PCR was demonstrated to be an accurate reference method for conducting homogeneity study, stability study, and collaborative characterization. The minimum intake for one measurement was determined to be 2 μL, and the gDNA RMs were stable during transport at 37 °C for 14 days and storage at -20 °C for 18 months. Each gDNA RM was certified for three property values: DBN9936 event copy number concentration, zSSIIb reference gene copy number concentration, and DBN9936/zSSIIb copy number ratio. The measurement uncertainty of the certified values took the uncertainty components related to possible inhomogeneity, instability, and characterization into account. This batch of gDNA RMs can be used for calibration and quality control when quantifying DBN9936 events.
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Affiliation(s)
- Jun Li
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Hongfei Gao
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yunjing Li
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Shanshan Zhai
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Fang Xiao
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Gang Wu
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yuhua Wu
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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Nakamura Y, Hashimoto M. Droplet size affects the degree of separation between fluorescence-positive and fluorescence-negative droplet populations in droplet digital PCR. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:656-666. [PMID: 38113037 DOI: 10.1039/d3ay01689g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
In droplet digital polymerase chain reaction (ddPCR) tests, a single sample solution is divided into many water-in-oil droplets. At the endpoint of PCR amplification, individual droplets are classified as either fluorescence-positive (FL(+)) or fluorescence-negative (FL(-)) droplets based upon their fluorescence amplitudes. Populations of FL(+) and FL(-) droplets can be seen in the histogram of fluorescence amplitude. The absolute copy number of a target molecule can be calculated from the fraction of FL(+) droplets relative to the total droplet number analyzed using Poisson statistics. It is crucial that the population of FL(+) droplets can be distinctly separated from that of the FL(-) droplets for accurately estimating the FL(+) droplet fraction and the absolute copy number. However, the distinct separation of the two populations is often impaired in actual ddPCR tests. Although many factors have been suggested to affect population separation, no study has addressed whether the droplet size influences the degree of separation. In this study, we compared the degrees of separation for ddPCR runs with three different droplet sizes. The experimental results showed an increasing degree of separation with decreasing droplet size. This discovery will potentially guide researchers to use smaller droplets in ddPCR to achieve higher accuracy and precision.
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Affiliation(s)
- Yusuke Nakamura
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321, Japan.
| | - Masahiko Hashimoto
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321, Japan.
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Pessoa FMCDP, Viana VBDJ, de Oliveira MB, Nogueira BMD, Ribeiro RM, Oliveira DDS, Lopes GS, Vieira RPG, de Moraes Filho MO, de Moraes MEA, Khayat AS, Moreira FC, Moreira-Nunes CA. Validation of Endogenous Control Genes by Real-Time Quantitative Reverse Transcriptase Polymerase Chain Reaction for Acute Leukemia Gene Expression Studies. Genes (Basel) 2024; 15:151. [PMID: 38397141 PMCID: PMC10887733 DOI: 10.3390/genes15020151] [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: 12/07/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Reference genes are used as internal reaction controls for gene expression analysis, and for this reason, they are considered reliable and must meet several important criteria. In view of the absence of studies regarding the best reference gene for the analysis of acute leukemia patients, a panel of genes commonly used as endogenous controls was selected from the literature for stability analysis: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Abelson murine leukemia viral oncogene human homolog 1 (ABL), Hypoxanthine phosphoribosyl-transferase 1 (HPRT1), Ribosomal protein lateral stalk subunit P0 (RPLP0), β-actin (ACTB) and TATA box binding protein (TBP). The stability of candidate reference genes was analyzed according to three statistical methods of assessment, namely, NormFinder, GeNorm and R software (version 4.0.3). From this study's analysis, it was possible to identify that the endogenous set composed of ACTB, ABL, TBP and RPLP0 demonstrated good performances and stable expressions between the analyzed groups. In addition to that, the GAPDH and HPRT genes could not be classified as good reference genes, considering that they presented a high standard deviation and great variability between groups, indicating low stability. Given these findings, this study suggests the main endogenous gene set for use as a control/reference for the gene expression in peripheral blood and bone marrow samples from patients with acute leukemias is composed of the ACTB, ABL, TBP and RPLP0 genes. Researchers may choose two to three of these housekeeping genes to perform data normalization.
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Affiliation(s)
- Flávia Melo Cunha de Pinho Pessoa
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Vitória Beatriz de Jesus Viana
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Marcelo Braga de Oliveira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Beatriz Maria Dias Nogueira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | | | - Deivide de Sousa Oliveira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Hematology, Fortaleza General Hospital (HGF), Fortaleza 60150-160, CE, Brazil
| | - Germison Silva Lopes
- Department of Hematology, César Cals General Hospital, Fortaleza 60015-152, CE, Brazil;
| | | | - Manoel Odorico de Moraes Filho
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Maria Elisabete Amaral de Moraes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Fabiano Cordeiro Moreira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
- Central Unity, Molecular Biology Laboratory, Clementino Fraga Group, Fortaleza 60115-170, CE, Brazil
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Schmitz D, Li Z, Lo Faro V, Rask-Andersen M, Ameur A, Rafati N, Johansson Å. Copy number variations and their effect on the plasma proteome. Genetics 2023; 225:iyad179. [PMID: 37793096 PMCID: PMC10697815 DOI: 10.1093/genetics/iyad179] [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: 08/25/2023] [Revised: 08/25/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
Structural variations, including copy number variations (CNVs), affect around 20 million bases in the human genome and are common causes of rare conditions. CNVs are rarely investigated in complex disease research because most CNVs are not targeted on the genotyping arrays or the reference panels for genetic imputation. In this study, we characterize CNVs in a Swedish cohort (N = 1,021) using short-read whole-genome sequencing (WGS) and use long-read WGS for validation in a subcohort (N = 15), and explore their effect on 438 plasma proteins. We detected 184,182 polymorphic CNVs and identified 15 CNVs to be associated with 16 proteins (P < 8.22×10-10). Of these, 5 CNVs could be perfectly validated using long-read sequencing, including a CNV which was associated with measurements of the osteoclast-associated immunoglobulin-like receptor (OSCAR) and located upstream of OSCAR, a gene important for bone health. Two other CNVs were identified to be clusters of many short repetitive elements and another represented a complex rearrangement including an inversion. Our findings provide insights into the structure of common CNVs and their effects on the plasma proteome, and highlights the importance of investigating common CNVs, also in relation to complex diseases.
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Affiliation(s)
- Daniel Schmitz
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
| | - Zhiwei Li
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
| | - Valeria Lo Faro
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
| | - Mathias Rask-Andersen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
| | - Nima Rafati
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Box 582, 751 23 Uppsala, Sweden
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
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Sahoo NR, D R P, Yadav V, Santhosh A, Maurya R, Gaur GK, Kumar P, Ravikumar GVPPS. Selection of a stable reference gene for relative copy number profiling of porcine chromosomal genes using SYBR green qPCR. Anim Biotechnol 2023; 34:2384-2390. [PMID: 35767335 DOI: 10.1080/10495398.2022.2092742] [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] [Indexed: 11/01/2022]
Abstract
Reference gene with stable copy number is essential for normalization in qPCR based copy number assay. Present study aims to identify a suitable reference gene in pigs for qPCR based relative copy number profiling of chromosomal genes. A total of 30 crossbred pigs of both sexes were cyto-screened and gDNA was extracted from the pigs having numerically normal karyotypes. The copy number stability was studied for 7 genes (FSHB, IL4, IGF1R, TCF24, BRMS1L, ARMC1 and SRSF4) selected on the basis of the chromosomal location, reports of single copy and lack of involvement in structural chromosomal abnormalities. The copy number was estimated from Ct values in 3 technical replicates using 6 animals from either sex for each gene. The stability was evaluated from the variations in Ct values using different (Delta Ct, geNorm, BestKeeper and normFinder) algorithms. While the moderate variation was observed among relative copy number stabilities among the genes, comprehensive ranking revealed the most stable gene for normalization (IGF1R > FSHB > TCF24 > IL4 > ARMC1> SRSF4 > BRMS1L) across the samples. The selected reference gene was validated using DNA of cyto-screened pigs to find out ratio of X and Y chromosome fragments using qPCR based copy number analysis.
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Affiliation(s)
- Nihar Ranjan Sahoo
- Swine Production Farm, ICAR- Indian Veterinary Research Institute, Izatnagar, UP, India
- International Centre for FMD, ICAR-Directorate of Foot and Mouth Disease, Bhubaneswar, Odisha, India
- Division of Animal Genetics, ICAR- Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Pruthviraj D R
- Division of Animal Genetics, ICAR- Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Vandana Yadav
- Division of Animal Genetics, ICAR- Indian Veterinary Research Institute, Izatnagar, UP, India
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Ameya Santhosh
- Division of Animal Genetics, ICAR- Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Rajveer Maurya
- Swine Production Farm, ICAR- Indian Veterinary Research Institute, Izatnagar, UP, India
| | - G K Gaur
- Swine Production Farm, ICAR- Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Pushpendra Kumar
- Division of Animal Genetics, ICAR- Indian Veterinary Research Institute, Izatnagar, UP, India
| | - G V P P S Ravikumar
- Veterinary Biotechnology Division, ICAR- Indian Veterinary Research Institute, Izatnagar, UP, India
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Yang Y, Feng X, Pan Y, Wang X, Peng T, Niu C, Qu W, Zou Q, Dong L, Dai X, Li M, Fang X. A culture-free method for rapidly and accurately quantifying active SARS-CoV-2. Anal Bioanal Chem 2023; 415:5745-5753. [PMID: 37486370 DOI: 10.1007/s00216-023-04855-9] [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: 05/03/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023]
Abstract
Determining the quantity of active virus is the most important basis to judge the risk of virus infection, which usually relies on the virus median tissue culture infectious dose (TCID50) assay performed in a biosafety level 3 laboratory within 5-7 days. We have developed a culture-free method for rapid and accurate quantification of active severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by targeting subgenomic RNA (sgRNA) based on reverse transcription digital PCR (RT-dPCR). The dynamic range of quantitative assays for sgRNA-N and sgRNA-E by RT-dPCR was investigated, and the result showed that the limits of detection (LoD) and quantification (LoQ) were 2 copies/reaction and 10 copies/reaction, respectively. The delta strain (NMDC60042793) of SARS-CoV-2 was cultured at an average titer of 106.13 TCID50/mL and used to evaluate the developed quantification method. Copy number concentrations of the cultured SARS-CoV-2 sgRNA and genomic RNA (gRNA) gave excellent linearity (R2 = 0.9999) with SARS-CoV-2 titers in the range from 500 to 105 TCID50/mL. Validation of 63 positive clinical samples further proves that the quantification of sgRNA-N by RT-dPCR is more sensitive for active virus quantitative detection. It is notable that we can infer the active virus titer through quantification of SARS-CoV-2 sgRNA based on the linear relationship in a biosafety level 2 laboratory within 3 h. It can be used to timely and effectively identify infectious patients and reduce unnecessary isolation especially when a large number of COVID-19 infected people impose a burden on medical resources.
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Affiliation(s)
- Yi Yang
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, 518107, China
| | - Xiaoli Feng
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, Yunnan, China
| | - Yang Pan
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Control and Prevention, Beijing, 100029, China
| | - Xia Wang
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Tao Peng
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Chunyan Niu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Wang Qu
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, 518107, China
| | - Qingcui Zou
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, 518107, China
| | - Lianhua Dong
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China.
| | - Xinhua Dai
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China.
| | - Minghua Li
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, 518107, China.
| | - Xiang Fang
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China.
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Rong N, Chen K, Shao J, Ouyang Q, Luo C. A 3D Scalable Chamber-Array Chip for Digital LAMP. Anal Chem 2023; 95:7830-7838. [PMID: 37115526 DOI: 10.1021/acs.analchem.2c05288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
As an absolute quantification method at the single-molecule level, digital PCR (dPCR) offers the highest accuracy. In this work, we developed a 3D scalable chamber-array chip that multiplied the number of partitions by stacking chamber-array layers and realized digital loop-mediated isothermal amplification to quantify DNA molecules. It greatly increases the number of partitions to improve the performance of dPCR without increasing the chip size, the operation workflow complicity, and operation time. For the three-chamber-array-layer chip which contains 200,000 reactors of a 0.125 nL volume, it has been proved that the reagent filling and partition were finished within 3 min, and the whole detection could be finished within 1 h. The method demonstrated that it could be scalable to a six-chamber-array layer, which contains 400,000 reactors without increasing the size of the chip and the complication of filling/partition workflow but only takes an additional hour for scanning. Due to its potential for high throughput, low cost, and simple operation, our device may significantly expand the clinical application range of dPCR.
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Affiliation(s)
- Nan Rong
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Kaiyue Chen
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Jiqi Shao
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Qi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
| | - Chunxiong Luo
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
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Establishment and evaluation of digital PCR methods for HER2 copy number variation in breast cancer. Anal Bioanal Chem 2023; 415:725-733. [PMID: 36571590 DOI: 10.1007/s00216-022-04466-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/20/2022] [Accepted: 11/24/2022] [Indexed: 12/27/2022]
Abstract
Accurate measurement of human epidermal growth factor receptor 2 (HER2) copy number variation (CNV) is very important for guiding the tumor target therapy in breast cancer. Digital PCR (dPCR) is a sensitive and an absolute quantitative method, which can be used to detect HER2 CNV. Three HER2 exon-specific digital PCR assays along with three new reference genes assays (homo sapiens ribonuclease P RNA component H1 (RPPH1), glucose-6-phosphate isomerase (GPI), and chromosome 1 open reading frame 43 (C1ORF43), on different chromosomes) were established and validated by using standard reference material, 8 different cell lines and 110 clinical Formalin-fixed and paraffin-embedded (FFPE) samples. DPCR can achieve precise quantification of HER2 CNV by calculating the ratio of HER2/reference gene. The positive and negative coincidence rates were 98% (53/54) and 95% (53/56), respectively, compared with fluorescence in situ hybridization (FISH) diagnostic result 110 of FFPE samples. The common reference gene CEP17 used for FISH diagnostic was not suitable as single reference gene for HER2 CNV measurements by dPCR. The best practice of HER2 CNV determination by dPCR is to conduct the three duplex assays of H1 (HER2 exon 4) with the proposed three new reference genes, with a positive cut-off value of H1/RPPH1 ≥ 2.0 or H1/averaged reference gene ≥ 2.0. The proposed dPCR method in our study can accurately provide absolute copy number of HER2 and reference gene on an alternative chromosome, thus avoiding false negative caused by polysomy of chromosome 17. The improved molecular typing and diagnosis of breast cancer will better guide clinical medication.
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9
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Shum EY, Lai JH, Li S, Lee HG, Soliman J, Raol VK, Lee CK, Fodor SP, Fan HC. Next-Generation Digital Polymerase Chain Reaction: High-Dynamic-Range Single-Molecule DNA Counting via Ultrapartitioning. Anal Chem 2022; 94:17868-17876. [PMID: 36508568 PMCID: PMC9798378 DOI: 10.1021/acs.analchem.2c03649] [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] [Indexed: 12/14/2022]
Abstract
Digital PCR (dPCR) was first conceived for single-molecule quantitation. However, current dPCR systems often require DNA templates to share partitions due to limited partitioning capacities. Here, we introduce UltraPCR, a next-generation dPCR system where DNA counting is performed in a single-molecule regimen through a 6-log dynamic range using a swift and parallelized workflow. Each UltraPCR reaction is divided into >30 million partitions without microfluidics to achieve single template occupancy. Combined with a unique emulsion chemistry, partitions are optically clear, enabling the use of a three-dimensional imaging technique to rapidly detect DNA-positive partitions. Single-molecule occupancy also allows for more straightforward multiplex assay development due to the absence of partition-specific competition. As a proof of concept, we developed a 222-plex UltraPCR assay and demonstrated its potential use as a rapid, low-cost screening assay for noninvasive prenatal testing for as low as 4% trisomy fraction samples with high precision, accuracy, and reproducibility.
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10
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Doleschall M, Darvasi O, Herold Z, Doleschall Z, Nyirő G, Somogyi A, Igaz P, Patócs A. Quantitative PCR from human genomic DNA: The determination of gene copy numbers for congenital adrenal hyperplasia and RCCX copy number variation. PLoS One 2022; 17:e0277299. [PMID: 36454796 PMCID: PMC9714944 DOI: 10.1371/journal.pone.0277299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/25/2022] [Indexed: 12/05/2022] Open
Abstract
Quantitative PCR (qPCR) is used for the determination of gene copy number (GCN). GCNs contribute to human disorders, and characterize copy number variation (CNV). The single laboratory method validations of duplex qPCR assays with hydrolysis probes on CYP21A1P and CYP21A2 genes, residing a CNV (RCCX CNV) and related to congenital adrenal hyperplasia, were performed using 46 human genomic DNA samples. We also performed the verifications on 5 qPCR assays for the genetic elements of RCCX CNV; C4A, C4B, CNV breakpoint, HERV-K(C4) CNV deletion and insertion alleles. Precision of each qPCR assay was under 1.01 CV%. Accuracy (relative error) ranged from 4.96±4.08% to 9.91±8.93%. Accuracy was not tightly linked to precision, but was significantly correlated with the efficiency of normalization using the RPPH1 internal reference gene (Spearman's ρ: 0.793-0.940, p>0.0001), ambiguity (ρ = 0.671, p = 0.029) and misclassification (ρ = 0.769, p = 0.009). A strong genomic matrix effect was observed, and target-singleplex (one target gene in one assay) qPCR was able to appropriately differentiate 2 GCN from 3 GCN at best. The analysis of all GCNs from the 7 qPCR assays using a multiplex approach increased the resolution of differentiation, and produced 98% of GCNs unambiguously, and all of which were in 100% concordance with GCNs measured by Southern blot, MLPA and aCGH. We conclude that the use of an internal (in one assay with the target gene) reference gene, the use of allele-specific primers or probes, and the multiplex approach (in one assay or different assays) are crucial for GCN determination using qPCR or other methods.
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Affiliation(s)
- Márton Doleschall
- Molecular Medicine Research Group, Eotvos Lorand Research Network and Semmelweis University, Budapest, Hungary
- * E-mail:
| | - Ottó Darvasi
- Hereditary Tumours Research Group, Eotvos Lorand Research Network and Semmelweis University, Budapest, Hungary
| | - Zoltán Herold
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Zoltán Doleschall
- Department of Pathogenetics, National Institute of Oncology, Budapest, Hungary
| | - Gábor Nyirő
- Molecular Medicine Research Group, Eotvos Lorand Research Network and Semmelweis University, Budapest, Hungary
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Anikó Somogyi
- Department of Internal Medicine and Hematology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Péter Igaz
- Molecular Medicine Research Group, Eotvos Lorand Research Network and Semmelweis University, Budapest, Hungary
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- Department of Endocrinology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Attila Patócs
- Hereditary Tumours Research Group, Eotvos Lorand Research Network and Semmelweis University, Budapest, Hungary
- Department of Internal Medicine and Hematology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
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11
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Liang X, Lan J, Xu M, Qin K, Liu H, Sun G, Liu X, Chen Y, He Z. Impact of KIT Editing on Coat Pigmentation and Fresh Meat Color in Yorkshire Pigs. CRISPR J 2022; 5:825-842. [PMID: 36315201 DOI: 10.1089/crispr.2022.0039] [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] [Indexed: 11/06/2022] Open
Abstract
The white coat color of Yorkshire pigs is caused by the dominant white I allele, which has been associated with at least one copy of the 450-kb duplication encompassing the entire KIT gene and a splice mutation (G > A) at the first base of intron 17. The splice mutation in KIT has an adverse effect on pigmentation in mice. Therefore, removing the 450 kb duplications harboring the KIT copy with splice mutations is expected to affect Yorkshire pig pigmentation. In this study, we describe the use of a Yorkshire pig kidney cell strain with the I?/IBe-ed genotype, previously created by CRISPR-Cas9, as donor cells for somatic cell nuclear transfer to generate gene-edited Yorkshire pigs. The removal of the 450 kb duplications harboring the KIT copy with splice mutation did not alter the white coat color of Yorkshire pigs, which was confirmed by the absence of fully mature melanocytes and melanin accumulation in the hair follicles. Except for the improved transcription of tyrosinase, and slight increase in microphthalmia transcription factor and tyrosinase-related protein 1 protein expression, there was no significant impact of the removal of splice mutations on genes and signaling pathways (PI3K/AKT) involved in melanogenesis. However, the removal of the 450 kb duplications harboring the KIT copy with splice mutation substantially improved fresh meat color accompanied by significantly increased red blood cell number, which merits further investigation. Our study provides new insights into the role of structural mutations of the KIT gene in the formation of white coat color and erythropoiesis in Yorkshire pigs.
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Affiliation(s)
- Xinyu Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jin Lan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Meina Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ke Qin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Hongbo Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Guanjie Sun
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
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12
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Liu M, Huang C, Dai R, Ren W, Li X, Wu X, Ma X, Chu M, Bao P, Guo X, Pei J, Xiong L, Yan P, Liang C. Copy Number Variations in the MICALL2 and MOGAT2 Genes Are Associated with Ashidan Yak Growth Traits. Animals (Basel) 2022; 12:ani12202779. [PMID: 36290165 PMCID: PMC9597734 DOI: 10.3390/ani12202779] [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: 09/05/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/29/2022] Open
Abstract
Copy number variations (CNVs) are a result of genomic rearrangement affecting DNA regions over 1 kb in length, and can include inversions, translocations, deletions, and duplications. The molecule interacting with CasL-like protein 2 (MICALL2) gene is primarily associated with mitochondrial protein targeting and exhibits predicted stress fiber colocalization. The monoacylglycerol O-acyltransferase 2 (MOGAT2) gene encodes an enzyme responsible for catalyzing diacylglycerol synthesis from 2-monoacylglycerol and fatty acyl-CoA. For this study, blood samples were obtained from 315 yaks, and the body weight, body length, withers height, and chest girth of these animals were measured at 6, 12, 18, and 30 months of age. Genomic DNA was harvested from the collected blood samples, and CNVs in these samples were detected by qPCR. The resultant data were compared using ANOVAs, revealing significant associations between MICALL2 gene CNVs and body weight at 6 months of age (p < 0.05), body length and chest girth at 30 months of age (p < 0.05), and withers height at 18 months of age (p < 0.01) in Ashidan yaks. Similarly, MOGAT2 CNVs were significantly associated with body weight at 6 and 30 months of age (p < 0.05), and with withers height at 18 months of age (p < 0.01) in these Ashidan yaks. MICALL2 and MOGAT2 gene expression was further analyzed in yak tissue samples, revealing that MICALL2 was most highly expressed in the adipose tissue, whereas MOGAT2 was most highly expressed in the lung. These results thus confirmed the relationship between CNVs in the MICALL2 and MOGAT2 genes and Ashidan yak growth traits, providing a valuable gene locus that can be leveraged for future marker-assisted yak breeding efforts.
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Affiliation(s)
- Modian Liu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chun Huang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Rongfeng Dai
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Wenwen Ren
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xinyi Li
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xiaoming Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Lin Xiong
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Correspondence: (P.Y.); (C.L.)
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Correspondence: (P.Y.); (C.L.)
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13
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Luo S, Chen X, Zeng D, Tang N, Yuan D, Liu B, Chen L, Zhong Q, Li J, Liu Y, Chen J, Wang X, Yan T. Detection of four rare thalassemia variants using Single-molecule realtime sequencing. Front Genet 2022; 13:974999. [PMID: 36159974 PMCID: PMC9493964 DOI: 10.3389/fgene.2022.974999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/01/2022] [Indexed: 11/18/2022] Open
Abstract
Conventional methods for the diagnosis of thalassemia include gap polymerase chain reaction (Gap-PCR), reverse membrane hybridization (RDB), multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. In this study, we used single molecule real-time technology (SMRT) sequencing and discovered four rare variants that have not been identified by conventional diagnostic methods for thalassemia. We also performed genotype and phenotype analyses on family members of thalassemia patients. The SMRT technology detected five cases in which the proband had abnormal results by conventional diagnostic methods or inconsistencies between the genotype and phenotype. The variants included two cases of an α-globin gene cluster 27,311 bp deletion, --27.3/αα (hg38 chr16:158664-185974), one case of an HS-40 region 16,079 bp deletion (hg38 chr16:100600-116678), one case of a rearrangement of -α3.7α1α2 on one allele and one case of a ß-globin gene cluster HBG1-HBG2 4,924 bp deletion (hg38 chr11:5249345-5254268). This study clarified the hematological phenotypes of four rare variants and indicated the application value of SMRT in the diagnosis of rare α-globin and ß-globin gene cluster deletions, gene recombination and deletion breakpoints. The SMRT method is a comprehensive one-step technology for the genetic diagnosis of thalassemia and is particularly suitable for the diagnosis of thalassemia with rare deletions or genetic recombination.
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Affiliation(s)
- Shiqiang Luo
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
| | - Xingyuan Chen
- Department of Laboratory Medicine, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Academy of Medical Sciences, Nanning, China
| | - Dingyuan Zeng
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, Liuzhou, China
| | - Ning Tang
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, Liuzhou, China
| | - Dejian Yuan
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
| | - Bailing Liu
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
| | - Lizhu Chen
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
| | - Qingyan Zhong
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
| | - Jiaqi Li
- Berry Genomics Corporation, Beijing, China
| | - Yinyin Liu
- Berry Genomics Corporation, Beijing, China
| | - Jianping Chen
- Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
| | - Xiaoyuan Wang
- Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- *Correspondence: Xiaoyuan Wang, ; Tizhen Yan,
| | - Tizhen Yan
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
- *Correspondence: Xiaoyuan Wang, ; Tizhen Yan,
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14
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Shirai R, Osumi T, Sato-Otsubo A, Nakabayashi K, Ishiwata K, Yamada Y, Yoshida M, Yoshida K, Shioda Y, Kiyotani C, Terashima K, Tomizawa D, Takasugi N, Takita J, Miyazaki O, Kiyokawa N, Yoneda A, Kanamori Y, Hishiki T, Matsumoto K, Hata K, Yoshioka T, Kato M. Quantitative assessment of copy number alterations by liquid biopsy for neuroblastoma. Genes Chromosomes Cancer 2022; 61:662-669. [PMID: 35655408 DOI: 10.1002/gcc.23073] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/27/2022] [Accepted: 05/10/2022] [Indexed: 11/08/2022] Open
Abstract
Liquid biopsy, a method of detecting genomic alterations using blood specimens, has recently attracted attention as a non-invasive alternative to surgical tissue biopsy. We attempted quantitative analysis to detect amplification of MYCN (MYCNamp) and loss of heterozygosity at 11q (11qLOH), which are clinical requisites as prognostic factors of neuroblastoma. In this study, cell-free DNA (cfDNA) was extracted from plasma samples from 24 neuroblastoma patients at diagnosis. Copy numbers of MYCN and NAGK genes were quantitatively analyzed by droplet digital PCR (ddPCR). 11qLOH was also assessed by detecting allelic imbalances of heterozygous single nucleotide polymorphisms in the 11q region. The results obtained were compared to those of specimens from tumor tissues. The correlation coefficient of MYCN copy number of cfDNA and tumor DNA was 0.88 (P < 0.00001). 11qLOH was also accurately detected from cfDNA, except for one case with localized NB. Given the high accuracy of liquid biopsy, to investigate components of cfDNA, the proportion of tumor-derived DNA was estimated by examining the variant allele frequency of tumor-specific mutations in cfDNA. The proportion of tumor-derived DNA in cfDNA was 42.5% (range, 16.9%-55.9%), suggesting sufficient sensitivity of liquid biopsy for neuroblastoma. In conclusion, MYCN copy number and 11qLOH could be quantitatively analyzed in plasma cfDNA by ddPCR assay. These results suggest that plasma cfDNA can be substituted for tumor DNA and can also be applied for comprehensive genomic profiling analysis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ryota Shirai
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Tomoo Osumi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Aiko Sato-Otsubo
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, University of Tokyo, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Keisuke Ishiwata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yuji Yamada
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masanori Yoshida
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Kaoru Yoshida
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yoko Shioda
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Chikako Kiyotani
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Keita Terashima
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Daisuke Tomizawa
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Nao Takasugi
- Department of Pediatrics, University of Tokyo, Tokyo, Japan
| | - Junko Takita
- Department of Pediatrics, University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Graduate School of Medicine Kyoto University, Kyoto City, Japan
| | - Osamu Miyazaki
- Department of Radiology, National Center for Child Health and Development, Tokyo, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akihiro Yoneda
- Division of Surgical Oncology, Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Yutaka Kanamori
- Division of Surgery, Department of Surgical Specialties, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoro Hishiki
- Division of Surgical Oncology, Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Kimikazu Matsumoto
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Takako Yoshioka
- Department of Pathology, National Center for Child Health and Development, Tokyo, Japan
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, University of Tokyo, Tokyo, Japan
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15
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Wong ATC, Lam DK, Poon ESK, Chan DTC, Sin SYW. Intra-specific copy number variation of MHC class II genes in the Siamese fighting fish. Immunogenetics 2022; 74:327-346. [PMID: 35229174 DOI: 10.1007/s00251-022-01255-8] [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: 09/12/2021] [Accepted: 02/04/2022] [Indexed: 11/28/2022]
Abstract
Duplicates of genes for major histocompatibility complex (MHC) molecules can be subjected to selection independently and vary markedly in their evolutionary rates, sequence polymorphism, and functional roles. Therefore, without a thorough understanding of their copy number variation (CNV) in the genome, the MHC-dependent fitness consequences within a species could be misinterpreted. Studying the intra-specific CNV of this highly polymorphic gene, however, has long been hindered by the difficulties in assigning alleles to loci and the lack of high-quality genomic data. Here, using the high-quality genome of the Siamese fighting fish (Betta splendens), a model for mate choice studies, and the whole-genome sequencing (WGS) data of 17 Betta species, we achieved locus-specific amplification of their three classical MHC class II genes - DAB1, DAB2, and DAB3. By performing quantitative PCR and depth-of-coverage analysis using the WGS data, we revealed intra-specific CNV at the DAB3 locus. We identified individuals that had two allelic copies (i.e., heterozygous or homozygous) or one allele (i.e., hemizygous) and individuals without this gene. The CNV was due to the deletion of a 20-kb-long genomic region harboring both the DAA3 and DAB3 genes. We further showed that the three DAB genes were under different modes of selection, which also applies to their corresponding DAA genes that share similar pattern of polymorphism. Our study demonstrates a combined approach to study CNV within a species, which is crucial for the understanding of multigene family evolution and the fitness consequences of CNV.
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Affiliation(s)
- Anson Tsz Chun Wong
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Derek Kong Lam
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Emily Shui Kei Poon
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - David Tsz Chung Chan
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China.
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16
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Bianca C, Sidhartha E, Tiribelli C, El-Khobar KE, Sukowati CHC. Role of hepatitis B virus in development of hepatocellular carcinoma: Focus on covalently closed circular DNA. World J Hepatol 2022; 14:866-884. [PMID: 35721287 PMCID: PMC9157711 DOI: 10.4254/wjh.v14.i5.866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/31/2022] [Accepted: 04/25/2022] [Indexed: 02/06/2023] Open
Abstract
Chronic infection with hepatitis B virus (HBV) remains a major global health problem, especially in developing countries. It may lead to prolonged liver damage, fibrosis, cirrhosis, and hepatocellular carcinoma. Persistent chronic HBV infection is related to host immune response and the stability of the covalently closed circular DNA (cccDNA) in human hepatocytes. In addition to being essential for viral transcription and replication, cccDNA is also suspected to play a role in persistent HBV infections or hepatitis relapses since cccDNA is very stable in non-dividing human hepatocytes. Understanding the pathogenicity and oncogenicity of HBV components would be essential in the development of new diagnostic tools and treatment strategies. This review summarizes the role and molecular mechanisms of HBV cccDNA in hepatocyte transformation and hepatocarcinogenesis and current efforts to its detection and targeting.
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Affiliation(s)
- Claryssa Bianca
- Department of Biomedicine, Indonesia International Institute for Life Sciences, Jakarta 13210, Indonesia
| | - Elizabeth Sidhartha
- Department of Biomedicine, Indonesia International Institute for Life Sciences, Jakarta 13210, Indonesia
| | - Claudio Tiribelli
- Centro Studi Fegato, Fondazione Italiana Fegato ONLUS, Trieste 34149, Italy
| | - Korri Elvanita El-Khobar
- Eijkman Center for Molecular Biology, National Research and Innovation Agency (BRIN), Jakarta 10340, Indonesia
| | - Caecilia H C Sukowati
- Centro Studi Fegato, Fondazione Italiana Fegato ONLUS, Trieste 34149, Italy
- Eijkman Center for Molecular Biology, National Research and Innovation Agency (BRIN), Jakarta 10340, Indonesia
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17
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Long S. In pursuit of sensitivity: Lessons learned from viral nucleic acid detection and quantification on the Raindance ddPCR platform. Methods 2022; 201:82-95. [PMID: 33839286 PMCID: PMC8501152 DOI: 10.1016/j.ymeth.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/27/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Sensitive PCR detection of viral nucleic acids plays a critical role in infectious disease research, diagnosis and monitoring. In the context of SARS-CoV-2 detection, recent reports indicate that digital PCR-based tests are significantly more sensitive than traditional qPCR tests. Numerous factors can influence digital PCR reaction sensitivity. In this review, using a model for human HIV infection and the Raindance ddPCR platform as an example, we describe technical aspects that contribute to sensitive viral signal detection in DNA and RNA from tissue samples, which often harbor viral reservoirs and serve as better predictors of disease outcome and indicators of treatment efficacy.
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Affiliation(s)
- Samuel Long
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States.
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18
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Long S, Berkemeier B. Ultrasensitive detection and quantification of viral nucleic acids with Raindance droplet digital PCR (ddPCR). Methods 2022; 201:49-64. [PMID: 33957204 PMCID: PMC8563494 DOI: 10.1016/j.ymeth.2021.04.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/22/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
Sensitive detection of viral nucleic acids is critically important for diagnosis and monitoring of the progression of infectious diseases such as those caused by SARS-CoV2, HIV-1, and other viruses. In HIV-1 infection cases, assessing the efficacy of treatment interventions that are superimposed on combination antiretroviral therapy (cART) has benefited tremendously from the development of sensitive HIV-1 DNA and RNA quantitation assays. Simian immunodeficiency virus (SIV) infection of Rhesus macaques is similar in many key aspects to human HIV-1 infection and consequently this non-human primate (NHP) model has and continues to prove instrumental in evaluating HIV prevention, treatment and eradication approaches. Cell and tissue associated HIV-1 viral nucleic acids have been found to serve as useful predictors of disease outcome and indicators of treatment efficacy, highlighting the value of and the need for sensitive detection of viruses in cells/tissues from infected individuals or animal models. However, viral nucleic acid detection and quantitation in such sample sources can often be complicated by high nucleic acid input (that is required to detect ultralow level viruses in, for example, cure research) or inhibitors, leading to reduced detection sensitivity and under-quantification, and confounded result interpretation. Here, we present a step-by-step procedure to quantitatively recover cell/tissue associated viral DNA and RNA, using SIV-infected Rhesus macaque cells and tissues as model systems, and subsequently quantify the viral DNA and RNA with an ultrasensitive SIV droplet digital PCR (ddPCR) assay and reverse transcription ddPCR (RT-ddPCR) assay, respectively, on the Raindance ddPCR platform. The procedure can be readily adapted for a broad range of applications where highly sensitive nucleic acid detection and quantitation are required.
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Affiliation(s)
- Samuel Long
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States.
| | - Brian Berkemeier
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States
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19
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Zou Z, Zhuang J, Xia L, Li Y, Yin J, Mu Y. DCD-chip designed for the digital and ultraprecise quantification of copy number variation. Analyst 2022; 147:4371-4378. [DOI: 10.1039/d2an00982j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The progress of CNV detection in DCD-chip.
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Affiliation(s)
- Zheyu Zou
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, P. R. China
- College of Life Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Jianjian Zhuang
- Department of Clinical pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Cancer Center, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, P. R. China
| | - Liping Xia
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, P. R. China
- College of Life Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Ying Li
- Department of Public Health, School of Medicine, Zhejiang University, Hangzhou, P. R. China
| | - Juxin Yin
- School of information and Electrical Engineering, Zhejiang University City College, Hangzhou, Zhejiang Province, P. R. China
| | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, P. R. China
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20
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Grimholt RM, Fjeld B, Klingenberg O. Hemoglobinopathy gone astray-three novel forms of α-thalassemia in Norwegian patients characterized by quantitative real-time PCR and DNA sequencing. Scandinavian Journal of Clinical and Laboratory Investigation 2021; 81:670-678. [PMID: 34791962 DOI: 10.1080/00365513.2021.2004218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
α-thalassemia is one of the most common monogenic diseases worldwide and is caused by reduced or absent synthesis of α-globin chains, most commonly due to deletions of one or more of the α-globin genes. α-thalassemia occurs with high frequency in tropical and subtropical regions of the world and are very rarely found in the indigenous Scandinavian population. Here, we describe four rare forms of α-thalassemia out of which three are novel, found in together 20 patients of Norwegian origin. The study patients were diagnosed during routine hemoglobinopathy evaluation carried out at the Department of Medical Biochemistry, Oslo University Hospital, Norway. The patients were selected for their thalassemic phenotype, despite Norway as country of origin. All samples went through standard hemoglobinopathy evaluation. DNA sequencing and copy number variation (CNV) analysis using quantitative real-time polymerase chain reaction (qPCR) was applied to detect sequence variants and uncommon deletions in the α-globin gene cluster, respectively. Deletion breakpoints were characterized using gap-PCR and DNA sequencing. DNA sequencing revealed a single nucleotide deletion in exon 3 of the HBA2 gene (NM_000517.4(HBA2):c.345del) and a novel deletion of 20 nucleotides in exon 2 of the HBA2 gene (NM_000517.4(HBA2):c.142_161del). qPCR CNV analysis detected two novel large deletions in the α-globin gene cluster, -(NOR) deletion covering both α-globin genes and (αα)Aurora Borealis affecting the regulatory region, leaving the downstream α-globin genes intact. Even though inherited globin gene disorders are extremely rare in indigenous Scandinavians, the possibility of a carrier state should not be ignored.
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Affiliation(s)
- Runa M Grimholt
- Department of Medical Biochemistry, Oslo University Hospital, Ullevaal, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Life Sciences and Health, Oslo Metropolitan University, Oslo, Norway
| | - Bente Fjeld
- Department of Medical Biochemistry, Oslo University Hospital, Ullevaal, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Olav Klingenberg
- Department of Medical Biochemistry, Oslo University Hospital, Ullevaal, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway
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21
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Trick AY, Chen FE, Schares JA, Freml BE, Lor P, Yun Y, Wang TH. High resolution estimates of relative gene abundance with quantitative ratiometric regression PCR (qRR-PCR). Analyst 2021; 146:6463-6469. [PMID: 34605831 PMCID: PMC8627783 DOI: 10.1039/d1an01397a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Quantification of the relative abundance of genetic traits has broad applications for biomarker discovery, diagnostics, and assessing gene expression in biological research. Relative quantification of genes is traditionally done with the 2-ΔΔCT method using quantitative real-time polymerase chain reaction (qPCR) data, which is often limited in resolution beyond orders of magnitude difference. The latest techniques for quantification of nucleic acids employ digital PCR or microarrays which involve lengthy sample preparation and complex instrumentation. In this work, we describe a quantitative ratiometric regression PCR (qRR-PCR) method for computing relative abundance of genetic traits in a sample with high resolution from a single duplexed real-time quantitative PCR assay. Instead of comparing the individual cycle threshold (Ct) values as is done for the 2-ΔΔCT method, our qRR-PCR algorithm leverages the innate relationship of co-amplified PCR targets to measure their relative quantities using characteristic curves derived from the normalized ratios of qPCR fluorescence curves. We demonstrate the utility of this technique for discriminating the fractional abundance of mixed alleles with resolution below 5%.
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Affiliation(s)
- Alexander Y Trick
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Fan-En Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | | | | | - Pa Lor
- Corteva Agriscience, Johnston, IA 50131, USA
| | - Yue Yun
- Corteva Agriscience, Johnston, IA 50131, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBiotechnology, Johns Hopkins University, Baltimore, MD 21218, USA
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22
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Emerging methods for and novel insights gained by absolute quantification of mitochondrial DNA copy number and its clinical applications. Pharmacol Ther 2021; 232:107995. [PMID: 34592204 DOI: 10.1016/j.pharmthera.2021.107995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023]
Abstract
The past thirty years have seen a surge in interest in pathophysiological roles of mitochondria, and the accurate quantification of mitochondrial DNA copy number (mCN) in cells and tissue samples is a fundamental aspect of assessing changes in mitochondrial health and biogenesis. Quantification of mCN between studies is surprisingly variable due to a combination of physiological variability and diverse protocols being used to measure this endpoint. The advent of novel methods to quantify nucleic acids like digital polymerase chain reaction (dPCR) and high throughput sequencing offer the ability to measure absolute values of mCN. We conducted an in-depth survey of articles published between 1969 -- 2020 to create an overview of mCN values, to assess consensus values of tissue-specific mCN, and to evaluate consistency between methods of assessing mCN. We identify best practices for methods used to assess mCN, and we address the impact of using specific loci on the mitochondrial genome to determine mCN. Current data suggest that clinical measurement of mCN can provide diagnostic and prognostic value in a range of diseases and health conditions, with emphasis on cancer and cardiovascular disease, and the advent of means to measure absolute mCN should improve future clinical applications of mCN measurements.
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23
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Borchardt MA, Boehm AB, Salit M, Spencer SK, Wigginton KR, Noble RT. The Environmental Microbiology Minimum Information (EMMI) Guidelines: qPCR and dPCR Quality and Reporting for Environmental Microbiology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10210-10223. [PMID: 34286966 DOI: 10.1021/acs.est.1c01767] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Real-time quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) methods have revolutionized environmental microbiology, yielding quantitative organism-specific data of nucleic acid targets in the environment. Such data are essential for characterizing interactions and processes of microbial communities, assessing microbial contaminants in the environment (water, air, fomites), and developing interventions (water treatment, surface disinfection, air purification) to curb infectious disease transmission. However, our review of recent qPCR and dPCR literature in our field of health-related environmental microbiology showed that many researchers are not reporting necessary and sufficient controls and methods, which would serve to strengthen their study results and conclusions. Here, we describe the application, utility, and interpretation of the suite of controls needed to make high quality qPCR and dPCR measurements of microorganisms in the environment. Our presentation is organized by the discrete steps and operations typical of this measurement process. We propose systematic terminology to minimize ambiguity and aid comparisons among studies. Example schemes for batching and combining controls for efficient work flow are demonstrated. We describe critical reporting elements for enhancing data credibility, and we provide an element checklist in the Supporting Information. Additionally, we present several key principles in metrology as context for laboratories to devise their own quality assurance and quality control reporting framework. Following the EMMI guidelines will improve comparability and reproducibility among qPCR and dPCR studies in environmental microbiology, better inform engineering and public health actions for preventing disease transmission through environmental pathways, and for the most pressing issues in the discipline, focus the weight of evidence in the direction toward solutions.
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Affiliation(s)
- Mark A Borchardt
- Environmentally Integrated Dairy Management Research Unit, USDA Agricultural Research Service, 2615 Yellowstone Drive, Marshfield, Wisconsin 54449, United States
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Marc Salit
- Departments of Pathology and Bioengineering, Stanford University, Stanford, California 94305, United States
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Susan K Spencer
- Environmentally Integrated Dairy Management Research Unit, USDA Agricultural Research Service, 2615 Yellowstone Drive, Marshfield, Wisconsin 54449, United States
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor Michigan 48109, United States
| | - Rachel T Noble
- Insitute for the Environment, University of North Carolina, Chapel Hill, North Carolina 27517, United States
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24
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Sallustio F, Curci C, Solimando AG, Leone P, Pontrelli P, Gesualdo L, Vacca A, Racanelli V, Gallone A. Identification and monitoring of Copy Number Variants (CNV) in monoclonal gammopathy. Cancer Biol Ther 2021; 22:404-412. [PMID: 34288806 DOI: 10.1080/15384047.2021.1946458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Monoclonal gammopathy of undetermined significance (MGUS) represents the pre-clinical stage of Multiple Myeloma (MM) with the 5% of MGUS progresses to MM. Although the progression from MGUS to MM has not been completely characterized, it is possible to monitor the DNA modifications of patients diagnosed with MGUS to detect early specific genomic abnormalities, including copy number variations (CNV). The CNVs of chromosome 1q and chromosome 13q are associated with a worse prognosis in MM.In the present study, we showed that it is possible to monitor the 1q21 gain and 13q deletion frequencies in gDNA using digital PCR. The CNV analysis of three cell lines with a well-characterized cytogenetic profile were compared with measures performed by a real-time PCR approach and with a digital PCR approach. Then, we analyzed CNVs in CD138+ plasma cells isolated from bone marrow of MGUS and MM patients.Our results show that digital PCR and targeted DNA monitoring represent a specific and accurate technique for the early detection of specific genomic abnormalities both in MM and in MGUS patients.Our results could represent a remarkable advancement in MM and MGUS diagnosis and in CNV analysis for the evaluation of the risk of progression from MGUS to MM.
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Affiliation(s)
- Fabio Sallustio
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Claudia Curci
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Antonio Giovanni Solimando
- Department of Biomedical Sciences and Human Oncology, Internal Medicine Unit "G. Baccelli", University of Bari Aldo Moro, Bari, Italy.,IRCCS Istituto Tumori Giovanni Paolo II of Bari, Italy
| | - Patrizia Leone
- Department of Biomedical Sciences and Human Oncology, Internal Medicine Unit "G. Baccelli", University of Bari Aldo Moro, Bari, Italy
| | - Paola Pontrelli
- Department of Emergency and Organ Transplantation, Nephrology, Dialysis and Transplantation Unit, University of Bari Aldo Moro, Bari, Italy
| | - Loreto Gesualdo
- Department of Emergency and Organ Transplantation, Nephrology, Dialysis and Transplantation Unit, University of Bari Aldo Moro, Bari, Italy
| | - Angelo Vacca
- Department of Biomedical Sciences and Human Oncology, Internal Medicine Unit "G. Baccelli", University of Bari Aldo Moro, Bari, Italy
| | - Vito Racanelli
- Department of Biomedical Sciences and Human Oncology, Internal Medicine Unit "G. Baccelli", University of Bari Aldo Moro, Bari, Italy
| | - Anna Gallone
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Bari, Italy
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25
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Willemse D, Kaushal D. Using genomic DNA copies to enumerate Mycobacterium tuberculosis load in macaque tissue samples. Tuberculosis (Edinb) 2021; 129:102102. [PMID: 34139570 DOI: 10.1016/j.tube.2021.102102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/30/2021] [Accepted: 06/06/2021] [Indexed: 11/29/2022]
Abstract
It is important to accurately quantify Mycobacterium tuberculosis (Mtb) load in laboratory-based tuberculosis (TB) research. This study aims to determine if real-time quantitative PCR (qPCR) and digital PCR (dPCR) can be used instead of colony forming unit (CFU) enumeration, to quantify Mtb load in rhesus and cynomolgus macaque tissue samples. Tissue samples of actively infected high Mtb-burden rhesus and cynomolgus macaques were selected from historic sample collections. CFUs were enumerated by plating, and Chelex-extracted genomic DNA used to quantify bacterial load by qPCR and dPCR. Three genes, sigA, 16S and CFP10, were assessed for their ability to quantify Mtb. All genes showed comparable quantification of Mtb between 2 and 20 000 copies/μl in the qPCR and 5-4000 copies/μl in the dPCR assay. The highest bacterial load was observed with dPCR, followed by qPCR, and CFU enumeration. Although the CFU count was consistently lower than the genomic copy numbers predicted by qPCR and dPCR, a significant correlation was observed. Quantification of Mtb by PCR was, however, only possible in higher-Mtb-load samples, suggesting that qPCR and dPCR quantification assays can predict bacterial load in actively infected and higher-Mtb-burden macaque tissue samples.
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Affiliation(s)
- Danicke Willemse
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, TX, 78227, Texas, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, TX, 78227, Texas, USA.
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26
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Development and assessment of a duplex droplet digital PCR method for quantification of GM rice Kemingdao. Anal Bioanal Chem 2021; 413:4341-4351. [PMID: 34023912 DOI: 10.1007/s00216-021-03390-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/26/2021] [Accepted: 05/03/2021] [Indexed: 10/21/2022]
Abstract
The implementation of genetically modified organism (GMO) labeling policies requires accurate quantitative methods to measure the GMO content in test samples. A Kemingdao/phospholipase D (KMD/PLD) duplex ddPCR method was established with rice genomic DNA (gDNA) of homozygous KMD as template by optimizing the annealing temperature and cycle number. Duplex ddPCR showed a linear response over the dynamic range from 68 to 175,000 copies, covering four orders of magnitude. The limit of detection (LOD) and limit of quantification (LOQ) for duplex ddPCR were determined to be 9 copies and 34 copies of the rice haploid genome, respectively. A very high dilution factor would result in unacceptable bias and coefficients of variation for determining copy number of the gDNA solution, and more than 1000 copies of the DNA template in one reaction is preferred to obtain accurate quantitative results by duplex PCR. Five blinded DNA samples with copy number ratio of 10%, 5%, 1%, 0.1%, and 0.05%, and three blinded real-life matrix samples with mass fraction of 5%, 1%, and 0.5% were quantified by duplex ddPCR, simplex ddPCR, and qPCR. These three methods all gave comparable GMO content and copy numbers within the required precision, but the duplex ddPCR showed the narrowest uncertainty interval and provided the highest precision in comparison to simplex ddPCR and qPCR. The ddPCR is a more appealing and reliable technology for the accurate quantification of GMO content than simplex ddPCR and qPCR considering the uncertainty and precision of quantitative results, the time consumption of generating droplets, and the cost of ddPCR reagents.
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27
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Wang X, Zhang Y, Niu C, Wang S, Li L, Guo Y, Zhu L, Jin X, Gao H, Xu W, Zhu P, Lan Q, Du M, Cheng X, Gao Y, Dong L. Establishment of primary reference measurement procedures and reference materials for EGFR variant detection in non-small cell lung cancer. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2114-2123. [PMID: 33870958 DOI: 10.1039/d1ay00328c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Circulating tumor DNA (ctDNA)-based mutation detection is promising to change the clinical practice of genotype-directed therapy for cancer. A growing number of non-invasive tests for cancer screening and monitoring that involve the detection of ctDNA have been commercialized. Primary reference measurement procedures (PRMPs) and reference materials (RMs) are urgently needed to assess the non-invasive tests. In this study, a PRMP based on digital PCR (dPCR) and ctDNA RMs for quantification of the frequently occurring variant in epidermal growth factor receptor (EGFR L858R, T790M, and 19Del) in non-small cell lung cancer (NSCLC) were established. The candidate dPCR PRMP showed high specificity (false positive rate 0-0.003%), good repeatability (coefficient of variance (CV), 2-3% for 104 copies/reaction), and high interlaboratory reproducibility (3-10%). A good linearity (0.97 < slope < 1.03, R2 ≥ 0.9999) between the measured mutant (MU) value and prepared value was observed for all assays over the fractional abundance (FA) range, between 25% and 0.05%. The limit of quantification (LoQ) was determined to be 34 L858R, 23 T790M, and 34 19Del copies/reaction, corresponding to a FA of 0.2%. An inter-laboratory study of using the EGFR ctDNA RMs and dPCR assays demonstrated that the participating laboratories produced consistent concentrations of MU and wild-type (WT), as well as FA. This study demonstrates that dPCR can act as a potential PRMP for EGFR mutation for validation of NSCLC genotyping tests and ctDNA quantitative tests. The PRMP and RMs established here could improve interlaboratory repeatability and reproducibility, which supports rapid translation and application of non-invasive tests into clinical practice.
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Affiliation(s)
- Xia Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Yongzhuo Zhang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Chunyan Niu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Shangjun Wang
- Nanjing Institute of Measurement and Testing Technology, Nanjing 210049, People's Republic of China
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, People's Republic of China
| | - Lingxiang Zhu
- Human Genetic Resource Center, National Research Institute for Health and Family Planning, Beijing 100081, People's Republic of China
| | - Xiaohua Jin
- Human Genetic Resource Center, National Research Institute for Health and Family Planning, Beijing 100081, People's Republic of China
| | - Huafang Gao
- Human Genetic Resource Center, National Research Institute for Health and Family Planning, Beijing 100081, People's Republic of China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
| | - Pengyu Zhu
- Chinese Academy of Inspection and Quarantine, Beijing 100176, People's Republic of China
| | - Qingkuo Lan
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin 300381, People's Republic of China
| | - Meihong Du
- Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical & Chemical Analysis, Beijing 100093, People's Republic of China
| | - Xiaoyan Cheng
- Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical & Chemical Analysis, Beijing 100093, People's Republic of China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Lianhua Dong
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
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28
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Volokhina I, Gusev Y, Moiseeva Y, Gutorova O, Fadeev V, Chumakov M. Gene Expression in Parthenogenic Maize Proembryos. PLANTS (BASEL, SWITZERLAND) 2021; 10:964. [PMID: 34066123 PMCID: PMC8151209 DOI: 10.3390/plants10050964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022]
Abstract
Angiosperm plants reproduce both sexually and asexually (by apomixis). In apomictic plants, the embryo and endosperm develop without fertilization. Modern maize seems to have a broken apomixis-triggering mechanism, which still works in Tripsacum and in Tripsacum-maize hybrids. For the first time, maize lines characterized by pronounced and inheritable high-frequency maternal parthenogenesis were generated 40 years ago, but there are no data on gene expression in parthenogenic maize proembryos. Here we examined for the first time gene expression in parthenogenic proembryos isolated from unpollinated embryo sacs (ESs) of a parthenogenic maize line (AT-4). The DNA-methylation genes (dmt103, dmt105) and the genes coding for the chromatin-modifying enzymes (chr106, hdt104, hon101) were expressed much higher in parthenogenic proembryos than in unpollinated ESs. The expression of the fertilization-independent endosperm (fie1) genes was found for the first time in parthenogenic proembryos and unpollinated ESs. In parthenogenic proembryos, the Zm_fie2 gene was expressed up to two times higher than it was expressed in unpollinated ESs.
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Affiliation(s)
- Irina Volokhina
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, 410049 Saratov, Russia; (I.V.); (Y.G.); (Y.M.); (V.F.)
| | - Yury Gusev
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, 410049 Saratov, Russia; (I.V.); (Y.G.); (Y.M.); (V.F.)
| | - Yelizaveta Moiseeva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, 410049 Saratov, Russia; (I.V.); (Y.G.); (Y.M.); (V.F.)
| | - Olga Gutorova
- Genetics Department, Saratov State University, 83 Ulitsa Astrakhanskaya, 410012 Saratov, Russia;
| | - Vladimir Fadeev
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, 410049 Saratov, Russia; (I.V.); (Y.G.); (Y.M.); (V.F.)
| | - Mikhail Chumakov
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, 410049 Saratov, Russia; (I.V.); (Y.G.); (Y.M.); (V.F.)
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29
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Zhang W, Bream JH, Leng SX, Margolick JB. Validation of Preamplification to Improve Quantification of Cytomegalovirus DNA Using Droplet Digital Polymerase Chain Reaction. Anal Chem 2021; 93:3710-3716. [PMID: 33596050 PMCID: PMC10074994 DOI: 10.1021/acs.analchem.0c02890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Subclinical cytomegalovirus (CMV) replication is associated with strong cellular immune response and chronic inflammation, which could contribute to aging-related conditions such as cardiovascular disease and frailty. However, because of very low levels of CMV DNA present in people with chronic CMV infection, it has been difficult to explore the virologic and immunologic mechanisms of chronic low-level CMV infection and a sensitive method to monitor CMV replication is needed. Droplet digital PCR (ddPCR) has been shown to have higher precision and reproducibility than real-time quantitative PCR (qPCR) in quantifying low levels of CMV DNA, but it is not always sensitive enough for this purpose. Through rigorous validation experiments, we demonstrated that sensitivity and precision of quantification of very low levels of CMV DNA by ddPCR can be significantly increased by preamplification of samples with 10-20 cycles of conventional PCR, especially when testing CMV DNA in the presence of cellular DNA. With preamplification, we could reliably quantify down to two copies of CMV DNA, as opposed to five copies without preamplification. Further studies are needed to determine if ddPCR with preamplification can facilitate mechanistic studies of the characteristics and consequences of chronic CMV infection in aging adults.
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Affiliation(s)
- Weiying Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, United States
| | - Jay H Bream
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, United States.,Graduate Program in Immunology, Johns Hopkins School of Medicine, Baltimore, Maryland 21224, United States
| | - Sean X Leng
- Division of Geriatric Medicine and Gerontology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21224, United States
| | - Joseph B Margolick
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, United States
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30
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Highly accurate and sensitive diagnostic detection of SARS-CoV-2 by digital PCR. Talanta 2021; 224:121726. [PMID: 33379001 PMCID: PMC7588801 DOI: 10.1016/j.talanta.2020.121726] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/30/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023]
Abstract
The outbreak of COVID-19 caused by a novel Coronavirus (termed SARS-CoV-2) has spread to over 210 countries around the world. Currently, reverse transcription quantitative qPCR (RT-qPCR) is used as the gold standard for diagnosis of SARS-CoV-2. However, the sensitivity of RT-qPCR assays of pharyngeal swab samples are reported to vary from 30% to 60%. More accurate and sensitive methods are urgently needed to support the quality assurance of the RT-qPCR or as an alternative diagnostic approach. A reverse transcription digital PCR (RT-dPCR) method was established and evaluated. To explore the feasibility of RT-dPCR in diagnostic of SARS-CoV-2, a total of 196 clinical pharyngeal swab samples from 103 suspected patients, 77 close contacts and 16 supposed convalescents were analyzed by RT-qPCR and then measured by the proposed RT-dPCR. For the 103 fever suspected patients, 19 (19/25) negative and 42 (42/49) equivocal tested by RT-qPCR were positive according to RT-dPCR. The sensitivity of SARS-CoV-2 detection was significantly improved from 28.2% by RT-qPCR to 87.4% by RT-dPCR. For 29 close contacts (confirmed by additional sample and clinical follow up), 16 (16/17) equivocal and 1 negative tested by RT-qPCR were positive according to RT-dPCR, which is implying that the RT-qPCR is missing a lot of asymptomatic patients. The overall sensitivity, specificity and diagnostic accuracy of RT-dPCR were 91%, 100% and 93%, respectively. RT-dPCR is highly accurate method and suitable for detection of pharyngeal swab samples from COVID-19 suspected patients and patients under isolation and observation who may not be exhibiting clinical symptoms.
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31
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Long S, Berkemeier B. Development of a reverse transcription droplet digital PCR (RT-ddPCR) assay for sensitive detection of simian immunodeficiency virus (SIV). Virol J 2021; 18:35. [PMID: 33588884 PMCID: PMC7883996 DOI: 10.1186/s12985-021-01503-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/01/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Simian immunodeficiency virus (SIV)-infected rhesus macaques constitute an excellent model of human HIV infection. Sensitive detection of SIV RNA in cell and tissue samples from infected animals subjected to treatment regimens becomes especially critical in determining which therapeutic attempts are successful, and consequently, which interventions should be prioritized in HIV cure research. RESULTS In this report, we describe the design and testing of a Raindance ddPCR platform-based, sensitive SIV reverse transcription droplet digital PCR (RT-ddPCR) assay by exploring the combinations of various priming conditions and reverse transcriptases, and testing one-step vs. two-step procedures, to eliminate background signal(s) and enable detection and quantification of low level target signals. CONCLUSIONS Similar reaction conditions and assay validation procedures can be explored for potential development of additional assays for other applications that require sensitive detection of low-level targets in RNA samples.
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Affiliation(s)
- Samuel Long
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
| | - Brian Berkemeier
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
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Anoshkin K, Vasilyev I, Karandasheva K, Shugay M, Kudryavtseva V, Egorov A, Gurevich L, Mironova A, Serikov A, Kutsev S, Strelnikov V. New Regions With Molecular Alterations in a Rare Case of Insulinomatosis: Case Report With Literature Review. Front Endocrinol (Lausanne) 2021; 12:760154. [PMID: 34737724 PMCID: PMC8563021 DOI: 10.3389/fendo.2021.760154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
Insulinomatosis is characterized by monohormonality of multiple macro-tumors and micro-tumors that arise synchronously and metachronously in all regions of the pancreas, and often recurring hypoglycemia. One of the main characteristics of insulinomatosis is the presence of insulin-expressing monohormonal endocrine cell clusters that are exclusively composed of proliferating insulin-positive cells, are less than 1 mm in size, and show solid islet-like structure. It is presumed that insulinomatosis affects the entire population of β-cells. With regards to molecular genetics, this phenomenon is not related to mutation in MEN1 gene and is more similar to sporadic benign insulinomas, however, at the moment molecular genetics of this disease remains poorly investigated. NGS sequencing was performed with a panel of 409 cancer-related genes. Results of sequencing were analyzed by bioinformatic algorithms for detecting point mutations and copy number variations. DNA copy number variations were detected that harbor a large number of genes in insulinoma and fewer genes in micro-tumors. qPCR was used to confirm copy number variations at ATRX, FOXL2, IRS2 and CEBPA genes. Copy number alterations involving FOXL2, IRS2, CEBPA and ATRX genes were observed in insulinoma as well as in micro-tumors samples, suggesting that alterations of these genes may promote malignization in the β-cells population.
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Affiliation(s)
- Kirill Anoshkin
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Ivan Vasilyev
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Mikhail Shugay
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Valeriya Kudryavtseva
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexey Egorov
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Larisa Gurevich
- Morphological Department of Oncology, M.F. Vladimirsky Moscow Regional Research and Clinical Institute, Moscow, Russia
| | - Anna Mironova
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexey Serikov
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Sergei Kutsev
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Vladimir Strelnikov
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
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Bilous NI, Abramenko IV, Chumak AA, Diagil IS, Martina ZV. EXPRESSION OF LIPOPROTEIN LIPASE AND c-MYC ONCOGENE IN PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA AFFECTED BY THE CHORNOBYL ACCIDENT. PROBLEMY RADIAT︠S︡IĬNOÏ MEDYT︠S︡YNY TA RADIOBIOLOHIÏ 2020; 25:421-429. [PMID: 33361851 DOI: 10.33145/2304-8336-2020-25-421-429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Indexed: 11/10/2022]
Abstract
OBJECTIVE to determine the association between the expression of lipoprotein lipase (LPL) and c-MYC genes inperipheral blood cells of chronic lymphocytic leukemia (CLL) patients affected by the Chornobyl catastrophedepending on the mutational status of IGHV genes. METHODS Analysis was performed in the group of 69 CLL patients irradiated due to the Chornobyl NPP accident (58clean-up workers of 1986 year, 6 inhabitants of radionuclide contaminated areas, and 5 evacuees). The IGHV genemutational status was studied by polymerase chain reaction (PCR) followed by direct sequencing. LPL and c-MYCexpression was evaluated by Quantitative Real-time PCR. Data were analyzed with the SPSS software package, version 20.0. RESULTS Relative LPL expression levels in CLL samples ranged from 0 to 1663.5 (mean 138.47 ± 30.69, median 26.1).A strong correlation between individual LPL expression levels and IGHV mutational status was found (r = 0.684;p < 0.0001). The average relative c-MYC expression level was 5.7 ± 0.87 (median 2.86; range 0-48.5). No association between c-MYC expression and IGHV mutational status was found. Among unmutated IGHV cases, a correlationbetween LPL and c-MYC gene expression levels was identified: r = 0.351; p = 0.013. CONCLUSIONS Our data confirm the dominant concept that unmutated IGHV CLL cases are more sensitive to the actionof proliferative stimuli compared to mutated IGHV CLL cases. This is manifested by an increase in the expression ofa functionally significant LPL gene, is one for the strongest negative prognostic markers in CLL.
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Affiliation(s)
- N I Bilous
- State Institution «National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine», 53 Yuriia Illienka St., Kyiv, 04050, Ukraine
| | - I V Abramenko
- State Institution «National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine», 53 Yuriia Illienka St., Kyiv, 04050, Ukraine
| | - A A Chumak
- State Institution «National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine», 53 Yuriia Illienka St., Kyiv, 04050, Ukraine
| | - I S Diagil
- State Institution «National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine», 53 Yuriia Illienka St., Kyiv, 04050, Ukraine
| | - Z V Martina
- State Institution «National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine», 53 Yuriia Illienka St., Kyiv, 04050, Ukraine
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Ternovoi VA, Lutkovsky RY, Ponomareva EP, Gladysheva AV, Chub EV, Tupota NL, Smirnova AM, Nazarenko AA, Loktev VB, Gavrilova EV, Agafonov AP, Maksyutov RA. Detection of SARS-CoV-2 RNA in nasopharyngeal swabs from COVID-19 patients and asymptomatic cases of infection by real-time and digital PCR. ACTA ACUST UNITED AC 2020; 65:785-792. [DOI: 10.18821/0869-2084-2020-65-12-785-792] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In this work we tested two reagent kits developed by us for detecting SARS-CoV-2 RNA using a fragment of the ORF1ab gene in digital PCR and real-time PCR formats. Data were obtained on the detection of SARS-CoV-2 virus RNA in nasopharyngeal swabs of patients with COVID-19 and asymptomatic carriers. The developed reagent kits provided 100% sensitivity and a detection limit of 103 GE / ml for qPCR, and at least 200 copies / ml of viral RNA when performing digital PCR. These methods were tested using a panel of 1,328 samples collected from patients with suspected COVID-19 at the beginning of 2020 in the Russian Federation. It has been shown that dPCR is more sensitive and can be used to analyze samples with low viral load, including those from patients without clinical symptoms. dPCR significantly improves the accuracy of laboratory research and significantly reduces the number of false negative results in the diagnosis of SARS-CoV-2. Determination of the concentration of SARS-CoV-2 RNA in patients with different clinical course of the disease showed that the concentration of viral RNA can sharply decrease in the first days of the disease. A low concentration of viral RNA in samples from patients is also characteristic of asymptomatic disease. Digital PCR provides a higher detection rate for asymptomatic cases, which is approximately 75% of those infected, as opposed to 45% for real-time PCR. The results obtained on the use of the digital PCR method for detecting SARS-CoV-2 RNA showed that this method is especially suitable for detecting RNA in case of its low concentration in contacts, as well as for monitoring changes in viral load in convalescent patients.
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Affiliation(s)
- V. A. Ternovoi
- State Research Center of Virology and Biotechnology VECTOR, World-class Genomic Research Center for Ensuring Biological Safety and Technological Independence within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies
| | - R. Yu. Lutkovsky
- State Research Center of Virology and Biotechnology VECTOR, World-class Genomic Research Center for Ensuring Biological Safety and Technological Independence within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies
| | - E. P. Ponomareva
- State Research Center of Virology and Biotechnology VECTOR, World-class Genomic Research Center for Ensuring Biological Safety and Technological Independence within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies
| | - A. V. Gladysheva
- State Research Center of Virology and Biotechnology VECTOR, World-class Genomic Research Center for Ensuring Biological Safety and Technological Independence within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies
| | - E. V. Chub
- State Research Center of Virology and Biotechnology VECTOR, World-class Genomic Research Center for Ensuring Biological Safety and Technological Independence within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies
| | - N. L. Tupota
- State Research Center of Virology and Biotechnology VECTOR, World-class Genomic Research Center for Ensuring Biological Safety and Technological Independence within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies
| | - A. M. Smirnova
- State Research Center of Virology and Biotechnology VECTOR, World-class Genomic Research Center for Ensuring Biological Safety and Technological Independence within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies
| | - A. A. Nazarenko
- State Research Center of Virology and Biotechnology VECTOR, World-class Genomic Research Center for Ensuring Biological Safety and Technological Independence within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies
| | - V. B. Loktev
- State Research Center of Virology and Biotechnology VECTOR, World-class Genomic Research Center for Ensuring Biological Safety and Technological Independence within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies
| | - E. V. Gavrilova
- State Research Center of Virology and Biotechnology VECTOR, World-class Genomic Research Center for Ensuring Biological Safety and Technological Independence within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies
| | - A. P. Agafonov
- State Research Center of Virology and Biotechnology VECTOR, World-class Genomic Research Center for Ensuring Biological Safety and Technological Independence within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies
| | - R. A. Maksyutov
- State Research Center of Virology and Biotechnology VECTOR, World-class Genomic Research Center for Ensuring Biological Safety and Technological Independence within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies
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Kockerols CC, Valk PJ, Levin MD, Pallisgaard N, Cornelissen JJ, Westerweel PE. Digital PCR for BCR-ABL1 Quantification in CML: Current Applications in Clinical Practice. Hemasphere 2020; 4:e496. [PMID: 33283168 PMCID: PMC7710259 DOI: 10.1097/hs9.0000000000000496] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023] Open
Abstract
Molecular monitoring of the BCR-ABL1 transcript for patients with chronic phase chronic myeloid leukemia (CML) has become increasingly demanding. Real-time quantitative PCR (qPCR) is the routinely used method, but has limitations in quantification accuracy due to its inherent technical variation. Treatment recommendations rely on specific BCR-ABL1 values set at timed response milestones, making precise measurement of BCR-ABL1 a requisite. Furthermore, the sensitivity of qPCR may be insufficient to reliably quantify low levels of residual BCR-ABL1 in patients in deep molecular response (DMR) who could qualify for an attempt to discontinue Tyrosine Kinase Inhibitor (TKI) therapy. We reviewed the current use of digital PCR (dPCR) as a promising alternative for response monitoring in CML. dPCR offers an absolute BCR-ABL1 quantification at various disease levels with remarkable precision and a clinical sensitivity reaching down to at least MR5.0. Moreover, dPCR has been validated in multiple studies as prognostic marker for successful TKI treatment discontinuation, while this could not be achieved using classical qPCR. dPCR may thus prospectively be the preferred method to reliably identify patients achieving treatment milestones after initiation of TKI therapy as well as for the selection and timing for TKI discontinuation.
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Affiliation(s)
| | - Peter J.M. Valk
- Department of Molecular Biology and Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mark-David Levin
- Department of Internal Medicine, Albert Schweitzer Hospital, Dordrecht, The Netherlands
| | | | - Jan J. Cornelissen
- Department of Molecular Biology and Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Peter E. Westerweel
- Department of Internal Medicine, Albert Schweitzer Hospital, Dordrecht, The Netherlands
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Long S, Berkemeier B. Development and optimization of a simian immunodeficiency virus (SIV) droplet digital PCR (ddPCR) assay. PLoS One 2020; 15:e0240447. [PMID: 33035247 PMCID: PMC7546489 DOI: 10.1371/journal.pone.0240447] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/27/2020] [Indexed: 12/12/2022] Open
Abstract
Accurate and sensitive quantification of rebound competent HIV that persists despite combination antiretroviral treatment (cART), including in latently infected cells (i.e., viral reservoir), is critical for evaluating cure strategies for decreasing or eliminating this reservoir. Simian immunodeficiency virus (SIV)-infected Rhesus macaques are an important non-human primate (NHP) system for studying potential cure strategies as they model many key aspects of human HIV-infection including the persistence of a latent viral reservoir in resting memory CD4+ T cells in animals receiving prolonged cART. In this report, we describe the design and testing of a sensitive SIV droplet digital PCR (ddPCR) assay through exploring the combination and optimization of different probe systems (including single, double quencher probes and minor groove binder (MGB) probes) and reaction conditions to eliminate background signal(s), ensure distinct target signal cluster separation from non-target signals, and enable detection and quantification of low level authentic target signals. Similar reaction conditions and assay validation procedures can be explored for potential development of additional assays for other applications that require sensitive detection of low-level targets in a large background of nucleic acid input derived from cell or tissue sources.
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Affiliation(s)
- Samuel Long
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- * E-mail:
| | - Brian Berkemeier
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
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Digital PCR for the Analysis of MYC Copy Number Variation in Lung Cancer. DISEASE MARKERS 2020; 2020:4176376. [PMID: 33014186 PMCID: PMC7525309 DOI: 10.1155/2020/4176376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 06/29/2020] [Accepted: 09/06/2020] [Indexed: 12/24/2022]
Abstract
Background MYC (v-myc avian myelocytomatosis viral oncogene homolog) is one of the most frequently amplified genes in lung tumors. For the analysis of gene copy number variations, dPCR (digital PCR) is an appropriate tool. The aim of our study was the assessment of dPCR for the detection of MYC copy number variations (CNV) in lung tissue considering clinicopathological parameters. Material and Methods. MYC status was analyzed with dPCR as well as qPCR (quantitative PCR) using gDNA (genomic DNA) from tumor and adjacent nontumor tissue samples of lung cancer patients. The performance of MYC was estimated based on the AUC (area under curve). Results The results of the MYC amplification correlated significantly between dPCR and qPCR (r S = 0.81, P < 0.0001). The MYC copy number revealed by dPCR showed statistically significant differences between tumor and adjacent nontumor tissues. For discrimination, a sensitivity of 43% and a specificity of 99% were calculated, representing 55 true-positive and one false-positive tests. No statistically significant differences could be observed for age, sex, and smoking status or the clinicopathological parameters (histological subtype, grade, and stage). Conclusion The results of the study show that dPCR is an accurate and reliable method for the determination of MYC copy numbers. The application is characterized by high specificity and moderate sensitivity. MYC amplification is a common event in lung cancer patients, and it is indicated that the determination of the MYC status might be useful in clinical diagnostics.
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Dolata J, Zielezinski A, Stepien A, Kruszka K, Bielewicz D, Pacak A, Jarmolowski A, Karlowski W, Szweykowska-Kulinska Z. Quantitative Analysis of Plant miRNA Primary Transcripts. Methods Mol Biol 2020; 2170:53-77. [PMID: 32797451 DOI: 10.1007/978-1-0716-0743-5_5] [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] [Indexed: 03/07/2023]
Abstract
MicroRNAs control plant development and are key regulators of plant responses to biotic and abiotic stresses. Thus, their expression must be carefully controlled since both excess and deficiency of a given microRNA may be deleterious to plant cell. MicroRNA expression regulation can occur at several stages of their biogenesis pathway. One of the most important of these regulatory checkpoints is transcription efficiency. mirEX database is a tool for exploration and visualization of plant pri-miRNA expression profiles. It includes results obtained using high-throughput RT-qPCR platform designed to monitor pri-miRNA expression in different miRNA biogenesis mutants and developmental stages of Arabidopsis, barley, and Pellia plants. A step-by-step instruction for browsing the database and detailed protocol for high-throughput RT-qPCR experiments, including list of primers designed for the amplification of pri-miRNAs, are presented.
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Affiliation(s)
- Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland
| | - Andrzej Zielezinski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland
| | - Agata Stepien
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland
| | - Wojciech Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland.
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poznań, Poland.
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Newkirk SJ, Kong L, Jones MM, Habben CE, Dilts VL, Ye P, An W. Subfamily-specific quantification of endogenous mouse L1 retrotransposons by droplet digital PCR. Anal Biochem 2020; 601:113779. [PMID: 32442414 DOI: 10.1016/j.ab.2020.113779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/06/2020] [Accepted: 05/14/2020] [Indexed: 11/18/2022]
Abstract
Long interspersed element type 1 (LINE-1; L1) mobilizes during early embryogenesis, neurogenesis, and germ cell development, accounting for 25% of disease-causing heritable insertions and 98% of somatic insertions in cancer. To better understand the regulation and impact of L1 mobilization in the genome, reliable methods for measuring L1 copy number variation (CNV) are needed. Here we present a comprehensive analysis of a droplet digital PCR (ddPCR) based method for quantifying endogenous mouse L1. We provide experimental evidence that ddPCR assays can be designed to target specific L1 subfamilies using diagnostic single nucleotide polymorphisms (SNPs). The target and off-target L1 subfamilies form distinct droplet clusters, which were experimentally verified using both synthetic gene fragments and endogenous L1 derived plasmid clones. We further provide a roadmap for in silico assay design and evaluation of target specificity, ddPCR testing, and optimization for L1 CNV quantification. The assay can achieve a sensitivity of 5% CNV with 8 technical replicates. With 24 technical replicates, it can detect 2% CNV because of the increased precision. The same approach will serve as a guide for the development of ddPCR based assays for quantifying human L1 copy number and any other high copy genomic target sequences.
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Affiliation(s)
- Simon J Newkirk
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
| | - Lingqi Kong
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
| | - Mason M Jones
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
| | - Chase E Habben
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
| | - Victoria L Dilts
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
| | - Ping Ye
- Department of Pharmacy Practice, South Dakota State University, Brookings, SD, 57007, United States; Avera Research Institute, Sioux Falls, SD, 57108, United States.
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
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Long S, Berkemeier B. Maximizing viral detection with SIV droplet digital PCR (ddPCR) assays. PLoS One 2020; 15:e0233085. [PMID: 32407343 PMCID: PMC7224504 DOI: 10.1371/journal.pone.0233085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/28/2020] [Indexed: 11/19/2022] Open
Abstract
Highly sensitive detection of HIV-1 nucleic acids is of critical importance for evaluating treatment interventions superimposed on combination antiretroviral therapy (cART) in HIV-1 infected individuals. SIV infection of rhesus macaques models many key aspects of human HIV-1 infection and plays a key role in evaluation of approaches for prevention, treatment and attempted eradication of HIV infection. Here we describe two droplet digital PCR (ddPCR) assays, a ddPCR DNA assay and an RT-ddPCR RNA assay for detecting simian immunodeficiency virus (SIV) on the RainDance platform. We demonstrate that RainDance ddPCR can tolerate significantly higher cell DNA input without inhibition on a per reaction basis (compared to both qPCR and Bio-Rad ddPCR), thus allowing a large quantity of sample to be analyzed in each reaction. In addition, the combination of a high processivity RT enzyme and RainDance ddPCR could overcome inhibition in severely inhibited (99.99% inhibition in qPCR quantification) viral RNA samples. These assays offer valuable tools for assessing low level viral production/replication and strategies for targeting residual virus in the setting of cART suppression of viral replication. The methodologies presented here can be adapted for a broad range of applications where highly sensitive nucleic acid detection is required.
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Affiliation(s)
- Samuel Long
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- * E-mail:
| | - Brian Berkemeier
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
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Zhang K, Qin S, Wu S, Liang Y, Li J. Microfluidic systems for rapid antibiotic susceptibility tests (ASTs) at the single-cell level. Chem Sci 2020; 11:6352-6361. [PMID: 34094102 PMCID: PMC8159419 DOI: 10.1039/d0sc01353f] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Infectious diseases caused by multidrug resistant (MDR) bacterial pathogens are impending threats to global health. Since delays in identifying drug resistance would significantly increase mortality, fast and accurate antibiotic susceptibility tests (ASTs) are critical for addressing the antibiotic resistance issue. However, the conventional methods for ASTs are always labor-intensive, imprecise, complex and slow (taking 2-3 days). To address these issues, some advanced microfluidic systems have been designed for rapid phenotypic and genotypic analysis of antibiotic resistance. This review highlights the recent development of microfluidics-based ASTs at the single-cell or single-molecule level for guiding antibiotic treatment decisions and predicting therapeutic outcomes.
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Affiliation(s)
- Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
| | - Sixuan Wu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
| | - Yan Liang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
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Li L, Yang P, Shi S, Zhang Z, Shi Q, Xu J, He H, Lei C, Wang E, Chen H, Huang Y. Association Analysis to Copy Number Variation (CNV) of Opn4 Gene with Growth Traits of Goats. Animals (Basel) 2020; 10:ani10030441. [PMID: 32155759 PMCID: PMC7143651 DOI: 10.3390/ani10030441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/11/2020] [Accepted: 03/05/2020] [Indexed: 01/03/2023] Open
Abstract
Simple Summary Copy number variation is a common genetic polymorphism and is mainly represented by submicroscopic levels of deletion and duplication which are caused by rearrangement of the genome. It is well known that copy number variations of genes are associated with growth traits of livestock. In this study, we detected the correlation between the copy number variation of the Opn4 gene and growth traits of Guizhou goats. We found that the copy number variation of the Opn4 gene had a significant influence on the body length and body weight of Guizhou goats. The results may provide preliminary suggestions into Guizhou goat breeding and new insights into the future of CNV as a new promising molecular marker in animal breeding. Abstract Extensive research has been carried out regarding the correlation between the growth traits of livestock and genetic polymorphisms, including single nucleotide polymorphisms and copy number variations (CNV). The purpose of this study was to analyze the CNV and its genetic effects of the Opn4 gene in 284 Guizhou goats (Guizhou black goat: n = 186, Guizhou white goat: n = 98). We used qPCR to detect the CNV of the Opn4 gene in Guizhou goats, and the classification results were correlated with the corresponding individual growth traits by SPSS software. The results showed that the Opn4 gene had a superior effect on growth traits with multiple copy variants in Guizhou black goats, and there was a significant correlation between copy number variation sites and body length traits. Contrary to the former conclusion, in Guizhou white goats, individuals with the Normal copy number type showed superior growth traits and copy number variant sites were significantly associated with body weight traits. Therefore, the CNV of the Opn4 gene can be used as a candidate molecular genetic marker to improve goat growth traits, speeding up the breeding process of goat elite varieties.
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Affiliation(s)
- LiJuan Li
- Institute of Bijie Test Area, Guizhou University of Engineering Science, Bijie, Guizhou 551700, China; (L.L.)
| | - Peng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China; (P.Y.)
| | - ShuYue Shi
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China; (P.Y.)
| | - ZiJing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 45002, China; (Z.Z.); (Q.S.)
| | - QiaoTing Shi
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 45002, China; (Z.Z.); (Q.S.)
| | - JiaWei Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China; (P.Y.)
| | - Hua He
- Institute of Bijie Test Area, Guizhou University of Engineering Science, Bijie, Guizhou 551700, China; (L.L.)
- College of Veterinary Medicine, Northwest A&F University, Yangling Shaanxi 712100, China
| | - ChuZhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China; (P.Y.)
| | - ErYao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 45002, China; (Z.Z.); (Q.S.)
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China; (P.Y.)
| | - YongZhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China; (P.Y.)
- Correspondence: ; Tel.: +86-29-87092102; Fax: +86-29-87092164
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Jouanin A, Tenorio-Berrio R, Schaart JG, Leigh F, Visser RG, Smulders MJ. Optimisation of droplet digital PCR for determining copy number variation of α-gliadin genes in mutant and gene-edited polyploid bread wheat. J Cereal Sci 2020. [DOI: 10.1016/j.jcs.2019.102903] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Cao Y, Yu M, Dong G, Chen B, Zhang B. Digital PCR as an Emerging Tool for Monitoring of Microbial Biodegradation. Molecules 2020; 25:E706. [PMID: 32041334 PMCID: PMC7037809 DOI: 10.3390/molecules25030706] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 11/16/2022] Open
Abstract
Biodegradation of contaminants is extremely complicated due to unpredictable microbial behaviors. Monitoring of microbial biodegradation drives us to determine (1) the amounts of specific degrading microbes, (2) the abundance, and (3) expression level of relevant functional genes. To this endeavor, the cultivation independent polymerase chain reaction (PCR)-based monitoring technique develops from endpoint PCR, real-time quantitative PCR, and then into novel digital PCR. In this review, we introduce these three categories of PCR techniques and summarize the timely applications of digital PCR and its superiorities than qPCR for biodegradation monitoring. Digital PCR technique, emerging as the most accurately absolute quantification method, can serve as the most promising and robust tool for monitoring of microbial biodegradation.
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Affiliation(s)
| | | | | | - Bing Chen
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John’s, NL A1B 3X5, Canada; (Y.C.); (M.Y.); (G.D.)
| | - Baiyu Zhang
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John’s, NL A1B 3X5, Canada; (Y.C.); (M.Y.); (G.D.)
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Abstract
Individuals within a species can exhibit vast variation in copy number of repetitive DNA elements. This variation may contribute to complex traits such as lifespan and disease, yet it is only infrequently considered in genotype-phenotype associations. Although the possible importance of copy number variation is widely recognized, accurate copy number quantification remains challenging. Here, we assess the technical reproducibility of several major methods for copy number estimation as they apply to the large repetitive ribosomal DNA array (rDNA). rDNA encodes the ribosomal RNAs and exists as a tandem gene array in all eukaryotes. Repeat units of rDNA are kilobases in size, often with several hundred units comprising the array, making rDNA particularly intractable to common quantification techniques. We evaluate pulsed-field gel electrophoresis, droplet digital PCR, and Nextera-based whole genome sequencing as approaches to copy number estimation, comparing techniques across model organisms and spanning wide ranges of copy numbers. Nextera-based whole genome sequencing, though commonly used in recent literature, produced high error. We explore possible causes for this error and provide recommendations for best practices in rDNA copy number estimation. We present a resource of high-confidence rDNA copy number estimates for a set of S. cerevisiae and C. elegans strains for future use. We furthermore explore the possibility for FISH-based copy number estimation, an alternative that could potentially characterize copy number on a cellular level.
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Yadav V, Sahoo NR, Kumar P, Gaur GK, Sahoo AP, Ravikumar GVPPS, Singh KP. Identification and copy number profiling of sex chromosome specific gene fragments in crossbred pigs with numerically normal karyotype. ANIMAL PRODUCTION SCIENCE 2020. [DOI: 10.1071/an19287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We examined the copy number profile of sex chromosome specific genes in crossbred pigs with numerically normal karyotype. A total of 30 (15M + 15F) Landlly (Landrace crossbred) pigs from a research farm were cyto-screened by karyotyping to determine the number of chromosomes per diploid cell using short-term peripheral lymphocyte culture technique. All pigs had numerically normal karyotype with 38, XX (female) and 38, XY (male). Genomic DNA was extracted from cyto-screened pigs of both sexes. A set of sex chromosome (X and Y) specific single copy gene fragments along with an autosomal gene fragment were selected out of 12 pairs of primers on the basis of male specific PCR amplification, PCR and qPCR specificity. Quantitative real-time PCR was performed to study the relative copy number change of selected Phosphate repressible alkaline phosphatase X linked (PHOX) gene, using the Eukaryotic Translation Initiation Factor 1A Y-Linked (EIF1AY) gene as control and Breast Cancer Metastasis-Suppressor 1-Like (BRMS1 L- autosomal gene) as the reference gene. The relative copy number of the PHOX gene in females was found to be 1.873 times higher compared with the EIF1AY gene in males. The present study indicates that the real-time quantitative real-time PCR based copy number analysis can be helpful for the detection of sex chromosome ratio in pigs to aid as a preliminary screening for numerical sex chromosomal aneuploidies, adding to the rate of throughput of traditional cyto-screening.
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Cassinari K, Quenez O, Joly-Hélas G, Beaussire L, Le Meur N, Castelain M, Goldenberg A, Guerrot AM, Brehin AC, Deleuze JF, Boland A, Rovelet-Lecrux A, Campion D, Saugier-Veber P, Gruchy N, Frebourg T, Nicolas G, Sarafan-Vasseur N, Chambon P. A Simple, Universal, and Cost-Efficient Digital PCR Method for the Targeted Analysis of Copy Number Variations. Clin Chem 2019; 65:1153-1160. [PMID: 31292136 DOI: 10.1373/clinchem.2019.304246] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 06/13/2019] [Indexed: 11/06/2022]
Abstract
BACKGROUND Rare copy number variations (CNVs) are a major cause of genetic diseases. Simple targeted methods are required for their confirmation and segregation analysis. We developed a simple and universal CNV assay based on digital PCR (dPCR) and universal locked nucleic acid (LNA) hydrolysis probes. METHODS We analyzed the mapping of the 90 LNA hydrolysis probes from the Roche Universal ProbeLibrary (UPL). For each CNV, selection of the optimal primers and LNA probe was almost automated; probes were reused across assays and each dPCR assay included the CNV amplicon and a reference amplicon. We assessed the assay performance on 93 small and large CNVs and performed a comparative cost-efficiency analysis. RESULTS UPL-LNA probes presented nearly 20000000 occurrences on the human genome and were homogeneously distributed with a mean interval of 156 bp. The assay accurately detected all the 93 CNVs, except one (<200 bp), with coefficient of variation <10%. The assay was more cost-efficient than all the other methods. CONCLUSIONS The universal dPCR CNV assay is simple, robust, and cost-efficient because it combines a straightforward design allowed by universal probes and end point PCR, the advantages of a relative quantification of the target to the reference within the same reaction, and the high flexibility of the LNA hydrolysis probes. This method should be a useful tool for genomic medicine, which requires simple methods for the interpretation and segregation analysis of genomic variations.
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Affiliation(s)
- Kévin Cassinari
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Olivier Quenez
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and CNR-MAJ, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Géraldine Joly-Hélas
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Ludivine Beaussire
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Nathalie Le Meur
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Mathieu Castelain
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Anne-Marie Guerrot
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Anne-Claire Brehin
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Génomique, CEA, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Institut de Génomique, CEA, Evry, France
| | - Anne Rovelet-Lecrux
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and CNR-MAJ, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Dominique Campion
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and CNR-MAJ, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France.,Department of Research, Rouvray Psychiatric Hospital, Sotteville-lés-Rouen, France
| | - Pascale Saugier-Veber
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Nicolas Gruchy
- Caen University Hospital, Department of Genetics, F 14000, Normandy Center for Genomic and Personalized Medicine, Caen, France
| | - Thierry Frebourg
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Gaël Nicolas
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and CNR-MAJ, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Nasrin Sarafan-Vasseur
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Pascal Chambon
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France;
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Zhu J, Zhao Y, Liu M, Gonzalez-Rivas D, Xu X, Cai W, Qi H, Dai L, Wang Z, Song X, Jiang G, Yang Y. Developing a New qPCR-Based System for Screening Mutation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805285. [PMID: 30677225 DOI: 10.1002/smll.201805285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/04/2019] [Indexed: 06/09/2023]
Abstract
An accurate genotyping analysis is one of the critical prerequisites for lung cancer targeted therapy. Here, a quantitative polymerase chain reaction (qPCR)-based mutation detection system, mutation-selected amplification-specific system PCR (MASS-PCR), is developed. The specific primers and probes used in MASS-PCR exactly match with the mutant sequence that only allows mutant gene to emit the fluorescence peak. To determine the sensitivity of MASS-PCR, 717 lung cancer specimens, 61 formalin-fixed paraffin-embedded (FFPE) tissues, and 656 fresh reaction tissues are collected and undergo mutation detection of lung cancer driver genes (EGFR, KRAS, BRAF, HER2, MET, ALK, and ROS1). These samples are divided into two groups. Mutations in Group I, which has 631 fresh reaction tissues, are analyzed by MASS-PCR and the amplification refractory mutation system PCR (ARMS-PCR). While group II samples, 25 fresh reaction tissues and 61 FFPE tissues, are screened through MASS-PCR and next-generation sequencing (NGS). All results are verified by direct sequencing. MASS-PCR shows high consistency with ARMS-PCR (kappa value > 0.733) and NGS (kappa value = 0.79) (P < 0.001). For the samples with inconsistent MASS-PCR and ARMS-PCR results, DS results more likely support the MASS-PCR results. These data suggest that MASS-PCR is a convenient, accurate, and economical method for the detection of lung cancer driver gene mutations in clinical practice.
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Affiliation(s)
- Junjie Zhu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, 200433, China
| | - Yanfeng Zhao
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, 200433, China
| | - Ming Liu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, 200433, China
| | - Diego Gonzalez-Rivas
- Department of Thoracic Surgery and Minimally Invasive Thoracic Surgery Unit (UCTMI), Coruña University Hospital, Coruña, 15706, Spain
| | - Xinnan Xu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, 200433, China
| | - Weijing Cai
- Shanghai Tongshu Biotechnology Co., Ltd, Shanghai, 200444, China
| | - Huiwei Qi
- Shanghai Tongshu Biotechnology Co., Ltd, Shanghai, 200444, China
| | - Lei Dai
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, 200433, China
| | - Zijian Wang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, 200433, China
| | - Xiao Song
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, 200433, China
| | - Gening Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, 200433, China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, 200433, China
- Institute for Advanced Study, Tongji University, Shanghai, 200430, China
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Burjanivova T, Malicherova B, Grendar M, Minarikova E, Dusenka R, Vanova B, Bobrovska M, Pecova T, Homola I, Lasabova Z, Plank L. Detection of BRAFV600E Mutation in Melanoma Patients by Digital PCR of Circulating DNA. Genet Test Mol Biomarkers 2019; 23:241-245. [PMID: 30676087 DOI: 10.1089/gtmb.2018.0193] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AIMS About 50% of melanomas have the BRAFV600E mutation. This mutation is an attractive therapeutic target. The aims of our study were to detect BRAFV600E mutations within circulating cell-free DNA in plasma ("liquid biopsy") by a droplet digital PCR (ddPCR) method, and to investigate how well the Breslow-Clark score can be predicted by ddPCR. MATERIALS AND METHODS We analyzed 113 patients with malignant melanoma. ddPCR was performed using the QX200 system (BIO-RAD®, Hercules). All samples were tested in duplicate. Besides the results of the liquid biopsy, we have collected data on gender and age of the patients, as well as the mitotic activity of the tumor; the tumor subtype and localization, and the Breslow-Clark score. The limit of detection (LoD) was determined by the method of Tzonev. The LoD was found to be five events per well. RESULTS The BRAFV600E mutation was detected in 37 of 113 samples. A moderate predictive accuracy of the Breslow-Clark score can be attained with the mitotic activity and the type of melanoma as the most important predictors. CONCLUSION Our results show that ddPCR is a highly sensitive method and could be used for a routine laboratory detection of the BRAFV600E mutation as well as for follow-up monitoring to determine the treatment response in patients with malignant melanomas.
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Affiliation(s)
- Tatiana Burjanivova
- 1 Division of Oncology, Biomedical Center Martin JFM CU, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia.,2 Department of Molecular Biology, and Biomedical Center Martin JFM CU, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia
| | - Bibiana Malicherova
- 1 Division of Oncology, Biomedical Center Martin JFM CU, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia.,2 Department of Molecular Biology, and Biomedical Center Martin JFM CU, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia
| | - Marian Grendar
- 3 Bioinformatic Unit, Biomedical Center Martin JFM CU, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia
| | - Eva Minarikova
- 4 Clinic of Dermatovenerology, Jessenius Faculty of Medicine and University Hospital in Martin, Martin, Slovakia
| | - Robert Dusenka
- 5 Department of Urology, Jessenius Faculty of Medicine and University Hospital in Martin, Martin, Slovakia
| | - Barbora Vanova
- 1 Division of Oncology, Biomedical Center Martin JFM CU, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia.,2 Department of Molecular Biology, and Biomedical Center Martin JFM CU, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia
| | - Martina Bobrovska
- 6 Department of Pathological Anatomy, and Jessenius Faculty of Medicine and University Hospital in Martin, Martin, Slovakia
| | - Tatiana Pecova
- 4 Clinic of Dermatovenerology, Jessenius Faculty of Medicine and University Hospital in Martin, Martin, Slovakia
| | - Igor Homola
- 7 Department of Plastic Surgery, Jessenius Faculty of Medicine and University Hospital in Martin, Martin, Slovakia
| | - Zora Lasabova
- 1 Division of Oncology, Biomedical Center Martin JFM CU, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia.,2 Department of Molecular Biology, and Biomedical Center Martin JFM CU, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia
| | - Lukas Plank
- 1 Division of Oncology, Biomedical Center Martin JFM CU, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia.,6 Department of Pathological Anatomy, and Jessenius Faculty of Medicine and University Hospital in Martin, Martin, Slovakia
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Tang L, Zhao P, Kong D. Muscleblind‑like 1 destabilizes Snail mRNA and suppresses the metastasis of colorectal cancer cells via the Snail/E‑cadherin axis. Int J Oncol 2019; 54:955-965. [PMID: 30664186 PMCID: PMC6365040 DOI: 10.3892/ijo.2019.4691] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/13/2018] [Indexed: 12/11/2022] Open
Abstract
RNA-binding proteins (RBPs) play a fundamental role in the recurrence and metastasis of colorectal cancer (CRC). In this study, we identified muscleblind-like 1 (MBNL1), an RBP implicated in developmental control, as a robust suppressor of CRC cell metastasis in vitro. By using a scratch assay coupled with time-lapse live cell imaging, our findings revealed that the knockdown of MBNL1 induced epithelial-to-mesenchymal transition (EMT)-like morphological changes in the HCT-116 cells, accompanied by an enhanced cell motility, and by the downregulation of E-cadherin and the upregulation of Snail expression. By contrast, the ectopic overexpression of MBNL1 suppressed EMT, characterized by the upregulation of E-cadherin and the downregulation of Snail expression. Mechanistically, Snail rather than E-cadherin, was identified as a direct downstream target gene of MBNL1. The ectopic the overexpression of MBNL1 markedly enhanced the recruitment of Snail transcripts to processing bodies (P-bodies), leading to the increased degradation of Snail mRNA and consequent translational silencing. Furthermore, the effect of MBNL1 on CRC cell migration was confirmed in additional CRC cell lines. SW480 and HT-29 cells exhibited similar changes in migratory capacity and the expression of Snail/E-cadherin to those observed in HCT-116 cells. On the whole, this study demonstrates that MBNL1 destabilizes Snail transcripts and, in turn, suppresses the EMT of CRC cells through the Snail/E-cadherin axis in vitro. Therefore, this EMT-related MBNL1/Snail/E-cadherin axis may prove to be a novel therapeutic target for CRC metastasis.
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Affiliation(s)
- Liang Tang
- Department of Colorectal Cancer, Cancer Hospital of Tianjin Medical University, Key Laboratory of Cancer Prevention and Therapy, and National Clinical Research Center of Cancer, Tianjin 300060, P.R. China
| | - Peng Zhao
- Department of Colorectal Cancer, Cancer Hospital of Tianjin Medical University, Key Laboratory of Cancer Prevention and Therapy, and National Clinical Research Center of Cancer, Tianjin 300060, P.R. China
| | - Dalu Kong
- Department of Colorectal Cancer, Cancer Hospital of Tianjin Medical University, Key Laboratory of Cancer Prevention and Therapy, and National Clinical Research Center of Cancer, Tianjin 300060, P.R. China
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