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Li M, Yin F, Song L, Mao X, Li F, Fan C, Zuo X, Xia Q. Nucleic Acid Tests for Clinical Translation. Chem Rev 2021; 121:10469-10558. [PMID: 34254782 DOI: 10.1021/acs.chemrev.1c00241] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.
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Affiliation(s)
- Min Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fangfei Yin
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Song
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Xia
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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A narrative review of single-nucleotide polymorphism detection methods and their application in studies of Staphylococcus aureus. JOURNAL OF BIO-X RESEARCH 2021. [DOI: 10.1097/jbr.0000000000000071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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de Sanctis L, Galliano I, Montanari P, Matarazzo P, Tessaris D, Bergallo M. Combining Real-Time COLD- and MAMA-PCR TaqMan Techniques to Detect and Quantify R201 GNAS Mutations in the McCune-Albright Syndrome
. Horm Res Paediatr 2018; 87:342-349. [PMID: 28334704 DOI: 10.1159/000463384] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 02/14/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIM The McCune-Albright syndrome (MAS) is a potentially severe disorder hallmarked by fibrous bone dysplasia, café-au-lait skin spots, and endocrine hyperfunction. It is caused by postzygotic activating mutations at the R201 codon of the GNAS gene, leading to a state of somatic mosaicism. Our aim was to improve the mutation detection rate and to quantify the presence of R201 GNAS mutations in different DNA samples from MAS patients. METHODS Real-time COLD- and MAMA-PCR TaqMan techniques were combined to search for R201 mutations in the DNA of blood or affected tissues from 16 previously molecularly characterized MAS patients, from a further 84 subjects with MAS signs who were R201 negative at RFLP analysis, and from 36 controls. The ability of this new method to provide quantitative data was tested in the serial dilution of wild-type, R201H, or R201C cloned plasmid DNA samples; the mutant abundance was measured by spectrophotometry. RESULTS A linear correlation between the true and the relative mutant abundance was observed until 2.5%, indicating a reliable quantification of R201 mutations. The assay's sensitivity was 0.05%, similar to that of previously described molecular methods. CONCLUSION The real-time COLD-MAMA-PCR approach is a rapid, efficient, and inexpensive molecular technique for the identification of mutant alleles poorly represented in DNA samples.
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Affiliation(s)
- Luisa de Sanctis
- Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children's Hospital-AOU Città della Salute e della Scienza, Turin, Italy.,Department of Pediatric Endocrinology and Diabetology, Regina Margherita Children's Hospital-AOU Città della Salute e della Scienza, Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children's Hospital-AOU Città della Salute e della Scienza, Turin, Italy
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children's Hospital-AOU Città della Salute e della Scienza, Turin, Italy
| | - Patrizia Matarazzo
- Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children's Hospital-AOU Città della Salute e della Scienza, Turin, Italy.,Department of Pediatric Endocrinology and Diabetology, Regina Margherita Children's Hospital-AOU Città della Salute e della Scienza, Turin, Italy
| | - Daniele Tessaris
- Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children's Hospital-AOU Città della Salute e della Scienza, Turin, Italy.,Department of Pediatric Endocrinology and Diabetology, Regina Margherita Children's Hospital-AOU Città della Salute e della Scienza, Turin, Italy
| | - Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children's Hospital-AOU Città della Salute e della Scienza, Turin, Italy
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Li M, Zhang T, Zhu L, Wang R, Jin Y. Liposomal andrographolide dry powder inhalers for treatment of bacterial pneumonia via anti-inflammatory pathway. Int J Pharm 2017; 528:163-171. [DOI: 10.1016/j.ijpharm.2017.06.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 12/14/2022]
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Han M, Kang X, Liu Z, Zhang T, Li Y, Chen C, Wang H. Rapid and Reliable Genotyping of HLA-B*57:01 in Four Chinese Populations Using a Single-Tube Duplex Real-Time Polymerase Chain Reaction Assay. AIDS Res Hum Retroviruses 2017; 33:711-717. [PMID: 28346841 DOI: 10.1089/aid.2016.0280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
HLA-B*57:01 is strongly associated with severe adverse drug reaction induced by the anti-HIV drug abacavir (ABC) and antibiotic flucloxacillin. This study was dedicated to establishing a new method for HLA-B*57:01 genotyping and investigating the HLA-B*57:01 distribution pattern in four Chinese populations. A single-tube duplex real-time polymerase chain reaction (PCR) system was established by combining the amplification refractory mutation system and TaqMan probe. The reliability of this assay was validated by comparing the genotyping results with those by sequence-based typing. With this assay, the distribution of HLA-B*57:01 in 354 blood samples from four ethnic groups, namely, Han, Tibetan, Uighur, and Buyei, was determined. A 100% concordance was observed between the results of real-time PCR and sequence-based typing in 50 Uighur samples. As low as 0.016 ng DNA that carried HLA-B*57:01 could be detected with this assay. HLA-B*57:01 carriers identified in 100 Northern Han Chinese, 104 Buyeis, 100 Tibetans, and 50 Uighurs were 0, 1 (0.96%), 3 (3%), and 6 (12%), respectively. The carrier rate of HLA-B*57:01 in Uighur was significantly higher than those in Northern Han (p = .001) and Buyei (p = .005). The newly established real-time PCR assay provides a rapid and reliable tool for HLA-B*57:01 allele screening before the prescription of ABC and flucloxacillin in clinical practice.
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Affiliation(s)
- Min Han
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, China
| | - Xing Kang
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, China
| | - Zhengbin Liu
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, China
| | - Tingting Zhang
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, China
| | - Yanwei Li
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, China
| | - Chao Chen
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, China
| | - Huijuan Wang
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, China
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Savino F, Sardo A, Montanari P, Galliano I, Di Stasio L, Bergallo M, Silvestro L. Polymorphisms in Lep and Lepr Genes in Infants: Correlation with Serum Leptin Values in the First 6 Months of Life. J Am Coll Nutr 2017. [PMID: 28628399 DOI: 10.1080/07315724.2017.1318723] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
OBJECTIVE Because several studies indicate that polymorphisms in leptin (Lep) and leptin receptor (Lepr) genes play a central role in determining obesity, we analyzed 2 single nucleotide polymorphisms (SNPs) in the Lep gene (Lep G2548A and A19G) and one in the Lepr gene (Lepr A668G) to verify the effect of the 3 SNPs on leptin concentrations in infancy. METHODS We enrolled 80 healthy Caucasian infants under 6 months of age, who were genotyped for the 3 SNPs with amplification refractory mutation system-mismatch amplification mutation assay (ARMS-MAMA) real-time polymerase chain reaction (PCR). Serum leptin values were measured with a radioimmunoassay method. Statistical significance was set at p < 0.05. RESULTS There were no significant differences between individually analyzed leptin polymorphisms Lep G2548A and A19G and serum leptin levels (p > 0.05). Because we found that Lep G2548A and A19G are in linkage disequilibrium on chromosome 7, we performed the haplotype analysis for Lep G2548A and Lep A19G. We obtained higher serum leptin levels in infants with the GG/GG haplotype (p < 0.05). Regarding receptor, we found higher leptin levels in GG-genotype infants for Lepr A668G (p < 0.001). Considering the 3 SNPs together, we found higher serum leptin values in GG/GG-GG infants (LepG2548A/A19G-Lepr A668G; p < 0.001). CONCLUSION We obtained higher serum leptin levels in infants with the GG genotype for Lepr A668G, with haplotype GG/GG for Lep G2548A/A19G, and with GG/GG-GG (LepG2548A/A19G-Lepr A668G); thus, it seems that the genotype GG could be a protector against obesity development in infancy and adulthood. Moreover, these data confirm that not variations in the Lep gene as well as in the Lepr gene could play a role in weight gain. Further studies are needed to evaluate the role of genetics and the environment in a predisposition toward obesity later in life.
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Affiliation(s)
- Francesco Savino
- a Department of Pediatrics , Azienda Ospedaliera Universitaria Città della Salute e della Scienza di Torino , Turin , Italy
| | - Allegra Sardo
- a Department of Pediatrics , Azienda Ospedaliera Universitaria Città della Salute e della Scienza di Torino , Turin , Italy
| | - Paola Montanari
- b Dipartimento delle Scienze di Sanità Pubblica e Pediatriche , Università degli Studi di Torino, Scuola di Medicina , Turin , Italy
| | - Ilaria Galliano
- b Dipartimento delle Scienze di Sanità Pubblica e Pediatriche , Università degli Studi di Torino, Scuola di Medicina , Turin , Italy
| | - Liliana Di Stasio
- c Department of Agricultural , Forest and Food Science, University of Torino , Turin , Italy
| | - Massimiliano Bergallo
- b Dipartimento delle Scienze di Sanità Pubblica e Pediatriche , Università degli Studi di Torino, Scuola di Medicina , Turin , Italy
| | - Leandra Silvestro
- b Dipartimento delle Scienze di Sanità Pubblica e Pediatriche , Università degli Studi di Torino, Scuola di Medicina , Turin , Italy
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Savino F, Rossi L, Di Stasio L, Galliano I, Montanari P, Bergallo M. Mismatch Amplification Mutation Assay Real-Time PCR Analysis of the Leptin Gene G2548A and A19G Polymorphisms and Serum Leptin in Infancy: A Preliminary Investigation. Horm Res Paediatr 2017; 85:318-24. [PMID: 27008407 DOI: 10.1159/000444484] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/05/2016] [Indexed: 11/19/2022] Open
Abstract
Leptin is a hormone that regulates food intake and energy metabolism. Its coding gene (LEP) is one of the most promising candidates for obesity. Although some studies have detected associations of different single nucleotide polymorphisms (SNPs) in the LEP gene with serum leptin levels and obesity-related traits, the results are still conflicting. We investigated two SNPs to find relationships with leptin concentrations. Thirty healthy Caucasian infants younger than 6 months were genotyped for the SNPs G2548A and A19G with polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and amplification refractory mutation system-mismatch amplification mutation assay (ARMS- MAMA) real-time PCR, and serum leptin concentrations were measured with a radioimmunoassay method. Considering the significant linkage disequilibrium observed between the two SNPs, we divided the sample according to the number of GG haplotypes and observed that individuals homozygous for the GG haplotype had higher serum leptin levels in early infancy than the others. Although these preliminary results are based on a limited sample, they suggest that the genetic background seems to play a role in modulating leptin levels in infancy, but changes in leptin levels over infancy and their correlation with obesity need to be further explored. We describe an ARMS-MAMA real-time PCR procedure which could be profitably applied in routine genetic screening.
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Affiliation(s)
- Francesco Savino
- Regina Margherita Children's Hospital, Cittx00E0; della Salute e della Scienza di Torino, Turin, Italy
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Khodakov D, Wang C, Zhang DY. Diagnostics based on nucleic acid sequence variant profiling: PCR, hybridization, and NGS approaches. Adv Drug Deliv Rev 2016; 105:3-19. [PMID: 27089811 DOI: 10.1016/j.addr.2016.04.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/21/2016] [Accepted: 04/06/2016] [Indexed: 12/22/2022]
Abstract
Nucleic acid sequence variations have been implicated in many diseases, and reliable detection and quantitation of DNA/RNA biomarkers can inform effective therapeutic action, enabling precision medicine. Nucleic acid analysis technologies being translated into the clinic can broadly be classified into hybridization, PCR, and sequencing, as well as their combinations. Here we review the molecular mechanisms of popular commercial assays, and their progress in translation into in vitro diagnostics.
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