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Zhou M, Zhang C, Chen M, Hu Z, Li M, Li Z, Wu L, Liang D. A protospacer adjacent motif-free, multiplexed, and quantitative nucleic acid detection platform with barcode-based Cas12a activity. MedComm (Beijing) 2023; 4:e310. [PMID: 37405277 PMCID: PMC10315165 DOI: 10.1002/mco2.310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 07/06/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-based biosensors have been developed to facilitate the rapid and sensitive detection of nucleic acids. However, most approaches using CRISPR-based detection have disadvantages associated with the limitations of CRISPR RNA (crRNA), protospacer adjacent motif (PAM) or protospacer flanking sequence restriction, single channel detection, and difficulty in quantitative detection resulting in only some target sites being detected qualitatively. Here, we aimed to develop a barcode-based Cas12a-mediated DNA detection (BCDetection) strategy, which overcomes the aforementioned drawbacks and enables (1) detection with a universal PAM and crRNA without PAM or crRNA restriction, (2) simultaneous detection of multiple targets in a single reaction, and (3) quantitative detection, which can significantly distinguish copy number differences up to as low as a two-fold limit. We could efficiently and simultaneously detect three β-thalassemia mutations in a single reaction using BCDetection. Notably, samples from normal individuals, spinal muscular atrophy (SMA) carriers, and SMA patients were significantly and accurately distinguished using the quantitative detection ability of BCDetection, indicating its potential application in β-thalassemia and SMA carrier screening. Therefore, our findings demonstrate that BCDetection provides a new platform for accurate and efficient quantitative detection using CRISPR/Cas12a, highlighting its bioanalytical applications.
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Affiliation(s)
- Miaojin Zhou
- Center for Medical Genetics & Hunan Key Laboratory of Medical GeneticsSchool of Life SciencesCentral South UniversityChangshaHunanChina
| | - Chunhua Zhang
- Center for Medical Genetics & Hunan Key Laboratory of Medical GeneticsSchool of Life SciencesCentral South UniversityChangshaHunanChina
- Department of Medical GeneticsYunnan Maternal and Child Health Care HospitalKunmingYunnanChina
| | - Miaomiao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical GeneticsSchool of Life SciencesCentral South UniversityChangshaHunanChina
| | - Zhiqing Hu
- Center for Medical Genetics & Hunan Key Laboratory of Medical GeneticsSchool of Life SciencesCentral South UniversityChangshaHunanChina
| | - Menglin Li
- Center for Medical Genetics & Hunan Key Laboratory of Medical GeneticsSchool of Life SciencesCentral South UniversityChangshaHunanChina
| | - Zhuo Li
- Center for Medical Genetics & Hunan Key Laboratory of Medical GeneticsSchool of Life SciencesCentral South UniversityChangshaHunanChina
| | - Lingqian Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical GeneticsSchool of Life SciencesCentral South UniversityChangshaHunanChina
| | - Desheng Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical GeneticsSchool of Life SciencesCentral South UniversityChangshaHunanChina
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Lara-Hernandez F, Cortez J, Garcia-Sorribes S, Blesa S, Olivares MD, Alic AS, Garcia-Garcia AB, Chaves FJ, Ivorra C. EOSAL-CNV for Easy and Rapid Detection of CNVs by Fragment Analysis : EOSAL: A Fast and Reliable New Method for CNV Detection. Methods Mol Biol 2023; 2621:241-253. [PMID: 37041448 DOI: 10.1007/978-1-0716-2950-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Copy number variations (CNVs) are a type of genetic variation involving from 50 base pairs (bps) to millions of bps and, in a general point of view, can include alterations of complete chromosomes. As CNVs mean the gain or loss of DNA sequences, their detection requires specific techniques and analysis. We have developed Easy One-Step Amplification and Labeling for CNV Detection (EOSAL-CNV) by fragment analysis in a DNA sequencer. The procedure is based on a single PCR reaction for amplification and labeling of all fragments included. The protocol includes specific primers for the amplification of the regions of interest with a tail in each of the primers (one for forward and another for the reverse primers) together with primers for tail amplification. One of the primers for tail amplification is labeled with a fluorophore, allowing the amplification and labeling in the same reaction. Combination of several tail pairs and labels allows the detection of DNA fragment by different fluorophores and increases the number of fragments that can be analyzed in one reaction. PCR products can be analyzed without any purification on a DNA sequencer for fragment detection and quantification. Finally, simple and easy calculations allow the detection of fragments with deletions or extra copies. The use of EOSAL-CNV allows simplifying and reducing costs in sample analysis for CNV detection.
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Affiliation(s)
| | - Jessica Cortez
- I+D+I Department, Sequencing Multiplex SL Serra, Valencia, Spain
| | | | - Sebastian Blesa
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, Valencia, Spain
| | | | - Andy S Alic
- I+D+I Department, Sequencing Multiplex SL Serra, Valencia, Spain
| | - Ana-Barbara Garcia-Garcia
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, Valencia, Spain.
- CIBERDEM, ISCIII, Madrid, Spain.
| | - F Javier Chaves
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, Valencia, Spain
- I+D+I Department, Sequencing Multiplex SL Serra, Valencia, Spain
- CIBERDEM, ISCIII, Madrid, Spain
| | - Carmen Ivorra
- I+D+I Department, Sequencing Multiplex SL Serra, Valencia, Spain
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García-García AB, Martínez-Hervás S, Vernia S, Ivorra C, Pulido I, Martín-Escudero JC, Casado M, Carretero J, Real JT, Chaves FJ. A Very Rare Variant in SREBF2, a Possible Cause of Hypercholesterolemia and Increased Glycemic Levels. Biomedicines 2022; 10:biomedicines10051178. [PMID: 35625914 PMCID: PMC9138625 DOI: 10.3390/biomedicines10051178] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 02/01/2023] Open
Abstract
Patients with high cholesterol and glucose levels are at high risk for cardiovascular disease. The Sterol Regulatory Element Binding Protein (SREBP) system regulates genes involved in lipid, cholesterol and glucose pathways. Autosomal Dominant Hypercholesterolemias (ADHs) are a group of diseases with increased cholesterol levels. They affect 1 out of every 500 individuals. About 20–30% of patients do not present any mutation in the known genes (LDLR, APOB and PCSK9). ADHs constitute a good model to identify the genes involved in the alteration of lipid levels or possible therapeutic targets. In this paper, we studied whether a mutation in the SREBP system could be responsible for ADH and other metabolic alterations present in these patients. Forty-one ADH patients without mutations in the main responsible genes were screened by direct sequencing of SREBP system genes. A luciferase reporter assay of the found mutation and an oral glucose tolerance test in carriers and non-carriers were performed. We found a novel mutation in the SREBF2 gene that increases transcription levels and cosegregates with hypercholesterolemia, and we found increased glucose levels in one family. SREBP2 is known to be involved in cholesterol synthesis, plasma levels and glucose metabolism in humans. The found mutation may involve the SREBF2 gene in hypercholesterolemia combined with hyperglycemia.
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Affiliation(s)
- Ana-Bárbara García-García
- CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), 28029 Madrid, Spain; (A.-B.G.-G.); (S.M.-H.); (J.T.R.)
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain;
| | - Sergio Martínez-Hervás
- CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), 28029 Madrid, Spain; (A.-B.G.-G.); (S.M.-H.); (J.T.R.)
- Department of Medicine, University of Valencia, 46010 Valencia, Spain
- Endocrinology Service, University Clinical Hospital of Valencia, 46010 Valencia, Spain
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
| | - Santiago Vernia
- Biomedical Institute of Valencia (IBV-CSIC), 46010 Valencia, Spain; (S.V.); (M.C.)
| | - Carmen Ivorra
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain;
| | - Inés Pulido
- University of Illinois Hospital & Health Sciences System Cancer Center, University of Illinois Chicago, Chicago, IL 60612, USA;
- Department of Physiology, University of Valencia, 46010 Valencia, Spain;
| | | | - Marta Casado
- Biomedical Institute of Valencia (IBV-CSIC), 46010 Valencia, Spain; (S.V.); (M.C.)
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), 28029 Madrid, Spain
| | - Julián Carretero
- Department of Physiology, University of Valencia, 46010 Valencia, Spain;
| | - José T. Real
- CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), 28029 Madrid, Spain; (A.-B.G.-G.); (S.M.-H.); (J.T.R.)
- Department of Medicine, University of Valencia, 46010 Valencia, Spain
- Endocrinology Service, University Clinical Hospital of Valencia, 46010 Valencia, Spain
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
| | - Felipe Javier Chaves
- CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), 28029 Madrid, Spain; (A.-B.G.-G.); (S.M.-H.); (J.T.R.)
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain;
- Correspondence: ; Tel.: +34-96-38-64100 (ext. 51905)
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Hussen BM, Abdullah ST, Salihi A, Sabir DK, Sidiq KR, Rasul MF, Hidayat HJ, Ghafouri-Fard S, Taheri M, Jamali E. The emerging roles of NGS in clinical oncology and personalized medicine. Pathol Res Pract 2022; 230:153760. [PMID: 35033746 DOI: 10.1016/j.prp.2022.153760] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/29/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has been increasingly popular in genomics studies over the last decade, as new sequencing technology has been created and improved. Recently, NGS started to be used in clinical oncology to improve cancer therapy through diverse modalities ranging from finding novel and rare cancer mutations, discovering cancer mutation carriers to reaching specific therapeutic approaches known as personalized medicine (PM). PM has the potential to minimize medical expenses by shifting the current traditional medical approach of treating cancer and other diseases to an individualized preventive and predictive approach. Currently, NGS can speed up in the early diagnosis of diseases and discover pharmacogenetic markers that help in personalizing therapies. Despite the tremendous growth in our understanding of genetics, NGS holds the added advantage of providing more comprehensive picture of cancer landscape and uncovering cancer development pathways. In this review, we provided a complete overview of potential NGS applications in scientific and clinical oncology, with a particular emphasis on pharmacogenomics in the direction of precision medicine treatment options.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq; Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Sara Tharwat Abdullah
- Department of Pharmacology and Toxicology, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Abbas Salihi
- Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq; Department of Biology, College of Science, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Dana Khdr Sabir
- Department of Medical Laboratory Sciences, Charmo University, Kurdistan Region, Iraq
| | - Karzan R Sidiq
- Department of Biology, College of Education, University of Sulaimani, Sulaimani 334, Kurdistan, Iraq
| | - Mohammed Fatih Rasul
- Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Kurdistan Region, Erbil, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Elena Jamali
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Srebf2 Locus Overexpression Reduces Body Weight, Total Cholesterol and Glucose Levels in Mice Fed with Two Different Diets. Nutrients 2020; 12:nu12103130. [PMID: 33066385 PMCID: PMC7602228 DOI: 10.3390/nu12103130] [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: 09/22/2020] [Revised: 10/06/2020] [Accepted: 10/10/2020] [Indexed: 11/17/2022] Open
Abstract
Macronutrients represent risk factors for hyperlipidemia or diabetes. Lipid alterations and type 2 diabetes mellitus are global health problems. Overexpression of sterol regulatory element-binding factor (Srebf2) in transgenic animals is linked to elevated cholesterol levels and diabetes development. We investigated the impact of increased Srebf2 locus expression and the effects of control and high-fat, high-sucrose (HFHS) diets on body weight, glucose and lipid metabolisms in transgenic mice (S-mice). Wild type (WT) and S-mice were fed with both diets for 16 weeks. Plasma glucose, insulin and lipids were assessed (n = 25). Immunostainings were performed in liver, pancreas and fat (N = 10). Expression of Ldlr and Hmgcr in liver was performed by RT-PCR (N = 8). Control diet: S-mice showed reduced weight, insulin, total and HDL cholesterol and triglycerides (TG). HFHS diet widened differences in weight, total and HDL cholesterol, insulin and HOMA index but increased TG in S-mice. In S-mice, adipocyte size was lower while HFHS diet produced lower increase, pancreatic β-cell mass was lower with both diets and Srebf2, Ldlr and Hmgcr mRNA levels were higher while HFHS diet produced a rise in Srebf2 and Hmgcr levels. Srebf2 complete gene overexpression seems to have beneficial effects on metabolic parameters and to protect against HFHS diet effects.
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A three-year follow-up study evaluating clinical utility of exome sequencing and diagnostic potential of reanalysis. NPJ Genom Med 2020; 5:37. [PMID: 32963807 PMCID: PMC7484757 DOI: 10.1038/s41525-020-00144-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/14/2020] [Indexed: 01/05/2023] Open
Abstract
Exome sequencing (ES) has become one of the important diagnostic tools in clinical genetics with a reported diagnostic rate of 25–58%. Many studies have illustrated the diagnostic and immediate clinical impact of ES. However, up to 75% of individuals remain undiagnosed and there is scarce evidence supporting clinical utility beyond a follow-up period of >1 year. This is a 3-year follow-up analysis to our previous publication by Mak et al. (NPJ Genom. Med. 3:19, 2018), to evaluate the long-term clinical utility of ES and the diagnostic potential of exome reanalysis. The diagnostic yield of the initial study was 41% (43/104). Exome reanalysis in 46 undiagnosed individuals has achieved 12 new diagnoses. The additional yield compared with the initial analysis was at least 12% (increased from 41% to at least 53%). After a median follow-up period of 3.4 years, change in clinical management was observed in 72.2% of the individuals (26/36), leading to positive change in clinical outcome in four individuals (11%). There was a minimum healthcare cost saving of HKD$152,078 (USD$19,497; €17,282) annually for these four individuals. There were a total of six pregnancies from five families within the period. Prenatal diagnosis was performed in four pregnancies; one fetus was affected and resulted in termination. None of the parents underwent preimplantation genetic diagnosis. This 3-year follow-up study demonstrated the long-term clinical utility of ES at individual, familial and health system level, and the promising diagnostic potential of subsequent reanalysis. This highlights the benefits of implementing ES and regular reanalysis in the clinical setting.
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