1
|
Li P, Wei Y, Shi J, Wu J, Wu Y, Yan J, Liu S, Tan X, Huang KJ. CRISPR/Cas12a-triggered ordered concatemeric DNA probes signal-on/off multifunctional analytical sensing system for ultrasensitive detection of thalassemia. Int J Biol Macromol 2024; 276:133884. [PMID: 39013507 DOI: 10.1016/j.ijbiomac.2024.133884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/18/2024]
Abstract
Based on CRISPR/Cas12a triggered ordered concatemeric DNA probes, a "on/off" self-powered biosensor is developed to achieve highly sensitive detection of thalassemia gene CD142 through open-circuit potential-assisted visual signal output. The ingeniously constructed glucose oxidase (GOD)-functionalized ordered concatemeric DNA probe structure can significantly amplify signal output, while the coupled CRISPR/Cas12a system is served as a "signal switch" with excellent signal-transducing capabilities. When the ordered concatemeric DNA probe structure is anchored on electrode, the response signal of the sensing system is in the "signal on" mode. While, the presence of the target activates the non-specific cleavage activity of the CRISPR/Cas12a system, causing the sensing system to switch to the "signal off" mode. In the detection system, GOD catalyzes the oxidation of glucose to produce hydrogen peroxide, which further catalyzes the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) to form a color product, enabling visual signal of the target through naked-eye color contrast. By employing a multifunctional analytical mode combining electrochemical and visual signal outputs, accurate determination of the target is achieved, with linear ranges of 0.0001-100 pM, and detection limits of 48.1 aM (S/N = 3). This work provides a reference method for sensitive detection of thalassemia genes and holds great diagnostic potential in biomedical applications.
Collapse
Affiliation(s)
- Peiyuan Li
- Education Department of Guangxi Zhuang Autonomous Region, Laboratory of Optic-electric Chemo/Biosensing and Molecular Recognition, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Yashu Wei
- The Reproductive Hospital of Guangxi Zhuang Autonomous Region, Nanning 530021, China
| | - Jinyue Shi
- Education Department of Guangxi Zhuang Autonomous Region, Laboratory of Optic-electric Chemo/Biosensing and Molecular Recognition, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Jiawen Wu
- Education Department of Guangxi Zhuang Autonomous Region, Laboratory of Optic-electric Chemo/Biosensing and Molecular Recognition, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Yeyu Wu
- Education Department of Guangxi Zhuang Autonomous Region, Laboratory of Optic-electric Chemo/Biosensing and Molecular Recognition, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Jun Yan
- Education Department of Guangxi Zhuang Autonomous Region, Laboratory of Optic-electric Chemo/Biosensing and Molecular Recognition, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Shaogang Liu
- Education Department of Guangxi Zhuang Autonomous Region, Laboratory of Optic-electric Chemo/Biosensing and Molecular Recognition, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Xuecai Tan
- Education Department of Guangxi Zhuang Autonomous Region, Laboratory of Optic-electric Chemo/Biosensing and Molecular Recognition, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China.
| | - Ke-Jing Huang
- Education Department of Guangxi Zhuang Autonomous Region, Laboratory of Optic-electric Chemo/Biosensing and Molecular Recognition, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China.
| |
Collapse
|
2
|
Lin Z, Liang X, Wei X, Liang G, Zhu D, Xie H, Yan T, Shang X. SUPT5H mutations associated with elevation of Hb A 2 level: Identification of two novel variants and literature review. Gene 2024; 908:148294. [PMID: 38373659 DOI: 10.1016/j.gene.2024.148294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 02/21/2024]
Abstract
β-thalassemia is one of the most common monogenic disorders in areas of the tropics and subtropics, which represents a major familial and social burden to local people. The elevated Hb A2 level, generally specified as greater than 3.5 %, is commonly used as a high efficiency index for screening of β-thalassemia carriers. However, mutations in other genes such as GATA1 and KLF1, could also result in increased Hb A2 level. In this study, we identified two novel variants in the SUPT5H gene: a frameshift mutation (SUPT5H: c.3032_3033delTG, p.M1011Mfs*9) and a nonsense mutation (SUPT5H: c.397C > T, p.Arg133*) in two Chinese individuals. Utilizing a combination of phenotype analysis, bioinformatics analysis, and functional analysis, we deduced that these two variants modified the SUPT5H protein's structure, thereby impacting its function and consequently leading to the heightened Hb A2 level phenotype found in the carriers. Furthermore, through a comprehensive literature review, a mutation spectrum was consolidated for SUPT5H, an investigation into the genotype-phenotype correlation was conducted, and factors known to influence Hb A2 levels were identified. Based on this in-depth understanding, clinicians are better equipped to carry out large scale screenings in regions with high prevalence of β-thalassemia.
Collapse
Affiliation(s)
- Zezhang Lin
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiongda Liang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiaofeng Wei
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Guanxia Liang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Dina Zhu
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Hongting Xie
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Tizhen Yan
- Prenatal Diagnostic Center, Affiliated Dongguan Maternal and Child Health Care Hospital, Southern Medical University, Dongguan, China
| | - Xuan Shang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China; Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China.
| |
Collapse
|
3
|
Liu Y, Yu L, Chen L, Chen K, Xu H, Chen M, Yi K, Li Y, Chen T, Wang F, Wang F, Zhu J, Wang F, Xiao X, Yang Y. Gradient Hydrogels Spatially Trapped Optical Cell Profiling for Quantitative Blood Cellular Osmotic Analysis. ACS Sens 2024; 9:1592-1601. [PMID: 38477713 DOI: 10.1021/acssensors.4c00102] [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: 03/14/2024]
Abstract
The quantitative exploration of cellular osmotic responses and a thorough analysis of osmotic pressure-responsive cellular behaviors are poised to offer novel clinical insights into current research. This underscores a paradigm shift in the long-standing approach of colorimetric measurements triggered by red cell lysis. In this study, we engineered a purpose-driven optofluidic platform to facilitate the goal. Specifically, creating photocurable hydrogel traps surmounts a persistent challenge─optical signal interference from fluid disturbances. This achievement ensures a stable spatial phase of cells and the acquisition of optical signals for accurate osmotic response analysis at the single-cell level. Leveraging a multigradient microfluidic system, we constructed gradient osmotic hydrogel traps and developed an imaging recognition algorithm, empowering comprehensive analysis of cellular behaviors. Notably, this system has successfully and precisely analyzed individual and clustered cellular responses within the osmotic dimension. Prospective clinical testing has further substantiated its feasibility and performance in that it demonstrates an accuracy of 92% in discriminating complete hemolysis values (n = 25) and 100% in identifying initial hemolysis values (n = 25). Foreseeably, this strategy should promise to advance osmotic pressure-related cellular response analysis, benefiting further investigation and diagnosis of related blood diseases, blood quality, drug development, etc.
Collapse
Affiliation(s)
- Yantong Liu
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
- Shenzhen Research Institute, Wuhan University, Shenzhen 518000, China
| | - Le Yu
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Longfei Chen
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Keyu Chen
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Hongshan Xu
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Ming Chen
- Department of Blood Transfusion, Zhongnan Hospital, Wuhan University, Wuhan 430071, China
| | - Kezhen Yi
- Department of Laboratory Medicine, Zhongnan Hospital, Wuhan University, Wuhan 430071, China
| | - Ying Li
- Department of Ophthalmology, Renmin Hospital, Wuhan University, Wuhan 430060, China
| | - Ting Chen
- Department of Ophthalmology, Renmin Hospital, Wuhan University, Wuhan 430060, China
| | - Faxi Wang
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Fang Wang
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Jiaomeng Zhu
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Fubing Wang
- Department of Laboratory Medicine, Zhongnan Hospital, Wuhan University, Wuhan 430071, China
| | - Xuan Xiao
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
- Department of Ophthalmology, Renmin Hospital, Wuhan University, Wuhan 430060, China
| | - Yi Yang
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
- Shenzhen Research Institute, Wuhan University, Shenzhen 518000, China
| |
Collapse
|
4
|
Saleem M, Aslam W, Lali MIU, Rauf HT, Nasr EA. Predicting Thalassemia Using Feature Selection Techniques: A Comparative Analysis. Diagnostics (Basel) 2023; 13:3441. [PMID: 37998577 PMCID: PMC10670018 DOI: 10.3390/diagnostics13223441] [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: 08/20/2023] [Revised: 10/25/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
Thalassemia represents one of the most common genetic disorders worldwide, characterized by defects in hemoglobin synthesis. The affected individuals suffer from malfunctioning of one or more of the four globin genes, leading to chronic hemolytic anemia, an imbalance in the hemoglobin chain ratio, iron overload, and ineffective erythropoiesis. Despite the challenges posed by this condition, recent years have witnessed significant advancements in diagnosis, therapy, and transfusion support, significantly improving the prognosis for thalassemia patients. This research empirically evaluates the efficacy of models constructed using classification methods and explores the effectiveness of relevant features that are derived using various machine-learning techniques. Five feature selection approaches, namely Chi-Square (χ2), Exploratory Factor Score (EFS), tree-based Recursive Feature Elimination (RFE), gradient-based RFE, and Linear Regression Coefficient, were employed to determine the optimal feature set. Nine classifiers, namely K-Nearest Neighbors (KNN), Decision Trees (DT), Gradient Boosting Classifier (GBC), Linear Regression (LR), AdaBoost, Extreme Gradient Boosting (XGB), Random Forest (RF), Light Gradient Boosting Machine (LGBM), and Support Vector Machine (SVM), were utilized to evaluate the performance. The χ2 method achieved accuracy, registering 91.56% precision, 91.04% recall, and 92.65% f-score when aligned with the LR classifier. Moreover, the results underscore that amalgamating over-sampling with Synthetic Minority Over-sampling Technique (SMOTE), RFE, and 10-fold cross-validation markedly elevates the detection accuracy for αT patients. Notably, the Gradient Boosting Classifier (GBC) achieves 93.46% accuracy, 93.89% recall, and 92.72% F1 score.
Collapse
Affiliation(s)
- Muniba Saleem
- Department of Computer Science & Information Technology, The Government Sadiq College Women University Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Waqar Aslam
- Department of Information Security, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | | | - Hafiz Tayyab Rauf
- Centre for Smart Systems, AI and Cybersecurity, Staffordshire University, Stoke-on-Trent ST4 2DE, UK;
| | - Emad Abouel Nasr
- Industrial Engineering Department, College of Engineering, King Saud University, Riyadh 11421, Saudi Arabia;
| |
Collapse
|
5
|
Wang G, Zou S, Li J, Wang X, Wu H, Tao Z, Zhang Q, Xu X, Zhou Y. The diagnosis and molecular analysis of a novel 27.2 kb deletion causing α 0-thalassemia. Clin Biochem 2023; 116:20-23. [PMID: 36878345 DOI: 10.1016/j.clinbiochem.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/06/2023]
Abstract
BACKGROUND Thalassemia, one of the most prevalent monogenic diseases worldwide, is caused by an imbalance of α-like and non-α-like globin chain production. Copy number variations, which cause the most common genotype of α-thalassemia, can be detected by multiple diagnostic methods. CASE REPORT The proband was a 31-year-old female who was diagnosed with microcytic hypochromic anemia by antenatal screening. Hematological analysis and molecular genotyping were conducted on the proband and the proband's family members. Gap-polymerase chain reaction, Sanger sequencing, multiplex ligation-dependent probe amplification, and next-generation sequencing were used to detect potentially pathogenic genes. Familial studies and genetic analyses revealed a novel deletion of 27.2 kb located in the α-globin gene cluster (NC_000016.9: g. 204538_231777delinsTAACA). CONCLUSIONS We reported a novel α-thalassemia deletion and described the process of molecular diagnosis. The novel deletion extends the thalassemia mutation spectrum, which may be helpful in genetic counseling and clinical diagnosis in the future.
Collapse
Affiliation(s)
- Ge Wang
- Zhuhai Institute of Medical Genetics, Zhuhai Women and Children's Hospital, Zhuhai, Guangdong, China
| | - Shaomin Zou
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Jialong Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Xingmin Wang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Hongqiu Wu
- Zhuhai Institute of Medical Genetics, Zhuhai Women and Children's Hospital, Zhuhai, Guangdong, China
| | - Zhenzhong Tao
- Guangzhou Jiexu Gene Technology Co., Ltd., Guangzhou, Guangdong, China
| | - Qianqian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiangmin Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Innovative Research Center for Diagnosis and Therapy of Thalassemias, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Yuqiu Zhou
- Zhuhai Institute of Medical Genetics, Zhuhai Women and Children's Hospital, Zhuhai, Guangdong, China..
| |
Collapse
|
6
|
A Particular Focus on the Prevalence of α- and β-Thalassemia in Western Sicilian Population from Trapani Province in the COVID-19 Era. Int J Mol Sci 2023; 24:ijms24054809. [PMID: 36902239 PMCID: PMC10002525 DOI: 10.3390/ijms24054809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/22/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Thalassemia is a Mendelian inherited blood disease caused by α- and β-globin gene mutations, known as one of the major health problems of Mediterranean populations. Here, we examined the distribution of α- and β-globin gene defects in the Trapani province population. A total of 2,401 individuals from Trapani province were enrolled from January 2007 to December 2021, and routine methodologies were used for detecting the α- and β-globin genic variants. Appropriate analysis was also performed. Eight mutations in the α globin gene showed the highest frequency in the sample studied; three of these genetic variants represented the 94% of the total α-thalassemia mutations observed, including the -α3.7 deletion (76%), and the tripling of the α gene (12%) and of the α2 point mutation IVS1-5nt (6%). For the β-globin gene, 12 mutations were detected, six of which constituted 83.4% of the total number of β-thalassemia defects observed, including codon β039 (38%), IVS1.6 T > C (15.6%), IVS1.110 G > A (11.8%), IVS1.1 G > A (11%), IVS2.745 C > G (4%), and IVS2.1 G > A (3%). However, the comparison of these frequencies with those detected in the population of other Sicilian provinces did not demonstrate significant differences, but it contrarily revealed a similitude. The data presented in this retrospective study help provide a picture of the prevalence of defects on the α and β-globin genes in the province of Trapani. The identification of mutations in globin genes in a population is required for carrier screening and for an accurate prenatal diagnosis. It is important and necessary to continue promoting public awareness campaigns and screening programs.
Collapse
|