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Zhang Y, Liu H, Nakagawa Y, Nagasaka Y, Ding T, Tang SY, Yalikun Y, Goda K, Li M. Enhanced CRISPR/Cas12a-based quantitative detection of nucleic acids using double emulsion droplets. Biosens Bioelectron 2024; 257:116339. [PMID: 38688231 DOI: 10.1016/j.bios.2024.116339] [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: 03/04/2024] [Revised: 04/05/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Pairing droplet microfluidics and CRISPR/Cas12a techniques creates a powerful solution for the detection and quantification of nucleic acids at the single-molecule level, due to its specificity, sensitivity, and simplicity. However, traditional water-in-oil (W/O) single emulsion (SE) droplets often present stability issues, affecting the accuracy and reproducibility of assay results. As an alternative, water-in-oil-in-water (W/O/W) double emulsion (DE) droplets offer superior stability and uniformity for droplet digital assays. Moreover, unlike SE droplets, DE droplets are compatible with commercially available flow cytometry instruments for high-throughput analysis. Despite these advantages, no study has demonstrated the use of DE droplets for CRISPR-based nucleic acid detection. In our study, we conducted a comparative analysis to assess the performance of SE and DE droplets in quantitative detection of human papillomavirus type 18 (HPV18) DNA based on CRISPR/Cas12a. We evaluated the stability of SEs and DEs by examining size variation, merging extent, and content interaction before and after incubation at different temperatures and time points. By integrating DE droplets with flow cytometry, we achieved high-throughput and high-accuracy CRISPR/Cas12a-based quantification of target HPV18 DNA. The DE platform, when paired with CRISPR/Cas12a and flow cytometry techniques, emerges as a reliable tool for absolute quantification of nucleic acid biomarkers.
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Affiliation(s)
- Yang Zhang
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia; School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Hangrui Liu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Yuta Nakagawa
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yuzuki Nagasaka
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Tianben Ding
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Shi-Yang Tang
- School of Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK
| | - Yaxiaer Yalikun
- Division of Materials Science, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan; Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA; Institute of Technological Sciences, Wuhan University, Hubei, 430072, China
| | - Ming Li
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia; School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW, 2052, Australia.
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Yoon DE, Lee H, Kim K. Recent Research Trends in Stem Cells Using CRISPR/Cas-Based Genome Editing Methods. Int J Stem Cells 2024; 17:1-14. [PMID: 37904281 PMCID: PMC10899885 DOI: 10.15283/ijsc23030] [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: 03/19/2023] [Revised: 08/28/2023] [Accepted: 09/21/2023] [Indexed: 11/01/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system, a rapidly advancing genome editing technology, allows DNA alterations into the genome of organisms. Gene editing using the CRISPR system enables more precise and diverse editing, such as single nucleotide conversion, precise knock-in of target sequences or genes, chromosomal rearrangement, or gene disruption by simple cutting. Moreover, CRISPR systems comprising transcriptional activators/repressors can be used for epigenetic regulation without DNA damage. Stem cell DNA engineering based on gene editing tools has enormous potential to provide clues regarding the pathogenesis of diseases and to study the mechanisms and treatments of incurable diseases. Here, we review the latest trends in stem cell research using various CRISPR/Cas technologies and discuss their future prospects in treating various diseases.
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Affiliation(s)
- Da Eun Yoon
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
- Department of Physiology, Korea University College of Medicine, Seoul, Korea
| | - Hyunji Lee
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
- Department of Medicine, Korea University College of Medicine, Seoul, Korea
| | - Kyoungmi Kim
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
- Department of Physiology, Korea University College of Medicine, Seoul, Korea
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Hertz E, Perez G, Hao Y, Rytel K, Ma C, Kirby M, Anderson S, Wincovitch S, Andersh K, Ahfeldt T, Blanchard J, Qi YA, Lopez G, Tayebi N, Sidransky E, Chen Y. Comparative study of enriched dopaminergic neurons from siblings with Gaucher disease discordant for parkinsonism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.25.581985. [PMID: 38529501 PMCID: PMC10962709 DOI: 10.1101/2024.02.25.581985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Inducible pluripotent stem cells (iPSCs) derived from patient samples have significantly enhanced our ability to model neurological diseases. Comparative studies of dopaminergic (DA) neurons differentiated from iPSCs derived from siblings with Gaucher disease discordant for parkinsonism provides a valuable avenue to explore genetic modifiers contributing to GBA1 -associated parkinsonism in disease-relevant cells. However, such studies are often complicated by the inherent heterogeneity in differentiation efficiency among iPSC lines derived from different individuals. To address this technical challenge, we devised a selection strategy to enrich dopaminergic (DA) neurons expressing tyrosine hydroxylase (TH). A neomycin resistance gene (neo) was inserted at the C-terminus of the TH gene following a T2A self-cleavage peptide, placing its expression under the control of the TH promoter. This allows for TH+ DA neuron enrichment through geneticin selection. This method enabled us to generate comparable, high-purity DA neuron cultures from iPSC lines derived from three sisters that we followed for over a decade: one sibling is a healthy individual, and the other two have Gaucher disease (GD) with GBA1 genotype N370S/c.203delC+R257X (p.N409S/c.203delC+p.R296X). Notably, the younger sister with GD later developed Parkinson disease (PD). A comprehensive analysis of these high-purity DA neurons revealed that although GD DA neurons exhibited decreased levels of glucocerebrosidase (GCase), there was no substantial difference in GCase protein levels or lipid substrate accumulation between DA neurons from the GD and GD/PD sisters, suggesting that the PD discordance is related to of other genetic modifiers.
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Yeap YJ, Teddy TJW, Lee MJ, Goh M, Lim KL. From 2D to 3D: Development of Monolayer Dopaminergic Neuronal and Midbrain Organoid Cultures for Parkinson's Disease Modeling and Regenerative Therapy. Int J Mol Sci 2023; 24:ijms24032523. [PMID: 36768843 PMCID: PMC9917335 DOI: 10.3390/ijms24032523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Parkinson's Disease (PD) is a prevalent neurodegenerative disorder that is characterized pathologically by the loss of A9-specific dopaminergic (DA) neurons in the substantia nigra pars compacta (SNpc) of the midbrain. Despite intensive research, the etiology of PD is currently unresolved, and the disease remains incurable. This, in part, is due to the lack of an experimental disease model that could faithfully recapitulate the features of human PD. However, the recent advent of induced pluripotent stem cell (iPSC) technology has allowed PD models to be created from patient-derived cells. Indeed, DA neurons from PD patients are now routinely established in many laboratories as monolayers as well as 3D organoid cultures that serve as useful toolboxes for understanding the mechanism underlying PD and also for drug discovery. At the same time, the iPSC technology also provides unprecedented opportunity for autologous cell-based therapy for the PD patient to be performed using the patient's own cells as starting materials. In this review, we provide an update on the molecular processes underpinning the development and differentiation of human pluripotent stem cells (PSCs) into midbrain DA neurons in both 2D and 3D cultures, as well as the latest advancements in using these cells for drug discovery and regenerative medicine. For the novice entering the field, the cornucopia of differentiation protocols reported for the generation of midbrain DA neurons may seem daunting. Here, we have distilled the essence of the different approaches and summarized the main factors driving DA neuronal differentiation, with the view to provide a useful guide to newcomers who are interested in developing iPSC-based models of PD.
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Affiliation(s)
- Yee Jie Yeap
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Tng J. W. Teddy
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
- Interdisciplinary Graduate Programme (IGP-Neuroscience), Nanyang Technological University, Singapore 639798, Singapore
| | - Mok Jung Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Micaela Goh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Kah Leong Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
- National Neuroscience Institute, Singapore 308433, Singapore
- Department of Brain Sciences, Imperial College London, London SW7 2AZ, UK
- Department of Anatomy, Shanxi Medical University, Taiyuan 030001, China
- Correspondence:
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Coschiera A, Watts ME, Kere J, Tammimies K, Swoboda P. Human LUHMES and NES cells as models for studying primary cilia in neurons. Methods Cell Biol 2023; 176:27-41. [PMID: 37164541 DOI: 10.1016/bs.mcb.2022.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Primary cilia are antenna-like organelles emanating from the cell surface. They are involved in cell-to-cell communication and bidirectional signal transduction to/from the extracellular environment. During brain formation, cilia critically aid in neurogenesis and maturation of neuronal structures such as axons, dendrites and synapses. Aberrations in cilia function can induce neuron differentiation defects and pathological consequences of varying severity, resulting in ciliopathies and likely a number of neurodevelopmental disorders. Despite the documented relevance of cilia for proper brain development, human neuronal models to recognize and study cilia biology are still scarce. We have established two types of cell models, Lund Human Mesencephalic (LUHMES) cells and neuroepithelial stem (NES) cells derived from induced pluripotent stem cells (iPSC), to investigate cilia biology in both proliferating neuronal progenitors/precursors and during the entire neuron differentiation and maturation process. We employ improved immunocytochemistry assays able to specifically detect cilia by confocal and super-resolution microscopy. We provide straightforward and robust methods to easily maintain cells in culture, for immunostaining and characterization of cilia orientation, anatomy and shape in human neurons across all stages of differentiation.
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Affiliation(s)
- Andrea Coschiera
- Karolinska Institute, Department of Biosciences and Nutrition, Huddinge, Sweden
| | - Michelle Evelyn Watts
- Karolinska Institute, Department of Women's and Children's Health and Center for Psychiatry Research, Center of Neurodevelopmental Disorders (KIND), Division of Neuropsychiatry, Stockholm, Sweden; Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Juha Kere
- Karolinska Institute, Department of Biosciences and Nutrition, Huddinge, Sweden; University of Helsinki, Stem Cells and Metabolism Research Program and Folkhälsan Research Center, Helsinki, Finland
| | - Kristiina Tammimies
- Karolinska Institute, Department of Women's and Children's Health and Center for Psychiatry Research, Center of Neurodevelopmental Disorders (KIND), Division of Neuropsychiatry, Stockholm, Sweden; Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Peter Swoboda
- Karolinska Institute, Department of Biosciences and Nutrition, Huddinge, Sweden.
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Chen X, Peng M, Cai Y, Zhou C, Liu L. Human iPSC-derived neural stem cells with ALDH5A1 mutation as a model of succinic semialdehyde dehydrogenase deficiency. BMC Neurosci 2022; 23:77. [PMID: 36527006 PMCID: PMC9756581 DOI: 10.1186/s12868-022-00755-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 11/11/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Succinic semialdehyde dehydrogenase deficiency (SSADH-D) is an autosomal recessive gamma-aminobutyric acid (GABA) metabolism disorder that can arise due to ALDH5A1 mutations, resulting in severe, progressive, untreatable neurodegeneration. SSADH-D is primarily studied using simplified models, such as HEK293 cells overexpressing genes of interest, but such overexpression can result in protein aggregation or pathway saturation that may not be representative of actual underlying disease phenotypes. METHODS We used a CRISPR/Cas9 approach to generate human iPSC cell lines bearing ALDH5A1 mutations. Through screening, two different mutant cell lines, NM_001080.3: c.727_735del (p.L243_S245del) and NM_001080.3: c.730_738del (p.A244_Q246del), were obtained. We induced iPSCs to neural stem cells and analyzed the characteristics of ALDH5A1 mutations in stem cells. RESULTS The human iPSC and NSC cell lines presented typical stem cell-like morphology. We found changes in ALDH5A1 expression and GABA accumulation in the different cell lines. In addition, by analyzing the cDNA between the wild-type and the mutant cell lines, we found that the mutant cell lines had a splicing variant. CONCLUSIONS iPSCs represent a promising in vitro model for SSADH-D that can be used to study early central nervous system developmental alterations and pathogenic mechanisms.
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Affiliation(s)
- Xiaodan Chen
- grid.410737.60000 0000 8653 1072Department of Genetics and Endocrinology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Minzhi Peng
- grid.410737.60000 0000 8653 1072Department of Genetics and Endocrinology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Yanna Cai
- grid.410737.60000 0000 8653 1072Department of Genetics and Endocrinology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Chengcheng Zhou
- grid.410737.60000 0000 8653 1072Department of Genetics and Endocrinology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Li Liu
- grid.410737.60000 0000 8653 1072Department of Genetics and Endocrinology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, People’s Republic of China
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Sen T, Thummer RP. CRISPR and iPSCs: Recent Developments and Future Perspectives in Neurodegenerative Disease Modelling, Research, and Therapeutics. Neurotox Res 2022; 40:1597-1623. [PMID: 36044181 PMCID: PMC9428373 DOI: 10.1007/s12640-022-00564-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/17/2022] [Accepted: 08/19/2022] [Indexed: 11/15/2022]
Abstract
Neurodegenerative diseases are prominent causes of pain, suffering, and death worldwide. Traditional approaches modelling neurodegenerative diseases are deficient, and therefore, improved strategies that effectively recapitulate the pathophysiological conditions of neurodegenerative diseases are the need of the hour. The generation of human-induced pluripotent stem cells (iPSCs) has transformed our ability to model neurodegenerative diseases in vitro and provide an unlimited source of cells (including desired neuronal cell types) for cell replacement therapy. Recently, CRISPR/Cas9-based genome editing has also been gaining popularity because of the flexibility they provide to generate and ablate disease phenotypes. In addition, the recent advancements in CRISPR/Cas9 technology enables researchers to seamlessly target and introduce precise modifications in the genomic DNA of different human cell lines, including iPSCs. CRISPR-iPSC-based disease modelling, therefore, allows scientists to recapitulate the pathological aspects of most neurodegenerative processes and investigate the role of pathological gene variants in healthy non-patient cell lines. This review outlines how iPSCs, CRISPR/Cas9, and CRISPR-iPSC-based approaches accelerate research on neurodegenerative diseases and take us closer to a cure for neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, Amyotrophic Lateral Sclerosis, and so forth.
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Affiliation(s)
- Tirthankar Sen
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India.
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Rakovic A, Voß D, Vulinovic F, Meier B, Hellberg AK, Nau C, Klein C, Leipold E. Electrophysiological Properties of Induced Pluripotent Stem Cell-Derived Midbrain Dopaminergic Neurons Correlate With Expression of Tyrosine Hydroxylase. Front Cell Neurosci 2022; 16:817198. [PMID: 35401116 PMCID: PMC8983830 DOI: 10.3389/fncel.2022.817198] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Induced pluripotent stem cell (iPSC)-based generation of tyrosine hydroxylase-positive (TH+) dopaminergic neurons (DNs) is a powerful method for creating patient-specific in vitro models to elucidate mechanisms underlying Parkinson’s disease (PD) at the cellular and molecular level and to perform drug screening. However, currently available differentiation paradigms result in highly heterogeneous cell populations, often yielding a disappointing fraction (<50%) of the PD-relevant TH+ DNs. To facilitate the targeted analysis of this cell population and to characterize their electrophysiological properties, we employed CRISPR/Cas9 technology and generated an mCherry-based human TH reporter iPSC line. Subsequently, reporter iPSCs were subjected to dopaminergic differentiation using either a “floor plate protocol” generating DNs directly from iPSCs or an alternative method involving iPSC-derived neuronal precursors (NPC-derived DNs). To identify the strategy with the highest conversion efficiency to mature neurons, both cultures were examined for a period of 8 weeks after triggering neuronal differentiation by means of immunochemistry and single-cell electrophysiology. We confirmed that mCherry expression correlated with the expression of endogenous TH and that genetic editing did neither affect the differentiation process nor the endogenous TH expression in iPSC- and NPC-derived DNs. Although both cultures yielded identical proportions of TH+ cells (≈30%), whole-cell patch-clamp experiments revealed that iPSC-derived DNs gave rise to larger currents mediated by voltage-gated sodium and potassium channels, showed a higher degree of synaptic activity, and fired trains of mature spontaneous action potentials more frequently compared to NPC-derived DNs already after 2 weeks in differentiation. Moreover, spontaneous action potential firing was more frequently detected in TH+ neurons compared to the TH– cells, providing direct evidence that these two neuronal subpopulations exhibit different intrinsic electrophysiological properties. In summary, the data reveal substantial differences in the electrophysiological properties of iPSC-derived TH+ and TH– neuronal cell populations and that the “floor plate protocol” is particularly efficient in generating electrophysiologically mature TH+ DNs, which are the most vulnerable neuronal subtype in PD.
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Affiliation(s)
| | - Dorothea Voß
- Department of Anesthesiology and Intensive Care, Center of Brain, Behavior and Metabolism (CBBM), University of Lübeck, Lübeck, Germany
| | - Franca Vulinovic
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Britta Meier
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Ann-Katrin Hellberg
- Department of Anesthesiology and Intensive Care, Center of Brain, Behavior and Metabolism (CBBM), University of Lübeck, Lübeck, Germany
| | - Carla Nau
- Department of Anesthesiology and Intensive Care, Center of Brain, Behavior and Metabolism (CBBM), University of Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Enrico Leipold
- Department of Anesthesiology and Intensive Care, Center of Brain, Behavior and Metabolism (CBBM), University of Lübeck, Lübeck, Germany
- *Correspondence: Enrico Leipold,
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9
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Long S. Digital PCR: Methods and applications in infectious diseases. Methods 2022; 201:1-4. [DOI: 10.1016/j.ymeth.2022.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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10
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Competitiveness of Quantitative Polymerase Chain Reaction (qPCR) and Droplet Digital Polymerase Chain Reaction (ddPCR) Technologies, with a Particular Focus on Detection of Antibiotic Resistance Genes (ARGs). Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1030028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
With fast-growing polymerase chain reaction (PCR) technologies and various application methods, the technique has benefited science and medical fields. While having strengths and limitations on each technology, there are not many studies comparing the efficiency and specificity of PCR technologies. The objective of this review is to summarize a large amount of scattered information on PCR technologies focused on the two majorly used technologies: qPCR (quantitative polymerase chain reaction) and ddPCR (droplet-digital polymerase chain reaction). Here we analyze and compare the two methods for (1) efficiency, (2) range of detection and limitations under different disciplines and gene targets, (3) optimization, and (4) status on antibiotic resistance genes (ARGs) analysis. It has been identified that the range of detection and quantification limit varies depending on the PCR method and the type of sample. Careful optimization of target gene analysis is essential for building robust analysis for both qPCR and ddPCR. In our era where mutation of genes may lead to a pandemic of viral infectious disease or antibiotic resistance-induced health threats, this study hopes to set guidelines for meticulous detection, quantification, and analysis to help future prevention and protection of global health, the economy, and ecosystems.
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Rai SN, Singh P, Varshney R, Chaturvedi VK, Vamanu E, Singh MP, Singh BK. Promising drug targets and associated therapeutic interventions in Parkinson's disease. Neural Regen Res 2021; 16:1730-1739. [PMID: 33510062 PMCID: PMC8328771 DOI: 10.4103/1673-5374.306066] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/26/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022] Open
Abstract
Parkinson's disease (PD) is one of the most debilitating brain diseases. Despite the availability of symptomatic treatments, response towards the health of PD patients remains scarce. To fulfil the medical needs of the PD patients, an efficacious and etiological treatment is required. In this review, we have compiled the information covering limitations of current therapeutic options in PD, novel drug targets for PD, and finally, the role of some critical beneficial natural products to control the progression of PD.
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Affiliation(s)
| | - Payal Singh
- Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Ritu Varshney
- Department of Bioengineering and Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
| | | | - Emanuel Vamanu
- Faculty of Biotechnology, University of Agronomic Science and Veterinary Medicine, Bucharest, Romania
| | - M. P. Singh
- Centre of Biotechnology, University of Allahabad, Prayagraj, India
| | - Brijesh Kumar Singh
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
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12
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Current State-of-the-Art and Unresolved Problems in Using Human Induced Pluripotent Stem Cell-Derived Dopamine Neurons for Parkinson's Disease Drug Development. Int J Mol Sci 2021; 22:ijms22073381. [PMID: 33806103 PMCID: PMC8037675 DOI: 10.3390/ijms22073381] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022] Open
Abstract
Human induced pluripotent stem (iPS) cells have the potential to give rise to a new era in Parkinson's disease (PD) research. As a unique source of midbrain dopaminergic (DA) neurons, iPS cells provide unparalleled capabilities for investigating the pathogenesis of PD, the development of novel anti-parkinsonian drugs, and personalized therapy design. Significant progress in developmental biology of midbrain DA neurons laid the foundation for their efficient derivation from iPS cells. The introduction of 3D culture methods to mimic the brain microenvironment further expanded the vast opportunities of iPS cell-based research of the neurodegenerative diseases. However, while the benefits for basic and applied studies provided by iPS cells receive widespread coverage in the current literature, the drawbacks of this model in its current state, and in particular, the aspects of differentiation protocols requiring further refinement are commonly overlooked. This review summarizes the recent data on general and subtype-specific features of midbrain DA neurons and their development. Here, we review the current protocols for derivation of DA neurons from human iPS cells and outline their general weak spots. The associated gaps in the contemporary knowledge are considered and the possible directions for future research that may assist in improving the differentiation conditions and increase the efficiency of using iPS cell-derived neurons for PD drug development are discussed.
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13
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Kim DH, Lee J, Suh Y, Lee K. Necessity for Validation of Effectiveness of Selected Guide RNA In Silico for Application of CRISPR/Cas9. Mol Biotechnol 2021; 63:140-149. [PMID: 33386580 DOI: 10.1007/s12033-020-00290-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2020] [Indexed: 12/26/2022]
Abstract
Selection of guide RNA (gRNA) is important to increase the efficiency of gene editing in the CRISPR/Cas9 system. Due to the variation in actual efficiency of insertion/deletion (indel) mutation among selected gRNAs in silico, reliable methods for validation of efficiency of gRNA need to be developed. Three gRNAs with high on-target scores (72.0 for target 1, 65.4 for target 2, and 62.9 for target 3) were designed to target the quail retinol binding protein 7 (qRbp7) gene, and indel efficiencies were predicted by the Sanger sequencing and Inference of CRISPR Edits (ICE) analysis of sorted cell populations receiving the CRISPR/Cas9 vector. Unlike the order of on-target scores among 3 gRNAs, predicted rates of indel mutations were highest in gRNA2, intermediate in gRNA1, and lowest in gRNA3. This was confirmed by actual indel mutation rates, 51.8% in gRNA2, 31% in gRNA1, and 12.9% in gRNA3, which were calculated by sequencing individual allele cloned into a vector. These data showed a rapid and reliable method for estimation of the efficiency of selected gRNAs, providing a critical necessary step for successful gene editing for further applications.
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Affiliation(s)
- Dong-Hwan Kim
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Joonbum Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
- Interdisciplinary Ph.D. Program in Nutrition, The Ohio State University, Columbus, OH, 43210, USA
| | - Yeunsu Suh
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Kichoon Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA.
- Interdisciplinary Ph.D. Program in Nutrition, The Ohio State University, Columbus, OH, 43210, USA.
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