Applications of CRISPR technologies to the development of gene and cell therapy
BMB Rep. 2024 Jan 5:6122. Online ahead of print.ABSTRACTAdvancements in gene and cell therapy have resulted in novel therapeutics for diseases previously considered incurable or challenging to treat. Among the various contributing technologies, genome editing stands out as one of the most crucial for the progress in gene and cell therapy. The discovery of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and the subsequent evolution of genetic engineering technology have markedly expanded the field of target-specific gene editing. Originally studied in the immune systems of bacteria and archaea, the CRISPR...
Source: BMB Reports - January 5, 2024 Category: Biochemistry Authors: Chul-Sung Park Omer Habib Younsu Lee Junho K Hur Source Type: research

Mitochondrial genome editing: strategies, challenges, and applications
BMB Rep. 2024 Jan 5:6125. Online ahead of print.ABSTRACTMitochondrial DNA (mtDNA), a multicopy genome found in mitochondria, is crucial for oxidative phosphorylation. Mutations in mtDNA can lead to severe mitochondrial dysfunction in tissues and organs with high energy demand. MtDNA mutations are closely associated with mitochondrial and age-related disease. To better understand the functional role of mtDNA and work toward developing therapeutics, it is essential to advance technology that is capable of manipulating the mitochondrial genome. This review discusses ongoing efforts in mitochondrial genome editing with mtDNA n...
Source: BMB Reports - January 5, 2024 Category: Biochemistry Authors: Kayeong Lim Source Type: research

PDAT1 genome editing reduces hydroxy fatty acid production in transgenic Arabidopsis
In this study, we investigated changes in HFA content when endogenous Arabidopsis PDAT1 (AtPDAT1) of the P327 line was edited using the CRISPR/Cas9 technique. The successful mutation resulted in three independent lines with different mutation patterns, which were transmitted until the T4 generation. Fatty acid analysis of the seeds showed that HFA content decreased in all three mutant lines. These findings indicate that AtPDAT1 as well as RcPDAT1-2 in the P327 line are involved in transferring and increasing HFAs to triacylglycerol.PMID:38053289 (Source: BMB Reports)
Source: BMB Reports - December 6, 2023 Category: Biochemistry Authors: Mid-Eum Park Hyun Uk Kim Source Type: research

Harnessing CRISPR-Cas adaptation for RNA recording and beyond
BMB Rep. 2023 Dec 6:5906. Online ahead of print.ABSTRACTProkaryotes encode clustered regularly interspaced short palindromic repeat (CRISPR) arrays and CRISPR-associated (Cas) genes as an adaptive immune machinery. CRISPR-Cas systems effectively protect hosts from the invasion of foreign enemies, such as bacteriophages and plasmids. During a process called 'adaptation', non-self-nucleic acid fragments are acquired as spacers between repeats in the host CRISPR array, to establish immunological memory. The highly conserved Cas1-Cas2 complexes function as molecular recorders to integrate spacers in a time course manner, which...
Source: BMB Reports - December 6, 2023 Category: Biochemistry Authors: Gyeong-Seok Oh Seongjin An Sungchul Kim Source Type: research

Genome-wide in-locus epitope tagging of Arabidopsis proteins using prime editors
BMB Rep. 2023 Dec 6:5914. Online ahead of print.ABSTRACTPrime editors (PEs), which are CRISPR-Cas9 nickase (H840A)-reverse transcriptase fusion proteins programmed with prime editing guide RNAs (pegRNAs), can not only edit bases but also install transversions, insertions, or deletions without both donor DNA and double-strand breaks at the target DNA. As the demand for in-locus tagging is increasing, to reflect gene expression dynamics influenced by endogenous genomic contexts, we demonstrated that PEs can be used to introduce the hemagglutinin (HA) epitope tag to a target gene locus, enabling molecular and biochemical stud...
Source: BMB Reports - December 6, 2023 Category: Biochemistry Authors: Cheljong Hong Jun Hee Han Gue-Ho Hwang Sangsu Bae Pil Joon Seo Source Type: research

CRISPR base editor-based targeted random mutagenesis (BE-TRM) toolbox for directed evolution
BMB Rep. 2023 Dec 6:5950. Online ahead of print.ABSTRACTDirected evolution (DE) of desired locus by targeted random mutagenesis (TRM) tools is a powerful approach for generating genetic variations with novel or improved functions, particularly in complex genomes. TRM-based DE involves developing a mutant library of targeted DNA sequences and screening the variants for the desired properties. However, DE methods have for a long time been confined to bacteria and yeasts. Lately, CRISPR/Cas and DNA deaminase-based tools that circumvent enduring barriers such as longer life cycle, small library sizes, and low mutation rates ha...
Source: BMB Reports - December 6, 2023 Category: Biochemistry Authors: Rahul Mahadev Shelake Dibyajyoti Pramanik Jae-Yean Kim Source Type: research

Highly efficient genome editing via CRISPR-Cas9 ribonucleoprotein (RNP) delivery in mesenchymal stem cells
In this study, we compared and optimized plasmid DNA and RNP approaches for efficient genome engineering in MSCs. The RNP-mediated approach enabled genome editing with high indel frequency and low cytotoxicity in MSCs. By utilizing Cas9 RNPs, we successfully generated B2M-knockout MSCs, which reduced T-cell differentiation, and improved MSC survival. Furthermore, this approach enhanced the immunomodulatory effect of IFN-r priming. These findings indicate that the RNP-mediated engineering of MSC genomes can achieve high efficiency, and engineered MSCs offer potential as a promising therapeutic strategy.PMID:38053293 (Source: BMB Reports)
Source: BMB Reports - December 6, 2023 Category: Biochemistry Authors: A Reum Han Ha Rim Shin Jiyeon Kweon Soo Been Lee Sang Eun Lee Eun-Young Kim Eun-Ju Chang Yongsub Kim Seong Who Kim Source Type: research

Recent advances in genome engineering by CRISPR technology
BMB Rep. 2023 Dec 6:6038. Online ahead of print.ABSTRACTDue to the development of CRISPR technology, the era of effective editing of target genes has arrived. However, the offtarget problem that occurs when recognizing target DNA due to the inherent nature of CRISPR components remains the biggest task to be overcome in the future. In this review, the principle of inducing such unintended off-target editing is analyzed from the structural aspect of CRISPR, and the methodology that has been developed to reduce off-target editing until now is summarized.PMID:38053294 (Source: BMB Reports)
Source: BMB Reports - December 6, 2023 Category: Biochemistry Authors: Youngsik Lee Yeounsun Oh Seung Hwan Lee Source Type: research

Research progress on hydrogel-based drug therapy in melanoma immunotherapy
BMB Rep. 2023 Dec 6:6043. Online ahead of print.ABSTRACTMelanoma is one of the most aggressive skin tumors, and conventional treatment modalities are not effective in treating advanced melanoma. Although immunotherapy is an effective treatment for melanoma, it has disadvantages, such as a poor response rate and serious systemic immune-related toxic side effects. The main solution to this problem is the use of biological materials such as hydrogels to reduce these side effects and amplify the immune killing effect against tumor cells. Hydrogels have great advantages as local slow-release drug carriers, including the ability...
Source: BMB Reports - December 6, 2023 Category: Biochemistry Authors: Wei He Yanqin Zhang Yi Qu Mengmeng Liu Guodong Li Luxiang Pan Xinyao Xu Gege Shi Qiang Hao Fen Liu Yuan Gao Source Type: research

Integrative analysis of microRNA-mediated mitochondrial dysfunction in hippocampal neural progenitor cell death in relation with Alzheimer ’s disease
This study aims to elucidate the mechanisms through which miRNAs regulate HCN cell death and their potential involvement in neurodegenerative disorder. We performed a comprehensive microarray-based analysis to investigate changes in miRNA expression in insulin-deprived HCN cells, as an in vitro model for cognitive impairment. Remarkably, miR-150-3p, miR-323-5p, and miR-370-3p which increased significantly over time following insulin withdrawal, induced pronounced mitochondrial fission and dysfunction, ultimately leading to HCN cell death. Notably, these miRNAs collectively target the mitochondrial fusion protein OPA1, with...
Source: BMB Reports - December 6, 2023 Category: Biochemistry Authors: A Reum Han Tae Kwon Moon Im Kyeung Kang Dae Bong Yu Yechan Kim Cheolhwan Byon Sujeong Park Hae Lin Kim Kyoung Jin Lee Heuiran Lee Ha-Na Woo Seong Who Kim Source Type: research

Current Status and Future of Gene Engineering in Livestock
BMB Rep. 2023 Dec 6:6102. Online ahead of print.ABSTRACTThe application of gene engineering in livestock is necessary for various reasons, such as increasing productivity and producing disease resistance and biomedicine models. Overall, gene engineering provides benefits to the agricultural and research aspects, and humans. In particular, productivity can be increased by producing livestock with enhanced growth and improved feed conversion efficiency. In addition, the application of the disease resistance models prevents the spread of infectious diseases, which reduces the need for treatment, such as the use of antibiotics...
Source: BMB Reports - December 6, 2023 Category: Biochemistry Authors: Dong-Hyeok Kwon Gyeong-Min Gim Soo-Young Yum Goo Jang Source Type: research

PDAT1 genome editing reduces hydroxy fatty acid production in transgenic Arabidopsis
In this study, we investigated changes in HFA content when endogenous Arabidopsis PDAT1 (AtPDAT1) of the P327 line was edited using the CRISPR/Cas9 technique. The successful mutation resulted in three independent lines with different mutation patterns, which were transmitted until the T4 generation. Fatty acid analysis of the seeds showed that HFA content decreased in all three mutant lines. These findings indicate that AtPDAT1 as well as RcPDAT1-2 in the P327 line are involved in transferring and increasing HFAs to triacylglycerol.PMID:38053289 (Source: BMB Reports)
Source: BMB Reports - December 6, 2023 Category: Biochemistry Authors: Mid-Eum Park Hyun Uk Kim Source Type: research

Harnessing CRISPR-Cas adaptation for RNA recording and beyond
BMB Rep. 2023 Dec 6:5906. Online ahead of print.ABSTRACTProkaryotes encode clustered regularly interspaced short palindromic repeat (CRISPR) arrays and CRISPR-associated (Cas) genes as an adaptive immune machinery. CRISPR-Cas systems effectively protect hosts from the invasion of foreign enemies, such as bacteriophages and plasmids. During a process called 'adaptation', non-self-nucleic acid fragments are acquired as spacers between repeats in the host CRISPR array, to establish immunological memory. The highly conserved Cas1-Cas2 complexes function as molecular recorders to integrate spacers in a time course manner, which...
Source: BMB Reports - December 6, 2023 Category: Biochemistry Authors: Gyeong-Seok Oh Seongjin An Sungchul Kim Source Type: research

Genome-wide in-locus epitope tagging of Arabidopsis proteins using prime editors
BMB Rep. 2023 Dec 6:5914. Online ahead of print.ABSTRACTPrime editors (PEs), which are CRISPR-Cas9 nickase (H840A)-reverse transcriptase fusion proteins programmed with prime editing guide RNAs (pegRNAs), can not only edit bases but also install transversions, insertions, or deletions without both donor DNA and double-strand breaks at the target DNA. As the demand for in-locus tagging is increasing, to reflect gene expression dynamics influenced by endogenous genomic contexts, we demonstrated that PEs can be used to introduce the hemagglutinin (HA) epitope tag to a target gene locus, enabling molecular and biochemical stud...
Source: BMB Reports - December 6, 2023 Category: Biochemistry Authors: Cheljong Hong Jun Hee Han Gue-Ho Hwang Sangsu Bae Pil Joon Seo Source Type: research

CRISPR base editor-based targeted random mutagenesis (BE-TRM) toolbox for directed evolution
BMB Rep. 2023 Dec 6:5950. Online ahead of print.ABSTRACTDirected evolution (DE) of desired locus by targeted random mutagenesis (TRM) tools is a powerful approach for generating genetic variations with novel or improved functions, particularly in complex genomes. TRM-based DE involves developing a mutant library of targeted DNA sequences and screening the variants for the desired properties. However, DE methods have for a long time been confined to bacteria and yeasts. Lately, CRISPR/Cas and DNA deaminase-based tools that circumvent enduring barriers such as longer life cycle, small library sizes, and low mutation rates ha...
Source: BMB Reports - December 6, 2023 Category: Biochemistry Authors: Rahul Mahadev Shelake Dibyajyoti Pramanik Jae-Yean Kim Source Type: research