Identification of Cell Type-Specific Effects of DNMT3A Mutations on Relapse in Acute Myeloid Leukemia

Bae, Seo-Gyeong; Kim, Hyeoung-Joon; Kim, Mi Yeon; Kim, Dennis Dong Hwan; Shin, So-I; Ahn, Jae-Sook; Park, Jihwan

doi:10.14348/molcells.2023.0093

Cited by 4 publications

(2 citation statements)

References 79 publications

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“…[32][33][34] At single-cell resolution, PCR-or hybridization-based targeted sequencing methods have been applied, but previous studies applied targeted sequencing only for several tens to hundreds of transcripts, which is not enough to cover the entire lncRNA transcriptome. [35][36][37][38] We established a high-throughput method to selectively enrich and characterize over 10,000 lncRNAs in thousands of single cells. This method allowed us to discover various cell type-specific lncRNAs.…”

Section: Introductionmentioning

confidence: 99%

Cell Type– and Age-Specific Expression of lncRNAs across Kidney Cell Types

Kim,

Shin,

Jung

et al. 2024

JASN

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Background Accumulated evidence demonstrates that long non-coding RNAs (lncRNAs) regulate cell differentiation and homeostasis, influencing kidney aging and disease. Despite their versatility, the function of lncRNA remains poorly understood due to the lack of a reference map of lncRNA transcriptome in various cell types. Methods In this study, we employed a targeted single-cell RNA sequencing (scRNA-seq) method to enrich and characterize lncRNAs in individual cells. We applied this method to various mouse tissues, including normal and aged kidneys. Results Through tissue-specific clustering analysis, we identified cell type-specific lncRNAs that showed a high correlation with known cell-type marker genes. Furthermore, we constructed gene regulatory networks (GRNs) to explore the functional roles of differentially expressed lncRNAs in each cell type. In the kidney, we observed dynamic expression changes of lncRNAs during aging, with specific changes in glomerular cells. These cell type- and age-specific expression patterns of lncRNAs provide insights into their potential roles in regulating cellular processes, such as immune response and energy metabolism, during kidney aging. Conclusions Our study sheds light on the comprehensive landscape of lncRNA expression and function and provides a valuable resource for future analysis of lncRNAs (https://gist-fgl.github.io/sc-lncrna-atlas/).

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Section: Introductionmentioning

confidence: 99%

Cell Type– and Age-Specific Expression of lncRNAs across Kidney Cell Types

Kim,

Shin,

Jung

et al. 2024

JASN

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“…CRISPR/Cas9-mediated knockout is widely used because of its versatility and simplicity compared to traditional systems, such as zinc-finger nucleases and transcription activator-like effector nucleases. CRISPR-knockout cell lines are powerful tools for studying gene regulation, function, and downstream pathways in cell biology, genetics, and cancer biology ( Bae et al, 2023 , Carroll, 2023 , Zou et al, 2018 ). Several strategies are available for enhancing the efficiency and precision of CRISPR/Cas9 knockout, and these involve the consideration of (1) the number of sgRNAs transfected into cell lines and (2) the type of CRISPR/Cas9: plasmid, mRNA, and protein.…”

Section: Introductionmentioning

confidence: 99%