Genome-scale CRISPR-Cas9 knockout screening in nasopharyngeal carcinoma for radiosensitive and radioresistant genes

Zhou, Ziyan; Chen, Gang; Shen, Mo; Li, Jixi; Liu, Kang; Liu, Ming; Shi, Shuo; Yang, Dong; Chen, Wei; Chen, Sixia; Yin, Yuanxiu; Qin, Yating; Su, Xuejin; Chen, Weimin; Kang, Min

doi:10.1016/j.tranon.2023.101625

Cited by 6 publications

(3 citation statements)

References 53 publications

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“…These findings suggest that mef2d and cks1b may regulate cell proliferation and differentiation in skeletal muscle, thereby promoting individual growth. Furthermore, although snx22 has been proposed as a potential radioresistant gene in nasopharyngeal carcinoma ( Zhou et al, 2023 ), its precise role in growth-related processes requires further investigation. Collectively, these results underscore the robustness and reliability of GWAS focused on growth traits in P. leopardus .…”

Section: Discussionmentioning

confidence: 99%

Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper (<i>Plectropomus leopardus</i>)

Wu,

Zeng,

Han

et al. 2024

Zoological Research

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The leopard coral grouper ( Plectropomus leopardus ) is a species of significant economic importance. Although artificial cultivation of P. leopardus has thrived in recent decades, the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data. In this study, we identified over 8.73 million single nucleotide polymorphisms (SNPs) through whole-genome resequencing of 326 individuals spanning six distinct groups. Furthermore, we categorized 226 individuals with high-coverage sequencing depth (≥14×) into eight clusters based on their genetic profiles and phylogenetic relationships. Notably, four of these clusters exhibited pronounced genetic differentiation compared with the other populations. To identify potentially advantageous loci for P. leopardus , we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity ( θπ ) and fixation index ( F ST ) in these four clusters. Using these high-coverage resequencing data, we successfully constructed the first haplotype reference panel specific to P. leopardus . This achievement holds promise for enabling high-quality, cost-effective imputation methods. Additionally, we combined low-coverage sequencing data with imputation techniques for a genome-wide association study, aiming to identify candidate SNP loci and genes associated with growth traits. A significant concentration of these genes was observed on chromosome 17, which is primarily involved in skeletal muscle and embryonic development and cell proliferation. Notably, our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs, showing potential for genetic selective breeding efforts. These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P. leopardus .

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Section: Discussionmentioning

confidence: 99%

Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper (<i>Plectropomus leopardus</i>)

Wu,

Zeng,

Han

et al. 2024

Zoological Research

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“…A short-term and long-term heat stress experiment on honeybees ( Apis cerana ) has suggested that the stress-induced response of DNAJA1, and the decrease of heat tolerance after the knockdown of DNAJA1, proved its key role in heat stress resistances [ 77 ]. There are few reports on DNAJC17, but as a member of the heat shock protein (HSP40) family, it is speculated that may regulate cell proliferation [ 78 ]. Similar to Trpm2 , the differential expression pattern of Dnajc17, Dnaja1 in C. gigas , and C. angulata after heat stress suggested that the upregulation of these genes in C. angulata may play a critical role in mitigating the effects of heat stress.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Analysis of Heat Tolerance in F2 Progeny from the Hybridization between Two Congeneric Oyster Species

Du,

Jiang,

Wang

et al. 2023

IJMS

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As the world’s largest farmed marine animal, oysters have enormous economic and ecological value. However, mass summer mortality caused by high temperature poses a significant threat to the oyster industry. To investigate the molecular mechanisms underlying heat adaptation and improve the heat tolerance ability in the oyster, we conducted genome-wide association analysis (GWAS) analysis on the F2 generation derived from the hybridization of relatively heat-tolerant Crassostrea angulata ♀ and heat-sensitive Crassostrea gigas ♂, which are the dominant cultured species in southern and northern China, respectively. Acute heat stress experiment (semi-lethal temperature 42 °C) demonstrated that the F2 population showed differentiation in heat tolerance, leading to extremely differentiated individuals (approximately 20% of individuals die within the first four days with 10% survival after 14 days). Genome resequencing and GWAS of the two divergent groups had identified 18 significant SNPs associated with heat tolerance, with 26 candidate genes located near these SNPs. Eleven candidate genes that may associate with the thermal resistance were identified, which were classified into five categories: temperature sensor (Trpm2), transcriptional factor (Gata3), protein ubiquitination (Ube2h, Usp50, Uchl3), heat shock subfamily (Dnajc17, Dnaja1), and transporters (Slc16a9, Slc16a14, Slc16a9, Slc16a2). The expressional differentiation of the above genes between C. gigas and C. angulata under sublethal temperature (37 °C) further supports their crucial role in coping with high temperature. Our results will contribute to understanding the molecular mechanisms underlying heat tolerance, and provide genetic markers for heat-resistance breeding in the oyster industry.

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“…Nine genes were found to be associated with radiosensitivity of NPC cells (C666-1R, 6-8FR). Fanconi anemia pathway and the TGF-β signaling pathway were reported to be important contributors for radiosensitivity [136]. In the nervous system, neuroblastoma tumorigenesis was investigated via CRISPR genome-wide knockout screening, showed that ubiquitin-specific proteases (USPs) stabilize and increase half-life of repressor element-1 silencing transcription factor (REST), indicating its critical role in neuroblastoma generation [137].…”

Section: The Utilization Of Crispr-cas9 In Investigating Drug Resista...mentioning

confidence: 99%

CRISPR-Cas and CRISPR-based screening system for precise gene editing and targeted cancer therapy

Qin,

Deng,

Wen

et al. 2024

J Transl Med

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Target cancer therapy has been developed for clinical cancer treatment based on the discovery of CRISPR (clustered regularly interspaced short palindromic repeat) -Cas system. This forefront and cutting-edge scientific technique improves the cancer research into molecular level and is currently widely utilized in genetic investigation and clinical precision cancer therapy. In this review, we summarized the genetic modification by CRISPR/Cas and CRISPR screening system, discussed key components for successful CRISPR screening, including Cas enzymes, guide RNA (gRNA) libraries, target cells or organs. Furthermore, we focused on the application for CAR-T cell therapy, drug target, drug screening, or drug selection in both ex vivo and in vivo with CRISPR screening system. In addition, we elucidated the advantages and potential obstacles of CRISPR system in precision clinical medicine and described the prospects for future genetic therapy.In summary, we provide a comprehensive and practical perspective on the development of CRISPR/Cas and CRISPR screening system for the treatment of cancer defects, aiming to further improve the precision and accuracy for clinical treatment and individualized gene therapy.

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Genome-scale CRISPR-Cas9 knockout screening in nasopharyngeal carcinoma for radiosensitive and radioresistant genes

Cited by 6 publications

References 53 publications

Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper (<i>Plectropomus leopardus</i>)

Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper (<i>Plectropomus leopardus</i>)

Genome-Wide Association Analysis of Heat Tolerance in F2 Progeny from the Hybridization between Two Congeneric Oyster Species

CRISPR-Cas and CRISPR-based screening system for precise gene editing and targeted cancer therapy

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