Using genome-wide CRISPR library screening with library resistant DCK to find new sources of Ara-C drug resistance in AML

Kurata, Morito; Rathe, Susan K.; Bailey, Nathanael G.; Aumann, Natalie K.; Jones, Justine M.; Veldhuijzen, G. Willemijn; Moriarity, Branden S.; Largaespada, David A.

doi:10.1038/srep36199

Cited by 59 publications

(49 citation statements)

References 24 publications

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“…In cancer chemotherapy, dCK is an enzyme needed for phosphorylation of several deoxyribonucleosides and their nucleoside analogs such as gemcitabine and cytarabine and is known as a rate limiting enzyme in activation of these drugs. Furthermore, in addition to a report that the deficiency of dCK is involved in resistance to gemcitabine and cytarabine, it has also been reported that these drugs show very high anti-tumor efficacy in cancer cells that overexpress dCK (14)(15)(16)(17). We found for the first time that the expression levels of dCK increase with the acquisition of resistance to cetuximabin this study.…”

Section: Discussionsupporting

confidence: 70%

Exploration of Proteins Involved in Acquisition of Resistance to Cetuximab

Nakamura¹,

Nagamine²,

Yashima³

et al. 2019

Indo J Pharm

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Anti-epidermal growth factor receptor (EGFR) monoclonal antibodies (Mabs) show high efficacy in about 50% of colorectal cancer (CRC) patients with wild-type KRAS. However, < 20% of patients with KRAS wild-type CRC have continued therapeutic effects with these agents, and acquired resistance to treatment has become a serious clinical problem. In this study, to clarify the factors related to acquisition of resistance to cetuximab (Cmab) and establish countermeasures against such acquired resistance, we conducted a comprehensive protein analysis via a proteomics approach using acquired resistance cell lines derived from Cmab-sensitive CRC cell lines and original cell lines. Cmab-acquired resistance cell lines were generated by continuous exposure of SW48 and C99 cell lines to Cmab. Expression of dCK and zinc finger and BTB domain-containing protein 41 (ZBTB41) increased more than 10-fold, and dual specificity protein phosphatase 3 (DUS3) expression decreased by less than 1/10 with acquisition of resistance to Cmab in both C99 and SW48 cell lines. Because overexpression of dCK is known as a positive indicator of efficacy of nucleoside analogs such as cytarabine or gemcitabine, it is considered that nucleoside analogs activated by dCK may be useful agents in treatment of cancers with acquired Cmab-resistance. In the future, we need to clarify the usefulness of these drugs for the treatment of Cmab resistant CRC and to assess the possibility of restoration of Cmab sensitivity by regulation of ZBTB41 and DUS3 expression.Keyword : cetuximab, colorectal cancer, acquired resistance, protein, dCK, ZBTB41

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Section: Discussionsupporting

confidence: 70%

Exploration of Proteins Involved in Acquisition of Resistance to Cetuximab

Nakamura¹,

Nagamine²,

Yashima³

et al. 2019

Indo J Pharm

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“…Those sgRNAs with significant changes in frequency in the pool after selection presumably target genes involved in promoting or repressing the selected phenotype. Pooled screens have been used to identify essential genes Wang et al 2014bWang et al , 2015Hart et al 2015) and genes that are involved in drug resistance (Koike-Yusa et al 2014;Shalem et al 2014;Wang et al 2014b;Hart et al 2015;Doench et al 2016;Kurata et al 2016), toxin susceptibility (Koike-Yusa et al 2014;Zhou et al 2014;Tao et al 2016), and immune response (Parnas et al 2015;Schmid-Burgk et al 2016). More recent pooled screens have used single cell sequencing to determine the impact of each sgRNA on the transcriptome rather than examining a cellular phenotype (Adamson et al 2016;Dixit et al 2016;Jaitin et al 2016;Datlinger et al 2017).…”

Section: Introductionmentioning

confidence: 99%

MicroRNA-focused CRISPR-Cas9 library screen reveals fitness-associated miRNAs

Kurata

Lin

2018

RNA

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MicroRNAs (miRNAs) are post-transcriptional gene regulators that play important roles in the control of cell fitness, differentiation, and development. The CRISPR-Cas9 gene-editing system is composed of the Cas9 nuclease in complex with a single guide RNA (sgRNA) and directs DNA cleavage at a predetermined site. Several CRISPR-Cas9 libraries have been constructed for genome-scale knockout screens of protein function; however, few libraries have included miRNA genes. Here we constructed a miRNA-focused CRISPR-Cas9 library that targets 1594 (85%) annotated human miRNA stem-loops. The sgRNAs in our LX-miR library are designed to have high on-target and low off-target activity, and each miRNA is targeted by four to five sgRNAs. We used this sgRNA library to screen for miRNAs that affect cell fitness of HeLa or NCI-N87 cells by monitoring the change in frequency of each sgRNA over time. By considering the expression in the tested cells and the dysregulation of the miRNAs in cancer specimens, we identified five HeLa pro-fitness and cervical cancer up-regulated miRNAs (miR-31-5p, miR-92b-3p, miR-146b-5p, miR-151a-3p, and miR-194-5p). Similarly, we identified six NCI-N87 pro-fitness and gastric cancer up-regulated miRNAs (miR-95-3p, miR-181a-5p, miR-188-5p, miR-196b-5p, miR-584-5p, and miR-1304-3p), as well as three anti-fitness and down-regulated miRNAs (let-7a-3p, miR-100-5p, and miR-149-5p). Some of those miRNAs are known to be oncogenic or tumor-suppressive, but others are novel. Taken together, the LX-miR library is useful for genome-wide unbiased screening to identify miRNAs important for cellular fitness and likely to be useful for other functional screens.

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“…Previously, studies using CRISPR-Cas9 libraries were published. Most of these studies used the same type of genome-wide library, GeCKO CRISPR Library version 1 or 2, comprising of >120,000 sgRNAs targeting nearly the entire genome (53)(54)(55)(56). For example, Sustic et al identified the endoplasmic reticulum to nucleus signaling 1 (ERN1)-JNK-JUN pathway as a potential target for improving the anti-cancer effects of MET inhibitors in KRAS-mutated colon cancer (56).…”

Section: Dropout Viability Screening Under Drug Treatmentmentioning

confidence: 99%

Phenotypic screening using large‑scale genomic libraries to identify drug targets for the treatment of cancer (Review)

Sato

2020

Oncol Lett

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During malignant progression to overt cancer cells, normal cells accumulate multiple genetic and non-genetic changes, which result in the acquisition of various oncogenic properties, such as uncontrolled proliferation, drug resistance, invasiveness, anoikis-resistance, the ability to bypass oncogene-induced senescence and cancer stemness. To identify potential novel drug targets contributing to these malignant phenotypes, researchers have performed large-scale genomic screening using various in vitro and in vivo screening models and identified numerous promising cancer drug target genes. However, there are issues with these identified genes, such as low reproducibility between different datasets. In the present study, the recent advances in the functional screening for identification of cancer drug target genes are summarized, and current issues and future perspectives are discussed.

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Using genome-wide CRISPR library screening with library resistant DCK to find new sources of Ara-C drug resistance in AML

Cited by 59 publications

References 24 publications

Exploration of Proteins Involved in Acquisition of Resistance to Cetuximab

Exploration of Proteins Involved in Acquisition of Resistance to Cetuximab

MicroRNA-focused CRISPR-Cas9 library screen reveals fitness-associated miRNAs

Phenotypic screening using large‑scale genomic libraries to identify drug targets for the treatment of cancer (Review)

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