Tumor immunology CRISPR screening: present, past, and future

Dong, Matthew B.; Tang, Kaizhi; Zhou, Xiaoyu; Zhou, Jingjia J.; Chen, Sidi

doi:10.1016/j.trecan.2021.11.009

Cited by 23 publications

(12 citation statements)

References 129 publications

(160 reference statements)

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“…Presumably, this was associated with both the high level of Cas9 nuclease expression and the relatively high susceptibility of HEK cells to genomic editing. We believe that rapid and multifold increases in the expression of genome editors can be highly beneficial in CRISPR screens of cell lines that are difficult to genetically modify, since to date these screens are mostly used only for easily transfected tumor cell lines [ 28 , 29 ]. In this case, the large and difficult-to-deliver genes of the Cas9 programmable nuclease (or its modifications, CRISPRi, CRISPRa, CRISPR-BE, etc.)…”

Section: Discussionmentioning

confidence: 99%

A Novel Cre/lox71-Based System for Inducible Expression of Recombinant Proteins and Genome Editing

Karagyaur

Dyikanov

Tyurin‐Kuzmin

et al. 2022

Cells

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In this study, we developed a novel Cre/lox71-based system for the controlled transient expression of target genes. We used the bacteriophage P1 Cre recombinase, which harbors a short, highly specific DNA-binding site and does not have endogenous binding sites within mouse or human genomes. Fusing the catalytically inactive form of Cre recombinase and the VP64 transactivation domain (VP16 tetramer), we constructed the artificial transcription factor Cre-VP64. This transcription factor binds to the lox71 sites within the promoter region of the target gene and, therefore, upregulates its expression. We tested the Cre-VP64/lox71 system for the controlled expression of several genes, including growth factors and the genome editor CRISPR/Cas9, and obtained superior efficiency in the regulation of transgene expression, achieving a high expression level upon induction together with low basal activity. This system or its modified forms can be suggested as a novel effective tool for the transitory controlled expression of target genes for functional genomic studies, as well as for gene therapy approaches.

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Section: Discussionmentioning

confidence: 99%

A Novel Cre/lox71-Based System for Inducible Expression of Recombinant Proteins and Genome Editing

Karagyaur

Dyikanov

Tyurin‐Kuzmin

et al. 2022

Cells

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Section: Introductionmentioning

confidence: 99%

“…In the era of precision medicine, CRISPR–Cas screening has become a powerful tool to accelerate cancer research [ 4 , 16 ]. One of its main applications in oncology is to identify genotype-specific vulnerabilities with the aim of discovering novel potential drug targets [ 16 , 17 ]. Another application of CRISPR screening is investigating the underlying mechanisms of drug action, particularly in identifying genes that work synergistically with the drug or develop resistance to it [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

High-Throughput CRISPR Screening in Hematological Neoplasms

Ancos-Pintado

Bragado-García

Morales

et al. 2022

Cancers

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CRISPR is becoming an indispensable tool in biological research, revolutionizing diverse fields of medical research and biotechnology. In the last few years, several CRISPR-based genome-targeting tools have been translated for the study of hematological neoplasms. However, there is a lack of reviews focused on the wide uses of this technology in hematology. Therefore, in this review, we summarize the main CRISPR-based approaches of high throughput screenings applied to this field. Here we explain several libraries and algorithms for analysis of CRISPR screens used in hematology, accompanied by the most relevant databases. Moreover, we focus on (1) the identification of novel modulator genes of drug resistance and efficacy, which could anticipate relapses in patients and (2) new therapeutic targets and synthetic lethal interactions. We also discuss the approaches to uncover novel biomarkers of malignant transformations and immune evasion mechanisms. We explain the current literature in the most common lymphoid and myeloid neoplasms using this tool. Then, we conclude with future directions, highlighting the importance of further gene candidate validation and the integration and harmonization of the data from CRISPR screening approaches.

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“…The most notable examples come for targeted therapy, where a large consortium called the Cancer Dependency Map performed 1076 genome-wide CRISPR screens in 908 cell lines ( 4 , 5 ). Genome-wide CRISPR screening is also employed for immunotherapy ( 6 – 17 ). For example, pooled CRISPR screening in immune or cancer cells has been performed to evaluate immune regulatory molecules and identify potential therapeutic targets.…”

Section: Introductionmentioning

confidence: 99%

Computational Discovery of Cancer Immunotherapy Targets by Intercellular CRISPR Screens

et al. 2022

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Cancer immunotherapy targets the interplay between immune and cancer cells. In particular, interactions between cytotoxic T lymphocytes (CTLs) and cancer cells, such as PD-1 (PDCD1) binding PD-L1 (CD274), are crucial for cancer cell clearance. However, immune checkpoint inhibitors targeting these interactions are effective only in a subset of patients, requiring the identification of novel immunotherapy targets. Genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screening in either cancer or immune cells has been employed to discover regulators of immune cell function. However, CRISPR screens in a single cell type complicate the identification of essential intercellular interactions. Further, pooled screening is associated with high noise levels. Herein, we propose intercellular CRISPR screens, a computational approach for the analysis of genome-wide CRISPR screens in every interacting cell type for the discovery of intercellular interactions as immunotherapeutic targets. We used two publicly available genome-wide CRISPR screening datasets obtained while triple-negative breast cancer (TNBC) cells and CTLs were interacting. We analyzed 4825 interactions between 1391 ligands and receptors on TNBC cells and CTLs to evaluate their effects on CTL function. Intercellular CRISPR screens discovered targets of approved drugs, a few of which were not identifiable in single datasets. To evaluate the method’s performance, we used data for cytokines and costimulatory molecules as they constitute the majority of immunotherapeutic targets. Combining both CRISPR datasets improved the recall of discovering these genes relative to using single CRISPR datasets over two-fold. Our results indicate that intercellular CRISPR screens can suggest novel immunotherapy targets that are not obtained through individual CRISPR screens. The pipeline can be extended to other cancer and immune cell types to discover important intercellular interactions as potential immunotherapeutic targets.

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Tumor immunology CRISPR screening: present, past, and future

Cited by 23 publications

References 129 publications

A Novel Cre/lox71-Based System for Inducible Expression of Recombinant Proteins and Genome Editing

A Novel Cre/lox71-Based System for Inducible Expression of Recombinant Proteins and Genome Editing

High-Throughput CRISPR Screening in Hematological Neoplasms

Computational Discovery of Cancer Immunotherapy Targets by Intercellular CRISPR Screens

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