Common computational tools for analyzing CRISPR screens

Colic, Medina; Hart, Traver

doi:10.1042/etls20210222

Cited by 12 publications

(7 citation statements)

References 80 publications

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“…CRISPR-Cas tools can be utilized to screen GBM pathogenesis, providing insights into genes for drug targets, metastatic regulators, and reasons of drug resistance. There are computational tools and algorithms for the purpose of analyzing CRISPR screens [ 112 ]. CRISPR screening of E3 ubiquitin ligases identified ring-finger protein 185 as tumor GBM growth inhibitor, and moreover, discovered that promoter hypermethylation and miR-587T can repressed it [ 113 ].…”

Section: Crispr-cas Technique Against Glioblastomamentioning

confidence: 99%

Systems Medicine for Precise Targeting of Glioblastoma

Zeng¹,

Zeng

2023

Mol Biotechnol

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Glioblastoma (GBM) is a malignant cancer that is fatal even after standard therapy and the effects of current available therapeutics are not promising due its complex and evolving epigenetic and genetic profile. The mysteries that lead to GBM intratumoral heterogeneity and subtype transitions are not entirely clear. Systems medicine is an approach to view the patient in a whole picture integrating systems biology and synthetic biology along with computational techniques. Since the GBM oncogenesis involves genetic mutations, various therapies including gene therapeutics based on CRISPR-Cas technique, MicroRNAs, and implanted synthetic cells endowed with synthetic circuits against GBM with neural stem cells and mesenchymal stem cells acting as potential vehicles carrying therapeutics via the intranasal route, avoiding the risks of invasive methods in order to reach the GBM cells in the brain are discussed and proposed in this review. Systems medicine approach is a rather novel strategy, and since the GBM of a patient is complex and unique, thus to devise an individualized treatment strategy to tailor personalized multimodal treatments for the individual patient taking into account the phenotype of the GBM, the unique body health profile of the patient and individual responses according to the systems medicine concept might show potential to achieve optimum effects.

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Section: Crispr-cas Technique Against Glioblastomamentioning

confidence: 99%

Systems Medicine for Precise Targeting of Glioblastoma

Zeng¹,

Zeng

2023

Mol Biotechnol

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“…It concurrently identifies genes selected in both positive and negative directions, providing consistent outcomes across various experimental conditions ( 76 ). Distinct MAGeCK algorithms typically comprise two key steps (1): Analyzing raw read counts associated with sgRNAs by median normalization and (2) modeling the mean-variance relationship within replicates using a negative binomial distribution to assess the differences between treatments and controls ( 82 ).…”

Section: High-throughput Crispr Technologymentioning

confidence: 99%

High-throughput CRISPR technology: a novel horizon for solid organ transplantation

Li,

Chen,

et al. 2024

Front. Immunol.

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Organ transplantation is the gold standard therapy for end-stage organ failure. However, the shortage of available grafts and long-term graft dysfunction remain the primary barriers to organ transplantation. Exploring approaches to solve these issues is urgent, and CRISPR/Cas9-based transcriptome editing provides one potential solution. Furthermore, combining CRISPR/Cas9-based gene editing with an ex vivo organ perfusion system would enable pre-implantation transcriptome editing of grafts. How to determine effective intervention targets becomes a new problem. Fortunately, the advent of high-throughput CRISPR screening has dramatically accelerated the effective targets. This review summarizes the current advancements, utilization, and workflow of CRISPR screening in various immune and non-immune cells. It also discusses the ongoing applications of CRISPR/Cas-based gene editing in transplantation and the prospective applications of CRISPR screening in solid organ transplantation.

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“…The variety of screening platforms have caused the development of different algorithms for CRISPR analysis [ 111 ]. In a typical screen workflow, after the viral delivery of the library and the selection for transduced cells, deep sequencing of PCR-amplified genomic DNA from selected clones and unselected ones is performed to quantify the representation of sgRNAs and evaluate as to whether they are enriched or depleted.…”

Section: Bioinformatic Tools In Crispr Screening Of Hematological Dis...mentioning

confidence: 99%

“…The comparison of sgRNA abundance between conditions (e.g., beginning/end of an experiment or treated/untreated cells) is the key step to identify hit genes. For this purpose, each algorithm uses different methods [ 111 ].…”

Section: Bioinformatic Tools In Crispr Screening Of Hematological Dis...mentioning

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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Common computational tools for analyzing CRISPR screens

Cited by 12 publications

References 80 publications

Systems Medicine for Precise Targeting of Glioblastoma

Systems Medicine for Precise Targeting of Glioblastoma

High-throughput CRISPR technology: a novel horizon for solid organ transplantation

High-Throughput CRISPR Screening in Hematological Neoplasms

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