Surface antigen-guided CRISPR screens identify regulators of myeloid leukemia differentiation

Wang, Eric; Zhou, Hua; Nadorp, Bettina; Cayanan, Geraldine; Chen, Xufeng; Yeaton, Anna; Nomikou, Sofia; Witkowski, Matthew T; Narang, Sonali; Kloetgen, Andreas; Thandapani, Palaniraja; Ravn-Boess, Niklas; Tsirigos, Aristotelis; Aifantis, Iannis

doi:10.1016/j.stem.2020.12.005

Cited by 43 publications

(37 citation statements)

References 95 publications

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“…This pool of perturbed cells can then be subjected to a selective pressure, with phenotypes assigned to genetic perturbations by sequencing. Forward genetic screens provide powerful tools for the identification of cancer dependencies, essential cellular machinery, differentiation factors, and suppressors of genetic diseases (3)(4)(5)(6). In parallel, dramatic improvements in molecular phenotyping now allow for single-cell readouts of epigenetic, transcriptomic, proteomic, and imaging information (7).…”

Section: Main Textmentioning

confidence: 99%

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

Replogle¹,

Saunders²,

Pogson³

et al. 2021

Preprint

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A central goal of genetics is to define the relationships between genotypes and phenotypes. High-content phenotypic screens such as Perturb-seq (pooled CRISPR-based screens with single-cell RNA-sequencing readouts) enable massively parallel functional genomic mapping but, to date, have been used at limited scales. Here, we perform genome-scale Perturb-seq targeting all expressed genes with CRISPR interference (CRISPRi) across >2.5 million human cells and present a framework to power biological discovery with the resulting genotype-phenotype map. We use transcriptional phenotypes to predict the function of poorly-characterized genes, uncovering new regulators of ribosome biogenesis (including CCDC86, ZNF236, and SPATA5L1), transcription (C7orf26), and mitochondrial respiration (TMEM242). In addition to assigning gene function, single-cell transcriptional phenotypes allow for in-depth dissection of complex cellular phenomena – from RNA processing to differentiation. We leverage this ability to systematically identify the genetic drivers and consequences of aneuploidy and to discover an unanticipated layer of stress-specific regulation of the mitochondrial genome. Our information-rich genotype-phenotype map reveals a multidimensional portrait of gene function and cellular behavior.

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Section: Main Textmentioning

confidence: 99%

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

Replogle¹,

Saunders²,

Pogson³

et al. 2021

Preprint

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show abstract

“…A previous study demonstrated a convergence between AML and SCLC with respect to therapeutic ( vulnerabilities 47 and our data on the LSD1-ZFP36L1 pathway in SCLC and AML is another example of their convergence. Interestingly, recent data from an unbiased CRISPR/Cas9 screen to identify genes that promote differentiation in AML found that LSD1 and the ZFP36L1 paralog, ZFP36L2, were required to sustain AML dedifferentiation 48 . Analogous to our findings showing that ZFP36L1 promotes non-neuroendocrine differentiation in SCLC, they found that AMLs induce ZFP36L1 to differentiate.…”

Section: Discussionmentioning

confidence: 99%

Regulation of Neuroendocrine Plasticity by the RNA-Binding Protein ZFP36L1

Chen

Durmaz

et al. 2021

Preprint

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Some small cell lung cancers (SCLCs) are highly sensitive to inhibitors of the histone demethylase LSD1. LSD1 inhibitors are thought to induce their anti-proliferative effects by blocking neuroendocrine differentiation, but the mechanisms by which LSD1 controls the SCLC neuroendocrine phenotype are not well understood. To identify genes required for LSD1 inhibitor sensitivity in SCLC, we performed a positive selection genome-wide CRISPR/Cas9 loss of function screen and found that ZFP36L1, an mRNA-binding protein that destabilizes mRNAs, is required for LSD1 inhibitor sensitivity. LSD1 binds and represses ZFP36L1 and upon LSD1 inhibition, ZFP36L1 expression is restored, which is sufficient to block the SCLC neuroendocrine differentiation phenotype and induce a non-neuroendocrine inflammatory phenotype. Mechanistically, ZFP36L1 binds and destabilizes SOX2 and INSM1 mRNAs, two transcription factors that are required for SCLC neuroendocrine differentiation. This work identifies ZFP36L1 as an LSD1 target gene that controls the SCLC neuroendocrine phenotype and demonstrates that modulating mRNA stability of lineage transcription factors controls neuroendocrine to non-neuroendocrine plasticity.

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“…But epigenomic studies done in patients with AML have found enhancer modules near ZFP36L2 that are associated with distinct AML cell states. Thus, there are coordinated epigenetic and post-transcriptional mechanisms involved in leukemic differentiation 17 . CRISPR/Cas9 technology allowed the excision of the interferon regulatory factor-1 (IRF-1) gene from HL-60 cells.…”

Section: Fbxo1allows the Progression Of Mds To Aml 8 2 Bend3mentioning

confidence: 99%

The high-performance technology CRISPR/Cas9 improves knowledge and management of acute myeloid leukemia

Mihăilă¹,

Topircean²

2021

BIOMED PAP

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Knowledge on acute myeloid leukemia pathogenesis and treatment has progressed recently, but not enough to provide ideal management. Improving the prognosis of acute myeloid leukemia patients depends on advances in molecular biology for the detection of new therapeutic targets and the production of effective drugs. The CRISPR/Cas9 technology allows gene insertions and deletions and it is the first step in investigating the function of their encoded proteins. Thus, new experimental models have been developed and progress has been made in understanding protein metabolism, antitumor activity, leukemic cell maintenance, differentiation, growth, apoptosis, and self-renewal, the combined pathogenetic mechanisms involved in leukemogenesis. The CRISPR/Cas9 system is used to understand drug resistance and find solutions to overcome it. The therapeutic progress achieved using the CRISPR/Cas9 system is remarkable. FST gene removal inhibited acute myeloid leukemia cell growth. Lysine acetyltransferase gene deletion contributed to decreased proliferation rate, increased apoptosis, and favored differentiation of acute myelid leukemia cells carrying MLL-X gene fusions. The removal of CD38 gene from NK cells decreased NK fratricidal cells contributing to increased efficacy of new CD38 CAR-NK cells to target leukemic blasts. BCL2 knockout has synergistic effects with FLT3 inhibitors. Exportin 1 knockout is synergistic with midostaurin treatment in acute myeloid leukemia with FLT3-ITD mutation. Using the results of CRISPR/Cas9 libraries and technology application will allow us to get closer to achieving the goal of curing acute myeloid leukemia in the coming decades.

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Surface antigen-guided CRISPR screens identify regulators of myeloid leukemia differentiation

Cited by 43 publications

References 95 publications

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

Regulation of Neuroendocrine Plasticity by the RNA-Binding Protein ZFP36L1

The high-performance technology CRISPR/Cas9 improves knowledge and management of acute myeloid leukemia

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