Genome-wide pooled CRISPR screening in neurospheres

Tanaz Abid, Amy B. Goodale, Zohra Kalani, Meghan Wyatt, Elizabeth M. Gonzalez, Kevin Ning Zhou, Kenin Qian, Dana Novikov, Alexandra-Larisa Condurat, Pratiti Bandopadhayay, Federica Piccioni, Nicole S. Persky, David E. Root

Published: 2023-06-06 DOI: 10.1038/s41596-023-00835-6

CRISPR screening

neurospheres

spheroid cultures

genome-wide

cell line screening

AI 解读

Supplementary information

Supplementary Information

Supplementary Methods and Figs. 1 and 2.

Supplementary Table

Raw data for Fig. 4b

Using high-resolution microscopy data to generate realistic structures for electromagnetic FDTD simulations from complex biological models

Experimental modulation of physiological force application on leg joint neurons in intactDrosophila melanogaster

Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility

Identification, isolation and analysis of human gut-associated lymphoid tissues

Development of RNA G-quadruplex (rG4)-targetingl-RNA aptamers by rG4-SELEX

Self-assembled ultraflexible probes for long-term neural recordings and neuromodulation

Hyperpolarized water as universal sensitivity booster in biomolecular NMR

Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments

An analytical workflow for dynamic characterization and quantification of metal-bearing nanomaterials in biological matrices

A flow cytometry-based protocol for syngenic isolation of neurovascular unit cells from mouse and human tissues

查看全部

Sections

Figures

References

Supplementary information

Jensen, C. & Teng, Y. Is it time to start transitioning from 2D to 3D cell culture? Front. Mol. Biosci. 7, 33 (2020).
Cui, X., Hartanto, Y. & Zhang, H. Advances in multicellular spheroids formation. J. R. Soc. Interface 14, 20160877 (2017).
Han, K. et al. CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities. Nature 580, 136–141 (2020).
Takahashi, N. et al. 3D culture models with CRISPR screens reveal hyperactive NRF2 as a prerequisite for spheroid formation via regulation of proliferation and ferroptosis. Mol. Cell 80, 828–844.e6 (2020).
Ringel, T. et al. Genome-Scale CRISPR screening in human intestinal organoids identifies drivers of TGF-β resistance. Cell Stem Cell 26, 431–440.e8 (2020).
MacLeod, G. et al. Genome-Wide CRISPR-Cas9 screens expose genetic vulnerabilities and mechanisms of temozolomide sensitivity in glioblastoma stem cells. Cell Rep. 27, 971–986.e9 (2019).
Tsherniak, A. et al. Defining a cancer dependency map. Cell 170, 564–576.e16 (2017).
Piccioni, F., Younger, S. T. & Root, D. E. Pooled lentiviral-delivery genetic screens. Curr. Protoc. Mol. Biol. 121, 32.1.1–32.1.21 (2018).
Doench, J. G. Am I ready for CRISPR? A user’s guide to genetic screens. Nat. Rev. Genet. 19, 67–80 (2018).
Hanna, R. E. & Doench, J. G. Design and analysis of CRISPR–Cas experiments. Nat. Biotechnol. 38, 813–823 (2020).
Khadka, P. et al. PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation. Nat. Commun. 13, 604 (2022).
Bandopadhayay, P. et al. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nat. Commun. 10, 2400 (2019).
Kofman, S. et al. Human mini brains and spinal cords in a dish: modeling strategies, current challenges, and prospective advances. J. Tissue Eng. 13, 20417314221113390 (2022).
Gómez-Oliva, R. et al. Evolution of experimental models in the study of glioblastoma: toward finding efficient treatments. Front. Oncol. 10, 614295 (2020).
Bock, C. et al. High-content CRISPR screening. Nat. Rev. Methods Primers 2, 8 (2022).
Xiong, F. et al. Optimal time for passaging neurospheres based on primary neural stem cell cultures. Cytotechnology 63, 621–631 (2011).
Brewer, G. J. & Torricelli, J. R. Isolation and culture of adult neurons and neurospheres. Nat. Protoc. 2, 1490–1498 (2007).
Ligon, K. L. et al. Olig2-regulated lineage-restricted pathway controls replication competence in neural stem cells and malignant glioma. Neuron 53, 503–517 (2007).
Mehta, S. et al. The central nervous system-restricted transcription factor Olig2 opposes p53 responses to genotoxic damage in neural progenitors and malignant glioma. Cancer Cell 19, 359–371 (2011).
Meyers, R. M. et al. Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells. Nat. Genet. 49, 1779–1784 (2017).

Genome-wide pooled CRISPR screening in neurospheres

Supplementary information

推荐阅读