The paper uses base editor screens to assess phosphorylation site functionality in T cell activation, identifying novel sites that modulate transcriptional activity and signaling pathways.

bioRxiv · Nov 11, 2023 · PreprintSystems Biology

Optimization of Cas12a for multiplexed genome-scale transcriptional activation

Audrey L Griffith, Fengyi Zheng, Abby V. McGee, Nathan Miller, Zsofia M Szegletes, Ganna Reint, Fabian Gademann, Ifunanya Nwolah, Mudra Hegde, Yanjing V. Liu, Amy B. Goodale, John G. Doench

The paper optimizes Cas12a for multiplexed CRISPRa screens in human cells, enabling simultaneous activation of up to four genes and identifying criteria for selecting effective guides.

Cell Genomics · Sep 1, 2023Peer-reviewedGenomics

Benchmarking of SpCas9 variants enables deeper base editor screens of BRCA1 and BCL2

Annabel K. Sangree, Audrey L Griffith, Zsofia M Szegletes, Priyanka Roy, Peter C. DeWeirdt, Mudra Hegde, Abby V. McGee, Ruth E. Hanna, John G. Doench

The paper benchmarks SpCas9 variants to improve base editor screens for BRCA1 and BCL2, identifying new insights into their genetic variants.

Nature Communications · Mar 14, 2022Peer-reviewedGenomics

Massively parallel assessment of human variants with base editor screens

Ruth E. Hanna, Mudra Hegde, Christian R. Fagre, Peter C. DeWeirdt, Annabel K. Sangree, Zsofia M Szegletes, Audrey L Griffith, Marissa N. Feeley, Kendall R Sanson, Yossef Baidi, Luke W. Koblan, David R. Liu, James T. Neal, John G. Doench

This paper uses CRISPR-Cas9 base editors in pooled screens to assess the functional impact of human variants, identifying loss-of-function mutations and drug sensitivity/resistance mutations.

Cell · Feb 1, 2021Peer-reviewedGenetics

Optimization of AsCas12a for combinatorial genetic screens in human cells

Peter C. DeWeirdt, Kendall R Sanson, Annabel K. Sangree, Mudra Hegde, Ruth E. Hanna, Marissa N. Feeley, Audrey L Griffith, Teng Teng, Samantha M. Borys, Christine Strand, J. Keith Joung, Benjamin P. Kleinstiver, Xuewen Pan, Alan Huang, John G. Doench

This paper optimizes AsCas12a for combinatorial genetic screens in human cells by improving on-target and off-target activity and enabling higher-order multiplexing.

Nature Biotechnology · Jul 13, 2020Peer-reviewedGenetics

Genetic screens in isogenic mammalian cell lines without single cell cloning

Peter C. DeWeirdt, Annabel K. Sangree, Ruth E. Hanna, Kendall R Sanson, Mudra Hegde, Christine Strand, Nicole S. Persky, John G. Doench

The paper presents a method to generate isogenic cell pairs and screen them with CRISPR-Cas9 libraries to identify genetic interactions, demonstrating applications for BCL2L1, MCL1, and PARP1.

Nature Communications · Feb 6, 2020Peer-reviewedGenetics

Up, down, and out: optimized libraries for CRISPRa, CRISPRi, and CRISPR-knockout genetic screens

Kendall R Sanson, Ruth E. Hanna, Mudra Hegde, Katherine F. Donovan, Christine Strand, Meagan E. Sullender, Emma W Vaimberg, Amy B. Goodale, David E. Root, Federica Piccioni, John G. Doench

The paper evaluates and introduces optimized CRISPR libraries for knockout, interference, and activation screens, showing improved performance in gene function interrogation.

Nature Communications · Dec 17, 2018Peer-reviewedGenomics

Uncoupling of sgRNAs from their associated barcodes during PCR amplification of combinatorial CRISPR screens

Mudra Hegde, Christine Strand, Ruth E. Hanna, John G. Doench

The paper identifies PCR amplification as a major source of uncoupling between sgRNAs and their associated barcodes in combinatorial CRISPR screens and proposes strategies to mitigate this issue.

PLoS ONE · May 25, 2018Peer-reviewedMolecular Biology

Mapping protein function with CRISPR/Cas9-mediated mutagenesis

Katherine F Donovan, Mudra Hegde, Meagan Sullender, Emma W Vaimberg, Cory M Johannessen, David E Root, John G Doench

The paper uses CRISPR/Cas9 mutagenesis to generate allelic variants of MEK1 and BRAF, identifying gain-of-function alleles in the MAPK signaling pathway.

bioRxiv · Sep 23, 2016Genomics