Journal ArticleDOI
In vivo CD8+ T cell CRISPR screening reveals control by Fli1 in infection and cancer.
Zeyu Chen,Eri Arai,Omar Khan,Zhen Zhang,Shin Foong Ngiow,Yuan He,Hua Huang,Sasikanth Manne,Zhendong Cao,Amy E. Baxter,Zhangying Cai,Elizabeth Freilich,Mohammed Alkhatim A. Ali,Josephine R. Giles,Jennifer E. Wu,Allison R. Greenplate,Mohamed A. Hakeem,Qingzhou Chen,Makoto Kurachi,Kito Nzingha,Viktoriya Ekshyyan,Divij Mathew,Zhuoyu Wen,Nancy A. Speck,Alexis Battle,Shelley L. Berger,E. John Wherry,Junwei Shi +27 more
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TLDR
In this paper, the authors developed an in-vivo T-cell CRISPR screening platform and identified a key mechanism restraining TEFF biology through the ETS family TF, Fli1.About:
This article is published in Cell.The article was published on 2021-03-04. It has received 74 citations till now.read more
Citations
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Journal ArticleDOI
Improving T cell therapy: in vivo CRISPR-Cas9 screens tell us how to do
TL;DR: A commentary on “In vivo CD8+ T cell CRISPR screening reveals control by Fli1 in infection and cancer”.
Journal ArticleDOI
Enforced expression of Runx3 improved CAR-T cell potency in solid tumor via enhancing resistance to activation-induced cell death.
Yi Wang,Yonghong Zhang,Guoxiu Du,Hong Luo,Jingwen Su,Yansha Sun,Min Zhou,Bizhi Shi,Henry Q.X. Li,Hua-jiang Jiang,Zonghai Li +10 more
TL;DR: In this paper , the authors showed that Runx3-armored CAR-T cells showed increased antitumor activities and could be a new modality for the treatment of solid tumors.
Posted ContentDOI
Cas12a/Cpf1 knock-in mice enable efficient multiplexed immune cell engineering
Matthew B. Dong,Kaiyuan T. Tang,Xiaoyu Zhou,Johanna Shen,Hyunu Ray Kim,Jerry Zhou,Hanbing Cao,Erica Vandenbulcke,Yueqi Zhang,Ryan D. Chow,Andrew Du,Kazushi Suzuki,Shao-Yu Fang,Medha Majety,Xiaoyun Dai,Sidi Chen +15 more
TL;DR: In this article , conditional and constitutive LbCas12a/Cpf1 knock-in transgenic mice were used to demonstrate efficient multiplexed gene editing and surface protein knockdown within individual primary immune cells.
Journal ArticleDOI
The druggable transcription factor Fli-1 regulates T cell immunity and tolerance in graft-versus-host disease
Yongxia Wu,Xue-Zhong Yu +1 more
TL;DR: In this paper , the authors investigated Friend virus leukemia integration 1 (Fli-1) in GVHD pathogenesis and validated Fli-1 as a therapeutic target using genetic approaches and found that it dynamically regulated different T cell subsets in allogeneic responses and pathogenicity in the development of aGVHD and cGVHD.
Journal ArticleDOI
Dissection of the MEF2D-IRF8 transcriptional circuit dependency in acute myeloid leukemia
Bianca Pingul,Hua Huang,Qingzhou Chen,Fatemeh Alikarami,Zhen Zhang,J Qi,Kathrin M. Bernt,Shelley L. Berger,Zhendong Cao,Junwei Shi +9 more
TL;DR: In this paper , the authors systematically surveyed transcription factor (TF) vulnerabilities in leukemia and uncovered TF clusters that exhibit context-specific vulnerabilities within and between different subtypes of leukemia, and they demonstrated that acute myeloid leukemia (AML) with high IRF8 expression was addicted to MEF2D, and dual perturbation of these two TFs leads to a more robust inhibition of AML proliferation.
References
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Journal ArticleDOI
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
Journal ArticleDOI
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan,Ira M. Hall +1 more
TL;DR: A new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format, which allows the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks.
Journal ArticleDOI
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
TL;DR: An R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters and can be easily extended to other species and ontologies is presented.
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