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
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MicroRNA-29a attenuates CD8 T cell exhaustion and induces memory-like CD8 T cells during chronic infection
Erietta Stelekati,Zhangying Cai,Sasikanth Manne,Ze-jian Chen,Jean Christophe Beltra,L. Buchness,Xuebing Leng,Svetlana Ristin,Kito Nzingha,Viktoriya Ekshyyan,Christina Niavi,Mohamed S. Abdel-Hakeem,Mohammed-Alkhatim Ali,Sydney Drury,Chi Wai Lau,Zhen Gao,Yuguang Ban,Simon K Zhou,K. Mark Ansel,Makoto Kurachi,Martha S. Jordan,Alejandro V. Villarino,Shin Foong Ngiow,E. John Wherry +23 more
TL;DR: Enforced miR-29a expression enhances TEX responses, attenuates exhaustion, and represents a target for improving the outcome of immunotherapy.
Journal ArticleDOI
The immunometabolite S-2-hydroxyglutarate exacerbates perioperative ischemic brain injury and cognitive dysfunction by enhancing CD8+ T lymphocyte-mediated neurotoxicity
Faqiang Zhang,Mu Niu,Kaikai Guo,Yulong Ma,Qiang Fu,Yanhong Liu,Zeguo Feng,Weidong Mi,Long Wang +8 more
TL;DR: In this paper , S-2HG signaling-mediated activation and neurotoxicity of CD8+ T lymphocytes might exacerbate perioperative ischemic brain injury and may represent a promising immunotherapy target in per-operative stroke.
Journal ArticleDOI
The immunometabolite S-2-hydroxyglutarate exacerbates perioperative ischemic brain injury and cognitive dysfunction by enhancing CD8+ T lymphocyte-mediated neurotoxicity
Faqiang Zhang,Mu Niu,Kaikai Guo,Yulong Ma,Qiang Fu,Yanhong Liu,Zeguo Feng,Weidong Mi,Long Wang +8 more
TL;DR: In this paper , S-2HG signaling-mediated activation and neurotoxicity of CD8+ T lymphocytes might exacerbate perioperative ischemic brain injury and may represent a promising immunotherapy target in per-operative stroke.
Journal ArticleDOI
CRISPR screens for functional interrogation of immunity
Journal ArticleDOI
PRDM1 Drives Human Primary T Cell Hyporesponsiveness by Altering the T Cell Transcriptome and Epigenome
Huidong Guo,Ming Wang,Bixia Wang,Liping Guo,Yi-Fei Cheng,Zhi-Dong Wang,Yu-Qian Sun,Yu Wang,Ying-Jun Chang,Xiao-Jun Huang +9 more
TL;DR: Results indicated that PRDM1 is sufficient for inducing human primary T cell hyporesponsiveness by transcriptomic and epigenetic manners.
References
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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.
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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.
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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.
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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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