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Immune CRISPR Screening

Katerina Hatzi, Huimin Geng, Ashley S Doane, Cem Meydan, Reed LaRiviere, Mariano Cardenas, Cihangir Duy, Hao Shen, Maria Nieves Calvo Vidal, Timour Baslan, Helai P Mohammad, Ryan G Kruger, Rita Shaknovich, Ann M Haberman, Giorgio Inghirami, Scott W Lowe, Ari M Melnick
Germinal center (GC) B cells feature repression of many gene enhancers to establish their characteristic transcriptome. Here we show that conditional deletion of Lsd1 in GCs significantly impaired GC formation, associated with failure to repress immune synapse genes linked to GC exit, which are also direct targets of the transcriptional repressor BCL6. We found that BCL6 directly binds LSD1 and recruits it primarily to intergenic and intronic enhancers. Conditional deletion of Lsd1 suppressed GC hyperplasia caused by constitutive expression of BCL6 and significantly delayed BCL6-driven lymphomagenesis...
January 2019: Nature Immunology
Yiping Zhu, Gary Z Wang, Oya Cingöz, Stephen P Goff
The entry of foreign DNA into many mammalian cell types triggers the innate immune system, a complex set of responses to prevent infection by pathogens. One aspect of the response is the potent epigenetic silencing of incoming viral DNAs1 , including the extrachromosomal DNAs that are formed immediately after infection by retroviruses. These unintegrated viral DNAs are very poorly transcribed in all cells, even in permissive cells, in contrast to the robust expression that is observed after viral integration2-5 ...
November 28, 2018: Nature
Li Xue, Bin Tang, Wei Chen, Jiesi Luo
The CRISPR-Cas9 system derived from adaptive immunity in bacteria and archaea has been developed into a powerful tool for genome engineering with wide-ranging applications. Optimizing single guide RNA (sgRNA) design to improve efficiency of target cleavage is a key step for successful gene editing using the CRISPR-Cas9 system. Because not all sgRNAs that cognate to a given target gene are equally effective, computational tools have been developed based on experimental data to increase the likelihood of selecting effective sgRNAs...
November 28, 2018: Journal of Chemical Information and Modeling
Eric Shifrut, Julia Carnevale, Victoria Tobin, Theodore L Roth, Jonathan M Woo, Christina T Bui, P Jonathan Li, Morgan E Diolaiti, Alan Ashworth, Alexander Marson
Human T cells are central effectors of immunity and cancer immunotherapy. CRISPR-based functional studies in T cells could prioritize novel targets for drug development and improve the design of genetically reprogrammed cell-based therapies. However, large-scale CRISPR screens have been challenging in primary human cells. We developed a new method, single guide RNA (sgRNA) lentiviral infection with Cas9 protein electroporation (SLICE), to identify regulators of stimulation responses in primary human T cells...
November 13, 2018: Cell
Derek J Theisen, Jesse T Davidson, Carlos G Briseño, Marco Gargaro, Elvin J Lauron, Qiuling Wang, Pritesh Desai, Vivek Durai, Prachi Bagadia, Joshua R Brickner, Wandy L Beatty, Herbert W Virgin, William E Gillanders, Nima Mosammaparast, Michael S Diamond, L David Sibley, Wayne Yokoyama, Robert D Schreiber, Theresa L Murphy, Kenneth M Murphy
During the process of cross-presentation, viral or tumor-derived antigens are presented to CD8+ T cells by Batf3- dependent CD8α+ /XCR1+ classical dendritic cells (cDC1s). We designed a functional CRISPR screen for previously unknown regulators of cross-presentation, and identified the BEACH domain-containing protein WDFY4 as essential for cross-presentation of cell-associated antigens by cDC1s in mice. However, WDFY4 was not required for major histocompatibility complex class II presentation, nor for cross-presentation by monocyte-derived dendritic cells...
November 9, 2018: Science
Aleksandra Wroblewska, Maxime Dhainaut, Benjamin Ben-Zvi, Samuel A Rose, Eun Sook Park, El-Ad David Amir, Anela Bektesevic, Alessia Baccarini, Miriam Merad, Adeeb H Rahman, Brian D Brown
CRISPR pools are being widely employed to identify gene functions. However, current technology, which utilizes DNA as barcodes, permits limited phenotyping and bulk-cell resolution. To enable novel screening capabilities, we developed a barcoding system operating at the protein level. We synthesized modules encoding triplet combinations of linear epitopes to generate >100 unique protein barcodes (Pro-Codes). Pro-Code-expressing vectors were introduced into cells and analyzed by CyTOF mass cytometry. Using just 14 antibodies, we detected 364 Pro-Code populations; establishing the largest set of protein-based reporters...
November 1, 2018: Cell
Robert C Orchard, Meagan E Sullender, Bria F Dunlap, Dale R Balce, John G Doench, Herbert W Virgin
Noroviruses (NoVs) are a leading cause of gastroenteritis world-wide, yet host factors that restrict NoV replication are not well understood. Here, we use a CRISPR activation (CRISPRa) genome-wide screening to identify host genes that can inhibit murine norovirus (MNoV) replication in human cells. Our screens identified with high confidence 49 genes that can inhibit MNoV infection when overexpressed. A significant number of these genes are in interferon and immune regulation signaling networks, but surprising, the majority of the genes identified are not associated with innate or adaptive immunity nor with any antiviral activity...
October 10, 2018: Journal of Virology
Patrick H Lizotte, Ruey-Long Hong, Troy A Luster, Megan E Cavanaugh, Luke J Taus, Stephen Wang, Abha Dhaneshwar, Naomi Mayman, Aaron Yang, Meghana Kulkarni, Lauren Badalucco, Erica Fitzpatrick, Hsiang-Fong Kao, Mari Kuraguchi, Mark Bittinger, Paul T Kirschmeier, Nathanael S Gray, David A Barbie, Pasi A Jänne
We developed a screening assay in which luciferized ID8 expressing OVA was cocultured with transgenic CD8+ T cells specifically recognizing the model antigen in an H-2b-restricted manner. The assay was screened with a small-molecule library to identify compounds that inhibit or enhance T cell-mediated killing of tumor cells. Erlotinib, an EGFR inhibitor, was the top compound that enhanced T-cell killing of tumor cells. Subsequent experiments with erlotinib and additional EGFR inhibitors validated the screen results...
September 21, 2018: Cancer Immunology Research
Kyle E Watters, Christof Fellmann, Hua B Bai, Shawn M Ren, Jennifer A Doudna
Cas12a (Cpf1) is a CRISPR-associated nuclease with broad utility for synthetic genome engineering, agricultural genomics, and biomedical applications. Although bacteria harboring CRISPR-Cas9 or CRISPR-Cas3 adaptive immune systems sometimes acquire mobile genetic elements encoding anti-CRISPR proteins that inhibit Cas9, Cas3, or the DNA-binding Cascade complex, no such inhibitors have been found for CRISPR-Cas12a. Here we use a comprehensive bioinformatic and experimental screening approach to identify three different inhibitors that block or diminish CRISPR-Cas12a-mediated genome editing in human cells...
October 12, 2018: Science
Ping Zhou, Yang She, Na Dong, Peng Li, Huabin He, Alessio Borio, Qingcui Wu, Shan Lu, Xiaojun Ding, Yong Cao, Yue Xu, Wenqing Gao, Mengqiu Dong, Jingjin Ding, Da-Cheng Wang, Alla Zamyatina, Feng Shao
Immune recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors often activates proinflammatory NF-κB signalling1 . Recent studies indicate that the bacterial metabolite D-glycero-β-D-manno-heptose 1,7-bisphosphate (HBP) can activate NF-κB signalling in host cytosol2-4 , but it is unclear whether HBP is a genuine PAMP and the cognate pattern recognition receptor has not been identified. Here we combined a transposon screen in Yersinia pseudotuberculosis with biochemical analyses and identified ADP-β-D-manno-heptose (ADP-Hep), which mediates type III secretion system-dependent NF-κB activation and cytokine expression...
September 2018: Nature
Xihong Zhao, Zhixue Yu, Zhenbo Xu
Staphylococcus aureus is a foodborne pathogen that causes food contamination and food poisoning, which poses great harm to health, agriculture and other hosts. Clustered regularly interspaced short palindromic repeats (CRISPR) are a recently discovered bacterial immune system that resists foreign genes such as phage DNA. This system inhibits the transfer of specific movable genetic elements that match the CRISPR spacer sequences, thereby preventing the spread of drug-resistant genes between pathogens. In this study, 57 CRISPR loci were screened from 38 strains of S...
2018: Frontiers in Microbiology
Dana Elster, Marie Tollot, Karin Schlegelmilch, Alessandro Ori, Andreas Rosenwald, Erik Sahai, Björn von Eyss
Yes-associated protein (YAP), the downstream transducer of the Hippo pathway, is a key regulator of organ size, differentiation and tumorigenesis. To uncover Hippo-independent YAP regulators, we performed a genome-wide CRISPR screen that identifies the transcriptional repressor protein Trichorhinophalangeal Syndrome 1 (TRPS1) as a potent repressor of YAP-dependent transactivation. We show that TRPS1 globally regulates YAP-dependent transcription by binding to a large set of joint genomic sites, mainly enhancers...
August 6, 2018: Nature Communications
Muhammad R Javed, Maria Sadaf, Temoor Ahmed, Amna Jamil, Marium Nawaz, Hira Abbas, Anam Ijaz
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR or more precisely CRISPR-Cas) system has proven to be a highly efficient and simple tool for achieving site-specific genome modifications in comparison to Zinc Finger Nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs). The discovery of bacterial defense system that uses RNA-guided DNA cleaving enzymes for producing double-strand breaks along CRISPR has provided an exciting alternative to ZFNs and TALENs for gene editing & regulation, as the CRISPR-associated (Cas) proteins remain the same for different gene targets and only the short sequence of the guide RNA needs to be changed to redirect the site-specific cleavage...
December 2018: Current Microbiology
Vijaya L Simhadri, Joseph McGill, Shane McMahon, Junxia Wang, Haiyan Jiang, Zuben E Sauna
The repurposing of the CRISPR/Cas microbial adaptive immune system for gene editing has resulted in an exponential rise in new technologies and promising approaches for treating numerous human diseases. While some of the approaches being currently developed involve ex vivo editing by CRISPR/Cas9, many more potential applications will require in vivo editing. The in vivo use of this technology comes with challenges, one of which is the immune response to Cas9, a protein of microbial origin. Thus, the prevalence of pre-existing antibodies to Cas9 could also be a relevant parameter...
September 21, 2018: Molecular Therapy. Methods & Clinical Development
Emily A Stout, Rosemary Sanozky-Dawes, Yong Jun Goh, Alexandra B Crawley, Todd R Klaenhammer, Rodolphe Barrangou
Lactobacillus gasseri is a human commensal which carries CRISPR-Cas, an adaptive immune system that protects the cell from invasive mobile genetic elements (MGEs). However, MGEs occasionally escape CRISPR targeting due to DNA mutations that occur in sequences involved in CRISPR interference. To better understand CRISPR escape processes, a plasmid interference assay was used to screen for mutants that escape CRISPR-Cas targeting. Plasmids containing a target sequence and a protospacer adjacent motif (PAM) were transformed for targeting by the native CRISPR-Cas system...
September 2018: Microbiology
Yoshifumi Nishikawa, Naomi Shimoda, Ragab M Fereig, Tomoya Moritaka, Kousuke Umeda, Maki Nishimura, Fumiaki Ihara, Kaoru Kobayashi, Yuu Himori, Yutaka Suzuki, Hidefumi Furuoka
Neospora caninum is a protozoan parasite closely related to Toxoplasma gondii Neosporosis caused by N. caninum is considered one of the main causes of abortion in cattle and nervous-system dysfunction in dogs, and identification of the virulence factors of this parasite is important for the development of control measures. Here, we used a luciferase reporter assay to screen the dense granule proteins genes of N. caninum , and we found that NcGRA6, NcGRA7, and NcGRA14 are involved in the activation of the NF-κB, calcium/calcineurin, and cAMP/PKA signals...
September 15, 2018: Applied and Environmental Microbiology
Ahmed Mahas, Magdy Mahfouz
In prokaryotes, CRISPR/Cas adaptive immunity systems target and destroy nucleic acids derived from invading bacteriophages and other foreign genetic elements. In eukaryotes, the native function of these systems has been exploited to combat viruses in mammals and plants. Rewired CRISPR/Cas9 and CRISPR/Cas13 systems have been used to confer resistance against DNA and RNA viruses, respectively. Here, we discuss recent approaches employing CRISPR/Cas systems to combat viruses in eukaryotes, highlight key challenges, and provide future perspectives...
July 10, 2018: Current Opinion in Virology
Conor J Kearney, Stephin J Vervoort, Simon J Hogg, Kelly M Ramsbottom, Andrew J Freeman, Najoua Lalaoui, Lizzy Pijpers, Jessica Michie, Kristin K Brown, Deborah A Knight, Vivien Sutton, Paul A Beavis, Ilia Voskoboinik, Phil K Darcy, John Silke, Joseph A Trapani, Ricky W Johnstone, Jane Oliaro
Immunotherapy has revolutionized outcomes for cancer patients, but the mechanisms of resistance remain poorly defined. We used a series of whole-genome clustered regularly interspaced short palindromic repeat (CRISPR)-based screens performed in vitro and in vivo to identify mechanisms of tumor immune evasion from cytotoxic lymphocytes [CD8+ T cells and natural killer (NK) cells]. Deletion of key genes within the tumor necrosis factor (TNF) signaling, interferon-γ (IFN-γ) signaling, and antigen presentation pathways provided protection of tumor cells from CD8+ T cell-mediated killing and blunted antitumor immune responses in vivo...
May 18, 2018: Science Immunology
Harriet Prior, Lauren MacConnachie, Jose L Martinez, Georgina C B Nicholl, Asim A Beg
The clustered regularly interspersed palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) prokaryotic adaptive immune defense system has been co-opted as a powerful tool for precise eukaryotic genome engineering. Here, we present a rapid and simple method using chimeric single guide RNAs (sgRNA) and CRISPR-Cas9 Ribonucleoproteins (RNPs) for the efficient and precise generation of genomic point mutations in C. elegans. We describe a pipeline for sgRNA target selection, homology-directed repair (HDR) template design, CRISPR-Cas9-RNP complexing and delivery, and a genotyping strategy that enables the robust and rapid identification of correctly edited animals...
April 30, 2018: Journal of Visualized Experiments: JoVE
Qingxiang Liu, Yaoxing Wu, Yunfei Qin, Jiajia Hu, Weihong Xie, F Xiao-Feng Qin, Jun Cui
The innate immune response conferred by type I interferons is essential for host defense against viral infection but needs to be tightly controlled to avoid immunopathology. We performed a systematic functional screening by CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) knockout and overexpression to investigate the roles of the deubiquitinating enzyme (DUB) family in regulating antiviral immunity. We demonstrated that the expression of a large fraction of DUBs underwent complex temporal alteration, suggesting a dynamic program of feedback regulation...
May 2018: Science Advances
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