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Article ; Online: Corrigendum: CRISPR nuclease off-target activity and mitigation strategies.

Wienert, Beeke / Cromer, M Kyle

Frontiers in genome editing

2023 Volume 4, Page(s) 1112956

Abstract: This corrects the article DOI: 10.3389/fgeed.2022.1050507.]. ...

Abstract	[This corrects the article DOI: 10.3389/fgeed.2022.1050507.].
Language	English
Publishing date	2023-01-20
Publishing country	Switzerland
Document type	Published Erratum
ISSN	2673-3439
ISSN (online)	2673-3439
DOI	10.3389/fgeed.2022.1112956
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: CRISPR nuclease off-target activity and mitigation strategies.

Wienert, Beeke / Cromer, M Kyle

Frontiers in genome editing

2022 Volume 4, Page(s) 1050507

Abstract: The discovery of CRISPR has allowed site-specific genomic modification to become a reality and this technology is now being applied in a number of human clinical trials. While this technology has demonstrated impressive efficacy in the clinic to date, ... ...

Abstract	The discovery of CRISPR has allowed site-specific genomic modification to become a reality and this technology is now being applied in a number of human clinical trials. While this technology has demonstrated impressive efficacy in the clinic to date, there remains the potential for unintended on- and off-target effects of CRISPR nuclease activity. A variety of
Language	English
Publishing date	2022-11-10
Publishing country	Switzerland
Document type	Journal Article ; Review
ISSN	2673-3439
ISSN (online)	2673-3439
DOI	10.3389/fgeed.2022.1050507
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Article: Dual α-globin and truncated EPO receptor knockin restores hemoglobin production in α-thalassemia-derived red blood cells.

Chu, Simon N / Soupene, Eric / Wienert, Beeke / Yin, Han / Sharma, Devesh / McCreary, Travis / Jia, Kun / Homma, Shota / Hampton, Jessica P / Gardner, James M / Conklin, Bruce R / MacKenzie, Tippi C / Porteus, Matthew H / Cromer, M Kyle

bioRxiv : the preprint server for biology

2024

Language	English
Publishing date	2024-05-07
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.09.01.555926
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Article ; Online: CRISPR off-target detection with DISCOVER-seq.

Wienert, Beeke / Wyman, Stacia K / Yeh, Charles D / Conklin, Bruce R / Corn, Jacob E

Nature protocols

2020 Volume 15, Issue 5, Page(s) 1775–1799

Abstract: DISCOVER-seq (discovery of in situ Cas off-targets and verification by sequencing) is a broadly applicable approach for unbiased CRISPR-Cas off-target identification in cells and tissues. It leverages the recruitment of DNA repair factors to double- ... ...

Abstract	DISCOVER-seq (discovery of in situ Cas off-targets and verification by sequencing) is a broadly applicable approach for unbiased CRISPR-Cas off-target identification in cells and tissues. It leverages the recruitment of DNA repair factors to double-strand breaks (DSBs) after genome editing with CRISPR nucleases. Here, we describe a detailed experimental protocol and analysis pipeline with which to perform DISCOVER-seq. The principle of this method is to track the precise recruitment of MRE11 to DSBs by chromatin immunoprecipitation followed by next-generation sequencing. A customized open-source bioinformatics pipeline, BLENDER (blunt end finder), then identifies off-target sequences genome wide. DISCOVER-seq is capable of finding and measuring off-targets in primary cells and in situ. The two main advantages of DISCOVER-seq are (i) low false-positive rates because DNA repair enzyme binding is required for genome edits to occur and (ii) its applicability to a wide variety of systems, including patient-derived cells and animal models. The whole protocol, including the analysis, can be completed within 2 weeks.
MeSH term(s)	Animals ; CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA Breaks, Double-Stranded ; DNA Repair ; Gene Editing/methods ; Humans ; K562 Cells ; Mice ; Sequence Analysis, DNA
Language	English
Publishing date	2020-04-20
Publishing country	England
Document type	Evaluation Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2244966-8
ISSN	1750-2799 ; 1754-2189
ISSN (online)	1750-2799
ISSN	1754-2189
DOI	10.1038/s41596-020-0309-5
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Article ; Online: A natural regulatory mutation in the proximal promoter elevates fetal

Martyn, Gabriella E / Wienert, Beeke / Kurita, Ryo / Nakamura, Yukio / Quinlan, Kate G R / Crossley, Merlin

Blood

2019 Volume 133, Issue 8, Page(s) 852–856

Abstract: β-hemoglobinopathies, such as sickle cell disease and β-thalassemia, result from mutations in the ... ...

Abstract	β-hemoglobinopathies, such as sickle cell disease and β-thalassemia, result from mutations in the adult
MeSH term(s)	Anemia, Sickle Cell/genetics ; Anemia, Sickle Cell/metabolism ; Cell Line ; Fetal Hemoglobin/biosynthesis ; Fetal Hemoglobin/genetics ; GATA1 Transcription Factor/genetics ; GATA1 Transcription Factor/metabolism ; Gene Expression Regulation ; Point Mutation ; Response Elements ; beta-Globins/genetics ; beta-Globins/metabolism ; beta-Thalassemia/genetics ; beta-Thalassemia/metabolism
Chemical Substances	GATA1 Transcription Factor ; GATA1 protein, human ; beta-Globins ; Fetal Hemoglobin (9034-63-3)
Language	English
Publishing date	2019-01-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80069-7
ISSN	1528-0020 ; 0006-4971
ISSN (online)	1528-0020
ISSN	0006-4971
DOI	10.1182/blood-2018-07-863951
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Uh III Zs.140: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
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Article ; Online: METTL21B Is a Novel Human Lysine Methyltransferase of Translation Elongation Factor 1A: Discovery by CRISPR/Cas9 Knockout.

Hamey, Joshua J / Wienert, Beeke / Quinlan, Kate G R / Wilkins, Marc R

Molecular & cellular proteomics : MCP

2017 Volume 16, Issue 12, Page(s) 2229–2242

Abstract: Lysine methylation is widespread on human proteins, however the enzymes that catalyze its addition remain largely unknown. This limits our capacity to study the function and regulation of this modification. Here we used the CRISPR/Cas9 system to knockout ...

Abstract	Lysine methylation is widespread on human proteins, however the enzymes that catalyze its addition remain largely unknown. This limits our capacity to study the function and regulation of this modification. Here we used the CRISPR/Cas9 system to knockout putative protein methyltransferases
MeSH term(s)	CRISPR-Cas Systems ; Catalytic Domain ; Gene Knockout Techniques/methods ; Humans ; K562 Cells ; Lysine/chemistry ; Methylation ; Methyltransferases/chemistry ; Methyltransferases/genetics ; Methyltransferases/metabolism ; Models, Molecular ; Peptide Elongation Factor 1/chemistry ; Peptide Elongation Factor 1/metabolism ; Protein Conformation ; Proteomics/methods
Chemical Substances	Peptide Elongation Factor 1 ; EEF1AKMT3 protein, human (EC 2.1.1.-) ; Methyltransferases (EC 2.1.1.-) ; METTL3 protein, human (EC 2.1.1.62) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2017-06-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1074/mcp.M116.066308
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Zs.A 5599: Show issues

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Article ; Online: Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair.

Perez-Bermejo, Juan A / Efagene, Oghene / Matern, William M / Holden, Jeffrey K / Kabir, Shaheen / Chew, Glen M / Andreoletti, Gaia / Catton, Eniola / Ennis, Craig L / Garcia, Angelica / Gerstenberg, Trevor L / Hill, Kaisle A / Jain, Aayami / Krassovsky, Kristina / Lalisan, Cassandra D / Lord, Daniel / Quejarro, B Joy / Sales-Lee, Jade / Shah, Meet /

Silva, Brian J / Skowronski, Jason / Strukov, Yuri G / Thomas, Joshua / Veraz, Michael / Vijay, Twaritha / Wallace, Kirby A / Yuan, Yue / Grogan, Jane L / Wienert, Beeke / Lahiri, Premanjali / Treusch, Sebastian / Dever, Daniel P / Soros, Vanessa B / Partridge, James R / Seim, Kristen L

Nature communications

2024 Volume 15, Issue 1, Page(s) 2625

Abstract: Homology Directed Repair (HDR) enables precise genome editing, but the implementation of HDR-based therapies is hindered by limited efficiency in comparison to methods that exploit alternative DNA repair routes, such as Non-Homologous End Joining (NHEJ). ...

Abstract	Homology Directed Repair (HDR) enables precise genome editing, but the implementation of HDR-based therapies is hindered by limited efficiency in comparison to methods that exploit alternative DNA repair routes, such as Non-Homologous End Joining (NHEJ). In this study, we develop a functional, pooled screening platform to identify protein-based reagents that improve HDR in human hematopoietic stem and progenitor cells (HSPCs). We leverage this screening platform to explore sequence diversity at the binding interface of the NHEJ inhibitor i53 and its target, 53BP1, identifying optimized variants that enable new intermolecular bonds and robustly increase HDR. We show that these variants specifically reduce insertion-deletion outcomes without increasing off-target editing, synergize with a DNAPK inhibitor molecule, and can be applied at manufacturing scale to increase the fraction of cells bearing repaired alleles. This screening platform can enable the discovery of future gene editing reagents that improve HDR outcomes.
MeSH term(s)	Humans ; CRISPR-Cas Systems ; Recombinational DNA Repair ; Gene Editing/methods ; DNA Repair ; DNA End-Joining Repair
Language	English
Publishing date	2024-03-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46816-5
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Article: Wake-up Sleepy Gene: Reactivating Fetal Globin for β-Hemoglobinopathies.

Wienert, Beeke / Martyn, Gabriella E / Funnell, Alister P W / Quinlan, Kate G R / Crossley, Merlin

Trends in genetics : TIG

2018 Volume 34, Issue 12, Page(s) 927–940

Abstract: Disorders in hemoglobin (hemoglobinopathies) were the first monogenic diseases to be characterized and remain among the most common and best understood genetic conditions. Moreover, the study of the β-globin locus provides a textbook example of ... ...

Abstract	Disorders in hemoglobin (hemoglobinopathies) were the first monogenic diseases to be characterized and remain among the most common and best understood genetic conditions. Moreover, the study of the β-globin locus provides a textbook example of developmental gene regulation. The fetal γ-globin genes (HBG1/HBG2) are ordinarily silenced around birth, whereupon their expression is replaced by the adult β-globin genes (HBB primarily and HBD). Over 50 years ago it was recognized that mutations that cause lifelong persistence of fetal γ-globin expression ameliorate the debilitating effects of mutations in β-globin. Since then, research has focused on therapeutically reactivating the fetal γ-globin genes. Here, we summarize recent discoveries, focusing on the influence of genome editing technologies, including CRISPR-Cas9, and emerging gene therapy approaches.
MeSH term(s)	Adult ; CRISPR-Cas Systems/genetics ; Gene Editing/trends ; Genetic Therapy/trends ; Hemoglobinopathies/blood ; Hemoglobinopathies/genetics ; Hemoglobinopathies/pathology ; Humans ; Mutation ; beta-Globins/genetics ; beta-Globins/therapeutic use ; gamma-Globins/genetics ; gamma-Globins/therapeutic use
Chemical Substances	beta-Globins ; gamma-Globins
Language	English
Publishing date	2018-10-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	619240-3
ISSN	1362-4555 ; 0168-9525 ; 0168-9479
ISSN (online)	1362-4555
ISSN	0168-9525 ; 0168-9479
DOI	10.1016/j.tig.2018.09.004
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Zs.A 2272: Show issues

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Article ; Online: In vitro-transcribed guide RNAs trigger an innate immune response via the RIG-I pathway.

Beeke Wienert / Jiyung Shin / Elena Zelin / Kathleen Pestal / Jacob E Corn

PLoS Biology, Vol 16, Iss 7, p e

2018 Volume 2005840

Abstract: Clustered, regularly interspaced, short palindromic repeat (CRISPR)-CRISPR-associated 9 (Cas9) genome editing is revolutionizing fundamental research and has great potential for the treatment of many diseases. While editing of immortalized cell lines has ...

Abstract	Clustered, regularly interspaced, short palindromic repeat (CRISPR)-CRISPR-associated 9 (Cas9) genome editing is revolutionizing fundamental research and has great potential for the treatment of many diseases. While editing of immortalized cell lines has become relatively easy, editing of therapeutically relevant primary cells and tissues can remain challenging. One recent advancement is the delivery of a Cas9 protein and an in vitro-transcribed (IVT) guide RNA (gRNA) as a precomplexed ribonucleoprotein (RNP). This approach allows editing of primary cells such as T cells and hematopoietic stem cells, but the consequences beyond genome editing of introducing foreign Cas9 RNPs into mammalian cells are not fully understood. Here, we show that the IVT gRNAs commonly used by many laboratories for RNP editing trigger a potent innate immune response that is similar to canonical immune-stimulating ligands. IVT gRNAs are recognized in the cytosol through the retinoic acid-inducible gene I (RIG-I) pathway but not the melanoma differentiation-associated gene 5 (MDA5) pathway, thereby triggering a type I interferon response. Removal of the 5'-triphosphate from gRNAs ameliorates inflammatory signaling and prevents the loss of viability associated with genome editing in hematopoietic stem cells. The potential for Cas9 RNP editing to induce a potent antiviral response indicates that care must be taken when designing therapeutic strategies to edit primary cells.
Keywords	Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2018-07-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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Article ; Online: In vitro-transcribed guide RNAs trigger an innate immune response via the RIG-I pathway.

Wienert, Beeke / Shin, Jiyung / Zelin, Elena / Pestal, Kathleen / Corn, Jacob E

PLoS biology

2018 Volume 16, Issue 7, Page(s) e2005840

Abstract	Clustered, regularly interspaced, short palindromic repeat (CRISPR)-CRISPR-associated 9 (Cas9) genome editing is revolutionizing fundamental research and has great potential for the treatment of many diseases. While editing of immortalized cell lines has become relatively easy, editing of therapeutically relevant primary cells and tissues can remain challenging. One recent advancement is the delivery of a Cas9 protein and an in vitro-transcribed (IVT) guide RNA (gRNA) as a precomplexed ribonucleoprotein (RNP). This approach allows editing of primary cells such as T cells and hematopoietic stem cells, but the consequences beyond genome editing of introducing foreign Cas9 RNPs into mammalian cells are not fully understood. Here, we show that the IVT gRNAs commonly used by many laboratories for RNP editing trigger a potent innate immune response that is similar to canonical immune-stimulating ligands. IVT gRNAs are recognized in the cytosol through the retinoic acid-inducible gene I (RIG-I) pathway but not the melanoma differentiation-associated gene 5 (MDA5) pathway, thereby triggering a type I interferon response. Removal of the 5'-triphosphate from gRNAs ameliorates inflammatory signaling and prevents the loss of viability associated with genome editing in hematopoietic stem cells. The potential for Cas9 RNP editing to induce a potent antiviral response indicates that care must be taken when designing therapeutic strategies to edit primary cells.
MeSH term(s)	Cell Line ; Cytosol/metabolism ; DEAD Box Protein 58/metabolism ; Humans ; Immunity, Innate/genetics ; Interferon Type I/metabolism ; Models, Biological ; RNA, Guide, CRISPR-Cas Systems/genetics ; RNA, Guide, CRISPR-Cas Systems/metabolism ; Receptors, Immunologic ; Transcription, Genetic
Chemical Substances	Interferon Type I ; RNA, Guide, CRISPR-Cas Systems ; Receptors, Immunologic ; RIGI protein, human (EC 3.6.1.-) ; DEAD Box Protein 58 (EC 3.6.4.13)
Language	English
Publishing date	2018-07-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.2005840
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