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Article ; Online: VirScan: High-throughput Profiling of Antiviral Antibody Epitopes.

Shrock, Ellen L / Shrock, Christine L / Elledge, Stephen J

2022 Volume 12, Issue 13

Abstract: Profiling the specificities of antibodies can reveal a wealth of information about humoral immune responses and the antigens they target. Here, we present a protocol for VirScan, an application of the phage immunoprecipitation sequencing (PhIP-Seq) ... ...

Abstract	Profiling the specificities of antibodies can reveal a wealth of information about humoral immune responses and the antigens they target. Here, we present a protocol for VirScan, an application of the phage immunoprecipitation sequencing (PhIP-Seq) method for profiling the specificities of human antiviral antibodies. Accompanying this protocol is a video of the experimental procedure. VirScan and, more generally, PhIP-Seq are techniques that enable high-throughput antibody profiling by combining high-throughput DNA oligo synthesis and bacteriophage display with next-generation sequencing. In the VirScan method, human sera samples are screened against a library of peptides spanning the entire human viral proteome. Bound phage are immunoprecipitated and sequenced, identifying the viral peptides recognized by the antibodies. VirScan Is a powerful tool for uncovering individual viral exposure histories, mapping the epitope landscape of viruses of interest, and studying fundamental mechanisms of viral immunity. Graphical abstract.
Language	English
Publishing date	2022-07-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833269-6
ISSN	2331-8325 ; 2331-8325
ISSN (online)	2331-8325
ISSN	2331-8325
DOI	10.21769/BioProtoc.4464
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: CasPlay provides a gRNA-barcoded CRISPR-based display platform for antibody repertoire profiling.

Barber, Karl W / Shrock, Ellen / Elledge, Stephen J

Cell reports methods

2022 Volume 2, Issue 10, Page(s) 100318

Abstract: Protein display technologies link proteins to distinct nucleic acid sequences (barcodes), enabling multiplexed protein assays via DNA sequencing. Here, we develop Cas9 display (CasPlay) to interrogate customized peptide libraries fused to catalytically ... ...

Abstract	Protein display technologies link proteins to distinct nucleic acid sequences (barcodes), enabling multiplexed protein assays via DNA sequencing. Here, we develop Cas9 display (CasPlay) to interrogate customized peptide libraries fused to catalytically inactive Cas9 (dCas9) by sequencing the guide RNA (gRNA) barcodes associated with each peptide. We first confirm the ability of CasPlay to characterize antibody epitopes by recovering a known binding motif for a monoclonal anti-FLAG antibody. We then use a CasPlay library tiling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteome to evaluate vaccine-induced antibody reactivities. Using a peptide library representing the human virome, we demonstrate the ability of CasPlay to identify epitopes across many viruses from microliters of patient serum. Our results suggest that CasPlay is a viable strategy for customized protein interaction studies from highly complex libraries and could provide an alternative to phage display technologies.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2/genetics ; Peptide Library ; Antibodies ; Epitopes/chemistry
Chemical Substances	Peptide Library ; Antibodies ; Epitopes
Language	English
Publishing date	2022-10-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	2667-2375
ISSN (online)	2667-2375
DOI	10.1016/j.crmeth.2022.100318
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Article ; Online: CRISPR-based peptide library display and programmable microarray self-assembly for rapid quantitative protein binding assays.

Barber, Karl W / Shrock, Ellen / Elledge, Stephen J

Molecular cell

2021 Volume 81, Issue 17, Page(s) 3650–3658.e5

Abstract: CRISPR-inspired systems have been extensively developed for applications in genome editing and nucleic acid detection. Here, we introduce a CRISPR-based peptide display technology to facilitate customized, high-throughput in vitro protein interaction ... ...

Abstract	CRISPR-inspired systems have been extensively developed for applications in genome editing and nucleic acid detection. Here, we introduce a CRISPR-based peptide display technology to facilitate customized, high-throughput in vitro protein interaction studies. We show that bespoke peptide libraries fused to catalytically inactive Cas9 (dCas9) and barcoded with unique single guide RNA (sgRNA) molecules self-assemble from a single mixed pool to programmable positions on a DNA microarray surface for rapid, multiplexed binding assays. We develop dCas9-displayed saturation mutagenesis libraries to characterize antibody-epitope binding for a commercial anti-FLAG monoclonal antibody and human serum antibodies. We also show that our platform can be used for viral epitope mapping and exhibits promise as a multiplexed diagnostics tool. Our CRISPR-based peptide display platform and the principles of complex library self-assembly using dCas9 could be adapted for rapid interrogation of varied customized protein libraries or biological materials assembly using DNA scaffolding.
MeSH term(s)	CRISPR-Cas Systems/genetics ; CRISPR-Cas Systems/immunology ; Epitopes/genetics ; Epitopes/immunology ; Gene Editing/methods ; Humans ; Mutagenesis/genetics ; Peptide Library ; Protein Binding/genetics ; Protein Binding/immunology ; RNA, Guide, CRISPR-Cas Systems/genetics ; RNA, Guide, CRISPR-Cas Systems/immunology
Chemical Substances	Epitopes ; Peptide Library ; RNA, Guide, CRISPR-Cas Systems
Language	English
Publishing date	2021-08-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2021.07.027
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Article ; Online: CRISPR in Animals and Animal Models.

Shrock, Ellen / Güell, Marc

Progress in molecular biology and translational science

2017 Volume 152, Page(s) 95–114

Abstract: CRISPR-Cas9 has revolutionized the generation of transgenic animals. This system has demonstrated an unprecedented efficiency, multiplexability, and ease of use, thereby reducing the time and cost required for genome editing and enabling the production ... ...

Abstract	CRISPR-Cas9 has revolutionized the generation of transgenic animals. This system has demonstrated an unprecedented efficiency, multiplexability, and ease of use, thereby reducing the time and cost required for genome editing and enabling the production of animals with more extensive genetic modifications. It has also been shown to be applicable to a wide variety of animals, from early-branching metazoans to primates. Genome-wide screens in model organisms have been performed, accurate models of human diseases have been constructed, and potential therapies have been tested and validated in animal models. Several achievements in genetic modification of animals have been translated into products for the agricultural and pharmaceutical industries. Based on the remarkable progress to date, one may anticipate that in the future, CRISPR-Cas9 technology will enable additional far-reaching advances, including understanding the bases of diseases with complex genetic origins, engineering animals to produce organs for human transplantation, and genetically transforming entire populations of organisms to prevent the spread of disease.
MeSH term(s)	Animals ; Clustered Regularly Interspaced Short Palindromic Repeats ; Genetic Engineering ; Genetic Therapy ; Models, Animal
Language	English
Publishing date	2017
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2471995-X
ISSN	1878-0814 ; 0079-6603 ; 1877-1173
ISSN (online)	1878-0814
ISSN	0079-6603 ; 1877-1173
DOI	10.1016/bs.pmbts.2017.07.010
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Article: CRISPR-based peptide library display and programmable microarray self-assembly for rapid quantitative protein binding assays

Barber, Karl W. / Shrock, Ellen / Elledge, Stephen J.

Molecular cell. 2021 Sept. 02, v. 81, no. 17

2021

Abstract	CRISPR-inspired systems have been extensively developed for applications in genome editing and nucleic acid detection. Here, we introduce a CRISPR-based peptide display technology to facilitate customized, high-throughput in vitro protein interaction studies. We show that bespoke peptide libraries fused to catalytically inactive Cas9 (dCas9) and barcoded with unique single guide RNA (sgRNA) molecules self-assemble from a single mixed pool to programmable positions on a DNA microarray surface for rapid, multiplexed binding assays. We develop dCas9-displayed saturation mutagenesis libraries to characterize antibody-epitope binding for a commercial anti-FLAG monoclonal antibody and human serum antibodies. We also show that our platform can be used for viral epitope mapping and exhibits promise as a multiplexed diagnostics tool. Our CRISPR-based peptide display platform and the principles of complex library self-assembly using dCas9 could be adapted for rapid interrogation of varied customized protein libraries or biological materials assembly using DNA scaffolding.
Keywords	DNA ; DNA microarrays ; RNA ; blood serum ; diagnostic techniques ; epitopes ; genome ; humans ; monoclonal antibodies ; mutagenesis ; peptide libraries
Language	English
Dates of publication	2021-0902
Size	p. 3650-3658.e5.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2021.07.027
Database	NAL-Catalogue (AGRICOLA)

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Article: Atomically accurate de novo design of single-domain antibodies.

bioRxiv : the preprint server for biology

2024

Abstract: Despite the central role that antibodies play in modern medicine, there is currently no way to rationally design novel antibodies to bind a specific epitope on a target. Instead, antibody discovery currently involves time-consuming immunization of an ... ...

Abstract	Despite the central role that antibodies play in modern medicine, there is currently no way to rationally design novel antibodies to bind a specific epitope on a target. Instead, antibody discovery currently involves time-consuming immunization of an animal or library screening approaches. Here we demonstrate that a fine-tuned RFdiffusion network is capable of designing de novo antibody variable heavy chains (VHH's) that bind user-specified epitopes. We experimentally confirm binders to four disease-relevant epitopes, and the cryo-EM structure of a designed VHH bound to influenza hemagglutinin is nearly identical to the design model both in the configuration of the CDR loops and the overall binding pose.
Language	English
Publishing date	2024-03-18
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.14.585103
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Article ; Online: Germline-encoded amino acid-binding motifs drive immunodominant public antibody responses.

Shrock, Ellen L / Timms, Richard T / Kula, Tomasz / Mena, Elijah L / West, Anthony P / Guo, Rui / Lee, I-Hsiu / Cohen, Alexander A / McKay, Lindsay G A / Bi, Caihong / Leng, Yumei / Fujimura, Eric / Horns, Felix / Li, Mamie / Wesemann, Duane R / Griffiths, Anthony / Gewurz, Benjamin E / Bjorkman, Pamela J / Elledge, Stephen J

Science (New York, N.Y.)

2023 Volume 380, Issue 6640, Page(s) eadc9498

Abstract: Despite the vast diversity of the antibody repertoire, infected individuals often mount antibody responses to precisely the same epitopes within antigens. The immunological mechanisms underpinning this phenomenon remain unknown. By mapping 376 ... ...

Abstract	Despite the vast diversity of the antibody repertoire, infected individuals often mount antibody responses to precisely the same epitopes within antigens. The immunological mechanisms underpinning this phenomenon remain unknown. By mapping 376 immunodominant "public epitopes" at high resolution and characterizing several of their cognate antibodies, we concluded that germline-encoded sequences in antibodies drive recurrent recognition. Systematic analysis of antibody-antigen structures uncovered 18 human and 21 partially overlapping mouse germline-encoded amino acid-binding (GRAB) motifs within heavy and light V gene segments that in case studies proved critical for public epitope recognition. GRAB motifs represent a fundamental component of the immune system's architecture that promotes recognition of pathogens and leads to species-specific public antibody responses that can exert selective pressure on pathogens.
MeSH term(s)	Animals ; Humans ; Mice ; Antibody Formation ; Germ Cells ; Immunodominant Epitopes/chemistry ; Immunodominant Epitopes/genetics ; Immunoglobulin Heavy Chains/genetics ; Immunoglobulin Heavy Chains/immunology ; Amino Acid Motifs ; Immunoglobulin Light Chains/genetics ; Immunoglobulin Light Chains/immunology ; Epitope Mapping ; Host-Pathogen Interactions/genetics ; Host-Pathogen Interactions/immunology
Chemical Substances	Immunodominant Epitopes ; Immunoglobulin Heavy Chains ; Immunoglobulin Light Chains
Language	English
Publishing date	2023-04-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.adc9498
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Article ; Online: Atomically accurate de novo design of single-domain antibodies

bioRxiv

Abstract	Despite the central role that antibodies play in modern medicine, there is currently no way to rationally design novel antibodies to bind a specific epitope on a target. Instead, antibody discovery currently involves time-consuming immunization of an animal or library screening approaches. Here we demonstrate that a fine-tuned RFdiffusion network is capable of designing de novo antibody variable heavy chains (VHH9s) that bind user-specified epitopes. We experimentally confirm binders to four disease-relevant epitopes, and the cryo-EM structure of a designed VHH bound to influenza hemagglutinin is nearly identical to the design model both in the configuration of the CDR loops and the overall binding pose.
Keywords	covid19
Language	English
Publishing date	2024-03-18
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2024.03.14.585103
Database	COVID19

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Article ; Online: High-resolution epitope mapping by AllerScan reveals relationships between IgE and IgG repertoires during peanut oral immunotherapy.

Chen, Genghao / Shrock, Ellen L / Li, Mamie Z / Spergel, Jonathan M / Nadeau, Kari C / Pongracic, Jacqueline A / Umetsu, Dale T / Rachid, Rima / MacGinnitie, Andrew J / Phipatanakul, Wanda / Schneider, Lynda / Oettgen, Hans C / Elledge, Stephen J

Cell reports. Medicine

2021 Volume 2, Issue 10, Page(s) 100410

Abstract: Peanut allergy can result in life-threatening reactions and is a major public health concern. Oral immunotherapy (OIT) induces desensitization to food allergens through administration of increasing amounts of allergen. To dissect peanut-specific ... ...

Abstract	Peanut allergy can result in life-threatening reactions and is a major public health concern. Oral immunotherapy (OIT) induces desensitization to food allergens through administration of increasing amounts of allergen. To dissect peanut-specific immunoglobulin E (IgE) and IgG responses in subjects undergoing OIT, we have developed AllerScan, a method that leverages phage-display and next-generation sequencing to identify the epitope targets of peanut-specific antibodies. We observe a striking diversification and boosting of the peanut-specific IgG repertoire after OIT and a reduction in pre-existing IgE levels against individual epitopes. High-resolution epitope mapping reveals shared recognition of public epitopes in Ara h 1, 2, 3, and 7. In individual subjects, OIT-induced IgG specificities overlap extensively with IgE and exhibit strikingly similar antibody footprints, suggesting related clonal lineages or convergent evolution of peanut-specific IgE and IgG B cells. Individual differences in epitope recognition identified via AllerScan could inform safer and more effective personalized immunotherapy.
MeSH term(s)	2S Albumins, Plant/administration & dosage ; 2S Albumins, Plant/chemistry ; Antigens, Plant/administration & dosage ; Antigens, Plant/chemistry ; Arachis/chemistry ; Arachis/immunology ; B-Lymphocytes/immunology ; B-Lymphocytes/pathology ; Case-Control Studies ; Desensitization, Immunologic/methods ; Epitope Mapping/methods ; Epitopes/chemistry ; Epitopes/immunology ; High-Throughput Nucleotide Sequencing ; High-Throughput Screening Assays ; Humans ; Immunoglobulin E/blood ; Immunoglobulin G/blood ; Membrane Proteins/administration & dosage ; Membrane Proteins/chemistry ; Omalizumab/therapeutic use ; Peanut Hypersensitivity/genetics ; Peanut Hypersensitivity/immunology ; Peanut Hypersensitivity/pathology ; Peanut Hypersensitivity/therapy ; Peptide Library ; Plant Proteins/administration & dosage ; Plant Proteins/chemistry ; Precision Medicine ; Seed Storage Proteins
Chemical Substances	2S Albumins, Plant ; Antigens, Plant ; Ara h 1 protein, Arachis hypogaea ; Ara h 2 allergen, Arachis hypogaea ; Epitopes ; Immunoglobulin G ; Membrane Proteins ; Peptide Library ; Plant Proteins ; Seed Storage Proteins ; allergen Ara h3 ; Omalizumab (2P471X1Z11) ; Immunoglobulin E (37341-29-0)
Language	English
Publishing date	2021-10-19
Publishing country	United States
Document type	Journal Article ; Multicenter Study ; Randomized Controlled Trial ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2666-3791
ISSN (online)	2666-3791
DOI	10.1016/j.xcrm.2021.100410
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Article ; Online: High-resolution epitope mapping by AllerScan reveals relationships between IgE and IgG repertoires during peanut oral immunotherapy

Genghao Chen / Ellen L. Shrock / Mamie Z. Li / Jonathan M. Spergel / Kari C. Nadeau / Jacqueline A. Pongracic / Dale T. Umetsu / Rima Rachid / Andrew J. MacGinnitie / Wanda Phipatanakul / Lynda Schneider / Hans C. Oettgen / Stephen J. Elledge

Cell Reports Medicine, Vol 2, Iss 10, Pp 100410- (2021)

2021

Abstract: Summary: Peanut allergy can result in life-threatening reactions and is a major public health concern. Oral immunotherapy (OIT) induces desensitization to food allergens through administration of increasing amounts of allergen. To dissect peanut-specific ...

Abstract	Summary: Peanut allergy can result in life-threatening reactions and is a major public health concern. Oral immunotherapy (OIT) induces desensitization to food allergens through administration of increasing amounts of allergen. To dissect peanut-specific immunoglobulin E (IgE) and IgG responses in subjects undergoing OIT, we have developed AllerScan, a method that leverages phage-display and next-generation sequencing to identify the epitope targets of peanut-specific antibodies. We observe a striking diversification and boosting of the peanut-specific IgG repertoire after OIT and a reduction in pre-existing IgE levels against individual epitopes. High-resolution epitope mapping reveals shared recognition of public epitopes in Ara h 1, 2, 3, and 7. In individual subjects, OIT-induced IgG specificities overlap extensively with IgE and exhibit strikingly similar antibody footprints, suggesting related clonal lineages or convergent evolution of peanut-specific IgE and IgG B cells. Individual differences in epitope recognition identified via AllerScan could inform safer and more effective personalized immunotherapy.
Keywords	peanut allergy ; antibody ; antibody repertoire ; phage display ; oral immunotherapy ; food allergy ; Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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