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Article ; Online: Disease etiology and diagnosis by TCR repertoire analysis goes viral.

Attaf, Meriem / Sewell, Andrew K

2016 Volume 46, Issue 11, Page(s) 2516–2519

Abstract: The importance of T-cell receptor (TCR) repertoire diversity is highlighted in murine models of immunodeficiency and in many human pathologies. However, the true extent of TCR diversity and how this diversity varies in health and disease is poorly ... ...

Abstract	The importance of T-cell receptor (TCR) repertoire diversity is highlighted in murine models of immunodeficiency and in many human pathologies. However, the true extent of TCR diversity and how this diversity varies in health and disease is poorly understood. In a previous issue of the European Journal of Immunology, Lossius et al. [Eur. J. Immunol. 2014. 44: 3439-3452] dissected the composition of the TCR repertoire in the context of multiple sclerosis (MS) using high-throughput sequencing of TCR-β chains in cerebrospinal fluid samples and blood. The authors demonstrated that the TCR repertoire of the CSF was largely distinct from the blood and enriched in EBV-reactive CD8
MeSH term(s)	Animals ; Humans ; Mice ; Multiple Sclerosis/immunology ; Receptors, Antigen, T-Cell/genetics ; Receptors, Antigen, T-Cell, alpha-beta/genetics ; T-Lymphocytes
Chemical Substances	Receptors, Antigen, T-Cell ; Receptors, Antigen, T-Cell, alpha-beta
Language	English
Publishing date	2016
Publishing country	Germany
Document type	Journal Article ; Comment
ZDB-ID	120108-6
ISSN	1521-4141 ; 0014-2980
ISSN (online)	1521-4141
ISSN	0014-2980
DOI	10.1002/eji.201646649
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Article ; Online: αβ T cell receptors as predictors of health and disease.

Attaf, Meriem / Huseby, Eric / Sewell, Andrew K

Cellular & molecular immunology

2015 Volume 12, Issue 4, Page(s) 391–399

Abstract: The diversity of antigen receptors and the specificity it underlies are the hallmarks of the cellular arm of the adaptive immune system. T and B lymphocytes are indeed truly unique in their ability to generate receptors capable of recognizing virtually ... ...

Abstract	The diversity of antigen receptors and the specificity it underlies are the hallmarks of the cellular arm of the adaptive immune system. T and B lymphocytes are indeed truly unique in their ability to generate receptors capable of recognizing virtually any pathogen. It has been known for several decades that T lymphocytes recognize short peptides derived from degraded proteins presented by major histocompatibility complex (MHC) molecules at the cell surface. Interaction between peptide-MHC (pMHC) and the T cell receptor (TCR) is central to both thymic selection and peripheral antigen recognition. It is widely assumed that TCR diversity is required, or at least highly desirable, to provide sufficient immune coverage. However, a number of immune responses are associated with the selection of predictable, narrow, or skewed repertoires and public TCR chains. Here, we summarize the current knowledge on the formation of the TCR repertoire and its maintenance in health and disease. We also outline the various molecular mechanisms that govern the composition of the pre-selection, naive and antigen-specific TCR repertoires. Finally, we suggest that with the development of high-throughput sequencing, common TCR 'signatures' raised against specific antigens could provide important diagnostic biomarkers and surrogate predictors of disease onset, progression and outcome.
MeSH term(s)	Animals ; Antigens/immunology ; Biomarkers ; Histocompatibility Antigens/immunology ; Humans ; Receptors, Antigen, T-Cell, alpha-beta/immunology ; T-Lymphocytes/immunology ; T-Lymphocytes/pathology ; Thymus Gland/immunology ; Thymus Gland/pathology
Chemical Substances	Antigens ; Biomarkers ; Histocompatibility Antigens ; Receptors, Antigen, T-Cell, alpha-beta
Language	English
Publishing date	2015-01-26
Publishing country	China
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2435097-7
ISSN	2042-0226 ; 1672-7681
ISSN (online)	2042-0226
ISSN	1672-7681
DOI	10.1038/cmi.2014.134
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Article ; Online: αβ T cell receptor germline CDR regions moderate contact with MHC ligands and regulate peptide cross-reactivity.

Attaf, Meriem / Holland, Stephan J / Bartok, Istvan / Dyson, Julian

Scientific reports

2016 Volume 6, Page(s) 35006

Abstract: αβ T cells respond to peptide epitopes presented by major histocompatibility complex (MHC) molecules. The role of T cell receptor (TCR) germline complementarity determining regions (CDR1 and 2) in MHC restriction is not well understood. Here, we examine ... ...

Abstract	αβ T cells respond to peptide epitopes presented by major histocompatibility complex (MHC) molecules. The role of T cell receptor (TCR) germline complementarity determining regions (CDR1 and 2) in MHC restriction is not well understood. Here, we examine T cell development, MHC restriction and antigen recognition where germline CDR loop structure has been modified by multiple glycine/alanine substitutions. Surprisingly, loss of germline structure increases TCR engagement with MHC ligands leading to excessive loss of immature thymocytes. MHC restriction is, however, strictly maintained. The peripheral T cell repertoire is affected similarly, exhibiting elevated cross-reactivity to foreign peptides. Our findings are consistent with germline TCR structure optimising T cell cross-reactivity and immunity by moderating engagement with MHC ligands. This strategy may operate alongside co-receptor imposed MHC restriction, freeing germline TCR structure to adopt this novel role in the TCR-MHC interface.
MeSH term(s)	Amino Acid Substitution ; Animals ; Complementarity Determining Regions/chemistry ; Complementarity Determining Regions/genetics ; Cross Reactions ; Female ; Histocompatibility Antigens/metabolism ; Major Histocompatibility Complex/immunology ; Mice ; Models, Molecular ; Receptors, Antigen, T-Cell, alpha-beta/chemistry ; Receptors, Antigen, T-Cell, alpha-beta/genetics ; Receptors, Antigen, T-Cell, alpha-beta/immunology
Chemical Substances	Complementarity Determining Regions ; Histocompatibility Antigens ; Receptors, Antigen, T-Cell, alpha-beta
Language	English
Publishing date	2016-10-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/srep35006
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Article ; Online: Cytomegalovirus-Mediated T Cell Receptor Repertoire Perturbation Is Present in Early Life.

Attaf, Meriem / Roider, Julia / Malik, Amna / Rius Rafael, Cristina / Dolton, Garry / Predergast, Andrew J / Leslie, Alasdair / Ndung'u, Thumbi / Kløverpris, Henrik N / Sewell, Andrew K / Goulder, Philip J

Frontiers in immunology

2020 Volume 11, Page(s) 1587

Abstract: Human cytomegalovirus (CMV) is a highly prevalent herpesvirus, particularly in sub-Saharan Africa, where it is endemic from infancy. The T cell response against CMV is important in keeping the virus in check, with CD8 T cells playing a major role in the ... ...

Abstract	Human cytomegalovirus (CMV) is a highly prevalent herpesvirus, particularly in sub-Saharan Africa, where it is endemic from infancy. The T cell response against CMV is important in keeping the virus in check, with CD8 T cells playing a major role in the control of CMV viraemia. Human leukocyte antigen (HLA) B
MeSH term(s)	Adolescent ; Adult ; Age Factors ; Antigens, Viral/immunology ; CD8-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/metabolism ; Child ; Child, Preschool ; Coinfection ; Cytomegalovirus/immunology ; Cytomegalovirus Infections/immunology ; Cytomegalovirus Infections/metabolism ; Cytomegalovirus Infections/virology ; Epitopes, T-Lymphocyte/chemistry ; Epitopes, T-Lymphocyte/immunology ; Female ; HIV Infections/immunology ; HIV Infections/virology ; HLA Antigens/immunology ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Leukocytes, Mononuclear/immunology ; Leukocytes, Mononuclear/metabolism ; Peptides/chemistry ; Peptides/immunology ; Receptors, Antigen, T-Cell/genetics ; Receptors, Antigen, T-Cell/metabolism ; T-Cell Antigen Receptor Specificity ; T-Lymphocytes/immunology ; T-Lymphocytes/metabolism ; Viral Load ; Young Adult
Chemical Substances	Antigens, Viral ; Epitopes, T-Lymphocyte ; HLA Antigens ; Peptides ; Receptors, Antigen, T-Cell
Language	English
Publishing date	2020-09-30
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2020.01587
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Article ; Online: Corrigendum: Cytomegalovirus-Mediated T Cell Receptor Repertoire Perturbation Is Present in Early Life.

Attaf, Meriem / Roider, Julia / Malik, Amna / Rafael, Cristina Rius / Dolton, Garry / Prendergast, Andrew J / Leslie, Alasdair / Ndung'u, Thumbi / Kløverpris, Henrik N / Sewell, Andrew K / Goulder, Philip J

Frontiers in immunology

2020 Volume 11, Page(s) 633633

Abstract: This corrects the article DOI: 10.3389/fimmu.2020.01587.]. ...

Abstract	[This corrects the article DOI: 10.3389/fimmu.2020.01587.].
Language	English
Publishing date	2020-12-21
Publishing country	Switzerland
Document type	Published Erratum
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2020.633633
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Article ; Online: Targeting of multiple tumor-associated antigens by individual T cell receptors during successful cancer immunotherapy.

Dolton, Garry / Rius, Cristina / Wall, Aaron / Szomolay, Barbara / Bianchi, Valentina / Galloway, Sarah A E / Hasan, Md Samiul / Morin, Théo / Caillaud, Marine E / Thomas, Hannah L / Theaker, Sarah / Tan, Li Rong / Fuller, Anna / Topley, Katie / Legut, Mateusz / Attaf, Meriem / Hopkins, Jade R / Behiry, Enas / Zabkiewicz, Joanna /

Alvares, Caroline / Lloyd, Angharad / Rogers, Amber / Henley, Peter / Fegan, Christopher / Ottmann, Oliver / Man, Stephen / Crowther, Michael D / Donia, Marco / Svane, Inge Marie / Cole, David K / Brown, Paul E / Rizkallah, Pierre / Sewell, Andrew K

Cell

2023 Volume 186, Issue 16, Page(s) 3333–3349.e27

Abstract: The T cells of the immune system can target tumors and clear solid cancers following tumor-infiltrating lymphocyte (TIL) therapy. We used combinatorial peptide libraries and a proteomic database to reveal the antigen specificities of persistent cancer- ... ...

Abstract	The T cells of the immune system can target tumors and clear solid cancers following tumor-infiltrating lymphocyte (TIL) therapy. We used combinatorial peptide libraries and a proteomic database to reveal the antigen specificities of persistent cancer-specific T cell receptors (TCRs) following successful TIL therapy for stage IV malignant melanoma. Remarkably, individual TCRs could target multiple different tumor types via the HLA A
MeSH term(s)	Antigens, Neoplasm/metabolism ; Epitopes ; Immunotherapy ; Lymphocytes, Tumor-Infiltrating ; Neoplasms/immunology ; Neoplasms/therapy ; Proteomics ; Receptors, Antigen, T-Cell/metabolism
Chemical Substances	Antigens, Neoplasm ; Epitopes ; Receptors, Antigen, T-Cell
Language	English
Publishing date	2023-07-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2023.06.020
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Article ; Online: GPU-Accelerated Discovery of Pathogen-Derived Molecular Mimics of a T-Cell Insulin Epitope.

Whalley, Thomas / Dolton, Garry / Brown, Paul E / Wall, Aaron / Wooldridge, Linda / van den Berg, Hugo / Fuller, Anna / Hopkins, Jade R / Crowther, Michael D / Attaf, Meriem / Knight, Robin R / Cole, David K / Peakman, Mark / Sewell, Andrew K / Szomolay, Barbara

Frontiers in immunology

2020 Volume 11, Page(s) 296

Abstract: The strong links between (Human Leukocyte Antigen) HLA, infection and autoimmunity combine to implicate T-cells as primary triggers of autoimmune disease (AD). T-cell crossreactivity between microbially-derived peptides and self-peptides has been shown ... ...

Abstract	The strong links between (Human Leukocyte Antigen) HLA, infection and autoimmunity combine to implicate T-cells as primary triggers of autoimmune disease (AD). T-cell crossreactivity between microbially-derived peptides and self-peptides has been shown to break tolerance and trigger AD in experimental animal models. Detailed examination of the potential for T-cell crossreactivity to trigger human AD will require means of predicting which peptides might be recognised by autoimmune T-cell receptors (TCRs). Recent developments in high throughput sequencing and bioinformatics mean that it is now possible to link individual TCRs to specific pathologies for the first time. Deconvolution of TCR function requires knowledge of TCR specificity. Positional Scanning Combinatorial Peptide Libraries (PS-CPLs) can be used to predict HLA-restriction and define antigenic peptides derived from self and pathogen proteins.
MeSH term(s)	Clone Cells ; Combinatorial Chemistry Techniques ; Computational Biology ; Cross Reactions ; Epitope Mapping ; Epitopes, T-Lymphocyte/genetics ; Epitopes, T-Lymphocyte/immunology ; Epitopes, T-Lymphocyte/metabolism ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Insulin/immunology ; Insulin/metabolism ; Molecular Mimicry ; Pathogen-Associated Molecular Pattern Molecules/immunology ; Pathogen-Associated Molecular Pattern Molecules/metabolism ; Peptide Library ; Receptors, Antigen, T-Cell/metabolism ; T-Cell Antigen Receptor Specificity ; T-Lymphocytes/immunology
Chemical Substances	Epitopes, T-Lymphocyte ; Insulin ; Pathogen-Associated Molecular Pattern Molecules ; Peptide Library ; Receptors, Antigen, T-Cell
Language	English
Publishing date	2020-02-28
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2020.00296
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Article ; Online: A Molecular Switch Abrogates Glycoprotein 100 (gp100) T-cell Receptor (TCR) Targeting of a Human Melanoma Antigen.

Bianchi, Valentina / Bulek, Anna / Fuller, Anna / Lloyd, Angharad / Attaf, Meriem / Rizkallah, Pierre J / Dolton, Garry / Sewell, Andrew K / Cole, David K

The Journal of biological chemistry

2016 Volume 291, Issue 17, Page(s) 8951–8959

Abstract: Human CD8(+) cytotoxic T lymphocytes can mediate tumor regression in melanoma through the specific recognition of HLA-restricted peptides. Because of the relatively weak affinity of most anti-cancer T-cell receptors (TCRs), there is growing emphasis on ... ...

Abstract	Human CD8(+) cytotoxic T lymphocytes can mediate tumor regression in melanoma through the specific recognition of HLA-restricted peptides. Because of the relatively weak affinity of most anti-cancer T-cell receptors (TCRs), there is growing emphasis on immunizing melanoma patients with altered peptide ligands in order to induce strong anti-tumor immunity capable of breaking tolerance toward these self-antigens. However, previous studies have shown that these immunogenic designer peptides are not always effective. The melanocyte differentiation protein, glycoprotein 100 (gp100), encodes a naturally processed epitope that is an attractive target for melanoma immunotherapies, in particular peptide-based vaccines. Previous studies have shown that substitutions at peptide residue Glu(3) have a broad negative impact on polyclonal T-cell responses. Here, we describe the first atomic structure of a natural cognate TCR in complex with this gp100 epitope and highlight the relatively high affinity of the interaction. Alanine scan mutagenesis performed across the gp100(280-288) peptide showed that Glu(3) was critically important for TCR binding. Unexpectedly, structural analysis demonstrated that the Glu(3) → Ala substitution resulted in a molecular switch that was transmitted to adjacent residues, abrogating TCR binding and T-cell recognition. These findings help to clarify the mechanism of T-cell recognition of gp100 during melanoma responses and could direct the development of altered peptides for vaccination.
MeSH term(s)	CD8-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/pathology ; Humans ; Melanoma/genetics ; Melanoma/immunology ; Melanoma/pathology ; Protein Structure, Quaternary ; Receptors, Antigen, T-Cell/chemistry ; Receptors, Antigen, T-Cell/genetics ; Receptors, Antigen, T-Cell/immunology ; gp100 Melanoma Antigen/chemistry ; gp100 Melanoma Antigen/genetics ; gp100 Melanoma Antigen/immunology
Chemical Substances	Receptors, Antigen, T-Cell ; gp100 Melanoma Antigen
Language	English
Publishing date	2016-02-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M115.707414
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Article ; Online: Reversible Oligonucleotide Chain Blocking Enables Bead Capture and Amplification of T-Cell Receptor α and β Chain mRNAs.

Hanson, W Miachel / Chen, Zhe / Jackson, Laurie K / Attaf, Meriem / Sewell, Andrew K / Heemstra, Jennifer M / Phillips, John D

Journal of the American Chemical Society

2016 Volume 138, Issue 35, Page(s) 11073–11076

Abstract: Next-generation sequencing (NGS) has proven to be an exceptionally powerful tool for studying genetic variation and differences in gene expression profiles between cell populations. However, these population-wide studies are limited by their inability to ...

Abstract	Next-generation sequencing (NGS) has proven to be an exceptionally powerful tool for studying genetic variation and differences in gene expression profiles between cell populations. However, these population-wide studies are limited by their inability to detect variation between individual cells within a population, inspiring the development of single-cell techniques such as Drop-seq, which add a unique barcode to the mRNA from each cell prior to sequencing. Current Drop-seq technology enables capture, amplification, and barcoding of the entire mRNA transcriptome of individual cells. NGS can then be used to sequence the 3'-end of each message to build a cell-specific transcriptional landscape. However, current technology does not allow high-throughput capture of information distant from the mRNA poly-A tail. Thus, gene profiling would have much greater utility if beads could be generated having multiple transcript-specific capture sequences. Here we report the use of a reversible chain blocking group to enable synthesis of DNA barcoded beads having capture sequences for the constant domains of the T-cell receptor α and β chain mRNAs. We demonstrate that these beads can be used to capture and pair TCRα and TCRβ sequences from total T-cell RNA, enabling reverse transcription and PCR amplification of these sequences. This is the first example of capture beads having more than one capture sequence, and we envision that this technology will be of high utility for applications such as pairing the antigen receptor chains that give rise to autoimmune diseases or measuring the ratios of mRNA splice variants in cancer stem cells.
MeSH term(s)	High-Throughput Nucleotide Sequencing ; Microspheres ; Models, Molecular ; Nucleic Acid Amplification Techniques/methods ; Nucleic Acid Conformation ; Oligonucleotides/chemistry ; RNA, Messenger/chemistry ; RNA, Messenger/genetics ; Receptors, Antigen, T-Cell, alpha-beta/genetics ; Sequence Analysis, RNA
Chemical Substances	Oligonucleotides ; RNA, Messenger ; Receptors, Antigen, T-Cell, alpha-beta
Language	English
Publishing date	2016-08-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.6b04465
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Article: Reversible Oligonucleotide Chain Blocking Enables Bead Capture and Amplification of T-Cell Receptor Î± and Î² Chain mRNAs

Hanson, W. Miachel / Attaf Meriem / Chen Zhe / Heemstra Jennifer M / Jackson Laurie K / Phillips John D / Sewell Andrew K

Journal of the American Chemical Society. 2016 Sept. 07, v. 138, no. 35

2016

Abstract	Next-generation sequencing (NGS) has proven to be an exceptionally powerful tool for studying genetic variation and differences in gene expression profiles between cell populations. However, these population-wide studies are limited by their inability to detect variation between individual cells within a population, inspiring the development of single-cell techniques such as Drop-seq, which add a unique barcode to the mRNA from each cell prior to sequencing. Current Drop-seq technology enables capture, amplification, and barcoding of the entire mRNA transcriptome of individual cells. NGS can then be used to sequence the 3â²-end of each message to build a cell-specific transcriptional landscape. However, current technology does not allow high-throughput capture of information distant from the mRNA poly-A tail. Thus, gene profiling would have much greater utility if beads could be generated having multiple transcript-specific capture sequences. Here we report the use of a reversible chain blocking group to enable synthesis of DNA barcoded beads having capture sequences for the constant domains of the T-cell receptor Î± and Î² chain mRNAs. We demonstrate that these beads can be used to capture and pair TCRÎ± and TCRÎ² sequences from total T-cell RNA, enabling reverse transcription and PCR amplification of these sequences. This is the first example of capture beads having more than one capture sequence, and we envision that this technology will be of high utility for applications such as pairing the antigen receptor chains that give rise to autoimmune diseases or measuring the ratios of mRNA splice variants in cancer stem cells.
Keywords	antigens ; autoimmune diseases ; DNA barcoding ; gene expression ; genes ; genetic variation ; high-throughput nucleotide sequencing ; messenger RNA ; neoplasms ; oligonucleotides ; reverse transcriptase polymerase chain reaction ; stem cells ; T-lymphocytes ; transcription (genetics) ; transcriptome
Language	English
Dates of publication	2016-0907
Size	p. 11073-11076.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021%2Fjacs.6b04465
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