eISSN: 1644-4124
ISSN: 1426-3912
Central European Journal of Immunology
Current issue Archive Manuscripts accepted About the journal Abstracting and indexing Subscription Contact Instructions for authors
SCImago Journal & Country Rank

3/2018
vol. 43
 
Share:
Share:
more
 
 
abstract:
Clinical immunology

Comparison of T-cell receptor β chain variable region 23-1 open reading frame and 3-1 F CDR3 repertoire in cDNA and gDNA from peripheral blood mononuclear cells of healthy volunteers by high-throughput sequencing

Xiaoyan He, Bin Shi, Long Ma, Rui Ma, Aihua Peng, Suhong Sun, Xinsheng Yao

(Centr Eur J Immunol 2018; 43 (3): 295-305)
Online publish date: 2018/10/30
View full text
Get citation
ENW
EndNote
BIB
JabRef, Mendeley
RIS
Papers, Reference Manager, RefWorks, Zotero
AMA
APA
Chicago
Harvard
MLA
Vancouver
 
The TRBV germline gene can be classified into three types: open reading frame (ORF), functional gene (F), and pseudogene (P); however, the differences and connections among ORF, functional gene, and pseudogene rearrangements and expression characteristics remain unclear. Here, we compared the characteristics of the CDR3 repertoire that was rearranged by TRBV23-1(ORF) and TRBV3-1(F) in four cDNA samples and six gDNA samples from healthy volunteers. In this study, we show that the frequencies of in-frame sequences in the TRBV23-1 complementarity determining region 3 (CDR3) repertoire were significantly lower than those in the TRBV3-1 CDR3 repertoire. The TRBV23-1 CDR3 repertoire, which differed from the TRBV3-1 in-frame and out-of-frame CDR3 repertoire, consisted of 1/3 in-frame sequences and 2/3 out-of-frame sequences. The usage of TRBD1 was higher than that of TRBD2 in the TRBV23-1 in-frame and out-of-frame CDR3 repertoire. In four cDNA samples from PBMCs, the TRBV23-1 in-frame and out-of-frame CDR3 repertoire showed a longer N2 relative to that of N1. Therefore, our results demonstrate that the mechanisms of rearrangement in the TRBV23-1 and TRBV3-1 CDR3 repertoire were different, and thus offered new ideas and methods to resolve the discrepancies in reports on the functionality of TRBV23-1 and to better understand the mechanisms underlying VDJ recombination.
keywords:

T-cell receptor, T-cell receptor β variable, complementarity-determining region 3 repertoire, open reading frame, high-throughput sequencing

references:
Tonegawa S (1988): Antibody and T-cell receptors. JAMA 259: 1845-1847.
Rowen L, Koop BF, Hood L (1996): The complete 685-kilobase DNA sequence of the human beta T cell receptor locus. Science 272: 1755-1762.
http://www.imgt.org/
http://www.embl.org/
Currier JR, Yassai M, Robinson MA, Gorski J (1996): Molecular defects in TCRBV genes preclude thymic selection and limit the expressed TCR repertoire. J Immunol 157: 170-175.
Than S, Kharbanda M, Chitnis V, et al. (1999): Clonal dominance patterns of CD8 T cells in relation to disease progression in HIV-infected children. J Immunol 162: 3680-3686.
Manfras BJ, Terjung D, Boehm BO (1999): Non-productive human TCR beta chain genes represent V-D-J diversity before selection upon function: insight into biased usage of TCRBD and TCRBJ genes and diversity of CDR3 region length. Hum Immunol 60: 1090-1100.
Pommié C, Levadoux S, Sabatier R, et al. (2004): IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties. J Mol Recognit 17: 17-32.
Alamyar E, Duroux P, Lefranc MP, Giudicelli V (2012): IMGT(R) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS. Methods Mol Biol 882: 569-604.
Alamyar E, Giudicelli V, Li S, et al. (2012): IMGT/HighV-QUEST: the IMGT® web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. Immun Res 8: 26.
Li S, Lefranc MP, Miles JJ, et al. (2013): IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. Nat Commun 4: 2333.
Robins HS, Campregher PV, Srivastava SK, et al. (2009): Comprehensive assessment of T-cell receptor beta-chain diversity in alpha beta T cells. Blood 114: 4099-4107.
Robins HS, Srivastava SK, Campregher PV, et al. (2010): Overlap and effective size of the human CD8+ T cell receptor repertoire. Sci Transl Med 2: 47ra64.
Sherwood AM, Desmarais C, Livingston RJ, et al. (2011): Deep sequencing of the human TCRγ and TCRβ repertoires suggests that TCRβ rearranges after αβ and γδ T cell commitment. Sci Transl Med 3: 90ra61.
Wu D, Sherwood A, Fromm JR, et al. (2012): High-throughput sequencing detects minimal residual disease in acute
T lymphoblastic leukemia. Sci Transl Med 4: 134ra63.
http://www.immunoseq.com
Stewart JJ, Lee CY, Ibrahim S, et al. (1997): A Shannon entropy analysis of immunoglobulin and T cell receptor. Mol Immunol 34: 1067-1082.
Yousfi Monod M, Giudicelli V, Chaume D, Lefranc MP (2004): IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics 20 Suppl 1: i379-385.
Lefranc MP (2011): IMGT unique numbering for the variable (V), constant (C), and groove (G) domains of IG, TR, MH, IgSF, and MhSF. Cold Spring Harb Protoc 2011; 633-642.
Meyer-Olson D, Brady KW, Blackard JT, et al. (2003): Analysis of the TCR beta variable gene repertoire in chimpanzees: identification of functional homologs to human pseudogenes. J Immunol 170: 4161-4169.
Murphy KM (2011): Janeway’s immunobiology. Garland Science, New York.
FEATURED PRODUCTS
Quick links
© 2018 Termedia Sp. z o.o. All rights reserved.
Developed by Bentus.
PayU - płatności internetowe