scholarly journals The Usage of Human IGHJ Genes Follows a Particular Non-random Selection: The Recombination Signal Sequence May Affect the Usage of Human IGHJ Genes

2020 ◽  
Vol 11 ◽  
Author(s):  
Bin Shi ◽  
Xiaoheng Dong ◽  
Qingqing Ma ◽  
Suhong Sun ◽  
Long Ma ◽  
...  
Keyword(s):  
Proliferative Response ◽  
Gene Frequency ◽  
High Throughput Sequencing ◽  
Signal Sequence ◽  
Variable Region ◽  
Cell Receptor ◽  
Spacer Length ◽  
Recombination Signal ◽  
Pathological Conditions ◽  
Self Tolerance

The formation of the B cell receptor (BCR) heavy chain variable region is derived from the germline V(D)J gene rearrangement according to the “12/23” rule and the “beyond 12/23” rule. The usage frequency of each V(D)J gene in the peripheral BCR repertoires is related to the initial recombination, self-tolerance selection, and the clonal proliferative response. However, their specific differences and possible mechanisms are still unknown. We analyzed in-frame and out-of-frame BCR-H repertoires from human samples with normal physiological and various pathological conditions by high-throughput sequencing. Our results showed that IGHJ gene frequency follows a similar pattern which is previously known, where IGHJ4 is used at high frequency (>40%), IGHJ6/IGHJ3/IGHJ5 is used at medium frequencies (10∼20%), and IGH2/IGHJ1 is used at low frequency (<4%) under whether normal physiological or various pathological conditions. However, our analysis of the recombination signal sequences suggested that the conserved non-amer and heptamer and certain 23 bp spacer length may affect the initial IGHD-IGHJ recombination, which results in different frequencies of IGHJ genes among the initial BCR-H repertoire. Based on this “initial repertoire,” we recommend that re-evaluation and further investigation are needed when analyzing the significance and mechanism of IGHJ gene frequency in self-tolerance selection and the clonal proliferative response.

scholarly journals The usage of human IGHJ genes follows a particular nonrandom selection: The recombination signal sequence affects the usage of human IGHJ genes

2019 ◽  
Author(s):  
Bin Shi ◽  
Xiaoheng Dong ◽  
Qingqing Ma ◽  
Suhong Sun ◽  
Long Ma ◽  
...  
Keyword(s):  
Proliferative Response ◽  
Gene Frequency ◽  
High Throughput Sequencing ◽  
Signal Sequence ◽  
Variable Region ◽  
Cell Receptor ◽  
Spacer Length ◽  
Recombination Signal ◽  
Pathological Conditions ◽  
Self Tolerance

ABSTRACTThe formation of the B cell receptor (BCR) heavy chain variable region is derived from the germline V(D)J gene rearrangement according to the “12/23” rule and the “beyond 12/23” rule. The usage frequency of each V(D)J gene in the peripheral BCR repertoires is related to the initial recombination, self-tolerance selection, and the clonal proliferative response. However, their specific differences and possible mechanisms are still unknown. We analyzed in-frame and out-of-frame BCR-H repertoires from human samples with physiological and various pathological conditions by high-throughput sequencing. Our results showed that IGHJ gene frequency follows a similar pattern where IGHJ4 is used at high frequency (>40%), IGHJ6/IGHJ3/IGHJ5 is used at medium frequencies (10%∼20%), and IGH2/IGHJ1 is used at low frequency (<4%) under whether physiological or various pathological conditions. Furthermore, analysis of the recombination signal sequences suggested that the conserved nonamer and heptamer and certain 23 bp spacer length may affect the initial IGHD-IGHJ recombination, which results in different frequencies of IGHJ genes among the initial BCR-H repertoire. Based on this “background repertoire”, we recommend that re-evaluation and further investigation are needed when analyzing the significance and mechanism of IGHJ gene frequency in self-tolerance selection and the clonal proliferative response.

scholarly journals Poor Quality Vβ Recombination Signal Sequences Enforce TCRβ Allelic Exclusion by Limiting the Frequency of Vβ Recombination

2020 ◽  
Author(s):  
Glendon S. Wu ◽  
Katherine S. Yang-Iott ◽  
Morgann A. Reed ◽  
Katharina E. Hayer ◽  
Kyutae D. Lee ◽  
...  
Keyword(s):  
B Lymphocyte ◽  
Feedback Inhibition ◽  
Signal Sequence ◽  
Antigen Receptor ◽  
Cell Receptor ◽  
Poor Quality ◽  
Functional Gene ◽  
Monoallelic Expression ◽  
Allelic Exclusion ◽  
Recombination Signal

SUMMARYMonoallelic expression (allelic exclusion) of T and B lymphocyte antigen receptor genes is achieved by the assembly of a functional gene through V(D)J recombination on one allele and subsequent feedback inhibition of recombination on the other allele. There has been no validated mechanism for how only one allele of any antigen receptor locus assembles a functional gene prior to feedback inhibition. Here, we demonstrate that replacement of a single Vβ recombination signal sequence (RSS) with a better RSS increases Vβ rearrangement, reveals Tcrb alleles compete for utilization in the αβ T cell receptor (TCR) repertoire, and elevates the fraction of αβ T cells expressing TCRβ protein from both alleles. The data indicate that poor qualities of Vβ RSSs for recombination with Dβ and Jβ RSSs enforces allelic exclusion by stochastically limiting the incidence of functional Vβ rearrangements on both alleles before feedback inhibition terminates Vβ recombination.

scholarly journals Level of human TCRBV3S1 (V beta 3) expression correlates with allelic polymorphism in the spacer region of the recombination signal sequence.

1994 ◽  
Vol 179 (5) ◽  
pp. 1707-1711 ◽  
Author(s):  
D N Posnett ◽  
C S Vissinga ◽  
C Pambuccian ◽  
S Wei ◽  
M A Robinson ◽  
...  
Keyword(s):  
Peripheral Blood ◽  
Signal Sequence ◽  
Cell Receptor ◽  
Allelic Polymorphism ◽  
Nucleotide Position ◽  
Recombination Signal Sequence ◽  
Recombination Signal ◽  
Cis Acting ◽  
Human T Cell

One of the causes of variations in the expressed human T cell receptor (TCR) BV (V beta) repertoire is genetic variation in the germline DNA. Herein evidence is provided that allelic polymorphism may affect recombination frequency for a specific V gene. Two alleles of the TCR BV3 differ only at a single nucleotide position (C/T) within the 23-bp spacer region of the recombination signal sequence. These alleles are associated with variable percentages of BV3 cells in the peripheral blood, as shown in families and in unrelated normal donors. Individuals homozygous for allele 2 have a mean of 8.1% BV3 cells, heterozygous individuals have a mean of 4.7% BV3 cells, and homozygotes for allele 1 have a mean of 1.2% BV3 cells in CD3+ CD4+ peripheral blood T cells. Since the correlation is tight in unrelated individuals and other genetic differences were not found in the vicinity of BV3, we suggest that the spacer region sequence itself modifies recombination efficiency. This allelic system provides an example of a novel mechanism by which cis-acting genetic elements may affect recombination in a natural in vivo system.

scholarly journals T-cell receptor alpha locus V(D)J recombination by-products are abundant in thymocytes and mature T cells.

1996 ◽  
Vol 16 (2) ◽  
pp. 609-618 ◽  
Author(s):  
F Livak ◽  
D G Schatz
Keyword(s):  
T Cells ◽  
T Cell ◽  
T Cell Receptor ◽  
Signal Sequence ◽  
Cell Receptor ◽  
Recombination Reaction ◽  
Dna Molecules ◽  
Coding Region ◽  
Recombination Signal ◽  
By Products

In addition to the assembled coding regions of immunoglobulin and T-cell receptor (TCR) genes, the V(D)J recombination reaction can in principle generate three types of by-products in normal developing lymphocytes: broken DNA molecules that terminate in a recombination signal sequence or a coding region (termed signal or coding end molecules, respectively) and DNA molecules containing fused recombination signal sequences (termed reciprocal products). Using a quantitative Southern blot analysis of the murine TCR alpha locus, we demonstrate that substantial amounts of signal end molecules and reciprocal products, but not coding end molecules, exist in thymocytes, while peripheral T cells contain substantial amounts of reciprocal products. At the 5' end of the J alpha locus, 20% of thymus DNA exists as signal end molecules. An additional 30 to 40% of the TCR alpha/delta locus exists as remarkably stable reciprocal products throughout T-cell development, with the consequence that the TCR C delta region is substantially retained in alpha beta committed T cells. The disappearance of the broken DNA molecules occurs in the same developmental transition as termination of expression of the recombination activating genes, RAG-1 and RAG-2. These findings raise important questions concerning the mechanism of V(D)J recombination and the maintenance of genome integrity during lymphoid development.

scholarly journals Nonmyeloablative allogeneic transplantation achieves clinical and molecular remission in cutaneous T-cell lymphoma

2020 ◽  
Vol 4 (18) ◽  
pp. 4474-4482 ◽  
Author(s):  
Wen-Kai Weng ◽  
Sally Arai ◽  
Andrew Rezvani ◽  
Laura Johnston ◽  
Robert Lowsky ◽  
...  
Keyword(s):  
T Cell ◽  
High Throughput Sequencing ◽  
Residual Disease ◽  
Chronic Gvhd ◽  
Survival Rates ◽  
Stage Iv ◽  
Allogeneic Transplantation ◽  
Cell Receptor ◽  
Advanced Stage ◽  
Molecular Remission

Abstract The majority of patients with refractory, advanced-stage mycosis fungoides (MF) or Sézary syndrome (SS) have a life expectancy of &lt;5 years. Here, we report a phase 2 study of a novel nonmyeloablative allogeneic transplantation strategy tailored for this patient population. This study has completed the enrollment, and 35 patients (13 MF, 22 SS) have undergone transplant as planned. The majority (80%) of the patients had stage IV disease and received multiple previous systemic therapies. All patients had active disease at the time of conditioning using total skin electron beam therapy, total lymphoid irradiation, and antithymocyte globulin, and received allograft infusion as outpatients. Cyclosporine or tacrolimus and mycophenolate mofetil were used for graft-versus-host disease (GVHD) prophylaxis. Patients tolerated the transplant well, with 1- and 2-year nonrelapse mortality of 3% and 14%, respectively. The day +180 cumulative incidence of grade 2 to 4 acute GVHD was 16%, and the 2-year incidence of moderate/severe chronic GVHD was 32%. With a median posttransplant follow-up of 5.4 years, the 2-, 3-, and 5-year overall survival rates were 68%, 62%, and 56%. Using high-throughput sequencing of the T-cell receptor for minimal residual disease monitoring, we observed that 43% achieved molecular remission, which was associated with a lower incidence of disease progression or relapse (9% vs 87%; P = .02). Our study also showed that patients who were aged ≥65 years at the time of allotransplant had similar clinical outcomes compared with younger patients. Thus, we have developed an alternative and potentially curative nonmyeloablative allogeneic transplant regimen for patients with advanced stage MF/SS. This trial was registered at www.clinicaltrials.gov as #NCT00896493.

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