Comprehensive landscape of the T and B-cell repertoires of newly diagnosed gestational diabetes mellitus

This study conducted a high-throughput sequencing analysis of the T- and B- repertoires in the newly diagnosed GDM patients and evaluated the association between abnormal adaptive immunity and GDM. The unique TCR CDR3 clonotypes were mildly decreased in GDM patients, and the similarity of TCR V-J distributions was higher in the GDM group. Moreover, the usages of the V gene and V-J pair and the frequency distributions of some CDR3 amino acids (AAs) both in BCR and TCR were significantly different between groups. Moreover, the cytokines including IL-4, IL-6, IFN-γ and IL-17A were synchronously elevated in the GDM cases. Our findings provide a comprehensive view of BCR and TCR repertoires at newly diagnosed GDM patients, revealing the mild reduction in unique TCRB CDR3 sequences and slight alteration of the V gene, V-J combination and CDR3 (AA) usages of BCR and TCR. This work provides deep insight into the mechanism of maternal adaptive immunity in GDM and provides novel diagnostic biomarkers and potential immunotherapy targets for GDM.

High-throughput T cell receptor sequencing reveals differential immune repertoires in autoimmune thyroid diseases

BACKGROUND

Autoimmune thyroid diseases (AITDs) are chronic autoimmune diseases specific to thyroid and mainly include Graves' disease (GD) and Hashimoto' thyroiditis (HT). The adaptive immunoreactivity of CD4⁺ T cells plays a crucial role in the pathogenesis of AITDs, but very little has been known about its changes in disease status.

METHODS

We collected peripheral CD4⁺ T cells from 12 GD patients, including 6 newly diagnosed GD (NGD) and 6 refractory GD (RGD) patients, 6 HT patients and 6 healthy controls, and examined the gene expression profiles and colon types of T cells receptor (TCR) β chain complementarity determining region 3 (CDR3) using high-throughput sequencing.

RESULTS

The TCR repertoire were significantly expanded in AITDs groups, and some TCR genes were expressed more preferentially in AITDs group than in the healthy control group, including TRBV15 (P = 0.001), TRBV4-2 (P = 0.003), TRBV9 (P = 0.007), TRBV3-2 (P = 0.012), TRBV7-8 (P = 0.015), TRBV25-1 (P = 0.019), TRBV12-4 (P = 0.019) and TRBV27 (P = 0.02) in GD patients as well as TRBV29-1 (P = 0.004), TRBV12-4 (P = 0.004), TRBV6-5 (P = 0.011), TRBV7-2 (P = 0.012), TRBV27 (P = 0.012), TRBV9 (P = 0.031) and TRBV4-2 (P = 0.032) in HT patients. Moreover, subgroup analysis showed that the difference in the TCR spectrum between the normal group and NGD was not obvious, but a large number of differential genes appeared in the RGD group.

CONCLUSION

TCR spectrum has changed in patients with AITDs with expanded repertoire and many upregulated TRBV genes. Moreover, this difference is not apparent in GD patients at the initial stage, but as the disease progresses, the differences in TCR profiles became more pronounced.

Highly multiplexed immune repertoire sequencing links multiple lymphocyte classes with severity of response to COVID-19

BACKGROUND

Disease progression of subjects with coronavirus disease 2019 (COVID-19) varies dramatically. Understanding the various types of immune response to SARS-CoV-2 is critical for better clinical management of coronavirus outbreaks and to potentially improve future therapies. Disease dynamics can be characterized by deciphering the adaptive immune response.

METHODS

In this cross-sectional study we analyzed 117 peripheral blood immune repertoires from healthy controls and subjects with mild to severe COVID-19 disease to elucidate the interplay between B and T cells. We used an immune repertoire Primer Extension Target Enrichment method (immunoPETE) to sequence simultaneously human leukocyte antigen (HLA) restricted T cell receptor beta chain (TRB) and unrestricted T cell receptor delta chain (TRD) and immunoglobulin heavy chain (IgH) immune receptor repertoires. The distribution was analyzed of TRB, TRD and IgH clones between healthy and COVID-19 infected subjects. Using McFadden's Adjusted R2 variables were examined for a predictive model. The aim of this study is to analyze the influence of the adaptive immune repertoire on the severity of the disease (value on the World Health Organization Clinical Progression Scale) in COVID-19.

FINDINGS

Combining clinical metadata with clonotypes of three immune receptor heavy chains (TRB, TRD, and IgH), we found significant associations between COVID-19 disease severity groups and immune receptor sequences of B and T cell compartments. Logistic regression showed an increase in shared IgH clonal types and decrease of TRD in subjects with severe COVID-19. The probability of finding shared clones of TRD clonal types was highest in healthy subjects (controls). Some specific TRB clones seems to be present in severe COVID-19 (Figure S7b). The most informative models (McFadden´s Adjusted R2=0.141) linked disease severity with immune repertoire measures across all three cell types, as well as receptor-specific cell counts, highlighting the importance of multiple lymphocyte classes in disease progression.

INTERPRETATION

Adaptive immune receptor peripheral blood repertoire measures are associated with COVID-19 disease severity.

FUNDING

The study was funded with grants from the Berlin Institute of Health (BIH).

T cell receptor beta germline variability is revealed by inference from repertoire data

BACKGROUND

T and B cell receptor (TCR, BCR) repertoires constitute the foundation of adaptive immunity. Adaptive immune receptor repertoire sequencing (AIRR-seq) is a common approach to study immune system dynamics. Understanding the genetic factors influencing the composition and dynamics of these repertoires is of major scientific and clinical importance. The chromosomal loci encoding for the variable regions of TCRs and BCRs are challenging to decipher due to repetitive elements and undocumented structural variants.

METHODS

To confront this challenge, AIRR-seq-based methods have recently been developed for B cells, enabling genotype and haplotype inference and discovery of undocumented alleles. However, this approach relies on complete coverage of the receptors' variable regions, whereas most T cell studies sequence a small fraction of that region. Here, we adapted a B cell pipeline for undocumented alleles, genotype, and haplotype inference for full and partial AIRR-seq TCR data sets. The pipeline also deals with gene assignment ambiguities, which is especially important in the analysis of data sets of partial sequences.

RESULTS

From the full and partial AIRR-seq TCR data sets, we identified 39 undocumented polymorphisms in T cell receptor Beta V (TRBV) and 31 undocumented 5 ' UTR sequences. A subset of these inferences was also observed using independent genomic approaches. We found that a single nucleotide polymorphism differentiating between the two documented T cell receptor Beta D2 (TRBD2) alleles is strongly associated with dramatic changes in the expressed repertoire.

CONCLUSIONS

We reveal a rich picture of germline variability and demonstrate how a single nucleotide polymorphism dramatically affects the composition of the whole repertoire. Our findings provide a basis for annotation of TCR repertoires for future basic and clinical studies.

Genomic analysis of a second rainbow trout line (Arlee) leads to an extended description of the IGH VDJ gene repertoire

High-throughput sequencing technologies brought a renewed interest for immune repertoires. Fish Ab and B cell repertoires are no exception, and their comprehensive analysis can both provide new insights into poorly understood immune mechanisms, and identify markers of protection after vaccination. However, the lack of genomic description and standardized nomenclature of IG genes hampers accurate annotation of Ig mRNA deep sequencing data. Complete genome sequences of Atlantic salmon and rainbow trout (Swanson line) recently allowed us to establish a comprehensive and coherent annotation of Salmonid IGH genes following IMGT standards. Here we analyzed the IGHV, D, and J genes from the newly released genome of a second rainbow trout line (Arlee). We confirmed the validity of salmonid IGHV subgroups, and extended the description of the rainbow trout IGH gene repertoire with novel sequences, while keeping nomenclature continuity. This work provides an important resource for annotation of high-throughput Ab repertoire sequencing data.

PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST

BACKGROUND

Recent advances in DNA sequencing technologies have enabled significant leaps in capacity to generate large volumes of DNA sequence data, which has spurred a rapid growth in the use of bioinformatics as a means of interrogating antibody variable gene repertoires. Common tools used for annotation of antibody sequences are often limited in functionality, modularity and usability.

RESULTS

We have developed PyIR, a Python wrapper and library for IgBLAST, which offers a minimal setup CLI and API, FASTQ support, file chunking for large sequence files, JSON and Python dictionary output, and built-in sequence filtering.

CONCLUSIONS

PyIR offers improved processing speed over multithreaded IgBLAST (version 1.14) when spawning more than 16 processes on a single computer system. Its customizable filtering and data encapsulation allow it to be adapted to a wide range of computing environments. The API allows for IgBLAST to be used in customized bioinformatics workflows.