Antigen receptor repertoire profiling from RNA-seq data

Bolotin, Dmitriy A.; Poslavsky, S. V.; Davydov, Alexey N.; Frenkel, Felix; Fanchi, Lorenzo F.; Zolotareva, Olga; Hemmers, Saskia; Putintseva, Ekaterina V.; Obraztsova, Anna; Shugay, Mikhail; Ataullakhanov, Ravshan; Rudensky, Alexander Y.; Schumacher, Ton N.; Chudakov, Dmitriy M.

doi:10.1038/nbt.3979

Cited by 264 publications

(265 citation statements)

References 38 publications

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“…We asked whether TCR diversity of γδ T cells from pLNs also changes upon ageing in the variant Vγ4 + and Vγ1 + subsets using invariant Vγ6 + as a control. From the RNA‐Seq data (paired‐end, 125 bp sequencing) of purified γδ T‐cell subsets, we reconstructed CDR3 sequences using MiXCR in the RNA‐Seq mode . We confirmed the ability of MiXCR to reconstruct the correct Vγ chains for each of the γδ T‐cell subsets (Appendix Fig S7A and B).…”

Section: Resultsmentioning

confidence: 56%

IL ‐7‐dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti‐tumour response

et al. 2019

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How the age‐associated decline of immune function leads to increased cancer incidence is poorly understood. Here, we have characterised the cellular composition of the γδ T‐cell pool in peripheral lymph nodes ( pLN s) upon ageing. We find that ageing has minimal cell‐intrinsic effects on function and global gene expression of γδ T cells, and γδ TCR diversity remains stable. However, ageing alters TCR δ chain usage and clonal structure of γδ T‐cell subsets. Importantly, IL ‐17‐producing γδ17 T cells dominate the γδ T‐cell pool of aged mice—mainly due to the selective expansion of Vγ6 + γδ17 T cells and augmented γδ17 polarisation of Vγ4 + T cells. Expansion of the γδ17 T‐cell compartment is mediated by increased IL ‐7 expression in the T‐cell zone of old mice. In a Lewis lung cancer model, pro‐tumourigenic Vγ6 + γδ17 T cells are exclusively activated in the tumour‐draining LN and their infiltration into the tumour correlates with increased tumour size in aged mice. Thus, upon ageing, substantial compositional changes in γδ T‐cell pool in the pLN lead to an unbalanced γδ T‐cell response in the tumour that is associated with accelerated tumour growth.

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Section: Resultsmentioning

confidence: 56%

IL ‐7‐dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti‐tumour response

et al. 2019

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“…BCR repertoire sequencing can also be coupled with proteomics to reconstruct the antibody repertoire at the protein level . Alternatively, TCR or BCR repertoires can be extracted from bulk RNA sequencing data obtained from any immune cell‐containing tissue . Obviously, only a small portion of such sequencing reads will correspond to TCRs or BCRs, and a very high sequencing depth is therefore required to derive informative repertoires .…”

Section: Hts‐based Methods Of Immune Repertoire Profilingmentioning

confidence: 99%

T‐cell receptor and B‐cell receptor repertoire profiling in adaptive immunity

2019

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Summary B‐cell receptors and T‐cell receptors are the key molecules responsible for specific antigen recognition in adaptive immunity. The huge diversity of immune receptor repertoires constrained their comprehensive studies in the past. More recently, however, high‐throughput sequencing based techniques have revolutionized the field of immune receptor repertoire profiling enabling new insights into the development and function of the adaptive immune system. In this review we describe current methods for immune receptor profiling and software tools used for repertoire reconstruction from raw sequencing data. We also provide examples of how immune repertoire profiling can be used to study adaptive immunity in disease and in the course of organ and bone marrow transplantation.

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“…The transcripts encoding these immune receptors are of great interest to basic and translational research as well as diagnostic and other clinical purposes 5,11,12 . However, RNA-seq, the current gold-standard for whole transcriptome analysis, fails short of describing these immune receptors completely and accurately 7 . Accurate and deep full-length cDNA sequencing of immune cell transcriptomes could overcome this shortfall by providing 1) the isoforms of surface receptors targeted in immunotherapy, 2) allele-resolved HLA transcript sequences central to self/non-self discrimination, and 3) B cell receptor (BCR) and T cell receptor (TCR) repertoires instrumental to the adaptive immune response to pathogens.…”

Section: Introductionmentioning

confidence: 99%

Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing

Cole

Byrne

Adams

et al. 2019

Preprint

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ABSTRACTThe human immune system relies on highly complex and diverse transcripts and the proteins they encode. These include transcripts for Human Leukocyte Antigen (HLA) class I and II receptors which are essential for self/non-self discrimination by the immune system as well as transcripts encoding B cell and T cell receptors (BCR and TCR) which recognize, bind, and help eliminate foreign antigens.HLA genes are highly diverse within the human population with each individual possessing two of thousands of different alleles in each of the 9 major HLA genes. Determining which combination of alleles an individual possesses for each HLA gene (high-resolution HLA-typing) is essential to establish donor-recipient compatibility in organ and bone-marrow transplantations. BCR and TCR genes in turn are generated by recombining a diverse set of gene segments on the DNA level in each maturing B and T cell, respectively. This process generates adaptive immune receptor repertoires (AIRR) of composed of unique transcripts expressed by each B and T cells. These repertoires carry a vast amount of health relevant information. Both short-read RNA-seq based HLA-typing1 and adaptive immune receptor repertoire sequencing2–5 currently rely heavily on our incomplete knowledge of the genetic diversity at HLA6 and BCR/TCR loci7,8.Here we used our nanopore sequencing based Rolling Circle toConcatemeric Consensus (R2C2) protocol9 to generate over 10,000,000 full-length cDNA sequences at a median accuracy of 97.9%. We used this dataset to demonstrate that deep and accurate full-length cDNA sequencing can - in addition to providing isoform-level transcriptome analysis for over 9,000 loci - be used to generate accurate sequences of HLA alleles for HLA allele typing and discovery as well as detailed AIRR data for the analysis of the adaptive immune system without requiring specific knowledge of the diversity at HLA and BCR/TCR loci.

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Antigen receptor repertoire profiling from RNA-seq data

Cited by 264 publications

References 38 publications

IL ‐7‐dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti‐tumour response

IL ‐7‐dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti‐tumour response

T‐cell receptor and B‐cell receptor repertoire profiling in adaptive immunity

Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing

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