Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases

Barennes, Pierre; Quiniou, Valentin; Shugay, Mikhail; Egorov, Evgeniy S.; Davydov, Alexey N.; Chudakov, Dmitriy M.; Uddin, Imran; Ismail, Maznah; Oakes, Theres; Chain, Benjamin M.; Eugster, Anne; Kashofer, Karl; Rainer, Peter P.; Darko, Samuel; Ransier, Amy; Douek, Daniel C.; Klatzmann, David; Mariotti‐Ferrandiz, Encarnita

doi:10.1038/s41587-020-0656-3

Cited by 97 publications

(117 citation statements)

References 68 publications

Supporting

Mentioning

113

Contrasting

Order By: Relevance

“…Only single-cell sequencing can provide paired chains. Also, the accuracy of the technology that heavily relies on PCR amplification and its capacity to detect rare clonotypes might affect results (24). Despite all these limitations, TCR sequencing carries enormous potential in particular in combination with cytometric techniques discussed above.…”

Section: Tcr Repertoire Analysismentioning

confidence: 99%

“…• To sequence the bulk repertoire of at least 10 5 purified/ enriched T cell populations, at least always separating Treg from Teffs, and using a robust method (24). • To refrain from performing single-cell TCR sequencing from peripheral blood except if relevant subsets can be enriched, i.e., by antigen-specific cytometry assays as described above.…”

Section: Tcr Repertoire Analysismentioning

confidence: 99%

See 1 more Smart Citation

Phenotyping of Adaptive Immune Responses in Inflammatory Diseases

et al. 2020

Self Cite

View full text Add to dashboard Cite

Immunophenotyping on the molecular and cellular level is a central aspect for characterization of patients with inflammatory diseases, both to better understand disease etiopathogenesis and based on this to develop diagnostic and prognostic biomarkers which allow patient stratification and tailor-made treatment strategies. Technology-driven developments have considerably expanded the range of analysis tools. Especially the analysis of adaptive immune responses, often regarded as central though mostly poorly characterized disease drivers, is a major focus of personalized medicine. The identification of the disease-relevant antigens and characterization of corresponding antigen-specific lymphocytes in individual patients benefits significantly from recent developments in cytometry by sequencing and proteomics. The aim of this workshop was to identify the important developments for state-of-the-art immunophenotyping for clinical application and precision medicine. We focused here on recent key developments in analysis of antigen-specific lymphocytes, sequencing, and proteomics approaches, their relevance in precision medicine and the discussion of the major challenges and opportunities for the future.

show abstract

Section: Tcr Repertoire Analysismentioning

confidence: 99%

Section: Tcr Repertoire Analysismentioning

confidence: 99%

Phenotyping of Adaptive Immune Responses in Inflammatory Diseases

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…Compared to other methods the resolution of information is much higher using less input of biomaterial. However, several comparative studies have shown that the different approaches lead to significantly different results, even when using the same input material ( 27 , 30 ). These studies indicate that there is still a need to standardize the analysis of TCR repertoires for clinical application.…”

Section: Introduction: T Cell Immunitymentioning

confidence: 99%

T Cell Repertoire During Ontogeny and Characteristics in Inflammatory Disorders in Adults and Childhood

et al. 2021

View full text Add to dashboard Cite

Since the first day of life, a newborn has to deal with various pathogens from the environment. While passive immune protection is provided by diaplacental maternal antibodies, the development of cellular immunity is ongoing. A mature immune system should be able not only to defend against pathogens, but should also be able to differentiate between self- and non-self-antigens. Dysregulation in the development of cellular immunity can lead to severe disorders like immunodeficiency, autoimmunity and chronic inflammation. In this review, we explain the role of T cell immunity in antigen detection and summarize the characteristics of a mature TCR repertoire as well as the current state of knowledge about the development of the TCR repertoire in ontogenesis. In addition, methods of assessments are outlined, with a focus on the advantages and disadvantages of advanced methods such as next generation sequencing. Subsequently, we provide an overview of various disorders occuring in early childhood like immunodeficiencies, autoimmunity, allergic diseases and chronic infections and outline known changes in the TCR repertoire. Finally, we summarize the latest findings and discuss current research gaps as well as potential future developments.

show abstract

“…However, while the length of the CDR3 distribution is one parameter of T-cell diversity, most of the variability lies in the CDR3 sequence that is encoded within the V(D)J region, represented by b sequences, which comes in contact with an antigenic peptide (21,22). Further, previous studies leveraged mRNA-based complimentary DNA sequencing which is biased due to different mRNA content per cell and is affected by RNA input (23). Therefore, deep sequencing of the genomic CDR3 beta-region would allow a more accurate representation of the TCR diversity (23).…”

Section: Introductionmentioning

confidence: 99%

“…Further, previous studies leveraged mRNA-based complimentary DNA sequencing which is biased due to different mRNA content per cell and is affected by RNA input (23). Therefore, deep sequencing of the genomic CDR3 beta-region would allow a more accurate representation of the TCR diversity (23).…”

Section: Introductionmentioning

confidence: 99%

Response to Hypomethylating Agents in Myelodysplastic Syndrome Is Associated With Emergence of Novel TCR Clonotypes

et al. 2021

View full text Add to dashboard Cite

Aberrant T-cell function is implicated in the pathogenesis of myelodysplastic syndrome (MDS). Monitoring the T-cell receptor (TCR) repertoire can provide insights into T-cell adaptive immunity. Previous studies found skewed TCR repertoires in MDS compared to healthy patients; however these studies that leverage mRNA-based spectratyping have limitations. Furthermore, evaluating the TCR repertoire in context of hypomethylating agents (HMAs) treatment can provide insights into the dynamics of T-cell mediated responses in MDS. We conducted immunosequencing of the CDR3 regions of TCRβ chains in bone marrows of 11 MDS patients prior to treatment (n=11 bone marrows prior to treatment), and in at least 2 timepoints for each patient following treatment (n=26 bone marrow aspirates post-treatment) with (HMA), alongside analyzing bone marrows from 4 healthy donors as controls. TCR repertoires in MDS patients were more clonal and less diverse than healthy donors. However, unlike previous reports, we did not observe significant skewness in CDR3 length or spectratyping. The global metrics of TCR profiling including richness, clonality, overlaps were not significantly changed in responders or non-responders following treatment with HMAs. However, we found an emergence of novel clonotypes in MDS patients who responded to treatment, while non-responders had a higher frequency of contracted clonotypes following treatment. By applying GLIPH2 for antigen prediction, we found rare TCR specificity clusters shared by TCR clonotypes from different patients at pre- or following treatment. Our data show clear differences in TCR repertoires of MDS compared with healthy patients and that novel TCR clonotype emergence in response to HMA therapy was correlated with response. This suggests that response to HMA therapy may be partially driven by T-cell mediated immunity and that the immune-based therapies, which target the adaptive immune system, may play a significant role in select patients with MDS.

show abstract

Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases

Cited by 97 publications

References 68 publications

Phenotyping of Adaptive Immune Responses in Inflammatory Diseases

Phenotyping of Adaptive Immune Responses in Inflammatory Diseases

T Cell Repertoire During Ontogeny and Characteristics in Inflammatory Disorders in Adults and Childhood

Response to Hypomethylating Agents in Myelodysplastic Syndrome Is Associated With Emergence of Novel TCR Clonotypes

Contact Info

Product

Resources

About