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Tumor associated TCR Repertoire Profiling Services

Background Tumor-associated TCR Repertoires Profiling Advantage Published Data FAQ Resources

High-throughput next-generation sequencing (NGS) of T cell receptor (TCR) repertoires has provided a broad perspective of TCR diversity at an unprecedented level. Beyond profiling peripheral blood, analysis of tissue-resident T cells provides further insight into immune-related diseases. Creative Biolabs can provide the service of RNA-sequencing (RNA-seq), extract TCR information from RNA-seq datasets and use it to characterize tumor-associated TCR repertoires. Our method could inform future cancer immunotherapy strategies, and it will have value in exploring other immune-related pathologies. We are proud to introduce this high-quality service for our customers all over the world.

The Background of RNA-seq

TCR repertoire plays an essential role in the adaptive immune system. Classical TCR sequencing (TCR-seq) methods have provided a detailed view of TCR diversity. Typically, CDR3 sequence information is obtained by performing TCR-seq on peripheral blood mononuclear cells, amplifying the CDR3 region with a conserved gene primer. As they rely on targeted amplicon sequencing, they could not avoid PCR bias. Deep sequencing technology has made whole-genome and transcriptome sequencing become true. Deep sequencing technology also provides opportunities for the extraction of immunological data using specialized software tools. TCR-seq applied to tissue can provide insight into tumor-infiltrating lymphocytes, T cells associated autoimmune pathology and infection.

Schematic diagram of CDR3β sequence sharing.Fig.1 Sharing of CDR3 β sequences.1,3

Tumor-associated TCR Repertoires Profiling Service in Creative Biolabs

Creative Biolabs has optimized the strategy for the extraction of TCR repertoire information from RNA-seq datasets of solid tumors. After samples are prepared, we performed RNA-seq on our unique Magic™ platform. A summary of our analytical method is as follows: (1) extraction of CDR3 sequences from RNA-seq data by using positive and negative control, (2) assessing CDR3 extraction efficiency using simulated data, (3) approximation of TCR transcript abundance, gene expression and inferred pairing of TCR alpha and beta subunits. This method avoids the need for PCR amplification and provides TCR information in global gene expression level, allowing an integrated analysis of extensive RNA-seq data resources.

Key Advantages of Our Tumor-associated TCR Repertoires Profiling Service


As a long-term expert in the field of immunology, Creative Biolabs has extensive experience and advanced technology platform for RNA-seq. Our scientists have accomplished and analyzed over hundreds of RNA sequencing projects. We can provide the best service of the extraction of TCR information from RNA-seq datasets from solid tumors for our global customers.

Please contact us for more information and a detailed quote.

Other optional Magic™ TCR repertoire analysis services:

Published Data

T cell receptor β chain repertoire sequencing.Fig. 2 T-cell receptor β-chain (TRB) repertoire sequencing reveals RCC-associated TRB sequences that are expanded in RCC tumors.2, 3

The research focuses on profiling tumor-infiltrating T-cell receptor (TCR) repertoires in renal cell carcinoma (RCC) to identify clonally expanded T cells associated with tumors. The significance lies in understanding how these expanded T cells may contribute to immune responses, particularly in relation to immune checkpoint inhibitor therapies. Results revealed that T cells within the tumor microenvironment exhibit distinct clonal expansions, especially CD8+ T cells, which were highly enriched in clear cell RCC (ccRCC). These T cells demonstrated unique phenotypes, including both activated and exhausted markers. Tumor-associated TCR profiling highlighted the dominance of private clonotypes, unique to the tumor, suggesting their potential role in recognizing RCC-specific antigens. The profiling also provided insights into how these T-cell populations might influence tumor progression and treatment responses.

References
  1. Brown, S.D.; et al. Profiling tissue-resident T cell repertoires by RNA sequencing. Genome Medicine. 2015, 7:125.
  2. Xu, Y.; et al. Integrated TCR repertoire analysis and single-cell transcriptomic profiling of tumor-infiltrating T cells in renal cell carcinoma identifies shared and tumor-restricted expanded clones with unique phenotypes. Frontiers in Oncology. 2022, 12: 952252.
  3. Distributed under Open Access license CC BY 4.0, without modification.

FAQ

  1. What is tumor-associated TCR repertoire profiling

    Tumor-associated TCR repertoire profiling involves analyzing the T-cell receptor (TCR) sequences from T cells present within a tumor. This technique provides insights into the immune response to the tumor, revealing how diverse the TCRs are and identifying specific TCRs that may be targeting tumor antigens. This information can guide immunotherapy strategies.

  2. How does RNA-sequencing facilitate TCR repertoire profiling

    RNA-sequencing allows for high-throughput analysis of the TCR transcriptome from tumor samples. By sequencing the RNA, researchers can obtain detailed information about the TCR sequences and their expression levels, enabling the identification of both predominant and rare TCRs that may play critical roles in the anti-tumor immune response.

  3. What are the advantages of using RNA-sequencing over traditional methods

    Compared to traditional methods like PCR and Sanger sequencing, RNA-sequencing offers a more comprehensive view of the TCR repertoire. It can capture the full spectrum of TCRs present, including those expressed at low levels. Additionally, RNA-sequencing can simultaneously profile other RNA species, such as cytokines and immune-related genes, providing a broader context for the immune landscape.

  4. What types of tumors can be analyzed using this approach

    Tumor-associated TCR repertoire profiling by RNA-sequencing can be applied to a variety of tumor types, including solid tumors like melanoma, lung cancer, and breast cancer, as well as hematological malignancies like leukemia. Each tumor type presents unique antigens and T-cell responses, making this profiling valuable across different cancer contexts.

  5. How do researchers validate the findings from TCR repertoire profiling

    Validation of findings typically involves complementary techniques, such as flow cytometry or single-cell sequencing, to confirm the presence and functionality of identified TCRs. Researchers may also perform functional assays to assess the ability of specific TCRs to recognize tumor cells, further substantiating the relevance of the identified TCRs in the anti-tumor immune response.

  6. How does tumor microenvironment influence TCR repertoire profiles

    The tumor microenvironment can significantly impact TCR repertoire profiles by influencing T-cell activation, differentiation, and retention. Factors such as cytokines, tumor-derived exosomes, and immune cell interactions can shape the TCR repertoire, affecting the overall immune response to the tumor. Understanding these dynamics is essential for developing effective immunotherapies that can overcome the immunosuppressive environment.

Resources

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