Characteristics and Clinical Significance of T-Cell Receptor Repertoire in Hepatocellular Carcinoma

Distinct T Cell Subset Profiles and T-Cell Receptor Signatures in Metabolically Unhealthy Obesity

Metabolically unhealthy obesity (MUO) is associated with increased inflammation and a higher risk of metabolic disorders compared to metabolically healthy obesity (MHO). T cell dysregulation in blood and adipose tissue may contribute to obesity-induced metabolic dysfunction, yet the characteristics of T cell subset profiles and T-cell receptor (TCR) repertoires in MHO and MUO remain unclear. We analyzed T cell subsets and TCR repertoires in peripheral blood and omental adipose tissue (oAT) from age- and BMI-matched MHO and MUO individuals using flow cytometry and high-throughput TCR sequencing. MUO individuals exhibited a higher proportion of memory CD4+ T cells in both compartments, with an increased frequency of central memory T cells. Circulating CD8+ T cells were increased in MUO, whereas CD8+ T cell subset composition remained unchanged in both blood and oAT. The TCR repertoire in oAT was significantly more restricted than in blood and showed greater skewing in MUO, with selective amplification of specific TRB V genes (TRBV12-4, TRBV18, TRBV7-9) and altered CDR3 length distributions. These findings suggest that distinct CD4+ T cell populations and specific TCR signatures may serve as potential biomarkers for metabolic dysfunction in obesity, providing insights into immune mechanisms underlying the transition from MHO to MUO.

Comprehensive Analysis of TCR and BCR Repertoires: Insights into Methodologies, Challenges, and Applications

The diversity of T-cell receptors (TCRs) and B-cell receptors (BCRs) underpins the adaptive immune system's ability to recognize and respond to a wide array of antigens. Recent advancements in RNA sequencing have expanded its application beyond transcriptomics to include the analysis of immune repertoires, enabling the exploration of TCR and BCR sequences across various physiological and pathological contexts. This review highlights key methodologies and considerations for TCR and BCR repertoire analysis, focusing on the technical aspects of receptor sequence extraction, data processing, and clonotype identification. We compare the use of bulk and single-cell sequencing, discuss computational tools and pipelines, and evaluate the implications of examining specific receptor regions such as CDR3. By integrating immunology, bioinformatics, and clinical research, immune repertoire analysis provides valuable insights into immune function, therapeutic responses, and precision medicine approaches, advancing our understanding of health and disease.

T-cell Receptor Repertoire Analysis in the Context of Transarterial Chemoembolization Synergy with Systemic Therapy for Hepatocellular Carcinoma

T-cell receptor (TCR) sequencing provides a novel platform for insight into and characterization of intricate T-cell profiles, advancing the understanding of tumor immune heterogeneity. Recently, transarterial chemoembolization (TACE) combined with systemic therapy has become the recommended regimen for advanced hepatocellular carcinoma. The regulation of the immune microenvironment after TACE and its impact on tumor progression and recurrence has been a focus of research. By examining and tracking fluctuations in the TCR repertoire following combination treatment, novel perspectives on the modulation of the tumor microenvironment post-TACE and the underlying mechanisms governing tumor progression and recurrence can be gained. Clarifying the distinctive metrics and dynamic alterations of the TCR repertoire within the context of combination therapy is imperative for understanding the mechanisms of anti-tumor immunity, assessing efficacy, exploiting novel treatments, and further advancing precision oncology in the treatment of hepatocellular carcinoma. In this review, we initially summarized the fundamental characteristics of TCR repertoire and depicted immune microenvironment remodeling after TACE. Ultimately, we illustrated the prospective applications of TCR repertoires in TACE combined with systemic therapy.

The intratumoral landscape of T cell receptor repertoire in esophageal squamous cell carcinoma

BACKGROUND

Esophageal squamous cell carcinoma (ESCC) is a malignant neoplasm with detrimental implications for human health. The landscape of ESCC therapy has been revolutionized by the introduction of immunotherapy, specifically involving immune checkpoint inhibitors (ICIs). A number of studies have documented the prognostic significance of T-cell receptor (TCR) repertoire and its association with many tumors. Nevertheless, the TCR repertoire landscape and its significance in ESCC still need to be explored.

METHODS

In this study, we conducted RNA-Seq analysis to investigate the characteristics of the TCR repertoire in 90 patients. Moreover, high-throughput TCR sequencing was performed on tumor tissues from 41 patients who received immunotherapy. Additionally, a comprehensive analysis of the T-cell receptor repertoire landscape within ESCC tumors was carried out through immunohistochemical staining on all patient samples.

RESULTS

We noticed a diminished diversity of TCR repertoire within the tumor compared to its adjacent normal tissue. In terms of immunotherapy responses, non-responsive patients exhibited higher TCR repertoire diversity indices and an increased frequency of common V and J genes. Additionally, elevated TCR repertoire diversity correlated with improved overall survival rates. Lastly, immunohistochemical staining results indicated a correlation between TCR repertoire diversity and the tumor immune microenvironment (TIME).

CONCLUSIONS

Our study primarily describes the landscape of TCR repertoires in ESCC through three aspects: differences in tumor tissues, immune response to immunotherapy, and survival prognosis of patients. These results emphasize the importance of TCR repertoire characteristics as unique and relevant biomarkers for ESCC immunotherapy.

Characterization of the T-cell receptor repertoire associated with lymph node metastasis in colorectal cancer

Purpose

Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide, with lymph node (LN) metastasis playing a pivotal role in disease progression. This study aimed to explore the T-cell receptor (TCR) repertoire among CRC patients, distinguishing those with LN metastasis from those without, in order to uncover potential biomarkers for predicting metastasis.

Methods

We analyzed the TCR repertoire in CRC patients with and without LN metastasis. A classification model utilizing random forest analysis was developed to assess the predictive potential of the TCR repertoire.

Results

The findings demonstrated a significant increase in the number of V-J combinations and immune CDR3 sequences in patients with LN metastasis compared to the control group. The classification model achieved high accuracy in differentiating patients with LN metastasis, with AUC values ranging from 0.514 to 0.794. Specific V-J combinations and CDR3 sequences were identified as significant predictors of the model's predictive accuracy.

Conclusion

These results suggest that the TCR repertoire is altered in CRC patients exhibiting LN metastasis, potentially influencing disease progression. This study highlights the importance of TCR repertoire analysis as a non-invasive biomarker for predicting LN metastasis in CRC patients.

Exploring the potential of the TCR repertoire as a tumor biomarker (Review)

T cells play an important role in adaptive immunity. Mature T cells specifically recognize antigens on major histocompatibility complex molecules through T-cell receptors (TCRs). As the TCR repertoire is highly diverse, its analysis is vital in the assessment of T cells. Advances in sequencing technology have provided convenient methods for further investigation of the TCR repertoire. In the present review, the TCR structure and the mechanisms by which TCRs function in tumor recognition are described. In addition, the potential value of the TCR repertoire in tumor diagnosis is reviewed. Furthermore, the role of the TCR repertoire in tumor immunotherapy is introduced, and the relationships between the TCR repertoire and the effects of different tumor immunotherapies are discussed. Based on the reviewed literature, it may be concluded that the TCR repertoire has the potential to serve as a biomarker for tumor prognosis. However, a wider range of cancer types and more diverse subjects require evaluation in future research to establish the TCR repertoire as a biomarker of tumor immunity.

Similar usage of T-cell receptor β-chain between tumor and adjacent normal tissue in hepatocellular carcinoma

BACKGROUND

In this study, we comprehensively profiled the T-cell receptor (TCR) repertoire of the tumor and adjacent normal tissue in patients with HBV-associated hepatocellular carcinoma (HCC) and determined the baseline characteristics and clinical significance of TCR.

METHODS

High-throughput sequencing was used to determine the profile of complementarity-determining region 3 (CDR3) of the TCR-β chain variable (TRBV) in the tumor and normal tissue samples of 14 HCC patients. At the same time, TRBV diversity and differences in expression between tumor and normal tissues were investigated. The cumulative frequency of top 100 CDR3 (CF100), clonality, and Shannon entropy as indices to evaluate diversity, RESULTS: The diversity of TRBV CDR3 showed no significant difference between tumor and normal tissues. Of the 58 V gene segments in TRBV, TRBV16 and TRBV7-6 had a significantly higher frequency in the tumor group than in the normal group (p < 0.05). The frequency of 14 J gene segments showed no significant difference between tumor and normal tissues. In contrast, the frequency of 22 TRBVx/BJx combinations was significantly higher in the tumor than in the normal tissue. In addition, the length and type of TRBV CDR3 were similar in tumor and normal tissues, and a Gaussian distribution was observed in both groups.

CONCLUSION

This study provided a large amount of information about the TCR lineage in HBV-associated HCC, laying the foundation for further research. In addition, the fact that the immune repertoire (TRBV CDR3) hardly differs between tumor and adjacent normal tissue provides a new clue for exploring the mechanism of the liver as an organ with immune privileges.

Suppression of Type I Interferon Signaling in Myeloid Cells by Autoantibodies in Severe COVID-19 Patients

PURPOSE

Auto-antibodies (auto-abs) to type I interferons (IFNs) have been identified in patients with life-threatening coronavirus disease 2019 (COVID-19), suggesting that the presence of auto-abs may be a risk factor for disease severity. We therefore investigated the mechanism underlying COVID-19 exacerbation induced by auto-abs to type I IFNs.

METHODS

We evaluated plasma from 123 patients with COVID-19 to measure auto-abs to type I IFNs. We performed single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells from the patients with auto-abs and conducted epitope mapping of the auto-abs.

RESULTS

Three of 19 severe and 4 of 42 critical COVID-19 patients had neutralizing auto-abs to type I IFNs. Patients with auto-abs to type I IFNs showed no characteristic clinical features. scRNA-seq from 38 patients with COVID-19 revealed that IFN signaling in conventional dendritic cells and canonical monocytes was attenuated, and SARS-CoV-2-specific BCR repertoires were decreased in patients with auto-abs. Furthermore, auto-abs to IFN-α2 from COVID-19 patients with auto-abs recognized characteristic epitopes of IFN-α2, which binds to the receptor.

CONCLUSION

Auto-abs to type I IFN found in COVID-19 patients inhibited IFN signaling in dendritic cells and monocytes by blocking the binding of type I IFN to its receptor. The failure to properly induce production of an antibody to SARS-CoV-2 may be a causative factor of COVID-19 severity.

T-cell receptor sequencing reveals hepatocellular carcinoma immune characteristics according to Barcelona Clinic liver cancer stages within liver tissue and peripheral blood

Analysis of T-cell receptor (TCR) repertoires in different stages of hepatocellular carcinoma (HCC) might help to elucidate its pathogenesis and progression. This study aimed to investigate TCR profiles in liver biopsies and peripheral blood mononuclear cells (PBMCs) in different Barcelona Clinic liver cancer (BCLC) stages of HCC. Ten patients in early stage (BCLC_A), 10 patients in middle stage (BCLC_B), and 10 patients in late stage (BCLC_C) cancer were prospectively enrolled. The liver tumor tissues, adjacent tissues, and PBMCs of each patient were collected and examined by TCR β sequencing. Based on the ImMunoGeneTics (IMGT) database, we aligned the V, D, J, and C gene segments and identified the frequency of CDR3 sequences and amino acids sequence. Diversity of TCR in PBMCs was higher than in both tumor tissues and adjacent tissues, regardless of BCLC stage and postoperative recurrence. TCR clonality was increased in T cells from peripheral blood in advanced HCC, compared with the early and middle stages. No statistical differences were observed between different BCLC stages, either in tumors or adjacent tissues. TCR clonality revealed no significant difference between recurrent tumor and non-recurrent tumor, therefore PBMCs was better to be representative of TCR characteristics in different stages of HCC compared to tumor tissues. Clonal expansion of T cells was associated with low risk of recurrence in HCC patients.