Integrated analysis of B‑cell and T‑cell receptors by high‑throughput sequencing reveals conserved repertoires in IgA nephropathy

Characterization of T-Cell receptor repertoire in immunoglobulin a nephropathy

Immunoglobulin A nephropathy (IgAN) is an autoimmune disease characterized by abnormal IgA deposition in glomerulus. Current diagnosis of IgAN still depends on renal biopsy, an invasive method that might increase the risk of clinical outcomes. Therefore, we aimed to explore the characteristics of T cell repertoire in IgAN from peripheral blood samples for identifying innovative diagnostic biomarkers. Herein, we included 8 IgAN patients, 25 non-IgAN patients, and 10 healthy controls in the study. A high-throughput immune repertoire sequencing was conducted to investigate the T-cell receptor beta-chain (TCRβ) repertoire of peripheral blood. Characteristics of TCRβ repertoire were assessed for these three distinct groups. A reduced TCRβ repertoire diversity was observed in IgAN patients compared to non-IgAN and healthy individuals. A skewed distribution toward shorter TCRβ complementarity determining region (CDR3) length was found in non-IgAN relative to IgAN patients. In addition, the differences in usages of five TRBV genes (TRBV5-4, TRBV6-4, TRBV12-1, TRBV16, and TRBV21-1) were identified between IgAN, non-IgAN, and healthy subjects. Of note, the TRBV6-4 gene, which is associated with mucosal-associated invariant T (MAIT) cells, exhibited higher usage in IgAN patients, suggesting potential importance of MAIT cells in IgAN. In short, our findings supported TCR repertoire characteristics as potential biomarkers for IgAN diagnosis.

A novel approach to T-cell receptor beta chain (TCRB) repertoire encoding using lossless string compression

MOTIVATION

T-cell receptor beta chain (TCRB) repertoires are crucial for understanding immune responses. However, their high diversity and complexity present significant challenges in representation and analysis. The main motivation of this study is to develop a unified and compact representation of a TCRB repertoire that can efficiently capture its inherent complexity and diversity and allow for direct inference.

RESULTS

We introduce a novel approach to TCRB repertoire encoding and analysis, leveraging the Lempel-Ziv 76 algorithm. This approach allows us to create a graph-like model, identify-specific sequence features, and produce a new encoding approach for an individual's repertoire. The proposed representation enables various applications, including generation probability inference, informative feature vector derivation, sequence generation, a new measure for diversity estimation, and a new sequence centrality measure. The approach was applied to four large-scale public TCRB sequencing datasets, demonstrating its potential for a wide range of applications in big biological sequencing data.

AVAILABILITY AND IMPLEMENTATION

Python package for implementation is available https://github.com/MuteJester/LZGraphs.

The Diagnostic and Prognostic Potential of the B-Cell Repertoire in Membranous Nephropathy

Membranous nephropathy (MN), an autoimmune glomerular disease, is one of the most common causes of nephrotic syndrome in adults. In current clinical practice, the diagnosis is dependent on renal tissue biopsy. A new method for diagnosis and prognosis surveillance is urgently needed for patients. In the present study, we recruited 66 MN patients before any treatment and 11 healthy control (HC) and analyzed multiple aspects of the immunoglobulin heavy chain (IGH) repertoire of these samples using high-throughput sequencing. We found that the abnormalities of CDR-H3 length, hydrophobicity, somatic hypermutation (SHM), and germ line index were progressively more prominent in patients with MN, and the frequency of IGHV3-66 in post-therapy patients was significantly lower than that in pre-therapy patients. Moreover, we found that the IGHV3-38 gene was significantly related to PLA2R, which is the most commonly used biomarker. The most important discovery was that several IGHV, IGHD transcripts, CDR-H3 length, and SHM rate in pre-therapy patients had the potential to predict the therapeutic effect. Our study further demonstrated that the IGH repertoire could be a potential biomarker for prognosis prediction of MN. The landscape of circulating B-lymphocyte repertoires sheds new light on the detection and surveillance of MN.

The regulatory effect of Lactobacillus rhamnosus GG on T lymphocyte and the development of intestinal villi in piglets of different periods

The maturation and development of T cells were not completed until T cells were selected in thymus. It was not until the early 1960s that j.f.a.p. discovered the importance of thymus in T cell development. Twelve healthy piglets were randomly divided into two groups, the experimental group (LGG group) and the control group (saline group). The LGG group piglets were given 1 ml LGG (6 × 10⁹ CFU/ml) per day. The saline group was given 1 ml of normal saline per day. The piglets were slaughtered at 30 days and 45 days, respectively, and the MLN, jejunum and ileum PPs, LP of the piglets were taken. The expression of CD3⁺CD4⁺ T lymphocytes was detected by flow cytometry, and intestinal villi development was observed by intestinal paraffin section. The results showed that the flow cytometry results at 30 days and 45 days showed that the CD3⁺CD4⁺ T lymphocytes in the MLN group were significantly different from those in the saline group (P < 0.05, P < 0.01).The CD3⁺CD4⁺ T lymphocytes in the jejunum PP of piglets in LGG group were significantly different from those in saline group (P < 0.05). The CD3⁺CD4⁺ T lymphocytes in the ileum PP of the LGG group were significantly different from those in the saline group (P < 0.05, P < 0.01). CD3⁺CD4⁺ T lymphocytes and normal saline in the piglets of the LGG group There was a significant difference between the two groups (P < 0.001, P < 0.05). P < 0.001). HE staining results showed the length of the LGG group ileal villi in piglets at 30 days, 45 days was significantly different from that in normal saline group (P < 0.01, P < 0.01). LGG can also regulate the proliferation of T lymphocytes in the intestine of early weaned piglets at 30 days and 45 days increase the number of CD3⁺CD4⁺ T lymphocytes.