Human immune repertoire in hepatitis B virus infection

Hepatitis B virus(HBV)infection is a public health threat that affects 257 million people worldwide and can progress to liver cirrhosis,liver failure,and hepatocellular carcinoma.The HBV antigen-induced adaptive immune response plays an important role in HBV clearance.Immune repertoire sequencing(IRS)has been used to investigate the molecular mechanisms behind the immune system,find novel ways to treat HBV infection,and evaluate the genetic responses and immune characteristics of individuals infected by HBV or immunized by HBV vaccine.This review summarizes the human immune repertoire analysis methodology,and the application of the IRS in the prediction of HBV infection progression,treatment,and vaccination.

Characterization of heavy-chain antibody gene repertoires in Bactrian camels

Camelids are the only mammals that can produce functional heavy-chain antibodies(HCAbs).Although HCAbs were discovered over 30 years ago,the antibody gene repertoire of Bactrian camels remains largely underexplored.To characterize the diversity of variable genes of HCAbs(VHHs),germline and rearranged VHH repertoires are constructed.Phylogenetics analysis shows that all camelid VHH genes are derived from a common ancestor and the nucleotide diversity of VHHs is similar across all camelid species.While species-specific hallmark sites are identified,the non-canonical cysteines specific to VHHs are distinct in Bactrian camels and dromedaries compared with alpacas.Though low divergence at the germline repertoire between wild and domestic Bactrian camels,higher expression of VHHs is observed in some wild Bactrian camels than that of domestic ones.This study not only adds our understanding of VHH repertoire diversity across camelids,but also provides useful resources for HCAb engineering.

T Cell Repertoire Diversity Is Decreased in Type 1 Diabetes Patients

Type 1 diabetes mellitus （T1D） is an immune-mediated disease. The autoreactive T cells in T1D patients attack and destroy their own pancreatic cells. In order to systematically investigate the potential autoreactive T cell receptors （TCRs）, we used a high-throughput immune repertoire sequencing technique to profile the spectrum of TCRs in individual T1D patients and controls. We sequenced the T cell repertoire of nine T1D patients, four type 2 diabetes （T2D） patients,and six nondiabetic controls. The diversity of the T cell repertoire in T1D patients was significantly decreased in comparison with T2D patients （P = 7.0E-08 for CD4＋ T cells, P = 1.4E-04 for CD8＋ T cells） and nondiabetic controls （P = 2.7E-09 for CD4＋ T cells, P = 7.6E-06 for CD8 ＋ T cells）. Moreover, T1D patients had significantly more highly-expanded T cell clones than T2D patients （P = 5.2E-06 for CD4＋ T cells, P = 1.9E-07 for CD8＋ T cells） and nondiabetic controls （P = 1.7E-07 for CD4＋ T cells, P =Y3E-03 for CD8＋ T cells）. Furthermore, we iden- tified a group of highly-expanded T cell receptor clones that are shared by more than two TID patients. Although further validation in larger cohorts is needed, our data suggest that T cell receptor diversity measurements may become a valuable tool in investigating diabetes, such as using the diversity as an index to distinguish different types of diabetes.

Applications of species accumulation curves in arge-scale biological data analysis

The species accumulation curve, or collector＇s curve, of a population gives the expected number of observed species or distinct classes as a function of sampling effort. Species accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional sampling. Traditional applications have focused on ecological populations but emerging large-scale applications, for example in DNA sequencing, are orders of magnitude larger and present new challenges. We developed a method to estimate accumulation curves for predicting the complexity of DNA sequencing libraries. This method uses rational function approximations to a classical non- parametric empirical Bayes estimator due to Good and Toulmin [Biometrika, 1956, 43, 45~63]. Here we demonstrate how the same approach can be highly effective in other large-scale applications involving biological data sets. These include estimating microbial species richness, immune repertoire size, and R-mer diversity for genome assembly applications. We show how the method can be modified to address populations containing an effectively infinite number of species where saturation cannot practically be attained. We also introduce a flexible suite of tools implemented as an R package that make these methods broadly accessible.

Bone marrow stromal cell line co-transfected with IL-2 and IL-3 genes can accelerate restoration of T-cell immunity in allo-BMT mice

Background After T-cell depleted allogeneic bone marrow transplantation, impaired immune reconstitution is a major cause of morbidity and mortality in the recipient The purpose of this study was to observe the effects of the gene-engineered bone marrow stromal cell line QXMSC1-IL-2+IL-3 on the reconstitution of T-cell immunity in allo-BMT mice Methods The bone marrow stromal cell line QXMSC1 was co-transfected with IL-2 and IL-3 genes using a Tet-on gene expression system T lymphocyte subset counts per spleen were analyzed by flow cytometry Lymphocyte proliferation response to ConA was examined to evaluate T-cell function CDR3 spectratyping techniques were performed to evaluate TCR repertoire diversity at various time points post-transplantation Results Gene engineered bone marrow stromal cell line QXMSC1-IL-2+IL-3 could express IL-2 and IL-3 (1300 ng·day -1 ·10 -6 cells and 1100 ng·day -1 ·10 -6 cells, respectively) under the control of doxycycline QXMSC1-IL-2+IL-3 in combination with allogeneic bone marrow could significantly increase the counts of CD4 + and CD8 + T cell, 1.72 and 1.27-fold respectively at week 3 compared with TCD-BMT group ( P <0.01); make CD4 +/CD8 + ratio return to normal level at week 4; enhance splenocytes mitotic response to ConA ( P <0.01), and accelerate restoration of TCR repertoire diversity in the lethally irradiated mice ( P <0.05) KH*2/5DConclusion The gene transduced stromal cell line QXMSC1-IL-2+IL-3 is able to accelerate T-cell immunity in allo-BMT mice