Computational Analysis of B-Cell Receptor (BCR) Immune Repertoires with Abalign.

The widespread application of high-throughput sequencing technology has generated massive sequences of B-cell receptor (BCR) immune repertoires. Computational analysis of these data has gained significant attention due to the increasing importance of immunotherapy and precision medicine. It not only reveals the diversity and dynamic changes in immune responses, contributing to the study of associated diseases, but also provides valuable information for immunodiagnostics and drug development. Recently, we introduced a BCR-specific multiple sequence alignment (MSA) method along with a comprehensive platform software called Abalign, which stands out as an excellent choice for analyzing BCR immune repertoires due to its unique high-throughput processing capability. It offers ultra-fast MSA functionality and a wide range of analytical features, including BCR/antibody extraction, clonal grouping, lineage tree construction, mutation profiling, diversity statistics, VJ gene assignment, antibody humanization, and more. Importantly, users can perform these analyses using the graphical user interface without any programming skills or scripts. In this article, we present a series of protocols that integrate Abalign's analysis modules into a cohesive workflow. This step-by-step workflow provides detailed instructions for software installation, data preparation, and comprehensive analysis of BCR immune repertoires. This workflow facilitates the efficient acquisition of comprehensive results in profiling BCR immune repertoires, offering insights into the impacts of infectious diseases, allergies, autoimmune disorders, tumor immunology, and antibody drugs. Abalign is freely available at http://cao.labshare.cn/abalign/. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Resource preparation Basic Protocol 2: Analyzing BCR immune repertoires Support Protocol 1: Aiding antibody humanization Support Protocol 2: Constructing B-cell lineage trees Alternate Protocol: Running with Linux command line Basic Protocol 3: Comparing BCR immune repertoires.

Platelet microvesicles promote the recovery of neurological function in mouse model of cerebral infarction by inducing angiogenesis.

The aim of this study is to investigate the effect of PMVs on mice with ischemic cerebral infarction and its mechanism. Male C57BL/6 mice were selected, and the right focal cortical infarction model was established via cauterization under a microscope and randomly divided into sham operation (Sham) group, normal saline control (Saline) group and platelet microvesicles intervention (PMVs) group. At 1 h after modeling, 5 µL of PMVs (50 µg/mL) or normal saline was injected into the lateral ventricle. The neurological function of mice in each group was evaluated at 1, 3, 7, 14 and 28 d after modeling. After 28 d, the cerebral infarction area was detected via 2,3,5-triphenyltetrazolium chloride (TTC) staining. At 7 and 28 d after modeling, the blood vessel density, proliferation rate of new vessels and encapsulation rate of pericytes were detected via immunofluorescence staining. Moreover, the changes in cerebral cortical blood flow at the infarction side were detected before modeling and at 7 and 28 d after modeling, respectively. Finally, the expressions of proangiogenic factors vascular endothelial growth factor (VEGF), angiopoietin-1 (Ang-1) and N-Cadherin were detected via Western blotting at 3, 7 and 28 d after modeling. PMVs could promote the improvement of neurological function and significantly reduce the cerebral infarction volume in mice with cerebral infarction. PMVs promoted proliferation of new vessels and increased blood vessel density at the infarction edge in mice with cerebral infarction. PMVs could increase the encapsulation rate of pericytes at the infarction edge and improve the permeability of blood-brain barrier in mice with cerebral infarction. PMVs could increase the cerebral cortical blood flow perfusion in mice with cerebral infarction. PMVs could increase proangiogenic factors in brain tissues in mice with cerebral infarction. PMVs could significantly improve the recovery of neurological function in mice with cerebral infarction, which is closely related to the ability of PMVs to promote angiogenesis at the infarction edge. The possible mechanism is that PMVs facilitate angiogenesis after cerebral infarction through promoting the expressions of VEGF, Ang-1 and N-Cadherin. More importantly, the new vessels promoted by PMVs have complete structure and perfect function, and can improve the cerebral blood flow perfusion at the infarction side.

Impact of diabetes-related gene polymorphisms on the clinical characteristics of type 2 diabetes Chinese Han population.

We investigated the correlation between type 2 diabetes (T2D)-related genes and the clinical characteristics of T2D in the Chinese Han population. Our study included 319 patients and 387 controls. Age, gender, clinical features, medications intake and biochemical blood profiles were analyzed. Genotyping was performed on a total of 18 single nucleotide polymorphisms previously reported to be associated with T2D. Our analyses revealed that the CT genotype of ARHGAP22 rs4838605 is associated with T2D risk. Upon analyzing the subjects' clinical characteristics, we found that for rs2811893, the TT genotype correlated with high creatinine levels, while the AA genotype of rs17045754 and the TT genotype of rs4838605 correlated with elevated triglyceride levels. In addition, the AA genotype of rs17376456 and the TT genotype of rs6214 (p = 0.006) correlated with elevated hemoglobin A1c levels. Lastly, those carrying the TT genotype of rs7772697 and the CA genotype of rs3918227 exhibited higher mean body mass index and Cystatin C than controls. Our results showing that the ARHGAP22 gene is associated with an increased risk of T2D, and that seven SNPs in MYSM1, PLXDC2, ARHGAP22 and HS6ST3 promote T2D progression and could help predict the clinical course of T2D in patients at risk.

Influence of FasL gene expression on hepatic metastasis of colorectal carcinoma.

BACKGROUND: FasL expression was reported to be associated with hepatic metastasis of colorectal cancer. The aim of this study was to study FasL gene expression in colorectal carcinoma and its influences on biological behavior and hepatic metastasis of colorectal carcinoma. METHODS: FasL gene expressions were examined with reverse transcriptase-polymerase chain reaction (RT-PCR) in the primary focus of colorectal carcinoma, adjacent cancerous mucosae, and metastasized liver focus from colorectal cancer. HR-8348 cells of human rectal cancer cell line were transfected with FasL cDNA. Cell growth suppression rate and response to 5-FU and carboplatin were observed and analyzed with the MTT method. RESULTS: FasL gene expression was detected in the primary focus of colorectal cancer (n=58), adjacent cancerous mucosae (n=58), and metastasized hepatic tumor tissues (n=28). The positive rate of FasL expression was 24% (14/58), 8% (5/58), and 100% (58/58) in the primary focus, adjacent cancerous mucosae and metastasized hepatic tumor tissues respectively. FasL expression rate in the metastasized hepatic tumor tissues was higher than that in the primary focus (X(2)=43.49, P<0.01) and adjacent cancerous mucosae (X(2)=57.66, P<0.01). In a group of patients with hepatic metastasis, the FasL expression rate in primary focus was higher than that in patients without hepatic metastasis (X(2)=3.96, P<0.05). In vitro study positive expression of FasL was shown in transfected HR-8348 cells. When 5-FU or carboplatin was added, there was a significant difference in growth suppression rate between FasL positive and controlled cancer cells (t=9.02, t=11.93, P<0.01). Under the same concentration of chemotherapeutic agents, the survival rate of FasL positive HR-8348 cells was higher than that of controlled cells. CONCLUSIONS: FasL positive cancer cells are powerfully resistant to chemotherapeutic agents. The expression of the FasL gene in colorectal cancer cells is related to immune evasion to escape from being killed by immune cells, showing stronger drug-resistance, and it facilitates hepatic metastasis.

[The influence of FasL gene expression upon hepatic metastasis of colorectal carcinoma].

OBJECTIVE: To study FasL gene expression in colorectal carcinoma and its influences on biological behaviour of colorectal cancer and hepatic metastasis. METHODS: FasL gene expressions were examined with RT-PCR technique in the primary locus of colorectal cancer, mucosa adjacent to cancer, and hepatic metastasis. HR-8348 cells of human rectal cancer cell line were transfected with FasL cDNA. Cell growth suppression rates and cell response to 5-FU and carboplatin were observed and analysed with MTT method. RESULTS: FasL gene expressions were detected in the primary site of colorectal cancer (n = 58), cancer adjacent mucosa (n = 58), and hepatic metastasis (n = 28). The positive rate of FasL expression was 24% (14/58), 14% (8/58), 100% (28/28), respectively, in primary site, tumor adjacent mucoca and hepatic metastasis. FasL expression rate in hepatic metastasis was higher than that in the primary site (chi2 = 43.49, P < 0.01) and tumor adjacent mucosa (chi2 = 57.66, P < 0.01). In a group of patients with hepatic metastasis, FasL expression rate in primary site was higher than that in patients without hepatic metastasis (chi2 = 3.96, P < 0.05). In vitro experiment, positive expression of FasL was found in transfected HR-8348 cells. When 5-FU or carboplatin was added, there was a significant difference in growth suppression rate between FasL positive and control cancer cells (t = 9.02, t = 11.93, P < 0.01). Under same concentration of chemotheraputic agent, survival rate of FasL positive HR-8348 cells was higher than that of control cells. CONCLUSIONS: FasL positive cancer cells have more powerful resistance to chemotheraputic drugs. Expression of FasL gene in colorectal cancer cells is related with immune evasion to escape killing by immune cells, showing stronger drug-resistance, and it facilitates hepatic metastasis.