Airway B Cell Repertoire Fragmentation and Microbe-Driven Clonal Expansion in COPD-HIV comorbidity

This dataset contains immune repertoire and microbiome sequencing data from induced sputum samples collected from 160 Ugandan adults stratified by HIV and COPD status (HIV−/COPD−, HIV+/COPD−, HIV−/COPD+, HIV+/COPD+). A total of 5,726 B cell receptor (BCR) clonotypes were reconstructed using the TRUST4 algorithm from bulk RNA-seq data. Complementary 16S rRNA sequencing was performed to profile airway microbial communities. The dataset includes: Clonotype sequences (AIRR-formatted outputs). Repertoire features (diversity indices, CDR3 length, somatic hypermutation rates, V–J recombination usage). Sample-level metadata (HIV and COPD status, demographic variables). Genus-level microbiome abundance tables. Clonotype-microbe correlation matrices. BCR_Clonotyping_Analysis_FullPackage: a complete analysis workflow (Python code and Jupyter notebooks) for reproducing clonotype construction, repertoire statistics, network analyses, and repertoire–microbiome integration. Value of the Data: Provides the first airway BCR repertoire map in HIV, COPD, and their comorbidity. Enables analysis of repertoire diversity, V–J recombination biases, clonotype sharing, and network topology. Links immune repertoire data with microbiome profiles to investigate repertoire–microbiome associations. Includes BCR_Clonotyping_Analysis_FullPackage to allow reproducibility, benchmarking, and adaptation by other groups. Supports research on mucosal immunology, host-microbiome interactions, biomarker discovery, and microbiome-specific inflammotypes. Data Format: CSV files: clonotype tables, repertoire metrics, metadata, microbiome abundance. FASTA/CSV (AIRR format): reconstructed BCR sequences. TXT/TSV: processed 16S rRNA abundance tables. Excel/CSV: supplementary tables for clonotype–microbe correlations. Code: BCR_Clonotyping_Analysis_FullPackage (Python scripts and Jupyter notebooks for full pipeline). Ethics Statement: All participants provided written informed consent. The study was approved by the Mulago Hospital Research and Ethics Committee (MHREC; reference no. 2152) and the Uganda National Council for Science and Technology (UNCST) (reference no. HS2035ES) . Funding: This work was supported by the Fogarty International Center, National Institutes of Health (R21TW012354, 3R21TW012354-S1, 3R21TW012354-S2). Keywords: BCR repertoire, airway microbiome, HIV, COPD, clonotypes, immunoglobulin, induced sputum, repertoire–microbiome interaction, Uganda, BCR_Clonotyping_Analysis_FullPackage本数据集涵盖160名乌干达成人诱导痰样本的免疫组库与微生物组测序数据，按人类免疫缺陷病毒（HIV）与慢性阻塞性肺疾病（COPD）状态分为四组：HIV阴性/COPD阴性、HIV阳性/COPD阴性、HIV阴性/COPD阳性、HIV阳性/COPD阳性。研究团队利用TRUST4算法从批量RNA测序数据中重构得到总计5726个B细胞受体（B cell receptor, BCR）克隆型，并通过16S核糖体RNA（16S rRNA）测序对气道微生物群落进行分析。 本数据集包含以下内容： 1. 克隆型序列（采用AIRR格式输出）； 2. 免疫组库特征：包括多样性指数、互补决定区3（Complementarity Determining Region 3, CDR3）长度、体细胞超突变率、V-J基因重组使用偏好； 3. 样本元数据：涵盖HIV与COPD状态、人口统计学变量； 4. 属级微生物组丰度表； 5. 克隆型-微生物相关性矩阵； 6. BCR_Clonotyping_Analysis_FullPackage：一套完整的分析工作流，包含Python代码与Jupyter笔记本，可复现克隆型构建、免疫组库统计分析、网络分析以及免疫组库-微生物组整合分析。 数据价值： 本数据集首次提供了HIV感染、COPD及其共病状态下的气道BCR组库图谱，可支持以下研究方向： 1. 免疫组库多样性、V-J基因重组偏好、克隆型共享性与网络拓扑结构分析； 2. 免疫组库数据与微生物组谱的关联分析，以探究免疫组库-微生物组的相互作用； 3. 内置BCR_Clonotyping_Analysis_FullPackage工具包，保障分析可复现性，可供其他研究团队开展基准测试与适配改造； 4. 支持黏膜免疫学、宿主-微生物组互作、生物标志物发现以及微生物组特异性炎症型相关研究。 数据格式： 1. CSV格式文件：克隆型表、免疫组库指标表、样本元数据表、微生物组丰度表； 2. FASTA/CSV格式文件（AIRR格式）：重构得到的BCR序列； 3. TXT/TSV格式文件：处理后的16S rRNA丰度表； 4. Excel/CSV格式文件：克隆型-微生物相关性补充表； 5. 代码文件：BCR_Clonotyping_Analysis_FullPackage（包含完整分析流程的Python脚本与Jupyter笔记本）。 伦理声明： 所有受试者均签署书面知情同意书。本研究经穆拉戈医院研究与伦理委员会（Mulago Hospital Research and Ethics Committee, MHREC；编号2152）以及乌干达国家科学技术委员会（Uganda National Council for Science and Technology, UNCST；编号HS2035ES）批准。 资助： 本工作受美国国立卫生研究院（National Institutes of Health, NIH）下属福格蒂国际中心（Fogarty International Center）资助，资助编号为R21TW012354、3R21TW012354-S1、3R21TW012354-S2。 关键词：BCR组库、气道微生物组、HIV、COPD、克隆型、免疫球蛋白、诱导痰、免疫组库-微生物组互作、乌干达、BCR_Clonotyping_Analysis_FullPackage