Airway B Cell Repertoire Fragmentation and Microbe-Driven Clonal Expansion in COPD-HIV comorbidity
Description
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
Files
Steps to reproduce
# BCR Clonotyping Analysis Pipeline This package contains a complete, publication-ready Jupyter Notebook pipeline for BCR clonotyping analysis. ## Contents - **BCR_Clonotyping_Analysis.ipynb** — main analysis notebook - **requirements.txt** — Python environment dependencies - **/data/** — input files folder - `merged_trust4_airr.csv` - `TRUST4_metadata.csv` - `Species copy.txt` ## Setup Instructions 1. **Install dependencies** ```bash pip install -r requirements.txt ``` or, to create a conda environment: ```bash conda create -n bcr_env --file requirements.txt conda activate bcr_env ``` 2. **Data is placed in file named data** - `data/merged_trust4_airr.csv` - `data/TRUST4_metadata.csv` - `Species copy.txt` The metadata file has: - `PTID` (sample ID) - `Hiv_test` (0/1) - `COPD_NHANES` (0/1) 3. **Run the notebook** ```bash jupyter notebook BCR_Clonotyping_Analysis.ipynb ``` The notebook will generate outputs (figures, CSVs) in an `output/` folder. ## Outputs The pipeline produces: - Diversity metrics (Shannon, Simpson, richness, SHM, CDR3 length) - PCA & UMAP embeddings with ellipses - PERMANOVA test results - BCR–microbiome correlation scaffolding - Jaccard overlap heatmap - Public vs private clonotypes summary - V and J gene usage frequencies - Louvain network communities - Group-wise FDR-corrected statistical tests - Airway Microbiome-Clonotype Associations - All results saved as high-resolution figures (600 dpi) and CSVs --- **Author:** AMIC-Lab **Purpose:** Supplementary analysis code for BCR clonotyping manuscripts
Institutions
- Makerere University College of Health Sciences