Memory B Cells and Their Transcriptomic Profiles Associated with Belimumab Resistance in Systemic Lupus Erythematosus in the Maintenance Phase

Normalized count of RNA sequences from systemic lupus erythematosus patients treated with belimumab.

We collected blood samples from patients with systemic lupus erythematosus (n=44) before and approximately 3 and 6 months after treatment by belimumab, respectively. We also included healthy individuals (n=17). There were no missing samples in the before-treatment specimen for 44 patients; however, five samples were missing at the three-month time, and four were missing at the six-month time after treatment. Whole blood samples were stored in PAXgene tubes (QUIAGEN). RNA was extracted by PAXgene Blood RNA Kit (QUIAGEN). Library preparation was performed using TruSeq stranded Total RNA Library PrepKit with Ribo-Zero Globin Human. Sequencing was conducted by NovaSeq6000 in the 100-bp paired-end mode. Sequencing reads were trimmed using Trimmomatic ver. 0.36 (leading: 20, trailing: 20, slidingwindow: 4:15, minlen: 36) and aligned to hg38 reference genome using STAR (ver. 2.7.3a). Gene counts were generated by RSEM (ver. 1.3.1) using Homo_sapiens.GRCh38.95.gtf from the Ensembl database. Gene counts were normalized by size factor implemented in DESeq2 and converted to count per million (CPM), and log2(CPM+1) was calculated. 

Sample names starting with 'R_' indicate responders, while those ending with '_NR' indicate non-responders. '0M' represents before treatment, '3M' represents three months after treatment, and '6M' represents six months after treatment. The numeric ID, excluding the last two characters, represents individual patients.

If you use this data, please cite Iwasaki et al. Front. Immunol., 04 February 2025 https://doi.org/10.3389/fimmu.2025.1506298