Glycomic profiles in lupus nephritis

Analysis code for:

Nikolopoulos D, Cindrić A, Charitidis K, Sherina N, Radovani Trbojević B, Pučić-Baković M, Šimunović J, Patenaude A-M, Pribić T, Tamirou F, Lauc G, Houssiau FA, Parodis I. Glycomic Profiles of IgG, C3 and Alpha-1-Acid Glycoprotein (AGP) Before and One Year After Treatment for Active Lupus Nephritis. Cells. 2026;15(5):433. doi:10.3390/cells15050433

The scripts compare glycan markers of total IgG, IgG Fab and Fc, complement C3, alpha-1-acid glycoprotein (AGP) and the total serum N-glycome between baseline and month 12. They then relate the markers to clinical indices, kidney histology, treatment response and renal impairment.

Data

No patient data are included. As stated in the paper, the data are available upon reasonable request.

Scripts

Run them in this order:

Script	What it does
Glycans_Preparation.Rmd	Joins the six glycan datasets with the clinical data, computes log2 fold changes (month 12 over baseline) and runs paired Wilcoxon signed-rank tests with Benjamini-Hochberg FDR correction. Writes the tables in Output_Data/ that the figure scripts read
Other/Check_Stats.Rmd	Builds the glycan annotations (Gl_annotations.xlsx, Gl_annotations_clean.xlsx) that label the markers in the figures. Its later sections collect each figure's significant markers into one table, so run those after the figure scripts
Glycans_Figure_1.Rmd	Figure 1: volcano plot of glycan changes from baseline to month 12
Glycans_Figure_2.Rmd	Figure 2: Spearman correlations of glycan markers with clinical indices
Glycans_Figure_3.Rmd	Figure 3: Spearman correlations of glycan markers with clinical and histopathological features. Also writes Histology_data.csv, which Figure 4 reads
Glycans_Figure_4.Rmd	Figure 4: correlations of glycan deltas with clinical and histopathological measures
Glycans_Figure_5.Rmd	Figure 5: Firth-penalised logistic regression of glycan markers against clinical and histopathological response
Glycans_Figure_6.Rmd	Figure 6: univariable and Firth-penalised multivariable Cox regression of glycan markers against time to renal impairment

The write_csv() and write_xlsx() calls that save the intermediate tables are commented out. Uncomment them on a first run.

Paths

Paths are hard-coded under ~/SLE/Glycans/:

• Data/: input spreadsheets
• Output_Data/: intermediate tables and results
• Plots_2/Final_Figures/: figures

Edit them to match your own layout.

Requirements

The analyses in the paper used R 4.4.2. To install the packages:

install.packages(c(
  "tidyverse", "readxl", "writexl", "broom", "broom.helpers",
  "ggtext", "ggrepel", "patchwork", "glmnet", "logistf",
  "survival", "coxphf", "timereg", "ggfortify", "gtsummary"
))