Longitudinal proteomics and single-cell transcriptomic data of P. falciparum malaria-infected travellers

Comprehensive plasma proteomics and targeted single‑cell multi‑omics were generated from a longitudinal cohort of returning travelers treated for Plasmodium falciparum malaria. Plasma and peripheral blood mononuclear cells (PBMCs) were collected from symptomatic patients at Karolinska University Hospital after informed consent and followed with repeated sampling from acute disease up to one year post‑treatment in the absence of reinfection. Plasma protein profiling was performed in collaboration with the Human Protein Atlas using next‑generation affinity proteomics based on Proximity Extension Assay with NGS readout (Olink Explore 1536). Protein abundance was reported as Normalized Protein eXpression (NPX, log2 scale) after bridge normalization across batches. Proteins below the limit of detection in more than 70% of samples were excluded, resulting in a final dataset of 1,427 plasma proteins.
To infer potential cellular sources and targets of circulating proteins, targeted single‑cell multi‑omics profiling was performed on PBMCs from a subset of donors with overlapping time points. Gene expression of 399 immune‑related genes and 29 cell‑surface proteins was assessed using BD Rhapsody with AbSeq. Libraries were sequenced on a NovaSeq 6000 platform and processed using the BD Targeted Analysis Pipeline, and downstream analyses were conducted in R using Seurat. In addition, a publicly available scRNA‑seq dataset from an independent malaria cohort was reanalyzed to validate and extend the findings. Integrated proteomic and single‑cell analyses were used to stratify patients into subgroups associated with malaria disease severity.
The dataset consists of two data modalities:

Plasma proteomics: Olink NPX values for 132 samples across 1,427 proteins
PBMC single‑cell multi‑omics: targeted gene expression and AbSeq protein data from 12 samples

Parts of the plasma proteomics data are available in aggregated form through the Human Protein Atlas Disease Atlas. An interactive Shiny application accompanies the associated publication (Lautenbach et al., Immunity, 2025) to enable exploratory data analysis.

The dataset consists of 2 files:
Part1: Plasma proteomics (Olink PEA with NGS readout - Explore 1536)
File: Plasma_proteomics/Explore1536_tidy_long.rds (709 kB)

Part2: Targeted single-cell transcriptomics data (BD Rhapsody scRNA‑seq + AbSeq)
- Seurat object
File: MalariaTraveler_RhapsodyAbSeq_Cell_Calling_qc_cca_wnn_clustering_annotated_clean.rds (507.2 MB)