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)
Lautenbach, M. J., Wyss, K., Yman, V., Foroogh, F., Satarvandi, D., Mousavian, Z., Sondén, K., Wang, J., Alvez, M. B., Bergström, S., Nilsson, P., Edfors, F., Brodin, P., Uhlén, M., Sundling, C., & Färnert, A. (2025). Systems analysis of clinical malaria reveals proteomic perturbation and innate-adaptive crosstalk linked to disease severity. In Immunity. https://doi.org/10.1016/j.immuni.2025.06.014
Malaria treatment outcomes in travelers- addressing emerging drug resistance
Malaria is a potentially severe and fatal disease. Artemisinin combination therapy (ACT) is the first line therapy for malaria. Alarming emergence of resistance to artemisinin and partner drugs is now reported from Sub-Saharan Africa. Understanding treatment outcomes and identifying drug resistant markers could guide management and development of new treatment strategies. The purpose of this preparatory study is to plan: 1) a nationwide prospective treatment efficacy study using a new standardized follow-up protocol for all malaria patients in Sweden for detecting treatment failures, and 2) to plan a comprehensive prospective study in adults treated for Plasmodium falciparum malaria with more extensive sampling to assess parasite clearance time in relation to antimalarial drug concentrations, host immunity and parasite genomics. Within the preparatory study, we will assess current practice of diagnostics and management of malaria across Sweden. Moreover, we will perform a retrospective review of treatment outcomes since ACT was introduced, and also perform a pilot analysis of resistance mutations in available archived samples. The project involves experts in infectious diseases, pediatrics, microbiology and pharmacology; and the aim is to establish a nationwide collaborative network including all treating clinics. The findings from this project will lead to improved management and monitoring of malaria in travelers, and could also inform treatment strategies in endemic areas.
Specific diseases, disorders and medical conditions
Data on specific, diagnosed diseases, disorders or syndromes (often classified in ICD-10 or its earlier versions). For example, medical research on infectious diseases or the causes of diabetes, or data on the physical and mental recovery of people who have had heart surgery.
Medical Bioinformatics and Systems Biology
Malaria caused by PLASMODIUM FALCIPARUM. This is the severest form of malaria and is associated with the highest levels of parasites in the blood. This disease is characterized by irregularly recurring febrile paroxysms that in extreme cases occur with acute cerebral, renal, or gastrointestinal manifestations.