Longitudinal proteomics and single-cell transcriptomic data of P. falciparum malaria-infected travellers
type: Dataset
description: 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 Sh…
citation: CreativeWork
  name: 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
conditions of access: https://publications.europa.eu/resource/authority/access-right/NON_PUBLIC
conditions of access: info:eu-repo/semantics/restrictedAccess
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Maximilian Julius Lautenbach
creator: Christopher Sundling
creator: Anna Färnert
date modified: 2026-04-27
date published: 2026-02-16
funding: Malaria treatment outcomes in travelers- addressing emerging drug resistance
  type: Grant
  description: 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.
  funder: Swedish Research Council
language: English
is part of: https://doi.org/10.48723/ygcx-hw44
keywords: Specific diseases, disorders and medical conditions
keywords: Immunology
  type: DefinedTerm
  term code: 10605
keywords: Immunology in the Medical Area
  type: DefinedTerm
  description: Including: Cell and Immunotherapy
  term code: 30110
keywords: Infectious Medicine
  type: DefinedTerm
  term code: 30209
keywords: Medical Bioinformatics and Systems Biology
  type: DefinedTerm
  term code: 30113
keywords: Malaria, Falciparum
keywords: Plasmodium falciparum malaria
keywords: Systems immunology
license: https://creativecommons.org/licenses/by/4.0/
publisher: Karolinska Institutet
size: QuantitativeValue
  unit text: cases
  value: 72
spatial coverage: Sweden
temporal coverage: 2011/2021
distribution: data/MalariaTraveler_RhapsodyAbSeq_Cell_Calling_qc_cca_wnn_clustering_annotated_clean.rds
  type: DataDownload
  additional type: data
  conditions of access: https://publications.europa.eu/resource/authority/access-right/NON_PUBLIC
  conditions of access: info:eu-repo/semantics/restrictedAccess
  content size: 507200000
  encoding format: application/octet-stream
distribution: data/Plasma_proteomics/Explore1536_tidy_long.rds
  type: DataDownload
  additional type: data
  conditions of access: https://publications.europa.eu/resource/authority/access-right/NON_PUBLIC
  conditions of access: info:eu-repo/semantics/restrictedAccess
  content size: 709000
  encoding format: application/octet-stream
distribution: documentation/README.txt
  type: DataDownload
  additional type: documentation
  conditions of access: http://publications.europa.eu/resource/authority/access-right/PUBLIC
  conditions of access: info:eu-repo/semantics/openAccess
  content size: 6497
  encoding format: text/plain
version: 1

PropertyValue
property ID: DOI
value: 10.48723/cmgs-aj72

PropertyValue
property ID: DOI
value: 10.1016/j.immuni.2025.06.014

Maximilian Julius Lautenbach
type: Person
affiliation: Karolinska Institutet
family name: Lautenbach
given name: Maximilian Julius

Karolinska Institutet
type: Organization
department: Department of Medicine, Solna [K2]

Christopher Sundling
type: Person
affiliation: Karolinska Institutet
family name: Sundling
given name: Christopher

Anna Färnert
type: Person
affiliation: Karolinska Institutet
family name: Färnert
given name: Anna

Swedish Research Council
type: Organization

English
type: Language
alternate name: eng

Specific diseases, disorders and medical conditions
type: DefinedTerm
description: 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.
term code: Health.SpecificDiseasesDisordersAndMedicalConditions

Malaria, Falciparum
type: DefinedTerm
description: 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.
term code: D016778

Plasmodium falciparum malaria
type: DefinedTerm
term code: B50

Sweden
type: Place