scRNA-Seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with clinical malaria

Malaria causes significant morbidity and mortality worldwide, disproportionately impacting parts of Africa. Disease phenotypes associated with malarial infection can vary widely, from subclinical to life-threatening. To date, prevention efforts, particularly those related to vaccine development, have been hindered by an incomplete understanding of which factors impact host immune responses resulting in these divergent outcomes. We applied single-cell RNA-sequencing to compare the immunological phenotypes of peripheral blood mononuclear cells (PBMCs) isolated from children with clinical and subclinical malarial infections in an area of high malaria transmission in northern Ghana. On average, clinical pediatric malaria infections were characterized by a higher fractional abundance of monocytes and an upregulation of innate immune responses, including those to type I and type II interferons and tumor necrosis factor-alpha (TNF-a) signaling via NFkB. Further, in the clinical malaria group, we identified more putative interactions between antigen-presenting cells and proliferating CD4 T cells and naive CD8 T cells driven by MHC-I and MHC-II signaling pathways, respectively. Together, these findings highlight transcriptional differences between immune cell subsets associated with disease phenotypes that may help guide the development of improved malaria vaccines and new therapeutic interventions for individuals residing in endemic areas. ### Competing Interest Statement A.K.S. reports compensation for consulting and/or SAB membership from Honeycomb Biotechnologies, Cellarity, Ochre Bio, FL86, Relation Therapeutics, Senda Biosciences, IntrECate biotherapeutics, and Dahlia Biosciences unrelated to this work. ### Funding Statement The study was funded by a DELTAS Africa grant (DEL-15-007: Awandare). The DELTAS Africa Initiative is an independent funding scheme of the African Academy of Sciences (AAS)s Alliance for Accelerating Excellence in Science in Africa (AESA) and supported by the New Partnership for Africas Development Planning and Coordinating Agency (NEPAD Agency) with funding from the Wellcome Trust (107755/Z/15/Z: Awandare) and the UK government. TDO was supported by the Wellcome Trust (104111/Z/14/Z & A). The study was also supported by the Ragon Institute of MGH, MIT, and Harvard (AKS). The funders had no role in the study design and interpretation of the results. The views expressed in this publication are those of the author(s) and not necessarily those of AAS, NEPAD Agency, Wellcome Trust, or the UK government. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethical clearance was obtained from the Noguchi Memorial Institute of Medical Research, University of Ghana (IRB 0000908), and the Ghana Health Service (GHS-ERC 008/02/19). All participants were provided with written informed consent before inclusion in the study. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data generated or analyzed during this study are included in this published article and its supplementary information files. The scRNA-Seq data are available at https://cellatlas-cxg.mvls.gla.ac.uk/PBMC.Pediatric.Malaria.Ghana.