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Prenatal immune priming to Plasmodium falciparum is characterized by multi-lineage T-cell responses that are influenced by maternal microchimerism and predict malaria outcomes

姜永厚, Florian A. BachiD, John Houck, Marc Carlson, Almahamoudou MahamariD, Santara Gaoussou, Oumar Attaher, Robert Morrison, Sudhir KumariD, Blair ArmisteadiD, Irfan ZaidiiD, Stefan H. I. KappeiD, Alassane DickoiD, Patrick A. Duffy, Michal FriediD, Marion PepperiD, Whitney E. HarringtoniD

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Abstract

In malaria endemic settings, the fetus may be exposed to Plasmodium falciparum (Pf) antigens leading to prenatal immune primming (PIP). The fetus also acquires a graft of maternal cells in utero, a phenomenon known as maternal microchimerism (MMc). We have previously identified that MMc at birth predicts altered malaria susceptibility in early childhood, and we hypothesized that this association may be mediated via two potential mechanisms. First, the fetus may acquire Pf-specific MMc T-cells that directly respond to postnatal parasitemia. Alternatively, MMc may indirectly influence the quantity or quality of PIP. To investigate this hypothesis, infant cord bloods from 97 Malian primigravidae were screened for MMc using qPCR. A subset of ten cord blood mononuclear cells with variable MMc levels were stimulated with purified Pf merozoite extract and activated T-cells were sorted by flow cytometry for scRNAseq analysis. Transcriptional profile was used to differentiate Pf-responsive versus bystander activated T-cells, and MMc cells were identified using the Cellector algorithm. Among Pf-responsive cells, we identified four key populations: activated CD4 T-cells, ZBTB16+ CD4 T-cells, activated V{delta}1+ {gamma}{delta} T-cells, and cytotoxic V{gamma}9V{delta}2+ {gamma}{delta} T-cells. The minority of sorted cells were of MMc origin; however, there was a strong association between the presence of MMc and the quantity and quality of PIP. MMc+ infants had significantly fewer Pf-responsive T-cells, as well as a shifted distribution of these cells with fewer ZBTB16+ CD4 and cytotoxic V{gamma}9V{delta}2+ {gamma}{delta} T-cells. Clinically, MMc was protective from incident parasitemia and febrile malaria, whereas the frequencies of ZBTB16+ CD4 and activated CD4 T-cells were associated with increased risk. Together, these data demonstrate that MMc influences malaria outcomes through regulation of offspring inflammatory responses to Pf.

In-depth summary

Claude Sonnet 4.6 · xhigh effort · 8 Nov 2026 · from the full text of version 2 (19 Oct 2026) · CC BY 4.0

Maternal microchimerism in Malian cord blood is associated with fewer Pf-responsive ZBTB16+ CD4 and Vγ9Vδ2 T cells, and with infant malaria outcomes.

Cord blood T-cell responses to Plasmodium falciparum have been attributed to fetal antigen exposure, yet maternal cells acquired in utero might also shape them. This work profiles the origin and phenotype of responding cells at single-cell resolution and tests whether maternal microchimerism (MMc) modulates prenatal immune priming (PIP).

Key results

  1. SuggestedPfME stimulation of cord blood mononuclear cells produced a multi-lineage T-cell response. Four clusters showed the strongest Pf-responsiveness: activated CD4, ZBTB16+ CD4, activated Vδ1 and cytotoxic Vγ9Vδ2 T cells.

    29,343 cells retained after QC and doublet removal across ten CBMC samples; 15 Louvain clusters merged to 13; the four responder clusters were picked by cluster-level AIM gene-module scores and activation marker expression. · Identification of Pf-specific T cells; Stimulation with PfME induces a polyclonal…

  2. ShownCord bloods with experimental MMc had fewer Pf-responsive T cells overall, and fewer ZBTB16+ CD4, Vδ1 and cytotoxic Vγ9δ2 subsets. Activated CD4 cells did not differ.

    MMc+ (six infants) vs MMc- (four infants): total 6.6% vs 18.3% (p<0.001); ZBTB16+ CD4 2.9% vs 9.11% (p<0.001); Vδ1 0.7% vs 1.9% (p=0.03); Vγ9δ2 1.4% vs 6.4% (p=0.02); activated CD4 1.6% vs 1.0% (p=0.5). · Maternal microchimerism is associated with…

  3. SuggestedMaternal cells were rare among sorted activated T cells and were not the main Pf responders. Few genes differed by MMc status, so the MMc effect appears to be a shift in cell frequency rather than in cell state.

    25 MMc cells found in six infants; 11 cells from five infants survived QC. Pseudobulk differentially expressed genes (donor as replicate, Libra/edgeR): 70 (all T cells), 10 (activated cells), 6 (activated clusters). · Identification of Pf-specific T cells; Maternal microchimerism is associated with…

  4. SuggestedIn the eight-infant follow-up subset, experimental MMc was linked to lower parasitemia and febrile-malaria odds, while ZBTB16+ CD4 and activated CD4 frequencies were linked to higher parasitemia odds. Adding MMc to the model attenuated the ZBTB16+ association.

    102 visits, 15 incident parasitemias. MMc: AOR=0.47 (p=0.03), febrile AOR=0.10 (p=0.04). ZBTB16+ CD4 AOR=2.01, activated CD4 AOR=2.23 (both p<0.001). With MMc, ZBTB16+ AOR=1.39 (p=0.59); activated CD4 AOR=1.97 (p=0.005). · MMc and Pf-responsive T-cell populations display…

  5. SuggestedIn the wider screening cohort, qPCR-detected MMc at birth was linked to more incident parasitemia and a non-significant trend to less febrile malaria. This contrasts with the protective association seen for experimental MMc.

    97 pairs; informative marker in 70, of which 23 were MMc-positive by qPCR. Among 63 children with 890 visits: parasitemia AOR=2.01 (p=0.05), febrile malaria AOR=0.33 (p=0.1). · Samples for characterization of the interaction…; DISCUSSION

Methods, data and reproducibility

Cord blood mononuclear cells were stimulated with Pf merozoite extract. CD3+CD69+ cells were sorted for 10X scRNA-seq with antibody barcodes. Responders were scored with an activation-gene module, maternal cells were called with Cellector, and outcomes were modeled with GEE.

  • Immuno-Epidemiology maternal-infant cohort, Ouelessebougou, Mali (mostly primigravidae); qPCR screening for maternal microchimerism in cord blood · human · n = 97 maternal-infant pairs
  • Pairs with an informative maternal-specific marker for MMc qPCR; MMc-positive subset · human · n = 70 informative pairs; 23 MMc-positive
  • scRNA-seq of PfME-stimulated CD3+CD69+ cord blood T cells (two MMc-negative, eight high-MMc by screening) · human · n = ten CBMC samples; 29,343 cells after QC
  • Clinical follow-up for experimental-MMc and T-cell subset analyses (infants followed at least 4 weeks) · human · n = 8 infants; 102 visits; 15 incident parasitemias
  • Adult Pf-exposed donor PBMC for validating PfME vs uninfected RBC extract stimulation and the AIM score · human
Methods & tools
Cellector, Cell Ranger v7.2.0, Seurat, DoubletFinder, Harmony, Libra (edgeR likelihood ratio test), Generalized estimating equations (binomial), 10X Chromium 5' v2 and V(D)J v1.1, BD FACS Melody, qPCR MMc assay, AIM gene-module score, Pf merozoite extract (PfME)
Reagents & environment
Cell Ranger v7.2.0; Seurat, DoubletFinder, Harmony (theta = 1), Libra run_de with edgeR; 30 Harmony dimensions for UMAP; Louvain resolution 1.0. No container or other versions stated.
Reproducibility gaps
No code repository, sequencing data accession or data-availability statement appears in the text.
Limitations (6)
  • Single-cell PIP profiling covered only ten infants because of resource limits, although the authors report clear PIP in all of them and strong clinical associations. · stated by the authors
  • PfME contains little PfEMP1, so responses directed at PfEMP1 were not captured. · stated by the authors
  • The authors cannot exclude a role for MMc in modulating responses during acute Pf exposure. · stated by the authors
  • Febrile-malaria models for the combined subset and MMc analysis could not converge because there were too few outcomes. · stated by the authors
  • Clinical associations rest on eight infants with 15 parasitemia events and many adjusted GEE models; odds ratios are likely unstable and not externally validated. · noted in this summary
  • Experimental MMc status was assigned from 25 initial maternal cells, only 11 of which passed QC, and it conflicts with the qPCR-screened MMc associations; causality of MMc education is inferred, not tested. · noted in this summary

Read this if you study prenatal immune priming, maternal microchimerism, or the role of γδ and ZBTB16+ CD4 T cells in infant malaria risk.

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