Common host variation drives malaria parasite fitness in healthy human red cells
- Department of Biology, Stanford University, United States
- Department of Pediatrics, Stanford University School of Medicine, United States
- Children's Hospital Oakland Research Institute, United States
- Department of Microbiology & Immunology, Stanford University School of Medicine, United States
Figures
Figure 1
Overview of blood donors and study design.
(A) PCA of genetic variation across 35,759 unlinked exome SNPs. Donors from this study are plotted on coordinate space derived from 1000 Genomes reference populations. Points with white borders …
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Figure 1—source data 1
Individual genotypes, population frequencies, and protein annotations for exome variants passing quality filters (N~160,000).
- https://cdn.elifesciences.org/articles/69808/elife-69808-fig1-data1-v2.zip
Figure 2 with 2 supplements
Plasmodium falciparum replication rate varies widely among donor RBCs.
(A, B) Growth of P. falciparum lab strain 3D7 (A) or clinical isolate Th.026.09 (B) over a full 48-hr cycle in donor RBCs (see Figure 1C). Growth is presented relative to the average non-carrier …
Figure 2—figure supplement 1
Linear models of batch effects on parasite fitness.
PMR: parasite multiplication rate.
Figure 2—figure supplement 2
Repeatability of parasite assays in the same donors over time.
Twelve participants (including the weekly control, 1111) donated blood in multiple weeks for independent experiments. Repeated donors were non-carriers except 6443, who carried the HbAC allele; and …
Figure 3 with 5 supplements
Red cell phenotypes that are abnormal in carriers also vary widely among non-carriers.
(A–D) Red cell indices were measured by an ADVIA hematology analyzer. Additional indices are shown in Figure 3—figure supplement 1. MCV: mean corpuscular (RBC) volume; MCH: mean cellular hemoglobin; …
Figure 3—figure supplement 1
RBC indices data from complete blood counts in donor RBCs.
Donor classifications and statistical tests as in Figure 3. HCT, hematocrit; HDW, hemoglobin distribution width; HGB, hemoglobin; MCHC, mean corpuscular hemoglobin concentration; MPV, mean platelet …
Figure 3—figure supplement 2
RBC Matrix data from complete blood counts in donor RBCs.
Donor classifications and statistical tests as in Figure 3. RBC, red blood cell.
Figure 3—figure supplement 3
Heatmap of RBC phenotypes by carrier status.
Phenotypes were scaled and centered at 0 with the preProcess function from the caret package in R using all sample data (i.e., not limited to non-carriers). The mean value for each carrier group is …
Figure 3—figure supplement 4
Osmotic fragility diagram and summary data.
Donor classifications and statistical tests as in Figure 3.
Figure 3—figure supplement 5
Ektacytometry diagram and summary data.
Donor classifications and statistical tests as in Figure 3.
Figure 4 with 1 supplement
RBC phenotypes predict Plasmodium falciparum fitness in non-carriers.
(A) Phenotypes selected by LASSO in at least 40% of train data sets (blue shading; see Materials and methods) in at least one of four models of parasite replication (columns). Each model was trained …
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Figure 4—source data 1
Association statistics for individual phenotypic predictors with non-zero LASSO support.
- https://cdn.elifesciences.org/articles/69808/elife-69808-fig4-data1-v2.xlsx
Figure 4—figure supplement 1
Scatterplots of RBC phenotypes against parasite fitness in non-carriers.
Phenotypes from Figure 4A are shown if at least one OLS test had p<0.1. Lines of best fit are shown if p<0.1. All phenotypes except Fragility and Donor Age are clustered around the median as a …
Figure 5 with 6 supplements
Common variation in malaria-associated genes predicts Plasmodium falciparum fitness in non-carrier RBCs.
(A) Variants in 23 malaria-related genes (Figure 5—source data 1) and genetic PCs selected by LASSO in at least >40% of train data sets. Each model was trained on ~90% of the measured data (B C) and …
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Figure 5—source data 1
Twenty-three RBC genes with strong links to malaria in the literature.
- https://cdn.elifesciences.org/articles/69808/elife-69808-fig5-data1-v2.xlsx
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Figure 5—source data 2
Proteins present in mature RBCs.
This list was derived from the Red Blood Cell Collection database (rbcc.hegelab.org) using a medium-confidence filter.
- https://cdn.elifesciences.org/articles/69808/elife-69808-fig5-data2-v2.csv
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Figure 5—source data 3
All genetic and phenotypic predictors with non-zero LASSO support.
Growth predictors selected in at least 40% of train data sets are indicated in bold. Genetic predictors are summarized in Figure 5A. NA indicates predictors that were only present as singletons in the smaller invasion data set.
- https://cdn.elifesciences.org/articles/69808/elife-69808-fig5-data3-v2.xlsx
Figure 5—figure supplement 1
Variance in parasite fitness explained by permuted data in LASSO models.
Each model was trained on ~90% of the measured data and tested on the remaining 10%. Dashed lines indicate average R2 for the measured test data. Each histogram shows the same procedure on 1,000 …
Figure 5—figure supplement 2
Lack of association between RBC dehydration phenotypes and PIEZO1 rs59446030 or ATP2B4 rs1419114.
Each cell shows the p-value from a linear model between the genetic variant and trait in non-carriers. RBC, red blood cell.
Figure 5—figure supplement 3
Three non-carrier variants with potentially overdominant effects on 3D7 growth.
Homozygotes for the minor allele were ignored when estimating effect sizes for these alleles with OLS for Figure 6E. Effect size estimates that include all homozygotes are shown in Figure 5—source …
Figure 5—figure supplement 4
Variants undiscovered by previous GWAS drive most of the association signal between parasite replication rate and the 23 malaria-related genes.
‘Variance explained’ is the R2 of a linear model in non-carriers (excluding using only these variants as predictors. Details on the variants and previous GWAS traits are provided in Figure 5—source …
Figure 5—figure supplement 5
An outlier individual for PC2 drives an apparent association between PC2 and 3D7 growth.
See also Figure 1A.
Figure 5—figure supplement 6
A six-member family has unique ancestry and parasite susceptibility compared to other non-carrier donors.
Only PCs that distinguish the family from other non-carriers are shown. P-values are derived from t-tests. PC, principal component.
Figure 6 with 1 supplement
Little evidence of widespread selection in Africa for slower Plasmodium falciparum replication, protective alleles, or protective phenotypes in non-carriers.
(A–D) Parasite replication versus the exome-wide fraction of African ancestry in non-carriers, determined with ADMIXTURE by comparison to 1000 Genomes reference populations. R2 and p-values are …
Figure 6—figure supplement 1
Scatterplots of RBC phenotypes versus African ancestry in non-carriers.
Phenotypes from Figure 4A are shown. R2 and p-values were estimated from OLS regression. RBC, red blood cell.
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Biological sample (Homo sapiens) | Primary whole blood samples | This paper | Freshly drawn from de-identified human subjects into CPDA tubes (IRB #40479) | |
| Strain, strain background (Plasmodium falciparum) | 3D7 | PMID:3299700; Obtained from Walter and Eliza Hall Institute, Melbourne, Australia | ||
| Strain, strain background (P. falciparum) | Th026.09 | PMID:22430961; Gift from Daouda Ndiaye and Sarah Volkman, Senegal | ||
| Commercial assay or kit | DNeasy Blood and Tissue Kit | QIAGEN | ||
| Commercial assay or kit | KAPA Hyperplus Kit | Roche | ||
| Commercial assay or kit | SeqCap EZ Prime Exome Kit | Roche | ||
| Sequence-based reagent | Primers amplifying PIEZO1 exon 17 | PMID:32265284 | ||
| Software, algorithm | bwa mem | http://arxiv.org/abs/1303.3997 | 0.7.17-r1188 | |
| Software, algorithm | GATK | https://gatk.broadinstitute.org/hc/en-us | 4.0.0.0 | |
| Software, algorithm | vcftools | doi:10.1093/bioinformatics/btr330 | 0.1.15 | |
| Software, algorithm | ANNOVAR | PMID:20601685 | 2018-04-16 | |
| Software, algorithm | PLINK | PMID:17701901 | v1.90b6.8 64-bit | |
| Software, algorithm | ADMIXTURE | PMID:21682921 | 1.3.0 | |
| Software, algorithm | R | https://www.R-project.org/ | 3.5.1 | |
| Other | SYBR Green I nucleic acid stain | Invitrogen | S7563 | |
| Other | Drabkin’s Reagent | Ricca Chemical | 2660–32 |
