DOI: 10.5061/dryad.59zw3r2jw
title: Data from: Clone tracking through repeated malaria reveals high-fidelity CD4+ memory responses

description: Few studies have assessed the clonality and functional fidelity of human
 CD4+ T cells responding to repeated infections in vivo. We utilized broad,
 longitudinal single-cell RNA and TCR tracking to study the functional
 stability and memory potential of thousands of CD4+ T cell clonotypes
 through repeated Plasmodium falciparum (Pf) infections over the course of
 hundreds of days. Strikingly, nearly all memory CD4+ T cell clonotypes
 displayed a strong preference for one of seven different subsets—Tcm, Th1,
 cytotoxic Th1, Th2, Th17, Treg, and Tr1. This phenomenon, which we call
 “clonal fidelity,” was influenced by clonal expansion, demonstrating an in
 vivo relationship between T cell polarization and proliferation. Using
 clone tracking, we characterized subset-specific trajectories of CD4+ T
 cell activation and identified clonotypes with specific reactivity to
 Plasmodium falciparum (Pf) blood-stage antigens. Tr1 cells, a
 peripherally-induced regulatory subset distinct from FOXP3+ Tregs,
 accounted for nearly 90% of Pf-specific CD4+ T cells. Tracking T cell
 clones longitudinally in humans, we observed malaria-induced clonal
 expansion of Tr1 effectors, long-term persistence of Tr1 memory cells, and
 high-fidelity recall responses following reinfection. Ultimately, this
 work establishes clonal fidelity as a natural phenomenon and demonstrates
 the stable, long-term memory potential of the previously enigmatic Tr1
 cell.
description: These processed data files are seurat objects that were generated
 from raw data available from NCBI (BioProject PRJNA1129481).
 The code used to generate these files is available on GitHub
 (jason-nideffer/clone-tracking-in-malaria). These files
 can be used (in conjunction with code available on GitHub) to reproduce
 the figures in the manuscript titled: "Clone tracking through
 repeated malaria reveals high-fidelity CD4+ memory
 responses."
description: # Data from: Clone tracking through repeated malaria reveals high-fidelity
 CD4+ memory responses
 [https://doi.org/10.5061/dryad.59zw3r2jw](https://doi.org/10.5061/dryad.59zw3r2jw) ## Description of the data and file structure These processed data files are Seurat objects that were generated from raw data available from NCBI (BioProject PRJNA1129481). The code used to generate these files is available on GitHub (jason-nideffer/clone-tracking-in-malaria). These files can be used (in conjunction with code available on GitHub) to reproduce the figures in the manuscript titled: "Clone tracking through repeated malaria reveals high-fidelity CD4+ memory responses." ### Files and variables #### File: rna_tcr_malaria_specific.rds **Description:** seurat object containing single memory CD4+ T cells analyzed by RNA/TCRseq. This object is the product of a full data processing pipeline (GitHub: jason-nideffer/clone-tracking-in-malaria; Steps 1-11). The seurat object includes metadata on a per-cell basis. These metadata provide TCR/clonal information, annotations, and describe which sample a cell came from. **Metadata**: Metadata variables in this object are largely the same as metadata variables in rna_tcr_malaria_specific.rds. #### File: rna_tcr_tr1.rds **Description:** seurat object containing only Tr1 cells. It contains a subset of the cells in 'rna_tcr_malaria_specific.rds' that were reclustered. **Metadata**: The most relevant variables included in the metadata of this seurat object are as described below: * `cohortid` - the id of the study participant from which the cell was derived * `CTaa` - the amino acid sequences of the alpha and beta chains of the TCR * `sample` - the sample from which the cell was derived * `cell_type` - the annotation of a cell based on its effector functions * `timepoint` - the timepoint from which the cell was derived. The number simply indicated chronology relative to other sample timepoints of the same study participant. * `seurat_clusters` - the cluster annotation assigned using the Seurat function FindClusters. * `activation_status` - the annotation of a cell based on its activation status (i.e., whether it displays a transcriptional signature of recent TCR activation, interferon stimulation, proliferation, or resting). * `clonotype_count_per_sample` - the number of cells that are from the same sample and that have the same `CTaa` as that cell. * `clonotype.identity_count_per_sample` - the number of cells that are from the same sample and that have the same `CTaa` and `cell_type` as that cell. * `clonotype_freq_per_sample` - the frequency of cells within the sample that have the same `CTaa` as that cell. * `clonotype.identity_freq_per_sample` - the frequency of cells within the sample that have the same `CTaa` and `cell_type` as that cell. * `clone_family` - the clone family to which the cell belongs. In this context, clone family refers to the bias that a clone has for a particular phenotype (`cell_type`). 1 = Th2; 2 = Tcm; 3 = Th1; 4 = Th17; 5 = Cytotoxic Th1; 6 = Treg; 7 = Tr1. * `malaria_specific` - whether or not the cell encodes a TCR that recognized *Plasmodium falciparum* blood stage antigens. #### File: rna_tcr_MalNaive_ref_mapped_use.rds **Description:** seurat object containing single memory CD4+ T cells from 2 malaria-naive adults analyzed by RNA/TCRseq. **Metadata**: Metadata variables in this object are largely the same as metadata variables in rna_tcr_malaria_specific.rds. #### File: multiome_chromvar.rds **Description:** seurat object containing single memory CD4+ T cells analyzed by multiome sequencing. This object was annotated by mapping to 'rna_tcr_malaria_specific.rds' as a reference. **Metadata**: Metadata variables in this object represent standard variables from Seurat/Signac processing with some important exceptions: * `sample` - the sample from which the cell was derived. * `cohortid` - the id of the study participant from which the cell was derived * `timepoint` - the timepoint from which the cell was derived. The number does not necessarily indicate chronology. * `predicted.cell_type` - the cell type annotation transferred after mapping this multiome dataset to scRNAseq data. This annotation does not represent the final cell type annotation used for downstream analysis. ## Code/software In addition to Seurat, phenoclone (GitHub: jason-nideffer/phenoclone) is required to reproduce analyses using these data. ## Access information Other publicly accessible locations of the data: * NCBI (BioProject PRJNA1129481) Data was derived from the following sources: * NCBI (BioProject PRJNA1129481) * GitHub: jason-nideffer/clone-tracking-in-malaria ## Questions? For any questions about these data, please contact Prasanna Jagannathan ([prasj@stanford.edu](mailto:prasj@stanford.edu)). ## Human subjects data We have received explicit consent from all study participants to publish de-identified metadata and data derived from biological samples.