Fig. 1: HSPC clonal complexity, size and source time point of long-lasting clones.
From: Long-term lineage commitment in haematopoietic stem cell gene therapy
a, Clonal tracking through ISs begins with a patient’s autologous transplantation of vector-marked cells. Periodic sampling and DNA processing isolate markers for distinct lineages (myeloid, erythroid, B and T cells). ISs are retrieved by means of custom PCRs and deep sequencing, allowing clonal population diversity, abundance, lineage tracking and vector integration frequency to be assessed for treatment safety and efficacy. b, The cumulative number of ISs retrieved for each patient by disease (MLD, WAS and β-Thal) increases over time after gene therapy, with a log-based regression curve showing the progression (confidence interval (CI) 0.75). c, Clonal population diversity index (Shannon index, y axis) by clinical trial, tissue (BM and PB) and lineage (different colours), over time (months, x axis); spline CI 0.75. d, The analytical process of HSPC estimate, starting from ISs derived by short-lived myeloid cells in PB, filtering ISs by low sequencing reads (removing ISs with n < 3), and estimating HSPCs over time by triplets of consecutive time points using the Chao1 model. e, Results of estimated HSPCs (y axis) over time (x axis) for each clinical trial, normalized by in vivo VCN for samples with VCN > 1. f, Percentage of the estimated active HSPCs on the total number of infused CD34+ BM cells, stratified by clinical trial; statistical results obtained with Fisher’s exact test. g, Long-term clones are identified by tracking ISs back to their first observed time points, categorized into early (1–6 months), mid (12–18 months) and steady (24–30 months) phases. Statistical comparisons were made using the Kruskal–Wallis test corrected by FDR. h, Percentage of long-lasting clones, for each lineage (in colours) and clinical study, backtracked by the first observed time point grouped by the haematopoietic reconstitution phase (early, mid and steady). RBC, red blood cell; MK, megakaryocyte; NK, natural killer cell; DCs, dendritic cells; Mφ, macrophage. Graphics in a were created using BioRender (https://biorender.com).
