Targeted Application of Human Genetic Variation Can Improve Red Blood Cell Production from Stem Cells

Abstract

Multipotent and pluripotent stem cells are potential sources for cell and tissue replacement therapies. For example, stem cell-derived red blood cells (RBCs) are a potential alternative to donated blood, but yield and quality remain a challenge. Here, we show that application of insight from human population genetic studies can enhance RBC production from stem cells. The SH2B3 gene encodes a negative regulator of cytokine signaling and naturally occurring loss-of-function variants in this gene increase RBC counts in vivo. Targeted suppression of SH2B3 in primary human hematopoietic stem and progenitor cells enhanced the maturation and overall yield of in-vitro-derived RBCs. Moreover, inactivation of SH2B3 by CRISPR/Cas9 genome editing in human pluripotent stem cells allowed enhanced erythroid cell expansion with preserved differentiation. Our findings therefore highlight the potential for combining human genome variation studies with genome editing approaches to improve cell and tissue production for regenerative medicine.

Figure 1. From in vivo association of SH2B3 variants with hemoglobin levels to in vitro suppression in primary HSPCs

(A) A schematic of the protein structure of SH2B3, including the dimerization (Dimer. Domain), pleckstrin homology (PH), and Src homology 2 (SH2) domains. The amino acids of these different regions are shown below. The strict damaging missense variants in the PH/SH2 domains and the nonsense variant identified in the European American individuals analyzed are shown. (B) Box plots for hemoglobin levels in the individuals harboring putative damaging missense and nonsense variants in SH2B3 (n=19) or without such mutations (n = 1995). Details of the association parameters from gene burden testing of these rare variants are provided in Table S1. (C) Simplified scheme illustrating differentiation of human CD34+ HSPCs into mature RBCs. (D) Western blot showing SH2B3 protein levels 8 days following infection. (E, F) Representative histogram plots of CD235a and CD71, respectively, showing phenotypic surface marker expression of control and SH2B3-KD cells on the indicated day of differentiation. (G) Representative flow cytometry plots showing cells stained with CD235a and Hoechst 33342 on day 18 of differentiation. Numbers represent the mean percentage of CD235a⁺/Hoechst 33342⁻ cells, indicative of enucleated RBCs, within the depicted gate ± the standard deviation. (H) Representative cytocentrifuge images of May-Grünwald-Giemsa stained control and SH2B3-KD cells at the indicated days of differentiation. A scale bar is shown in upper left panel. (I) Scatter plot of mean gene expression values of control (Luc-KD for cells treated with control shLuc) and SH2B3-KD samples (n = 3 independent samples for shLuc, sh83, and sh84). The coefficient of determination (r) is shown. (J) Enrichment profiles from GSEA comparing the relative expression of genes in SH2B3-KD samples versus control. An enrichment plot showing an erythroid differentiation signature derived by comparing early erythroid progenitors with more differentiated cells is shown (P < 0.0001 using a modified Kolmogorov–Smirnov statistical test).

Figure 2. Improved expansion of erythroid cells with SH2B3 suppression in hematopoietic and pluripotent stem cells

(A, B) Mean yield of enucleated RBCs (CD235a⁺/Hoechst 33342⁻) observed for control and SH2B3 KD samples derived from adult mobilized peripheral blood (A) or cord blood (B) HSPCs. Values shown are mean ± the standard deviation and were normalized to the control. Comparisons were done by a two-tailed Student's t-test (n = 3 independent experiments; * P < 0.05; ** P < 0.01, *** P < 0.001). See also Figure S1. (C) Mean yield of enucleated RBCs (CD235a⁺/Hoechst 33342⁻) observed for control and SH2B3 KD samples derived from adult mobilized peripheral blood progenitors using a more efficient differentiation protocol involving a CD34+ expansion phase (discussed in Methods). Comparisons were done by a two-tailed Student's t-test (n = 4; *** P < 0.001). (D) Representative histogram plots showing eosin-5-maleimide signal on day 18 of mature RBCs derived from peripheral blood-mobilized CD34+ cells. See also Figure S2. (E) Simplified scheme illustrating differentiation of hESCs into RBCs. The hESCs were cultured in sequential cytokine combinations to induce the production of multipotent hematopoietic progenitor cells (HPCs) that were released into the medium around day 8. The HPCs were collected and cultured further in medium with EPO and SCF to support erythroid differentiation. (F, G) Erythroid cell expansion of HPCs derived from two independent pairs of isogenic hESC clones (KO, SH2B3-knockout; WT, wild type isogenic controls). The total cell numbers starting with 50,000 cells are shown at various time points as the mean ± the standard deviation. Comparisons were performed by a two-tailed Student's t-test (n = 3; * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001). See also Figure S2. (H) Representative cytospin images of May Grünwald-Giemsa stained control and SH2B3-KO erythroblasts at the indicated days of culture subsequent to HPC selection. (I) Representative flow cytometry plots depicting the expression of CD71 and CD235a on erythroblasts derived from SH2B3-KO and isogenic WT hESCs.