Somatic and Stem Cell Bank to study the contribution of African ancestry to dementia: African iPSC Initiative

Abstract

Introduction: Africa, home to 1.4 billion people and the highest genetic diversity globally, harbors unique genetic variants crucial for understanding complex diseases like neurodegenerative disorders. However, African populations remain underrepresented in induced pluripotent stem cell (iPSC) collections, limiting the exploration of population-specific disease mechanisms and therapeutic discoveries.

Methods: To address this gap, we established an open-access African Somatic and Stem Cell Bank.

Results: In this initial phase, we generated 10 rigorously characterized iPSC lines from fibroblasts representing five Nigerian ethnic groups and both sexes. These lines underwent extensive profiling for pluripotency, genetic stability, differentiation potential, and Alzheimer's disease and Parkinson's disease risk variants. Clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 technology was used to introduce frontotemporal dementia-associated MAPT mutations (P301L and R406W).

Discussion: This collection offers a renewable, genetically diverse resource to investigate disease pathogenicity in African populations, facilitating breakthroughs in neurodegenerative research, drug discovery, and regenerative medicine.

Highlights: We established an open-access African Somatic and Stem Cell Bank. 10 induced pluripotent stem cell lines from five Nigerian ethnic groups were rigorously characterized. Clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 technology was used to introduce frontotemporal dementia-causing MAPT mutations. The African Somatic and Stem Cell Bank is a renewable, genetically diverse resource for neurodegenerative research.

Keywords: African ancestry; Alzheimer's disease; Parkinson's disease; cell bank; clustered regularly interspaced palindromic repeats/CRISPR‐associated protein 9; fibroblasts; frontotemporal dementia; induced pluripotent stem cells; polygenic risk scores.

FIGURE 1

Establishing an African Somatic and Stem Cell Bank. A, Map of Nigeria indicating biopsy collection site (yellow) in the state of Yobe. Ethnic groups participating in the study indicated along with their regional distribution. Pink square, Babur. Green hexagon, Fulfude. Red circle, Hausa. Blue star, Kanuri. Yellow triangle, Kare‐Kare. B, Workflow to transform skin biopsies into fibroblasts and iPSCs. iPSC, induced pluripotent stem cells; WashU, Washington University.

FIGURE 2

Characterization of iPSC lines from African Somatic and Stem Cell Bank. Representative characterization data. A, Phase‐contrast images of iPSC BA‐001.1. B, qPCR for pluripotency markers normalized against GAPDH for all iPSCs profiled. Open circles represent individual iPSC clones. C, Immunocytochemistry for pluripotency markers OCT4, SOX2, SSEA4, and TRA‐1‐60 in iPSC BA‐001.1. D, G‐band karyotyping reveals no chromosomal abnormalities in iPSC BA‐001.1. See Figures S1–S10 for characterization of all iPSC described in this study. GAPDH, glyceraldehyde 3‐phosphate dehydrogenase; iPSC, induced pluripotent stem cell; qPCR, quantitative polymerase chain reaction.

FIGURE 3

Genomic profiling of iPSC lines from African Somatic and Stem Cell Bank. A, Workflow. B–I, Genetic analyses of iPSC. B, PCA of common genetic variants measured in unique iPSC lines (gray, cohort) compared to 1000 Genomes reference: AFR, AMR, EAS, EUR, SAS. C, Frequency of APOE genotypes among iPSC lines. D–I, PRS. D–E, Distribution of PRS represented using reference (salmon, REF) and iPSC samples (cyan, TRG). G–H, Distribution of PRS represented based on Nigerian ethnic group. D, G, PRS for AD including the APOE gene locus. E, H, PRS for AD excluding the APOE gene locus. F, I, PRS for PD. J, PCA of transcriptomic data generated from iPSCs (500 most variable gene transcripts). K, XIST, expressed on the inactivated X‐chromosome, in iPSC lines. Graphs represent CPM mean $\pm$ SEM. ****, p < 0.0001. Blue, female. Red, male. AD, Alzheimer's disease; AFR, Africans; AMR, admixed Americans; APOE, apolipoprotein E; CPM, counts per million; EAS, East Asians; EUR, Europeans; GWAS, genome‐wide association study; iPSC, induced pluripotent stem cell; PCA, principal component analysis; PD, Parkinson's disease; PRS, polygenic risk score; REF, reference; SAS, South Asian; SEM, standard error of the mean.

FIGURE 4

Genome engineering of the MAPT locus in iPSC BA‐001.1. A, Workflow. B–D, BA‐001.1 was edited from MAPT WT/WT to MAPT P301L/WT using CRISPR/Cas9. Characterization for one of the resulting clones: BA‐001.1.P301L Δ1D01. B, Sanger sequencing illustrating the heterozygous engineered SNP. C, Immunocytochemistry for pluripotency markers OCT4, SOX2, SSEA4, and TRA‐1‐60. D, G‐band karyotyping reveals no chromosomal abnormalities. E, F, BA‐001.1 was edited from MAPT WT/WT to MAPT R406W/WT using CRISPR/Cas9. Characterization for one of the resulting clones: BA‐001.1.R406W Δ1C09. E, Sanger sequencing illustrating the heterozygous engineered SNP. F, Immunocytochemistry for pluripotency markers OCT4, SOX2, SSEA4, and TRA1. CRISPR/Cas9, Clustered regularly interspaced palindromic repeats/CRISPR‐associated protein 9; G, G‐band karyotyping reveals no chromosomal abnormalities; iPSC, induced pluripotent stem cell; SNP, single nucleotide polymorphism.