Pressure-Driven Mitochondrial Transfer Pipeline Generates Mammalian Cells of Desired Genetic Combinations and Fates

Generating mammalian cells with desired mtDNA sequences is enabling for studies of mitochondria, disease modeling, and potential regenerative therapies. MitoPunch, a high-throughput mitochondrial transfer device, produces cells with specific mtDNA-nDNA combinations by transferring isolated mitochondria from mouse or human cells into primary or immortal mtDNA-deficient (p0) cells. Stable isolated mitochondrial recipient (SIMR) cells isolated in restrictive media permanently retain donor mtDNA and reacquire respiration. However, SIMR fibroblasts maintain a p0-like cell metabolome and transcriptome despite growth in restrictive media. We reprogram non-immortal SIMR fibroblasts into induced pluripotent stem cells (iPSCs) with subsequent differentiation into diverse functional cell types, including mesenchymal stem cells (MSCs), adipocytes, osteoblasts, and chondrocytes. Remarkably, following reprogramming and differentiation, SIMR fibroblasts molecularly and phenotypically resemble un-manipulated control fibroblasts carried through the same protocol. Thus, our MitoPunch ‘pipeline’ enables the production of SIMR cells with unique mtDNA-nDNA combinations for additional studies and applications in multiple cell types. Total ribo-depleted bulk RNA-sequencing of mtDNA depleted (p0) BJ human neonatal foreskin fibroblasts transferred HEK 293 DsRed mitochondria (n = 3) or human peripheral blood mononuclear cell (LP351 PBMC) mitochondria (n = 3), compared to wildtype (BJ, n = 3) and mtDNA depleted (BJ p0, n = 3) fibroblasts. Transferred BJ fibroblasts were reprogrammed into iPSC (n = 2 of three isolated clones each, 6 total) and each clone differentiated into MSC (n = 2 of each matched clone, 6 total) for functional assesment. Reprogramming and differentiations were compared to wildtype BJ fibroblast generation of iPSCs (n = 3) and MSCs (n = 3) (n = 60 total samples).