Mitochondrial Transfer by Photothermal Nanoblade Restores Metabolite Profile in Mammalian Cells

Abstract

mtDNA sequence alterations are challenging to generate but desirable for basic studies and potential correction of mtDNA diseases. Here, we report a new method for transferring isolated mitochondria into somatic mammalian cells using a photothermal nanoblade, which bypasses endocytosis and cell fusion. The nanoblade rescued the pyrimidine auxotroph phenotype and respiration of ρ0 cells that lack mtDNA. Three stable isogenic nanoblade-rescued clones grown in uridine-free medium showed distinct bioenergetics profiles. Rescue lines 1 and 3 reestablished nucleus-encoded anapleurotic and catapleurotic enzyme gene expression patterns and had metabolite profiles similar to the parent cells from which the ρ0 recipient cells were derived. By contrast, rescue line 2 retained a ρ0 cell metabolic phenotype despite growth in uridine-free selection. The known influence of metabolite levels on cellular processes, including epigenome modifications and gene expression, suggests metabolite profiling can help assess the quality and function of mtDNA-modified cells.

Figure 1. Generating Mitochondrial Rescue Clones by Photothermal Nanoblade

(A) Recipient 143BTK− ρ0 cells were seeded on a 400 μm × 400 μm square to facilitate nanoblade delivery, tracking, and clonal selection. (B) Schematic of mitochondrial delivery by photothermal nanoblade. A 3 μm inner diameter glass microcapillary pipette tip coated externally with titanium is positioned to lightly contact the cell surface. A 532 nm pulsed laser illumination triggers a cavitation bubble to open the membrane with coordinated delivery of donor mitochondria into a cell using a fluid pump. (C) Representative confocal image of two foci of DsRed labeled donor mitochondria from HEK293T cells in the cytosol of a single 143BTK− ρ0 cell whose endogenous mitochondria are stained with MitoTracker Green (upper left quadrant). (D) Isolated MDA-MB-453 donor and 143BTK− parent cell mitochondria remain functional and coupled. Mean ± s.d. (n=3). (E) Two weeks post-nanoblade delivery, donor MDA-MB-453 (and 143BTK− parent, not shown) mitochondria transferred into 143BTK− ρ0 recipient cells generated ‘rescue’ clones that emerged in uridine-free dialyzed media (Left). 143BTK− ρ0 control cells (or 143BTK− ρ0 cells that received 143BTK− ρ0 donor mitochondria, not shown) died and detached from the plate when grown in uridine-free dialyzed media (Right).

Figure 2. Recipient gDNA – Donor mtDNA Pairing Validates Rescue Clones

(A) PicoGreen staining of mtDNA in the cytoplasm of 143BTK− ρ0 cells containing nanoblade-transferred MDA-MB-453 mitochondria at 2 (top row) and 4 weeks (bottom row) post-delivery. 143BTK−ρ0 cells lack mtDNA, do not survive for 4 weeks in uridine⁻ medium, and show only nuclear staining. At 2 weeks in uridine⁻ medium, ~15% of rescue clones 2 and 3 cells have mtDNA, which appear as green puncta in the cytoplasm. By 4 weeks of uridine⁻ selection, >85% of cells in rescue clones 1–3 have mtDNA. Mean ± s.d. (B) PCR of mtDNA D-loop hypervariable region from rescue clones 1–3 with controls. (C) Sequencing of mtDNA D-loop hypervariable region revealed multiple single nucleotide polymorphisms (SNPs, red color, arrows) present in rescue clones 1–3 and donor MDA-MB-453. (D) Rescue clones 1–3 contained the same SNP in the FGFR2 nuclear gene as 143BTK− parent and 143BTK− ρ0 cells (arrow), but a distinct SNP from mitochondrial donor MDA-MB-453 cells. (E) Human leukocyte antigen (HLA) analysis of rescue 1 shows the same major histocompatibility complex (MHC) loci as 143BTK− parent and 143BTK− ρ0 cells.

Figure 3. Bioenergetic Profile of Rescue Clones

(A) Proliferation of 143BTK− parent, MDA-MB-453 donor, 143BTK− ρ0, and rescue clone 1–3 cells in the indicated media formulations. Mean ± s.d. (n=3). (B) Steady-state intracellular ATP levels in arbitrary units. Mean ± s.d. (n=3). (C) Mitochondria coupling assay (Left) and electron flow assay (Right) as measured by Seahorse XF24 Analyzer. Mean ± s.d. (n=3). (D) Ratio of citrate synthase enzyme activity to total cellular protein, normalized to 1.0 for the 143BTK− parent line. Mean ± s.d. (n=3). (E) mtDNA quantification by qPCR, normalized to 1.0 for the 143BTK− parent line. Mean ± s.d. (n=3). (F) mtDNA-encoded ND1 and ND2 transcript quantification by qRT-PCR, normalized to 1.0 for the 143BTK− parent line. Mean ± s.d. (n=3). (G) Representative mitochondrial membrane potential quantified by TMRM staining and flow cytometry.

Figure 4. Metabolic Gene Expression and Metabolite Profile of Rescue Clones

(A) Expression of 33 genes involved in TCA cycle metabolism quantified by qRT-PCR and normalized to the ribosomal 36B4 gene (see Figure S4B). PCA shows the grouped relationships between the six cell lines studied. (B) Relative levels of twelve TCA cycle proximate metabolites quantified by LC-MS/MS and normalized to the 143BTK− parental line. Mean ± s.d. (n=3). (C) Heatmap of 96 metabolites measured with an ANOVA p-value equal to or less than 0.05. Samples were clustered using a Pearson correlation matrix. (D) PCA using the fractional contribution from U-¹³C glucose to all measured metabolites. (E) PCA using the fractional contribution from U-¹³C glutamine to all measured metabolites.