Fig. 3: Effect of atomic vacancies in MoS₂ nanoflowers on nuclear-encoded mitochondrial genes.

A Heatmap showing the DEGs (Log₂FPKM of DEGs; P-adj < 0.01) known to encode mitochondrial proteins. Samples treated with vacancy rich MoS₂ show consistent upregulation of mitochondrial genes as compared to untreated hMSC samples. B Volcano plot highlighting genes involved in mitochondrial ATP synthesis coupled proton transport (GO:0042776) and mitochondrial electron transport, cytochrome c to oxygen (GO:0006123) for high vacancies MoS₂ nanoflowers (1:6). Gray, all of the expressed genes; Blue, all genes associated with the GO term; Red, genes associated with the GO term that show significant difference. MoS₂ nanoflowers with high atomic vacancies enhance the transcription of key MRC genes, including those in the adenosine triphosphate (ATP) and mitochondrial cytochrome c oxidase (COX) families. C RNA-seq tracks showing normalized mRNA expression (aligned reads normalized by total library size—transcript per million (TPM)) at the genomic locus of ATP5E and COX5A. D GSEA shows positive enrichment of MRC related terms. Positive NES indicates a significant number of genes belonging to these processes are upregulated. E GSEA enrichment results showing NES for Hallmark: Reactive oxygen species, Hallmark: OXPHOS and Hallmark: Fatty acid metabolism for MoS₂ (1:6) treatment. The vertical black lines (bar code) represent the projection onto the ranked gene list of individual genes of the gene set. The horizontal bar in graded color from red (left) to blue (right) represents the gene list ranked from up-regulated on the left to down-regulated on the right. F Sub-cellular localization of MoS₂ nanoflowers was determined by co-staining mitochondrial (green) and MoS₂ nanoflowers (purple). The nucleus and mitochondria were stained using DAPI and Mito tracker red, respectively. The arrow points towards MoS₂ nanoflowers that were visualized using reflective light imaging. G Quantification of mitochondrial morphology with and without MoS₂ exposure by Mito Hacker analysis. Mitochondrial network parameters were graphed to observe any effect of MoS₂ on mitochondrial morphology. (Data represented volin plots with horizontal lines indicating the median and quartiles. n = 28 cells analyzed from three distinct sets of confocal images. Statistical significance was determined using two-tailed student t test, n.s. p > 0.05).