Project description:Single-cell transcriptomic analysis is widely used to study human tumors. However it remains challenging to distinguish normal cell types in the tumor microenvironment from malignant cells and to resolve clonal substructure within the tumor. To address these challenges, we developed an integrative Bayesian segmentation approach called CopyKAT (Copynumber Karyotyping of Aneuploid Tumors) to estimate genomic copy number profiles at an average genomic resolution of 5Mb from read depth in high-throughput scRNA-seq data. We applied CopyKAT to analyze 46,501 single cells from 21 tumors, including triple-negative breast cancer, pancreatic ductal adenocarcinomas, anaplastic thyroid cancer, invasive ductal carcinoma and glioblastoma to accurately (98%) distinguish cancer cells from normal cell types. In three breast tumors, CopyKAT resolved clonal subpopulations that differed in the expression of cancer genes such as KRAS and signatures including EMT, DNA repair, apoptosis and hypoxia. These data show that CopyKAT can aid the analysis of scRNA-seq data in a variety of solid human tumors.
Project description:Peptide yield was enhanced through copy number amplification, and the resulting mCherry–GLP-1(9–37) can be directly used—following enterokinase cleavage—as a chemical precursor for semaglutide synthesis.
Project description:Eukaryotic cells maintain multiple copies of the mitochondrial genome, which is essential for cellular metabolism. Accordingly, alterations in the mitochondrial DNA (mtDNA) copy number are associated with severe human diseases and ageing. However, the mechanisms through which cells regulate mtDNA copy number and the cellular consequences of altered copy number remain poorly understood. Here, using budding yeast as a model, we show that mtDNA copy number is determined by the amount of three limiting factors, Mip1, Abf2, and Rim1. By synthetically tuning the concentrations of only these three proteins, we can modulate mtDNA dosage inside the cell. This revealed that cells are surprisingly robust to mtDNA copy number alterations, with increased copy numbers even accelerating cell growth. Our findings suggest that this robustness is due to protein dosage compensation and independent regulation of mitochondrial morphology. Mechanistically, we identified a critical role of the retrograde signalling pathway for this adaptation. We show that signalling from mitochondria to the nucleus is upregulated in cells with higher mtDNA copy number, and disruption of this regulation diminishes their faster growth. Taken together, our work reveals regulatory principles that allow cells to adapt to mtDNA copy number alterations.