Palatini, J. | bioRxiv Science

bioRxiv2026

Precision single-cell profiling of Circulating Tumour Cells: novel markers and data-driven characterization by CTCeek

Circulating tumour cells (CTCs) represent a minimally invasive method for monitoring cancer evolution in patients. CTCs are nowadays commonly isolated using antibodies against EPCAM protein. A key limitation regards the extent of EPCAM-negative CTCs, such as those that undergo EMT or whose tumour of origin is EPCAM-low or negative. We studied 3,302 RNA single-cell transcriptomes reported as CTCs in public repositories. Using copy number variation and cell type-specific markers, we discriminated bona fide CTCs from contaminating blood cells, often mislabelled as CTCs. The integration of bona fide CTCs and PBMCs, from multiple datasets, allowed us to identify novel markers, such as CLDN4, CLDN7, EFNA1 and TACSTD2 for epithelial CTCs, KCNK15 and LY6K for epithelial B CTCs, and ITGB4 for both epithelial B and mesenchymal CTCs. We revealed PODXL, AXL, CAV1, and TGM2 as markers of mesenchymal CTCs, which might be undetectable using anti-EPCAM antibodies, and TM4SF1 as universal marker, expressed in all CTC subclasses. Additionally, we found platelets to be physically associated with the epithelial A, but not with the epithelial B or the mesenchymal subtypes. Finally, we developed and implemented CTCeek, the first web-based and public reference tool that automatically annotates bona fide CTCs from scRNA-sequencing profiles.

cancer biology↗

bioRxiv2024

The energy-saving metabolic switch underlies survival of extremophilic red microalgae in extremely high nickel levels

The red microalga Cyanidioschyzon merolae inhabits extreme environments of high temperature (40-56{degrees}C), high acidity (pH 0.05-4), and the presence of high concentrations of heavy metals and sulphites that are lethal to most other forms of life. However, information is scarce on the precise adaptation mechanisms of this extremophile to such hostile conditions. Gaining such knowledge is important for understanding the evolution of microorganisms in the early stages of life on Earth characterized by such extreme environments. By analyzing the re-programming of the global transcriptome upon long-term (up to 15 days) exposure of C. merolae to extremely high concentrations of nickel (1 and 3 mM), the key adaptive metabolic pathways and associated molecular components were identified. Our work shows that long-term Ni exposure of C. merolae leads to the lagged metabolic switch demonstrated by the transcriptional upregulation of the metabolic pathways critical for cell survival. DNA replication, cell cycle, and protein quality control processes were upregulated while downregulation occurred of energetically costly processes including assembly of the photosynthetic apparatus and lipid biosynthesis. This study paves the way for the multi-omic studies of the molecular mechanisms of abiotic stress adaptation in phototrophs, as well as future development of the rational approaches for bioremediation of contaminated aquatic environments. ImportanceThis study provides the first comprehensive analysis of the global transcriptome re-programming in the extremophilic red microalga Cyanidioschyzon merolae during its long-term adaptation to heavy metals. We show that the lagged metabolic switch, demonstrated by the transcriptional upregulation of the metabolic pathways critical for cell survival, underlies the long-term Ni adaptation of this model extremophile. The transcriptomic results shed light on how life may have adapted to some of the harshest abiotic stresses on Earth including high temperatures, extreme acidity, and high levels heavy metals that are prohibitive to most other organisms. Additionally, the differentially regulated genes identified in this work provide important clues on the rational development of effective bioremediation strategies of removing heavy metals from the heavily contaminated aquatic environments.

plant biology↗