Fluorochromes for DNA Staining and Quantitation

Impact of heat and cold shock on epigenetics and chromatin structure

Cells are continuously exposed to various sources of insults, among which temperature variations are extremely common. Epigenetic mechanisms, critical players in gene expression regulation, undergo alterations due to these stressors, potentially leading to health issues. Despite the significance of DNA methylation and histone modifications in gene expression regulation, their changes following heat and cold shock in human cells remain poorly understood. In this study, we investigated the epigenetic profiles of human cells subjected to hyperthermia and hypothermia, revealing significant variations. Heat shock primarily led to DNA methylation increments and epigenetic modifications associated with gene expression silencing. In contrast, cold shock presented a complex scenario, with both methylation and demethylation levels increasing, indicating different epigenetic responses to the opposite thermal stresses. These temperature-induced alterations in the epigenome, particularly their impact on chromatin structural organization, represent an understudied area that could offer important insights into genome function and potential prospects for therapeutic targets.

DNA topoisomerase inhibition with the HIF inhibitor acriflavine promotes transcription of lncRNAs in endothelial cells

The transcription factor hypoxia-inducible factor 1 (HIF1) is an important driver of cancer and is therefore an attractive drug target. Acriflavine (ACF) has been suggested to inhibit HIF1, but its mechanism of action is unknown. Here we investigated the interaction of ACF with DNA and long non-coding RNAs (lncRNAs) and its function in human endothelial cells. ACF promoted apoptosis and reduced proliferation, network formation, and angiogenic capacity. It also induced changes in gene expression, as determined by RNA sequencing (RNA-seq), which could not be attributed to specific inhibition of HIF1. A similar response was observed in murine lung endothelial cells. Although ACF increased and decreased a similar number of protein-coding genes, lncRNAs were preferentially upregulated under normoxic and hypoxic conditions. An assay for transposase accessibility with subsequent DNA sequencing (ATAC-seq) demonstrated that ACF induced strong changes in chromatin accessibility at lncRNA promoters. Immunofluorescence showed displacement of DNA:RNA hybrids. Such effects might be due to ACF-mediated topoisomerase inhibition, which was indeed the case, as reflected by DNA unwinding assays. Comparison with other acridine derivatives and topoisomerase inhibitors suggested that the specific function of ACF is an effect of acridinium-class compounds. This study demonstrates that ACF inhibits topoisomerases rather than HIF specifically and that it elicits a unique expression response of lncRNAs.

Basic Quality Controls Used in Skin Tissue Engineering

Reconstruction of skin defects is often a challenging effort due to the currently limited reconstructive options. In this sense, tissue engineering has emerged as a possible alternative to replace or repair diseased or damaged tissues from the patient's own cells. A substantial number of tissue-engineered skin substitutes (TESSs) have been conceived and evaluated in vitro and in vivo showing promising results in the preclinical stage. However, only a few constructs have been used in the clinic. The lack of standardization in evaluation methods employed may in part be responsible for this discrepancy. This review covers the most well-known and up-to-date methods for evaluating the optimization of new TESSs and orientative guidelines for the evaluation of TESSs are proposed.

Rhodamine-Hoechst positional isomers for highly efficient staining of heterochromatin

Hoechst conjugates to fluorescent dyes are popular DNA stains for live-cell imaging, but the relationship between their structure and performance remains elusive. This study of carboxyrhodamine-Hoechst 33258 conjugates reveals that a minimal change in the attachment point of the dye has dramatic effects on the properties of the final probe. All tested 6'-carboxyl dye-containing probes exhibited dual-mode binding to DNA and formed a dimmer complex at high DNA concentrations. The 5'-carboxyl dye-containing probes exhibited single-mode binding to DNA which translated into increased brightness and lower cytotoxicity. Up to 10-fold brighter nuclear staining by the newly developed probes allowed acquisition of stimulated emission depletion (STED) nanoscopy images of outstanding quality in living and fixed cells. Therefore we were able to estimate a diameter of ∼155 nm of the heterochromatin exclusion zones in the nuclear pore region in living cells and intact chicken erythrocytes and to localize telomeres relative to heterochromatin in living U-2 OS cells. Employing the highly efficient probes for two-color STED allowed visualization of DNA and tubulin structures in intact nucleated erythrocytes - a system where imaging is greatly hampered by high haemoglobin absorbance.

The role of automated cytometry in the new era of cancer immunotherapy

The introduction in the clinical practice of several new approaches to cancer immunotherapy has greatly increased the interest in analytical methodologies that can define the immunological profile of patients in the clinical setting. This requires huge effort to obtain reliable monitoring tools that could be used to improve the patient's clinical outcome. The clinical applications of flow cytometry (FCM) in oncology started with the measurement of DNA content for the evaluation of both ploidy and cell cycle profile as potential prognostic parameters in the majority of human solid cancer types. The availability of monoclonal antibodies widely broadened the spectrum of clinical applications of this technique, which rapidly became a fundamental tool for the diagnosis and prognosis of malignant hematological diseases. Among the emerging clinical applications of FCM, the study of minimal residual disease in hematological malignancies, the quantification of blood dendritic cells in various types of tumors, the study of metastatic spread in solid tumors throughout both the analysis of circulating endothelial progenitor cells and the identification and characterization of circulating tumor cells, all appear very promising. More recently, an advanced single cell analysis technique has been developed that combines the precision of mass spectrometry with the unique advantages of FCM. This approach, termed mass cytometry, utilizes antibodies conjugated to heavy metal ions for the analysis of cellular proteins by a mass spectrometer. It provides measurement of over 100 simultaneous cellular parameters in a single sample and has evolved from a promising technology to a high recognized platform for multi-dimensional single-cell analysis. Should a careful standardization of the analytical procedures be reached, both FCM and mass cytometry could effectively become ideal tools for the optimization of new immunotherapeutic approaches in cancer patients.