The analysis of cell-free DNA (cfDNA) in plasma represents a rapidly advancing field in medicine, providing information on pathological processes in the body. Blood cfDNA is in the form of nucleosomes, which maintain their tissue-and cancer-specific epigenetic state. We developed EPINUC, a single-molecule multi-parametric assay to comprehensively profile the Epigenetics of Plasma Isolated Nucleosomes, DNA methylation and cancer-specific protein biomarkers. Our system allows high-resolution detection of six active and repressive histone modifications, their ratios and combinatorial patterns, on millions of individual nucleosomes by single-molecule imaging. In addition, it provides sensitive and quantitative data on plasma proteins, including detection of nonsecreted tumor-specific proteins such as mutant p53. Applying this analysis to a cohort of plasma samples detected colorectal cancer at high accuracy and sensitivity, even at early stages. Finally, combining EPINUC with direct single-molecule DNA sequencing revealed the tissue-of-origin of colorectal, pancreatic, lung and breast tumors. EPINUC provides multi-layered clinical-relevant information from limited liquid biopsy material, establishing a novel approach for cancer diagnostics.

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The analysis of cell-free DNA (cfDNA) in plasma represents a rapidly advancing field in medicine, providing information on pathological processes in the body. Blood cfDNA is in the form of nucleosomes, which maintain their tissue- and cancer-specific epigenetic state. We developed EPINUC, a single-molecule multi-parametric assay to comprehensively profile the Epigenetics of Plasma Isolated Nucleosomes, DNA methylation and cancer-specific protein biomarkers. Our system allows high-resolution detection of six active and repressive histone modifications, their ratios and combinatorial patterns, on millions of individual nucleosomes by single-molecule imaging. In addition, it provides sensitive and quantitative data on plasma proteins, including detection of non-secreted tumor-specific proteins such as mutant p53. Applying this analysis to a cohort of plasma samples detected colorectal cancer at high accuracy and sensitivity, even at early stages. Finally, combining EPINUC with direct single-molecule DNA sequencing revealed the tissue-of-origin of the tumor. EPINUC provides multi-layered clinical-relevant information from limited liquid biopsy material, establishing a novel approach for cancer diagnostics.

Ultra processed foods (UPF) consumption is becoming dominant in the global food system, to the point of being the most recent cause of malnutrition. Health outcomes of this diet include obesity and metabolic syndrome; however, its effect on skeletal development has yet to be examined. This project studied the influence of UPF diet on the development and quality of the post-natal skeleton. Young female mice were fed with regular chow diet, UPF diet, UPF diet supplemented with calcium or with multivitamin and mineral complex. Mice fed UPF diet presented unfavorable morphological parameters, evaluated by micro-CT, alongside inferior mechanical performance of the femora, evaluated by three-point bending tests. Growth-plate histology evaluation suggested a modification of the growth pattern. Accumulation of adipose tissue within the bone marrow was significantly higher in the group fed UPF diet. Finally, microbiome 16SrRNA sequencing was used to explore the connection between diets, gut microbial community and skeletal development. Together, we show that consumption of UPF diet during the postnatal developmental period alters the microbiome and has negative outcomes on bone parameters and bone marrow adiposity. Micronutrients improved these phenotypes only partially. Thus, consuming a wholesome diet that contributes to a healthy microbiota is of a great significance in order to achieve healthy skeletal development.