Capturing Chromosome Conformation

Decreased xCT activity in patients associated with Helicobacter pylori infection

Objective: In animals, Helicobacter pylori (Hp)-induced gastric injury is accompanied by a decrease in the activity of the cysteine/glutamate transporter (xCT), which regulates extracellular glutamate levels. However, the impact of xCT activity in patients with Hp infection remains unclear. This study aims to investigate variations of xCT activity in the gastric mucosa of patients with Hp infection and to provide a clinical basis for identifying targets related to Hp infection. Methods: Our study included a total of 67 patients with gastritis, which consisted of 44 Hp-negative and 23 Hp-positive peptic ulcer cases. The inclusion criteria used to select patients were as follows: gastric histology was determined with a gastroscope, antral biopsies were taken for urease tests, and pathology and culture were performed for analysis of Hp-colonization. The clinical characteristics of the patients were obtained, the expressions of microRNAs and xCT protein were detected using immune histochemical analysis, and the concentration of glutamate in their gastric secretion was determined. Results: The findings revealed that xCT expression was significantly lower in Hp-positive patients as compared to Hp-negative individuals, which was accompanied by a decrease in glutamate concentration in gastric juice. We also discovered a high expression of microRNAs that have been shown to negatively regulate xCT expression, in Hp-positive patients. Conclusion: Reduced xCT activity in patients may play an important role in gastric ulcers caused by Hp infection. Our findings suggest that the microRNA/xCT pathway could be a potential treatment target for Hp-infection-related ulcers.

Epigenetics of alcohol-related liver diseases

Alcohol-related liver disease (ARLD) is a primary cause of chronic liver disease in the United States. Despite advances in the diagnosis and management of ARLD, it remains a major public health problem associated with significant morbidity and mortality, emphasising the need to adopt novel approaches to the study of ARLD and its complications. Epigenetic changes are increasingly being recognised as contributing to the pathogenesis of multiple disease states. Harnessing the power of innovative technologies for the study of epigenetics (e.g., next-generation sequencing, DNA methylation assays, histone modification profiling and computational techniques like machine learning) has resulted in a seismic shift in our understanding of the pathophysiology of ARLD. Knowledge of these techniques and advances is of paramount importance for the practicing hepatologist and researchers alike. Accordingly, in this review article we will summarise the current knowledge about alcohol-induced epigenetic alterations in the context of ARLD, including but not limited to, DNA hyper/hypo methylation, histone modifications, changes in non-coding RNA, 3D chromatin architecture and enhancer-promoter interactions. Additionally, we will discuss the state-of-the-art techniques used in the study of ARLD (e.g. single-cell sequencing). We will also highlight the epigenetic regulation of chemokines and their proinflammatory role in the context of ARLD. Lastly, we will examine the clinical applications of epigenetics in the diagnosis and management of ARLD.

Circuit topology analysis of cellular genome reveals signature motifs, conformational heterogeneity, and scaling

Reciprocal regulation of genome topology and function is a fundamental and enduring puzzle in biology. The wealth of data provided by Hi-C libraries offers the opportunity to unravel this relationship. However, there is a need for a comprehensive theoretical framework in order to extract topological information for genome characterization and comparison. Here, we develop a toolbox for topological analysis based on Circuit Topology, allowing for the quantification of inter- and intracellular genomic heterogeneity, at various levels of fold complexity: pairwise contact arrangement, higher-order contact arrangement, and topological fractal dimension. Single-cell Hi-C data were analyzed and characterized based on topological content, revealing not only a strong multiscale heterogeneity but also highly conserved features such as a characteristic topological length scale and topological signature motifs in the genome. We propose that these motifs inform on the topological state of the nucleus and indicate the presence of active loop extrusion.

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Circuit topology quantifies heterogeneity in genomic arrangement

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Scale analysis reveals a characteristic length scale of 10 Mb in genome topology

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We identify highly conserved topological structures related to loop extrusion

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We suggest a topological model of chromatin arrangement for loop extrusion, the L-loop