Haitang Liao, Ruiyan Ma, Shuai Hao, Xuxin Tan, Xue Zeng, Rui Song, Bing Chen, Zhezhe Cao, Wei Shen, Zhenchun Luo, Jianfeng Huang, He Huang, Liangming Liu, Chenyang Duan <<<

Abstract Accurate early diagnosis and prognosis of sepsis remain major clinical challenges. This study explores specific plasma cell‐free mitochondrial DNA (cfmtDNA) breakage patterns as potential biomarkers for sepsis. Plasma samples from ten non‐sepsis control patients and 63 sepsis patients are analyzed using mitochondrial DNA fragmentomics, revealing distinct breakage sites in the RNR2 (positions 2474–2478) and COX2 (positions 7761, 7775, 7776, 7777, and 7783) regions, which are intact in healthy individuals but exhibited high‐frequency breakage in sepsis patients. Diagnostic models based on these breakage sites show superior accuracy for sepsis detection (AUC = 0.865) and prognosis prediction (AUC = 0.809) compared to traditional cfmtDNA copy number assessments. Notably, COX2 breakage frequency correlated with inflammatory markers and SOFA scores, highlighting its prognostic potential. Mechanistic analyses suggest that reduced protein binding in sepsis may increase cfmtDNA susceptibility to cleavage by bacterial restriction endonucleases. These findings indicate that plasma cfmtDNA breakage characteristics can serve as valuable biomarkers for early sepsis detection and therapeutic monitoring. <<<

AbstractCell cycle structures vary significantly across cell types, which exhibit distinct phase compositions. Asynchronous DNA replication and dynamic cellular characteristics during the cell cycle result in considerable heterogeneity in DNA dosage, chromatin accessibility, methylation, and expression. Nonetheless, the consequences of cell cycle disruption in the interpretation of multi‐omics data remain unclear. Here, we systematically assessed the influence of distinct cell phase structures on the interpretation of omics features in proliferating cells, and proposed solutions for each omics dataset. For copy number variation (CNV) calling, asynchronous replication timing (RT) interference induces false CNVs in cells with high S‐phase ratio (SPR), which are significantly decreased following replication timing domain (RTD) correction. Similar noise is observed in the chromatin accessibility data. Moreover, for DNA methylation and transcriptomic analyses, cell cycle‐sorted data outperformed direct comparison in elucidating the biological features of compared cells. Additionally, we established an integrated pipeline to identify differentially expressed genes (DEGs) after cell cycle phasing. Consequently, our study demonstrated extensive cell‐cycle heterogeneity, warranting consideration in future studies involving cells with diverse cell‐cycle structures. RTD correction or phase‐specific comparison could reduce the influence of cell cycle composition on the analysis of the differences observed between stem and differentiated cells. <<<