Cell identity genes are distinct from other genes with respect to the epigenetic mechanisms to activate their transcription, e.g. by super-enhancers and broad H3K4me3 domains. However, it remains unclear whether their post-transcriptional regulation is also unique. We performed a systematic analysis of transcriptome-wide RNA stability in nine cell types and found that unstable transcripts were enriched in cell identity-related pathways while stable transcripts were enriched in housekeeping pathways. Joint analyses of RNA stability and chromatin state revealed significant enrichment of super-enhancers and broad H3K4me3 domains at the gene loci of unstable transcripts. Intriguingly, the RNA m⁶A methyltransferase, METTL3, preferentially binds to chromatin at super-enhancers, broad H3K4me3 domains and their associated genes. METTL3 binding intensity is positively correlated with RNA m⁶A methylation and negatively correlated with RNA stability of cell identity genes, probably due to co-transcriptional m⁶A modifications promoting RNA decay. Nanopore direct RNA-sequencing showed that METTL3 knockdown has a stronger effect on RNA m⁶A and mRNA stability for cell identity genes. Our data suggest a run-and-brake model, where cell identity genes undergo both frequent transcription and fast RNA decay to achieve precise regulation of RNA expression.

Immunotherapy targeting tumor-associated macrophages (TAMs) is a promising approach to treating cancer. However, the limited drug targets and ambiguous mechanisms impede the development of clinical immunotherapy strategies. To elucidate the underlying processes involved in mononuclear phagocyte (MNP) infiltration and phenotypic changes in hepatocellular carcinoma (HCC), we integrated single-cell RNA-sequencing data from 100,030 cells derived from patients with HCC and healthy individuals and compared the phenotypes and origins of the MNPs in the tumor core, tumor periphery, adjacent normal tissue, and healthy liver samples. Using machine learning and multi-omics analyses, we identified 445 infiltration-associated genes and potential drug targets affecting this process. Through in vitro experiments, we found that the expression of macrophage migration inhibitory factor (MIF) is the upstream regulator of secreted phosphoprotein 1 (SPP1) and promote migration in TAMs. Our findings also indicate that MIF promotes tumor metastasis and invasion and is a promising potential target for treating HCC.

Bioinformatics has significantly advanced RNA-based therapeutics, particularly circular RNAs (circRNAs), which outperform mRNA vaccines, by offering superior stability, sustained expression, and enhanced immunogenicity due to their covalently closed structure. This review highlights how bioinformatics and computational biology optimise circRNA vaccine design, elucidates internal ribosome entry sites (IRES) selection, open reading frame (ORF) optimisation, codon usage, RNA secondary structure prediction, and delivery system development. While circRNA vaccines may not always surpass traditional vaccines in stability, their production efficiency and therapeutic efficacy can be enhanced through computational strategies. The discussion also addresses challenges and future prospects, emphasizing the need for innovative solutions to overcome current limitations and advance circRNA vaccine applications.

Derivation of human hepatocytes from pluripotent stem cells in vitro has important applications including cell therapy and drug discovery. However, the differentiation of pluripotent stem cells into hepatocytes in vitro was not well recapitulated the development of liver. Here, we developed a differentiation protocol by mimicking the two‐stage development of hepatoblasts, which permits the efficient generation of hepatic progenitor cells from chemically induced pluripotent stem cells (hCiPSCs). Single‐cell RNA sequencing (scRNA‐seq) indicates the similarity between hepatoblasts differentiated in vitro and in vivo. Moreover, hCiPSC‐derived hepatic progenitor cells can further differentiate into hepatocytes that are similar to primary human hepatocytes with respect to gene expression and key hepatic functions. Our results demonstrate the feasibility of generating hepatic progenitor cells and hepatocytes from hCiPSCs with high efficiency and set the foundation for broad translational applications of hCiPSC‐derived hepatocytes.

Background and Aims: Atherosclerosis is a chronic inflammatory disorder with high morbidity and mortality rates worldwide. Emerging evidence has reported that kinesin family member 13B (KIF13B), a crucial motor protein, integrates hepatic lipid metabolism and inflammatory response to protect liver disease. However, the relationship between KIF13B and atherosclerosis remains unknown. The present study aimed to elucidate the specific role of KIF13B in atherosclerosis and its potential therapeutic significance. Methods: The investigation first assessed the relationship between the expression levels of KIF13B and the progression of atherosclerosis in human cohort data and carotid plaques from patients. Subsequently, the authors generated Kif13b knockout (Kif13b−/−) mice on low-density lipoprotein receptor (Ldlr)-deficient background (Ldlr−/−) to obtain double knockouts (Kif13b−/−;Ldlr−/−) and myeloid-specific Kif13b knockout mice (Lyz2 Cre;Kif13bf/f) with adeno-associated virus 8 (AAV8)-mediated overexpression of proprotein convertase subtilisin/kexin type 9 (PCSK9). Moreover, Ldlr−/− mice received bone marrow transplants from either Kif13b−/−;Ldlr−/− or Ldlr−/− mice and were fed a Western diet (WD) for 12 weeks. Results: KIF13B expression was significantly reduced in patients with atherosclerosis and negatively associated with the severity of atherosclerotic progress in WD-fed Ldlr−/− mice. In contrast to Kif13b−/−;Ldlr−/− mice showing a significant increase in plasma total cholesterol and more atherosclerosis lesions compared with the corresponding control mice, depletion of myeloid-derived Kif13b and bone marrow transplantation with macrophages lacking Kif13b both did not alter plasma lipid levels but elicited the larger atherosclerotic plaques with increased macrophage infiltration and more apoptotic cells. In vitro studies showed that upon oxidized low-density lipoprotein treatment, macrophages with Kif13b deficiency also display significantly increased cholesterol accumulation and impaired efferocytosis with reduced MER proto-oncogene, tyrosine kinase (MERTK) expression. Mechanistic study revealed that loss of Kif13b decreased the expression of Itchy E3 ubiquitin protein ligase (ITCH), leading to accelerated ubiquitination and degradation of MERTK mediated by Casitas B-lineage lymphoma (CBL) in macrophages. Moreover, oral administration of NX-1607, a CBL antagonist, significantly reversed the reduction of MERTK protein level and defective efferocytosis, ultimately protecting against atherosclerotic development caused by Kif13b deficiency in vivo. Conclusions: The study results revealed that KIF13B is a crucial modulator responsible for maintaining proper macrophage efferocytosis to prevent atherosclerotic development through KIF13B/ITCH/CBL/MERTK axis, suggesting that KIF13B will be a potential therapeutic target for the treatment of atherosclerosis in future clinical trials.