Yu Liu

Fatty acid oxidation (FAO) is a major energy source in the adult heart, and disruption of cardiac metabolism is closely associated with heart failure. Here, we investigated the effects of cardiac-specific overexpression of the H19X-encoded miR-424(322)/-503 cluster using an inducible transgenic mouse model. Sustained miR-424(322)/-503 overexpression caused rapid metabolic and functional deterioration, with early impairment of fatty acid oxidation. Short-term induction reduced FAO activity and downregulated genes involved in lipid metabolism, while glycolytic enzyme activity remained largely unchanged. Continued miR-424(322)/-503 expression subsequently led to severe dilated cardiomyopathy characterized by ventricular dilation, wall thinning, fibrosis, reduced contractility, and high mortality. Importantly, disease progression was dependent on the level and duration of miR-424(322)/-503 expression, as intermittent or lower-dose induction delayed cardiac dysfunction and prolonged survival. Withdrawal of miR-424(322)/-503 expression after the onset of dysfunction promoted substantial functional recovery. Together, these findings identify miR-424(322)/-503 as a potent regulator of cardiac metabolic reprogramming that disrupts fatty acid metabolism and drives progressive heart failure.

Skeletal muscle is a highly plastic tissue with a robust capacity for regeneration, largely driven by resident satellite cells. Muscular dystrophies comprise a heterogeneous group of inherited disorders characterized by progressive muscle degeneration, chronic inflammation, and impaired regenerative capacity. Despite well-defined genetic etiologies, effective disease-modifying therapies for these disorders, as well as many acquired myopathies, remain limited. Emerging evidence identifies nuclear receptors (NRs) as key regulators of skeletal muscle homeostasis, integrating hormonal, metabolic, and environmental signals to control transcriptional programs governing mitochondrial function, metabolism, inflammation, and myogenesis. In this review, we summarize the diverse roles and mechanisms of action of NRs in skeletal muscle biology and discuss how their dysregulation contributes to muscle wasting and disease progression. We also highlight emerging NR-targeted therapeutic strategies aimed at enhancing metabolic function, suppressing inflammation and fibrosis, and promoting muscle regeneration. Finally, we outline critical knowledge gaps and future directions to advance the translation of NR-based therapies for muscular dystrophies and related neuromuscular disorders.

PHD2 is essential in modulating HIF-1α levels upon oxygen fluctuations. Hypoxia, a hallmark of uterus, and HIF-1α have recently emerged as opposing regulators of mesendoderm specification, suggesting a role for PHD2 therein. We found that PHD2 expression initially covered the epiblast and gradually receded from the primitive streak, which was identical to hypoxia and exclusive to HIF-1α. The investigations performed in mESCs, embryoids, and mouse embryos together demonstrated that PHD2 negatively regulated mesendoderm specification. Single-cell RNA sequencing revealed that PHD2 governed the transition from epiblast to mesendoderm. The downstream effect of PHD2 relied on the HIF-1α regulated Wnt/β-catenin pathway, while it was regulated upstream by miR-429. In summary, our research highlights PHD2’s essential role in mesendoderm specification and its interactions with hypoxia and HIF-1α.

Background: Skeletal muscle atrophy is a debilitating complication of many chronic diseases, disuse conditions, and ageing. Genome‐wide gene expression analyses have identified that elevated levels of microRNAs encoded by the H19X locus are among the most significant changes in skeletal muscles in a wide scope of human cachectic conditions. We have previously reported that the H19X locus is important for the establishment of striated muscle fate during embryogenesis. However, the role of H19X‐encoded microRNAs in regulating skeletal mass in adults is unknown.Methods: We have created a transgenic mouse strain in which ectopic expression of miR‐322/miR‐503 is driven by the skeletal muscle‐specific muscle creatine kinase promoter. We also used an H19X mutant mouse strain in which transcription from the locus is interrupted by a gene trap. Animal phenotypes were analysed by standard histological methods. Underlying mechanisms were explored by using transcriptome profiling and validated in the two animal models and cultured myotubes.Results: Our results demonstrate that the levels of H19X microRNAs are inversely related to postnatal skeletal muscle growth. Targeted overexpression of miR‐322/miR‐503 impeded skeletal muscle growth. The weight of gastrocnemius muscles of transgenic mice was only 54.5% of the counterparts of wild‐type littermates. By contrast, interruption of transcription from the H19X locus stimulates postnatal muscle growth by 14.4–14.9% and attenuates the loss of skeletal muscle mass in response to starvation by 12.8–21.0%. Impeded muscle growth was not caused by impaired IGF1/AKT/mTOR signalling or a hyperactive ubiquitin–proteasome system, instead accompanied by markedly dropped abundance of translation initiation factors in transgenic mice. miR‐322/miR‐503 directly targets eIF4E, eIF4G1, eIF4B, eIF2B5, and eIF3M.Conclusions: Our study illustrates a novel pathway wherein H19X microRNAs regulate skeletal muscle growth and atrophy through regulating the abundance of translation initiation factors, thereby protein synthesis. The study highlights how translation initiation factors lie at the crux of multiple signalling pathways that control skeletal muscle mass.

Type 2 diabetes condition mediated vascular smooth muscle cell (VSMCs) dysfunction. However, the mechanism of VSMCs dysfunction in diabetic patients needs further elucidation. VSMCs are an important component of the vascular wall, participate in the process of vascular remodeling, and play a vital role in the vascular complications of diabetes. Studies have found that circular RNAs (circRNAs) play a key regulatory role in the occurrence and development of VSMCs dysfunction. In this study, we stimulated VSMCs with high glucose and identified a new circular RNA, circYTHDC2, using circRNA chip analysis. circYTHDC2 was highly expressed in VSMCs treated with high glucose. Knockout of circYTHDC2 significantly inhibited the proliferation and migration of VSMCs. Metformin treatment significantly inhibited the expression of YTHDC2 and circYTHDC2. The upstream mechanism analysis revealed that the stability of circYTHDC2 was regulated by YTHDC2-mediated m6A modification. Furthermore, circYTHDC2 negatively regulates the expression of Ten-Eleven Translocation 2 (TET2) by targeting the unstable motif of TET2 3′UTR, thereby promoting dedifferentiated “synthetic type” transformation of VSMC. Taken together, these results suggest that the YTHDC2/circYTHDC2/TET2 pathway is an important target of metformin in preventing the progression of VSMCs dysfunction under high glucose.

Genomes are organized into self-interacting chromatin regions called topologically associated domains (TADs). A significant number of TAD boundaries are shared across multiple cell types and conserved across species. Disruption of TAD boundaries may affect the expression of nearby genes and could lead to several diseases. Even though detection of TAD boundaries is important and useful, there are experimental challenges in obtaining high resolution TAD locations. Here, we present computational prediction of TAD boundaries from high resolution Hi-C data in fruit flies. By extensive exploration and testing of several deep learning model architectures with hyperparameter optimization, we show that a unique deep learning model consisting of three convolution layers followed by a long short-term-memory layer achieves an accuracy of 96%. This outperforms feature-based models’ accuracy of 91% and an existing method's accuracy of 73–78% based on motif TRAP scores. Our method also detects previously reported motifs such as Beaf-32 that are enriched in TAD boundaries in fruit flies and also several unreported motifs.

In many fields of biology, especially in the field of developmental biology, LacZ reporter staining is an approach used to monitor gene expression patterns. In the LacZ reporter system, the LacZ gene is inserted in the endogenous location of the target gene via gene knock-in or by constructing a transgenic cassette in which LacZ is placed downstream of the promoter of the target gene being examined. Currently, the most common LacZ staining methods used are X-gal/FeCN staining and S-gal/TNBT staining. A serious limitation of both of these methods is that they are not effective when the LacZ gene is expressed at a low level. In an attempt to remedy this problem, we have established a new staining protocol which combines both methods. When compared to them, the method described here is better for visualizing lowly expressed genes and it has low background with high sensitivity.

Growing evidence indicates that Angiomotin (Amot)-p130 and Amot-p80 have different physiological functions. We hypothesized that Amot-p130 is a tumor suppressor gene in breast cancer, in contrast with the canonical oncogenicity of Amot-p80 or total Amot. To clarify the role of Amot-p130 in breast cancer, we performed real-time quantitative PCR, western blotting, flow cytometry, microarray, immunofluorescence, immunoprecipitation, and tumor sphere-formation assays in vitro, as well as tumorigenesis and limited-dilution analysis in vivo. In this study, we showed that Amot-p130 inhibited the proliferation, migration, and invasion of breast cancer cells. Interestingly, transcriptional profiles indicated that genes differentially expressed in response to Amot-p130 knockdown were mostly related to β-catenin signaling in MCF7 cells. More importantly, most of the downstream partners of β-catenin were associated with stemness. In a further validation, Amot-p130 inhibited the cancer stem cell potential of breast cancer cells both in vitro and in vivo. Mechanistically, Amot-p130 decreased β-catenin stability by competing with Axin for binding to tankyrase, leading to a further inhibition of the WNT pathway. In conclusions, Amot-p130 functions as a tumor suppressor gene in breast cancer, disrupting β-catenin stability by competing with Axin for binding to tankyrase. Amot-p130 was identified as a potential target for WNT pathway-targeted therapies in breast cancer.