Yan Li

ADAR1 is overexpressed in hepatocellular carcinoma (HCC) and has been linked to poor prognosis, metastasis, and recurrence; however, its precise functions and underlying mechanisms, particularly in the context of metastasis, remain inadequately elucidated. This study seeks to elucidate the functions and underlying mechanisms of the most abundantly expressed isoform of ADAR1, ADAR1p110, in the setting of HCC metastasis. In this study, hepatocyte-specific ADAR1p110 knock-in mice and engineered HCC cell lines were utilized to investigate the function of ADAR1p110 in vivo and in vitro. Genome sequencing, transcriptome sequencing, microRNA sequencing, RNA immunoprecipitation qPCR (RIP-qPCR), and RNA pull-down assays were performed to elucidate the mechanism of ADAR1p110 in HCC. We demonstrated that ADAR1p110 overexpression promotes HCC metastasis by improving the motility of HCC cells. Mechanistically, ADAR1p110 overexpression increases TUBA1A expression, which plays a crucial role in regulating HCC cell motility. At the molecular level, ADAR1p110 suppresses miR-451a biogenesis by competitively binding to pri-miR-451a, thereby preventing its cleavage by the Drosha/DGCR8 complex. Furthermore, we confirmed that TUBA1A is a direct downstream target of miR-451a.

While magnesium isoglycyrrhizinate (MgIG) is a clinically approved therapy for alcohol-associated liver disease (ALD), its precise molecular targets and mechanisms remain uncharacterized. This study aimed to define MgIG’s hepatoprotective actions in chronic-binge ALD mouse models and ethanol/palmitic acid-exposed AML-12 hepatocytes. Through an integrated strategy encompassing RNA sequencing, molecular docking, and microscale thermophoresis, we discovered that MgIG directly binds to hydroxysteroid 11-beta dehydrogenase 1 (HSD11B1) at residue 187, a finding corroborated by molecular dynamics simulations. In vivo, MgIG markedly attenuated alcohol-induced liver injury, evidenced by ameliorated histological damage, reduced hepatic steatosis, and normalized liver-to-body weight ratios. In vitro, it effectively reduced lipid accumulation, inflammation, and apoptosis. Mechanistically, RNA sequencing identified isopentenyl diphosphate delta isomerase 1 (IDI1) as a key downstream effector. Hepatocyte-specific genetic manipulations confirmed that MgIG modulates the SREBP2–IDI1 axis, thereby suppressing lipogenesis, inflammatory responses, and apoptotic pathways. We reveal HSD11B1 as a novel direct molecular target of MgIG and elucidate its therapeutic mechanism through the HSD11B1–SREBP2–IDI1 signaling axis, which profoundly impacts ALD pathogenesis. These findings not only validate MgIG’s clinical utility but also highlight a promising new therapeutic target for ALD.

Protein tyrosine phosphatase type IVA 3 (PTP4A3) is implicated in the metastasis of hepatocellular carcinoma (HCC), yet its precise regulatory mechanisms remain elusive. This study aimed to identify the interacting substrates and underlying mechanisms of PTP4A3 to inform the optimization of PTP4A3-targeted therapies in HCC. Using the TurboID system and protein mass spectrometry, over 500 candidate substrates for PTP4A3 were identified. A direct interaction between PTP4A3 and epidermal growth factor receptor (EGFR) was also validated. Ti-IMAC protein phosphorylation mass spectrometry revealed that PTP4A3 dephosphorylates Thr693 of EGFR. This dephosphorylation event enhanced EGFR-ERBB2 heterodimerization, leading to increased RhoA-GTPase activation, cell motility, and cytoskeletal rearrangement. EGFR/ERBB2 inhibition effectively suppressed PTP4A3-driven metastasis both in vitro and in vivo. This study reveals a novel mechanism by which PTP4A3 promotes HCC metastasis via direct dephosphorylation of EGFR at Thr693. Lapatinib, an inhibitor of EGFR/ERBB2, effectively suppressed PTP4A3-driven HCC metastasis, offering a potential therapeutic strategy for HCC patients with high PTP4A3 expression. The regulatory mechanism of PTP4A3 regulating HCC cell metastasis. PTP4A3 overexpression promotes EGFR-ERBB2 heterodimer formation by dephosphorylating EGFR at Thr693, inhibiting its degradation. This sustained EGFR activation enhances HCC cell motility via RhoA-GTP signaling. Lapatinib, an EGFR/ERBB2 inhibitor, effectively counteracts the pro-migratory effects of PTP4A3.

While magnesium isoglycyrrhizinate (MgIG) is a clinically approved therapy for alcohol-associated liver disease (ALD), its precise molecular targets and mechanisms remain uncharacterized. This study aimed to define MgIG’s hepatoprotective actions in chronic-binge ALD mouse models and ethanol/palmitic acid-exposed AML-12 hepatocytes. Through an integrated strategy encompassing RNA sequencing, molecular docking, and microscale thermophoresis, we discovered that MgIG directly binds to hydroxysteroid 11-beta dehydrogenase 1 (HSD11B1) at residue 187, a finding corroborated by molecular dynamics simulations. In vivo, MgIG markedly attenuated alcohol-induced liver injury, evidenced by ameliorated histological damage, reduced hepatic steatosis, and normalized liver-to-body weight ratios. In vitro, it effectively reduced lipid accumulation, inflammation, and apoptosis. Mechanistically, RNA sequencing identified isopentenyl diphosphate delta isomerase 1 (IDI1) as a key downstream effector. Hepatocyte-specific genetic manipulations confirmed that MgIG modulates the SREBP2-IDI1 axis, thereby suppressing lipogenesis, inflammatory responses, and apoptotic pathways. We reveal HSD11B1 as a novel direct molecular target of MgIG and elucidate its therapeutic mechanism through the HSD11B1-SREBP2-IDI1 signaling axis, which profoundly impacts ALD pathogenesis. These findings not only validate MgIG’s clinical utility but also highlight a promising new therapeutic target for ALD.

Post-transcriptional regulation via the mRNA poly(A) tail is fundamental to gene expression, yet a comprehensive dataset across an entire organism is still lacking. Here, we generated a pan-organ atlas of poly(A) tail lengths across 18 murine organs using full-length nanopore sequencing that totaled 422 million reads. This dataset enables robust, single-molecule poly(A) profiling for an average of 7421 genes per sample (≥20 reads). We observed notably heterogeneous and organ-specific poly(A) tail length landscapes, ranging from profiles peaking at ~45 nt in pancreas to ~180 nt in reproductive tissues. Clustering isoforms by cross-organ poly(A) dynamics reveals functionally coherent regulatory modules that are statistically orthogonal to those derived from transcript abundance. This orthogonality is biologically informative, as poly(A) length co-regulation predicts known functional interactions even among genes with divergent expression. Together, these findings establish poly(A) tail dynamics as an independent, functionally coherent regulatory layer and provide a foundational resource for deciphering this dimension of transcriptome regulation (https://zhailab.bio.sustech.edu.cn/mouse_atlas).

While magnesium isoglycyrrhizinate (MgIG) is a clinically approved therapy for alcohol-associated liver disease (ALD), its precise molecular targets and mechanisms remain uncharacterized. This study aimed to define MgIG’s hepatoprotective actions in chronic-binge ALD mouse models and ethanol/palmitic acid-exposed AML-12 hepatocytes. Through an integrated strategy encompassing RNA sequencing, molecular docking, and microscale thermophoresis, we discovered that MgIG directly binds to hydroxysteroid 11-beta dehydrogenase 1 (HSD11B1) at residue 187, a finding corroborated by molecular dynamics simulations. In vivo , MgIG markedly attenuated alcohol-induced liver injury, evidenced by ameliorated histological damage, reduced hepatic steatosis, and normalized liver-to-body weight ratios. In vitro , it effectively reduced lipid accumulation, inflammation, and apoptosis. Mechanistically, RNA sequencing identified isopentenyl diphosphate delta isomerase 1 (IDI1) as a key downstream effector. Hepatocyte-specific genetic manipulations confirmed that MgIG modulates the SREBP2-IDI1 axis, thereby suppressing lipogenesis, inflammatory responses, and apoptotic pathways. We reveal HSD11B1 as a novel direct molecular target of MgIG and elucidate its therapeutic mechanism through the HSD11B1-SREBP2-IDI1 signaling axis, which profoundly impacts ALD pathogenesis. These findings not only validate MgIG’s clinical utility but also highlight a promising new therapeutic target for ALD.

The liver exhibits extensive circadian regulation among organs. Epidemiological studies have substantiated that disruptions in circadian rhythm constitute a risk factor for the oncogenesis of liver cancer. Nonetheless, the molecular underpinnings of how circadian dysregulation influences liver cancer progression remain elusive. Our research aims to elucidate these mechanisms and develop a predictive model for prognosis and treatment responsiveness. Our multi-omics analysis revealed extensive dysregulation of liver circadian genes (LCGs) in liver cancer. Employing machine learning algorithms, we pinpointed four pivotal dysregulated LCGs. Through the integration of single-cell, bulk, and spatial transcriptomics, we further elucidated the interconnections between LCGs dysregulation and the tumor microenvironment. In vivo and in vitro experiments demonstrated that RBM17, identified as a crucial dysregulated LCG, promotes the progression of liver cancer and cisplatin resistance by facilitating cancer stem cell phenotype. The circadian prognosis scores (CPS), based on these four genes, effectively reflected the prognosis of liver cancer patients and their responses to various therapeutic interventions. Mechanism of Action (MOA) analysis suggested that high CPS level may sensitize tumors to cell cycle-targeted therapies. Collectively, our findings provide new insights into the interplay between liver circadian gene regulation and liver cancer progression, and propose novel therapeutic targets for liver cancer.

ADAR is highly expressed and correlated with poor prognosis in hepatocellular carcinoma (HCC), yet the role of its constitutive isoform ADARp110 in tumorigenesis remains elusive. We investigated the role of ADARp110 in HCC and underlying mechanisms using clinical samples, a hepatocyte-specific Adarp110 knock-in mouse model, and engineered cell lines. ADARp110 is overexpressed and associated with poor survival in both human and mouse HCC. It creates an immunosuppressive microenvironment by inhibiting total immune cells, particularly cytotoxic GZMB ⁺ CD8 ⁺ T cells infiltration, while augmenting Treg cells, MDSCs, and exhausted CD8 ⁺ T cells ratios. Mechanistically, ADARp110 interacts with SNRPD3 and RNPS1 to stabilize CD24 mRNA by inhibiting STAU1-mediated mRNA decay. CD24 protects HCC cells from two indispensable mechanisms: macrophage phagocytosis and oxidative stress. Genetic knockdown or monoclonal antibody treatment of CD24 inhibits ADARp110-overexpressing tumor growth. Our findings unveil different mechanisms for ADARp110 modulation of tumor immune microenvironment and identify CD24 as a promising therapeutic target for HCCs.

Hepatocellular carcinoma (HCC) often occurs in the context of fibrosis or cirrhosis. Methylation of histone is an important epigenetic mechanism, but it is unclear whether histone methyltransferases are potent targets for fibrosis‐associated HCC therapy. ASH1L, an H3K4 methyltransferase, is found at higher levels in activated hepatic stellate cells (HSCs) and hepatoma cells. To determine the role of ASH1L in vivo, transgenic mice with conditional Ash1l depletion in the hepatocyte cell lineage (Ash1l^flox/floxAlb^cre) or HSCs (Ash1l^flox/floxGFAP^creERT2) are generated, and these mice are challenged in a diethylnitrosamine (DEN)/carbon tetrachloride (CCl₄)‐induced model of liver fibrosis and HCC. Depleting Ash1l in both hepatocytes and HSCs mitigates hepatic fibrosis and HCC development. Multicolor flow cytometry, bulk, and single‐cell transcriptomic sequencing reveal that ASH1L creates an immunosuppressive microenvironment. Mechanically, ASH1L‐mediated H3K4me3 modification increases the expression of CCL2 and CSF1, which recruites and polarizes M2‐like pro‐tumorigenic macrophages. The M2‐like macrophages further enhance tumor cell proliferation and suppress CD8⁺ T cell activation. AS‐99, a small molecule inhibitor of ASH1L, demonstrates similar anti‐fibrosis and tumor‐suppressive effects. Of pathophysiological significance, the increased expression levels of mesenchymal ASH1L and M2 marker CD68 are associated with poor prognosis of HCC. The findings reveal ASH1L as a potential small‐molecule therapeutic target against fibrosis‐related HCC.